M gnu/local.mk => gnu/local.mk +4 -3
@@ 1927,7 1927,6 @@ dist_patch_DATA = \
%D%/packages/patches/ocaml-4.09-multiple-definitions.patch \
%D%/packages/patches/omake-fix-non-determinism.patch \
%D%/packages/patches/oneko-remove-nonfree-characters.patch \
- %D%/packages/patches/onionshare-cli-async-mode.patch \
%D%/packages/patches/online-judge-tools.patch \
%D%/packages/patches/onnx-optimizer-system-library.patch \
%D%/packages/patches/onnx-1.13.1-use-system-googletest.patch \
@@ 2006,9 2005,11 @@ dist_patch_DATA = \
%D%/packages/patches/prusa-slicer-fix-tests.patch \
%D%/packages/patches/prusa-wxwidgets-makefile-fix.patch \
%D%/packages/patches/pthreadpool-system-libraries.patch \
+ %D%/packages/patches/python-3.11-fix-tests.patch \
%D%/packages/patches/python-3.12-fix-tests.patch \
%D%/packages/patches/python-accupy-use-matplotx.patch \
%D%/packages/patches/python-accupy-fix-use-of-perfplot.patch \
+ %D%/packages/patches/python-bed-reader-use-store-samples.patch \
%D%/packages/patches/python-chai-drop-python2.patch \
%D%/packages/patches/python-clarabel-blas.patch \
%D%/packages/patches/python-docrepr-fix-tests.patch \
@@ 2023,7 2024,6 @@ dist_patch_DATA = \
%D%/packages/patches/python-sgmllib3k-assertions.patch \
%D%/packages/patches/python-sphobjinv-defer-ssl-import.patch \
%D%/packages/patches/python-sphinx-prompt-docutils-0.19.patch \
- %D%/packages/patches/python-wxwidgets-type-errors.patch \
%D%/packages/patches/qcodeeditor-qt6.patch \
%D%/packages/patches/qtdeclarative-5-disable-qmlcache.patch \
%D%/packages/patches/qtdeclarative-disable-qmlcache.patch \
@@ 2130,6 2130,7 @@ dist_patch_DATA = \
%D%/packages/patches/python-memcached-syntax-warnings.patch \
%D%/packages/patches/python-mox3-python3.6-compat.patch \
%D%/packages/patches/python-packaging-test-arch.patch \
+ %D%/packages/patches/python-property-cached-asyncio-3_11.patch \
%D%/packages/patches/python-pyan3-fix-absolute-path-bug.patch \
%D%/packages/patches/python-pyan3-fix-positional-arguments.patch \
%D%/packages/patches/python-pytorch-fix-codegen.patch \
@@ 2143,6 2144,7 @@ dist_patch_DATA = \
%D%/packages/patches/python-robotframework-sshlibrary-rf5-compat.patch \
%D%/packages/patches/python-unittest2-python3-compat.patch \
%D%/packages/patches/python-unittest2-remove-argparse.patch \
+ %D%/packages/patches/python-vaex-core-fix-tsl-use.patch \
%D%/packages/patches/python-vega-datasets-remove-la-riots-code.patch \
%D%/packages/patches/python-versioneer-guix-support.patch \
%D%/packages/patches/python-werkzeug-tests.patch \
@@ 2329,7 2331,6 @@ dist_patch_DATA = \
%D%/packages/patches/tpetra-remove-duplicate-using.patch \
%D%/packages/patches/transcode-ffmpeg.patch \
%D%/packages/patches/transmission-4.0.6-fix-build.patch \
- %D%/packages/patches/trytond-add-egg-modules-to-path.patch \
%D%/packages/patches/trytond-add-guix_trytond_path.patch \
%D%/packages/patches/ttf2eot-cstddef.patch \
%D%/packages/patches/tup-unbundle-dependencies.patch \
M gnu/packages/admin.scm => gnu/packages/admin.scm +22 -18
@@ 1065,25 1065,29 @@ memory, disks, network and processes.")
(uri (pypi-uri "bpytop" version))
(sha256
(base32 "1clvajbv7pzlya9s1xs6dvjic8rv3kx7aqiwnjxapiypx246gdjk"))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:tests? #f ; No tests in Pypi archive.
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'use-poetry-core
+ (lambda _
+ ;; Patch to use the core poetry API.
+ (substitute* "pyproject.toml"
+ (("poetry.masonry.api")
+ "poetry.core.masonry.api"))))
+ (add-after 'install 'install-themes
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((themes (string-append (site-packages inputs outputs)
+ "/bpytop-themes")))
+ (mkdir-p themes)
+ (copy-recursively "themes" themes)))))))
(inputs
(list python-psutil))
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- ;; sanity-check phase fail, but the application seems to be working
- (delete 'sanity-check)
- (add-after 'install 'install-themes
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((themes (string-append (assoc-ref outputs "out")
- "/lib/python"
- ,(version-major+minor
- (package-version python))
- "/site-packages/bpytop-themes")))
- (mkdir-p themes)
- (copy-recursively "themes" themes)))))))
- (home-page
- "https://github.com/aristocratos/bpytop")
+ (native-inputs
+ (list python-poetry-core))
+ (home-page "https://github.com/aristocratos/bpytop")
(synopsis "Resource monitor")
(description "Resource monitor that shows usage and stats for processor,
memory, disks, network and processes. It's a Python port and continuation of
@@ 3280,7 3284,7 @@ provides the following commands:
;; variable in the tests/cpan.scm test.
(list (search-path-specification
(variable "GUIX_PYTHONPATH")
- (files (list "lib/python3.10/site-packages")))))
+ (files (list "lib/python3.11/site-packages")))))
(home-page "https://www.ansible.com/")
(synopsis "Radically simple IT automation")
(description "Ansible aims to be a radically simple IT automation system.
M gnu/packages/aidc.scm => gnu/packages/aidc.scm +2 -2
@@ 179,7 179,7 @@ C/C++ programs to use its capabilities without restrictions or overhead.")
(define-public zbar
(package
(name "zbar")
- (version "0.23.92")
+ (version "0.23.93")
(source
(origin
(method git-fetch)
@@ 189,7 189,7 @@ C/C++ programs to use its capabilities without restrictions or overhead.")
(commit version)))
(file-name (git-file-name name version))
(sha256
- (base32 "0k3g0ql2m4dnflppp9r3k804d927g7zslczblzcrbvhp02g6n5an"))))
+ (base32 "0x71clkkm4w765c2d5h3svr29w08dj03r6785f9jwqx5r4ral0za"))))
(build-system glib-or-gtk-build-system)
(arguments
(list
M gnu/packages/android.scm => gnu/packages/android.scm +4 -1
@@ 738,7 738,10 @@ file system.")
(base32
"11as7n2mj3nbqsqb3ivyv9985n73i022s748qvjg36cs8ig50afx"))))
(build-system pyproject-build-system)
- (inputs (list python-requests python-argcomplete python-urllib3 gnupg))
+ (inputs (list python-requests
+ python-argcomplete
+ python-urllib3-1.26
+ gnupg))
(native-inputs (list python-setuptools python-wheel))
(arguments
(list #:phases #~(modify-phases %standard-phases
M gnu/packages/astronomy.scm => gnu/packages/astronomy.scm +62 -8
@@ 2059,7 2059,10 @@ simulated Astronomical data in Python.")
"--ignore=astroML/density_estimation/tests/test_bayesian_blocks.py"
"--ignore=astroML/density_estimation/tests/test_bayesian_blocks.py"
"--ignore=astroML/density_estimation/tests/test_hist_binwidth.py"
- "--ignore=astroML/density_estimation/tests/test_hist_binwidth.py")
+ "--ignore=astroML/density_estimation/tests/test_hist_binwidth.py"
+ ;; Disalbe tests with NumPy, see
+ ;; <https://github.com/astroML/astroML/issues/281>.
+ "--ignore=astroML/tests/test_resample.py")
#:phases
'(modify-phases %standard-phases
(add-after 'unpack 'patch-build-system
@@ 2085,11 2088,18 @@ simulated Astronomical data in Python.")
;; Some tests need this
(lambda _
(setenv "HOME" "/tmp"))))))
- (propagated-inputs (list python-astropy python-matplotlib python-numpy
- python-scikit-learn python-scipy))
- (native-inputs (list python-pytest-astropy-header python-pytest-cov
- python-pytest-doctestplus python-pytest-remotedata
- python-wheel))
+ (native-inputs
+ (list python-pytest-astropy-header
+ python-pytest-cov
+ python-pytest-doctestplus
+ python-pytest-remotedata
+ python-wheel))
+ (propagated-inputs
+ (list python-astropy
+ python-matplotlib
+ python-numpy
+ python-scikit-learn
+ python-scipy))
(home-page "https://astroml.org")
(synopsis "Tools for machine learning and data mining in astronomy")
(description "This package provides tools for machine learning and data
@@ 2136,7 2146,9 @@ mining in astronomy.")
"test_table_comp[t16-t26]"
;; UnboundLocalError: local variable 'ihd'
;; referenced before assignment
- "test_delay_doc_updates")
+ "test_delay_doc_updates"
+ ;; assert 13 == 1
+ "test_skip_meta")
" and not "))
#:phases
#~(modify-phases %standard-phases
@@ 2488,6 2500,46 @@ attempting to maintain ISTP compliance
"This package contains a helper functionality to test ROMAN and JWST.")
(license license:bsd-3)))
+(define-public python-cesium
+ (package
+ (name "python-cesium")
+ (version "0.12.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "cesium" version))
+ (sha256
+ (base32
+ "0jr0ycqz9ns6mcskm4sxx92k40fj3v0x9knjaw5ac9f3mpqxsfbv"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; The installed test files contain the /gnu/store location, not the
+ ;; location of the discovered test files from the build directory.
+ ;; The test framework doesn't like this. The easiest way around
+ ;; this mismatch is to jump to the output directory.
+ (add-before 'check 'check-chdir
+ (lambda _ (chdir #$output))))))
+ (propagated-inputs
+ (list python-click ;XXX required by python-dask
+ python-cloudpickle
+ python-dask
+ python-gatspy
+ python-joblib
+ python-numpy
+ python-pandas
+ python-scikit-learn
+ python-scipy
+ python-toolz))
+ (native-inputs (list python-cython python-pytest python-setuptools-scm
+ python-setuptools python-wheel))
+ (home-page "https://pypi.org/project/cesium/")
+ (synopsis "Library for time-series feature extraction and processing")
+ (description
+ "Cesium is a library for time-series feature extraction and processing.")
+ (license license:bsd-3)))
+
(define-public python-cmyt
(package
(name "python-cmyt")
@@ 3132,7 3184,9 @@ zooming windows, star catalog access, cuts, star pick/FWHM, thumbnails, etc.")
"--ignore=glue_astronomy/io/spectral_cube/tests/test_spectral_cube.py"
"--ignore=glue_astronomy/io/spectral_cube/tests/test_spectral_cube.py"
"--ignore=glue_astronomy/translators/tests/test_trace.py"
- "--ignore=glue_astronomy/translators/tests/test_trace.py")))
+ "--ignore=glue_astronomy/translators/tests/test_trace.py"
+ ;; This is a Numpy DeprecationWarning, remove it on next update.
+ "-k" "not test_spectral_cube_io")))
(propagated-inputs
(list python-astropy
python-glue-core
M gnu/packages/audio.scm => gnu/packages/audio.scm +33 -11
@@ 647,17 647,25 @@ Filter) modules follow the convention of 1V / Octave.")
"1npks71ljc48w6858l9bq30kaf5nph8z0v61jkfb70xb9np850nl"))))
(build-system waf-build-system)
(arguments
- `(#:tests? #f ; no check target
- #:configure-flags
- (list
- (string-append "LDFLAGS=-Wl,-rpath=" (assoc-ref %outputs "out") "/lib")
- "--enable-fftw3f"
- "--enable-jack"
- "--enable-sndfile"
- "--enable-samplerate"
- "--enable-avcodec")))
+ (list
+ #:tests? #f ; no check target
+ #:configure-flags
+ #~(list
+ (string-append "LDFLAGS=-Wl,-rpath=" #$output "/lib")
+ "--enable-fftw3f"
+ "--enable-jack"
+ "--enable-sndfile"
+ "--enable-samplerate"
+ "--enable-avcodec")
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'python3.11-compatibility
+ (lambda _
+ (substitute* '("waflib/Context.py"
+ "waflib/ConfigSet.py")
+ (("'rU'") "'r'")))))))
(inputs
- (list jack-1
+ (list jack-2
libsndfile
libsamplerate
ffmpeg-4 ;for libavcodec
@@ 2664,7 2672,13 @@ partial release of the General MIDI sound set.")
#:configure-flags
#~(list
;; Add the output lib directory to the RUNPATH.
- (string-append "--ldflags=-Wl,-rpath=" #$output "/lib"))))
+ (string-append "--ldflags=-Wl,-rpath=" #$output "/lib"))
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'python3.11-compatibility
+ (lambda _
+ (substitute* "wscript"
+ (("'rU'") "'r'")))))))
(inputs
(list libsndfile
boost
@@ 2872,6 2886,14 @@ synchronous execution of all clients, and low latency operation.")
#:configure-flags '("--dbus" "--alsa")
#:phases
(modify-phases %standard-phases
+ ;; Python 3.11 has removed the 'U' (universal newline) mode. It has
+ ;; been the default since Python 3.3.
+ (add-after 'unpack 'python-compatibility
+ (lambda _
+ (substitute* '("waflib/Context.py"
+ "waflib/ConfigSet.py")
+ (("m='rU'") "m='r'")
+ (("read\\('rU'") "read('r'"))))
(add-before 'configure 'set-linkflags
(lambda _
;; Ensure -lstdc++ is the tail of LDFLAGS or the simdtests.cpp
M gnu/packages/backup.scm => gnu/packages/backup.scm +3 -1
@@ 1443,7 1443,9 @@ borgmatic is powered by borg.")
python-pytest-mock
python-pytest-qt
python-pytest-runner
- python-setuptools-git))
+ python-setuptools
+ python-setuptools-git
+ python-wheel))
(inputs
(list borg
python-appdirs
M gnu/packages/benchmark.scm => gnu/packages/benchmark.scm +25 -8
@@ 402,7 402,7 @@ setup against another one.")
(define-public python-locust
(package
(name "python-locust")
- (version "2.32.5")
+ (version "2.33.2")
;; The archive on Pypi has no tests.
(source (origin
(method git-fetch)
@@ 412,7 412,7 @@ setup against another one.")
(file-name (git-file-name name version))
(sha256
(base32
- "0nmhk2k0mbza9slqgms42s6hsfwwmyr275l90an02qaypx066l1n"))))
+ "055is6plxjajzp7v5q108n90j5mvdaylpna98kw9zsqn7mvfq7ms"))))
(build-system pyproject-build-system)
(arguments
(list
@@ 484,10 484,21 @@ setup against another one.")
"not test_ramp_up_from_0_to_100_000_users_with_50_user_classes_and_1000_workers_and_5000_spawn_rate"
;; This test fails with "AssertionError:
;; 'stopped' != 'stopping'".
- "not test_distributed_shape") " and "))
+ "not test_distributed_shape"
+ ;; This test fails with AssertionError:
+ ;; "locust [...] != .locust-real"
+ "not test_invalid_stop_timeout_string"
+ ) " and "))
#:phases
#~(modify-phases %standard-phases
;; The build system attempts to detect the version by spawning git.
+ (add-after 'unpack 'pretend-version
+ (lambda _
+ (substitute* "pyproject.toml"
+ (("^dynamic = \\[\"version\"\\].*$")
+ (format #f "version = ~s~%" #$version))
+ (("^source = \"vcs\".*$")
+ "source = \"static\"\n"))))
(add-after 'unpack 'fix-version
(lambda _
(let ((tuple (list
@@ 518,9 529,15 @@ version_tuple = __version_tuple__
")))))
(substitute* "pyproject.toml"
- (("setuptools = \">=70.0.0\"") "setuptools = \">=67.0.0\"")
- (("^version =.*") (string-append "version = \"" #$version "\"\n"))
- (("enable = true") "enable = false"))))
+ (("\"setuptools>=.*\",")
+ (string-append "\"setuptools>="
+ #$(package-version
+ (this-package-input "python-setuptools"))
+ "\","))
+ (("^version =.*")
+ (string-append "version = \"" #$version "\"\n"))
+ (("enable = true")
+ "enable = false"))))
(add-before 'check 'increase-resource-limits
(lambda _
;; XXX: Copied from ungoogled-chromium.
@@ 552,8 569,8 @@ version_tuple = __version_tuple__
python-werkzeug))
(native-inputs
(list nss-certs-for-test
- python-poetry-core
- python-poetry-dynamic-versioning
+ python-hatchling
+ python-hatch-vcs
python-pyquery
python-pytest
python-retry))
M gnu/packages/bioinformatics.scm => gnu/packages/bioinformatics.scm +568 -342
@@ 309,7 309,7 @@ single executable called @code{bam}.")
(define-public bcftools
(package
(name "bcftools")
- (version "1.14")
+ (version "1.21")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/samtools/bcftools/"
@@ 317,11 317,11 @@ single executable called @code{bam}.")
version "/bcftools-" version ".tar.bz2"))
(sha256
(base32
- "1jqrma16fx8kpvb3c0462dg0asvmiv5yi8myqmc5ddgwi6p8ivxp"))
+ "10p2ligd9pqn8wq6szw2s4zqknlm7hmb4057fpdnhlsmsg0lr2jj"))
(modules '((guix build utils)))
(snippet '(begin
;; Delete bundled htslib.
- (delete-file-recursively "htslib-1.14")))))
+ (delete-file-recursively "htslib-1.21")))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
@@ 453,7 453,7 @@ computational cluster.")
(define-public bedtools
(package
(name "bedtools")
- (version "2.30.0")
+ (version "2.31.1")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/arq5x/bedtools2/releases/"
@@ 461,7 461,7 @@ computational cluster.")
"bedtools-" version ".tar.gz"))
(sha256
(base32
- "1f2hh79l7dn147c2xyfgf5wfjvlqfw32kjfnnh2n1qy6rpzx2fik"))))
+ "15rbfg776pcjxqrsa22dk7sdlmx1lijh3jhap04f1cbr4866czpw"))))
(build-system gnu-build-system)
(arguments
(list
@@ 2185,6 2185,20 @@ Format (GFF) with Biopython integration.")
(modify-inputs (package-propagated-inputs python-bcbio-gff)
(replace "python-biopython" python-biopython-1.73))))))
+(define bed-sample-files
+ (let* ((name "bed-sample-files")
+ (commit "a06dc0450e484090f15656ffd5d317813a5e1e01")
+ (revision "0")
+ (version (git-version "0.0.0" revision commit)))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/fastlmm/bed-sample-files")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1ldr2lvgbcykxa9i2s2298mhfh0sz96aaxs5dx217aipa9vsrjwk")))))
+
(define-public python-bed-reader
(package
(name "python-bed-reader")
@@ 2194,80 2208,124 @@ Format (GFF) with Biopython integration.")
(method url-fetch)
(uri (pypi-uri "bed_reader" version))
(sha256
- (base32 "1c8ibwvz3b069w7ffh9aasz16lfkmx4z0249c2v909a21mrkkd6n"))))
+ (base32 "1c8ibwvz3b069w7ffh9aasz16lfkmx4z0249c2v909a21mrkkd6n"))
+ (modules '((guix build utils)))
+ ;; Bundled unused javascript & co.
+ (snippet #~(delete-file-recursively "_static"))
+ (patches
+ (search-patches "python-bed-reader-use-store-samples.patch"))))
(build-system cargo-build-system)
(arguments
(list
- ;; Many of the tests (both the Rust tests and the Python tests) require
- ;; Internet access to fetch samples.
- #:tests? #false
#:install-source? #false
#:features '(list "extension-module")
- #:cargo-test-flags '(list "--features=extension-module")
+ #:cargo-test-flags
+ '(list "--features=extension-module"
+ ;; Skip doc tests.
+ "--lib" "--bins" "--tests" "--"
+ ;; This test is the only one not matched by our regexp.
+ "--skip=http_one"
+ ;; These test require a 84 GB file.
+ "--skip=http_two"
+ "--skip=http_cloud_urls_md_3")
#:cargo-inputs
- `(("rust-anyinput" ,rust-anyinput-0.1)
- ("rust-bytecount" ,rust-bytecount-0.6)
- ("rust-byteorder" ,rust-byteorder-1)
- ("rust-bytes" ,rust-bytes-1)
- ("rust-cloud-file" ,rust-cloud-file-0.2)
- ("rust-derive-builder" ,rust-derive-builder-0.20)
- ("rust-dpc-pariter" ,rust-dpc-pariter-0.4)
- ("rust-fetch-data" ,rust-fetch-data-0.2)
- ("rust-futures-util" ,rust-futures-util-0.3)
- ("rust-itertools" ,rust-itertools-0.13)
- ("rust-ndarray" ,rust-ndarray-0.16)
- ("rust-ndarray-npy" ,rust-ndarray-npy-0.9)
- ("rust-num-traits" ,rust-num-traits-0.2)
- ("rust-numpy" ,rust-numpy-0.22)
- ("rust-pyo3" ,rust-pyo3-0.22)
- ("rust-pyo3-build-config" ,rust-pyo3-build-config-0.22)
- ("rust-rayon" ,rust-rayon-1)
- ("rust-statrs" ,rust-statrs-0.17)
- ("rust-thiserror" ,rust-thiserror-1)
- ("rust-tokio" ,rust-tokio-1))
+ (list rust-anyinput-0.1
+ rust-bytecount-0.6
+ rust-byteorder-1
+ rust-bytes-1
+ rust-cloud-file-0.2
+ rust-derive-builder-0.20
+ rust-dpc-pariter-0.4
+ rust-fetch-data-0.2
+ rust-futures-util-0.3
+ rust-itertools-0.13
+ rust-ndarray-0.16
+ rust-ndarray-npy-0.9
+ rust-num-traits-0.2
+ rust-numpy-0.22
+ rust-pyo3-0.22
+ rust-pyo3-build-config-0.22
+ rust-rayon-1
+ rust-statrs-0.17
+ rust-thiserror-1
+ rust-tokio-1)
#:cargo-development-inputs
- `(("rust-anyhow" ,rust-anyhow-1)
- ("rust-ndarray-rand" ,rust-ndarray-rand-0.15)
- ("rust-rusoto-credential" ,rust-rusoto-credential-0.48)
- ("rust-temp-testdir" ,rust-temp-testdir-0.2)
- ("rust-thousands" ,rust-thousands-0.2))
+ (list rust-anyhow-1
+ rust-ndarray-rand-0.15
+ rust-rusoto-credential-0.48
+ rust-temp-testdir-0.2
+ rust-thousands-0.2)
#:imported-modules
(append %cargo-build-system-modules
%pyproject-build-system-modules)
#:modules
'((guix build cargo-build-system)
((guix build pyproject-build-system) #:prefix py:)
- (guix build utils))
+ (guix build utils)
+ (ice-9 match)
+ (ice-9 rdelim))
#:phases
#~(modify-phases %standard-phases
+ (add-after 'configure 'set-data-path
+ (lambda _
+ ;; This var is still necessary despite the patch-data-path phase.
+ ;; Otherwise more tests fail with a read-only filesystem error.
+ (setenv "BED_READER_DATA_DIR" #+bed-sample-files)))
+ (add-after 'unpack 'patch-data-path
+ (lambda _
+ ;; If BED_READER_DATA_DIR is unset, default to bed-sample-files.
+ (substitute* "bed_reader/_sample_data.py"
+ (("os\\.environ\\.get\\(\"BED_READER_DATA_DIR\"" all)
+ (format #f "~a, ~s" all #+bed-sample-files)))
+ ;; XXX: More work is necessary to use another
+ ;; version of sample files with BED_READER_DATA_DIR
+ ;; Currently, only the hardcoded Guix version is working.
+ (substitute* '("bed_reader/tests/test_open_bed_cloud.py"
+ "src/bed_cloud.rs"
+ "src/lib.rs"
+ "src/supplemental_documents/cloud_urls_etc.md"
+ "tests/tests_api_cloud.rs")
+ (("\
+https://raw\\.githubusercontent\\.com/fastlmm/bed-sample-files/main")
+ (string-append "file://" #+bed-sample-files)))
+ (substitute* "src/tests.rs"
+ (("bed_reader/tests/data")
+ #+bed-sample-files))))
(add-after 'install 'prepare-python-module
(lambda _
- ;; We don't use maturin.
- (delete-file "pyproject.toml")
- (call-with-output-file "pyproject.toml"
- (lambda (port)
- (format port "\
+ ;; We don't use maturin. Conveniently, what we want to drop
+ ;; from pyproject.toml is at the end of the file.
+ (rename-file "pyproject.toml" "pyproject.toml.bak")
+ (call-with-input-file "pyproject.toml.bak"
+ (lambda (in)
+ (call-with-output-file "pyproject.toml"
+ (lambda (out)
+ (let loop ()
+ (match (read-line in)
+ ((? eof-object? eof)
+ eof)
+ ("[build-system]"
+ (and (format out "\
[build-system]
build-backend = 'setuptools.build_meta'
requires = ['setuptools']
-")))
- (call-with-output-file "setup.cfg"
- (lambda (port)
- (format port "\
-[metadata]
-name = bed-reader
-version = ~a
-
-[options]
-packages = find:
-[options.packages.find]
-exclude =
- src
- docs
- tests
- Cargo.toml
-" #$version)))))
+[tool.setuptools.packages.find]
+where = [\".\"]
+exclude = [\"src\", \"docs\", \"tests\", \"Cargo.toml\"]
+")))
+ ("samples = [\"pooch>=1.5.0\"]"
+ (and (format out "samples = []~%")
+ (loop)))
+ ("[project]"
+ (and (format out "\
+[project]
+version = ~s
+" #$version)
+ (loop)))
+ (line
+ (and (format out "~a~%" line)
+ (loop)))))))))))
(add-after 'prepare-python-module 'enable-bytecode-determinism
(assoc-ref py:%standard-phases 'enable-bytecode-determinism))
(add-after 'enable-bytecode-determinism 'build-python-module
@@ 2279,16 2337,35 @@ exclude =
(let ((site (string-append #$output "/lib/python"
#$(version-major+minor
(package-version python))
- "/site-packages")))
- (mkdir-p site)
+ "/site-packages/")))
+ (mkdir-p (string-append site "bed_reader"))
(copy-file "target/release/libbed_reader.so"
- (string-append site "/bed_reader/bed_reader.so")))))
+ (string-append site "bed_reader/bed_reader.so")))))
(add-after 'install-python-library 'add-install-to-pythonpath
(assoc-ref py:%standard-phases 'add-install-to-pythonpath))
(add-after 'add-install-to-pythonpath 'check-python
- (lambda* (#:key tests? test-flags #:allow-other-keys)
+ (lambda* (#:key tests? #:allow-other-keys)
(when tests?
- (apply invoke "pytest" "-v" #$output test-flags)))))))
+ (let ((site (string-append #$output "/lib/python"
+ #$(version-major+minor
+ (package-version python))
+ "/site-packages/"))
+ (data-dir "bed_reader/tests/data"))
+ (symlink (canonicalize-path data-dir)
+ (string-append site data-dir))
+ (invoke "pytest" "-v" #$output
+ ;; These test require a 84 GB file.
+ "-k" (string-join
+ (list "not test_http_two"
+ "test_http_cloud_urls_rst_3"
+ "test_http_cloud_urls_rst_4"
+ ;; XXX: python-pooch dependency removed
+ "test_optional_dependencies")
+ " and not "))
+ (delete-file-recursively
+ (string-append site "bed_reader/tests"))
+ (delete-file-recursively
+ (string-append #$output "/.pytest_cache")))))))))
(native-inputs (list python-pytest
python-pytest-cov
python-pytest-datadir
@@ 2296,7 2373,7 @@ exclude =
python-recommonmark
python-sphinx))
(inputs (list python-wrapper))
- (propagated-inputs (list python-numpy python-pandas python-pooch))
+ (propagated-inputs (list python-numpy python-pandas python-scipy))
(home-page "https://fastlmm.github.io/")
(synopsis "Read and write the PLINK BED format, simply and efficiently")
(description
@@ 2424,7 2501,7 @@ to explore and analyze bulk RNA-seq data.")
(define-public python-cell2cell
(package
(name "python-cell2cell")
- (version "0.6.8")
+ (version "0.7.4")
(source (origin
(method git-fetch)
(uri (git-reference
@@ 2433,7 2510,7 @@ to explore and analyze bulk RNA-seq data.")
(file-name (git-file-name name version))
(sha256
(base32
- "1hwww0rcv8sc4k312n4d0jhbyix1jjqgv5djg25bw8127q5iym3s"))
+ "02cqc5rm0qkm0np1k7bim1w7f5qjnwf1jcm5albd9cpvfs4bwgdr"))
(modules '((guix build utils)))
(snippet
'(begin
@@ 2449,6 2526,8 @@ to explore and analyze bulk RNA-seq data.")
(("'statannotations',") "")
;; We provide version 1.0.4, which should be fine.
(("'gseapy == 1.0.3'") "'gseapy'")
+ ;; We provide version 0.9.0, which should be fine.
+ (("'tensorly == 0.8.1'") "'tensorly'")
;; Using matplotlib 3.5.2 leads to this bug:
;; https://github.com/earmingol/cell2cell/issues/19 but we
;; can't package a different minor version of matplotlib
@@ 2717,16 2796,18 @@ parsing of Variant Call Format (VCF) files.")
(define-public python-decoupler-py
(package
(name "python-decoupler-py")
- (version "1.6.0")
+ ;; Upstream places release on a new branch, see
+ ;; <https://github.com/saezlab/decoupler-py/issues/175>.
+ (version "1.8.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/saezlab/decoupler-py")
- (commit (string-append "v" version))))
+ (commit version)))
(file-name (git-file-name name version))
(sha256
(base32
- "1mqkp0i8k5hzhfnka4nc2f0phmrs0k404ynbl1lqfjzywx25y75h"))))
+ "0c3yg7jjb1nxb6hsh9wn7wr8w0ba55gixdbf5fp443nhv1cwlajj"))))
(build-system pyproject-build-system)
(arguments
(list
@@ 2742,6 2823,11 @@ parsing of Variant Call Format (VCF) files.")
" and not test_get_collectri"))
#:phases
'(modify-phases %standard-phases
+ (add-after 'unpack 'relax-requirements
+ (lambda _
+ (substitute* "pyproject.toml"
+ ;; numba = "^0.60.0"; all tests passed.
+ (("0.60.0") "0.61.0"))))
(add-before 'check 'set-home
;; Some tests require a home directory to be set.
(lambda _ (setenv "HOME" "/tmp")))
@@ 2763,7 2849,7 @@ parsing of Variant Call Format (VCF) files.")
python-skranger
python-tqdm
python-typing-extensions))
- (native-inputs (list python-pytest python-wheel))
+ (native-inputs (list python-poetry-core python-pytest))
(home-page "https://github.com/saezlab/decoupler-py")
(synopsis
"Framework for modeling, analyzing and interpreting single-cell RNA-seq data")
@@ 3243,6 3329,8 @@ phylogenetic trees also goes by the name simulationmethods for phylogenetic
trees, synthetic data generation, or just phylogenetic tree simulation.")
(license license:expat)))
+;; XXX: Probably unmaintained, build fails with Python 3.11, see
+;; <https://github.com/cancerit/parabam/issues/10>.
(define-public python-parabam
(package
(name "python-parabam")
@@ 3302,19 3390,29 @@ encountered in PDB files prior to simulation tasks.")
(define-public python-peaks2utr
(package
(name "python-peaks2utr")
- (version "1.2.0")
+ (version "1.4.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "peaks2utr" version))
(sha256
(base32
- "1idp9cgwqxvryf4qqrc1xjsamfqn3jmr56kmjp2h1ysmckwmhw4v"))))
+ "104il0kk61q07b58g9xrss7xflwlbx4kzsmw9iih99lhfsii0wzg"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
- ;; These two tests fail because file names are not URLs.
- '(list "-k" "not test_annotation.py")))
+ ;; These tests fail because file names are not URLs.
+ '(list "-k" (string-join
+ (list "not test_forward_strand_annotations"
+ "test_matching_chr"
+ "test_reverse_strand_annotations")
+ " and not "))
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'relax-requirements
+ (lambda _
+ (substitute* "setup.cfg"
+ (("==") ">=")))))))
(propagated-inputs
(list python-asgiref
python-gffutils
@@ 3339,30 3437,31 @@ three prime UTR.")
(define-public python-pegasusio
(package
(name "python-pegasusio")
- (version "0.7.1")
+ (version "0.9.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "pegasusio" version))
(sha256
(base32
- "0gqygspdy398vjymdy6756jmk99s7fhwav9rivdx59kpqjcdxaz9"))))
+ "1vxi6z7jlznp7sgzlbjsl1dzf1h7ypinllnls0lb2773a8vavg5x"))))
(build-system pyproject-build-system)
;; There are no tests.
(arguments (list #:tests? #false))
(propagated-inputs
(list python-anndata
+ python-cython
python-docopt
python-h5py
- python-importlib-metadata
python-loompy
python-natsort
python-numpy
python-pandas
python-pillow
python-scipy
+ python-setuptools
python-zarr))
- (native-inputs (list python-cython python-setuptools-scm
- python-setuptools python-wheel))
+ (native-inputs (list python-cython python-setuptools python-setuptools-scm
+ python-wheel))
(home-page "https://github.com/lilab-bcb/pegasusio")
(synopsis "Read or write single-cell genomics data")
(description
@@ 3641,6 3740,49 @@ It emphasizes modularity and performance. The API will be immediately
familiar to anyone with experience of scikit-learn or scipy.")
(license license:asl2.0)))
+(define bgen-sample-files
+ (let* ((name "bgen-sample-files")
+ (commit "7b1bc74f58b326ca19606fa5f3c6093d48367993")
+ (revision "0")
+ (version (git-version "0.0.0" revision commit)))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/fastlmm/bgen-sample-files")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1b8jkscccyspfr3y1b66xvwnljcha08r2i24v9d6hcm5zii0l54w")))))
+
+(define pynsptools-examples-files
+ (let* ((name "pysnptools-examples-files")
+ ;; taken from pysnptools/util/pysnptools.hashdown.json
+ (commit "ed14e050b2b75e7f4ddb73d512fbe928bbdb2b85")
+ (revision "0")
+ (version (git-version "0.0.0" revision commit)))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/fastlmm/PySnpTools")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0hznpj15kx2sla16wlmcqz21n2vi2qb1493v30vz75hnm1m4iwm1"))
+ (modules '((guix build utils)
+ (ice-9 ftw)))
+ (snippet
+ #~(begin
+ ;; Delete everything except for examples directory:
+ (define (delete-except exceptions)
+ (lambda (file)
+ (unless (member file `("." ".." ,@exceptions))
+ (delete-file-recursively file))))
+ (for-each (delete-except '("pysnptools" "tests")) (scandir "."))
+ (with-directory-excursion "pysnptools"
+ (for-each (delete-except '("examples")) (scandir ".")))
+ (with-directory-excursion "tests"
+ (for-each (delete-except '("datasets")) (scandir "."))))))))
+
(define-public python-pysnptools
(package
(name "python-pysnptools")
@@ 3650,12 3792,39 @@ familiar to anyone with experience of scikit-learn or scipy.")
(method url-fetch)
(uri (pypi-uri "pysnptools" version))
(sha256
- (base32
- "1babnyky5fk93as1ybdvpz9x3x5099gkgscxflngzfswin23mspk"))))
+ (base32 "1babnyky5fk93as1ybdvpz9x3x5099gkgscxflngzfswin23mspk"))))
(build-system pyproject-build-system)
- ;; Tests require test data from python-bed-reader, which fetches data with
- ;; python-pooch.
- (arguments (list #:tests? #f))
+ (arguments
+ (list
+ #:test-flags
+ #~(list
+ ;; These tests require the bgen feature and an additional input.
+ "--ignore" "pysnptools/distreader/bgen.py"
+ "--ignore" "pysnptools/distreader/test_bgen2.py"
+ "--ignore" "pysnptools/distreader/distreader.py"
+ "-k" "not pysnptools.distreader.distdata.DistData.val \
+and not pysnptools.distreader.disthdf5.DistHdf5.write \
+and not pysnptools.distreader.distmemmap.DistMemMap.write"
+ ;; These tests require network connection.
+ "--ignore" "pysnptools/util/_example_file.py"
+ "--ignore" "pysnptools/util/filecache/hashdown.py")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'patch-data-path
+ (lambda _
+ (substitute* "pysnptools/util/pysnptools.hashdown.json"
+ (("https://github\\.com/fastlmm/PySnpTools/\
+raw/ed14e050b2b75e7f4ddb73d512fbe928bbdb2b85")
+ (string-append "file://" #+pynsptools-examples-files)))
+ (substitute* "pysnptools/util/bgen.hashdown.json"
+ (("https://raw\\.githubusercontent\\.com\
+/fastlmm/bgen-sample-files/7b1bc74f58b326ca19606fa5f3c6093d48367993")
+ (string-append "file://" #+bgen-sample-files)))))
+ (add-after 'unpack 'loosen-requirements
+ (lambda _
+ (substitute* "pyproject.toml"
+ (("(h5py|psutil|wheel)>=[0-9.]*" all target)
+ target)))))))
(propagated-inputs
(list python-bed-reader
python-cloudpickle
@@ 3903,7 4072,7 @@ use-case, we encourage users to compose functions to achieve their goals.")
(define-public python-biom-format
(package
(name "python-biom-format")
- (version "2.1.12")
+ (version "2.1.16")
(source
(origin
(method git-fetch)
@@ 3915,7 4084,7 @@ use-case, we encourage users to compose functions to achieve their goals.")
(file-name (git-file-name name version))
(sha256
(base32
- "06x2d8fv80jp86kd66fm3ragmxrpa2j0lzsbm337ziqjnpsdwc0f"))
+ "1npxjsi7r0w8diq6s37q21cqgrqifl7f483lfn72bn7qrvkvbpyz"))
(modules '((guix build utils)))
;; Delete generated C files.
(snippet
@@ 4214,21 4383,30 @@ sequencing.")
(define-public python-biopython
(package
(name "python-biopython")
- (version "1.80")
+ (version "1.85")
(source (origin
(method url-fetch)
;; use PyPi rather than biopython.org to ease updating
(uri (pypi-uri "biopython" version))
(sha256
(base32
- "0hqf3jsxn2sphcx81fx7x3i69sarpjsi70fzw98f8rw7z2d5x02j"))))
+ "19m03s5rwcyiq5cs1kq9dzj7qvmfvm76idgn967ygr4x0msapbsx"))))
(build-system pyproject-build-system)
(arguments
'(#:phases
(modify-phases %standard-phases
(add-before 'check 'set-home
;; Some tests require a home directory to be set.
- (lambda _ (setenv "HOME" "/tmp"))))))
+ (lambda _ (setenv "HOME" "/tmp")))
+ (add-after 'unpack 'numpy-compatibility
+ (lambda _
+ (substitute* "Bio/Cluster/__init__.py"
+ (("np.True_") "True"))))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (with-directory-excursion "Tests"
+ (invoke "python3" "run_tests.py" "--offline"))))))))
(propagated-inputs
(list python-numpy))
(native-inputs (list python-setuptools python-wheel))
@@ 4253,7 4431,87 @@ into separate processes; and more.")
(uri (pypi-uri "biopython" version))
(sha256
(base32
- "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh"))))))
+ "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh"))))
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'python3.11-compatibility
+ (lambda _
+ ;; Py_TYPE was changed to an inline static function in Python
+ ;; 3.11, so it cannot be used on the left-hand side.
+ (substitute* "Bio/triemodule.c"
+ (("Py_TYPE\\(&Trie_Type\\) = &PyType_Type;")
+ "Py_SET_TYPE(&Trie_Type, &PyType_Type);"))
+
+ ;; PY_SSIZE_T_CLEAN must be defined if s# notation is used.
+ ;; Note that this is no longer needed in Python 3.13.
+ (substitute* '("Bio/triemodule.c" "Bio/motifs/_pwm.c")
+ (("#include <Python.h>")
+ "#define PY_SSIZE_T_CLEAN\n#include <Python.h>")
+ (("int s;") "Py_ssize_t s;"))
+
+ ;; The U mode is implicit in Python 3.11.
+ (substitute* '("Tests/test_KGML_nographics.py"
+ "Tests/test_PDB.py")
+ (("'rU'") "'r'"))
+ (substitute* "Bio/SCOP/Cla.py"
+ (("\"rU\"") "\"r\""))
+
+ ;; ExactPosition class needs to define __str__.
+ (substitute* "Bio/SeqFeature.py"
+ (("class UncertainPosition" m)
+ (string-append "\
+ # Must define this on Python 3.8 onwards because we redefine __repr__
+ def __str__(self):
+ return str(int(self))
+
+ def __add__(self, offset):
+ # By default preserve any subclass
+ return self.__class__(int(self) + offset)
+" m)))
+ ;; This was removed in Python 3.9 already
+ (substitute* "Bio/KEGG/KGML/KGML_parser.py"
+ (("self.entry.getchildren\\(\\)")
+ "list(self.entry)")
+ (("element.getchildren\\(\\)")
+ "list(element)"))
+ (substitute* "Bio/Phylo/NeXMLIO.py"
+ (("node.getchildren\\(\\)")
+ "list(node)")
+ (("edge.getchildren\\(\\)")
+ "list(edge)"))
+ (substitute* "Bio/Entrez/Parser.py"
+ (("child.getiterator\\(\\)")
+ "list(child.iter())"))
+ (substitute* "Bio/SeqIO/UniprotIO.py"
+ (("alt_element.getiterator\\(NS \\+ ('.*')\\)" m something)
+ (string-append "list(alt_element.iter(NS + " something "))"))
+ (("link_element.getiterator\\(NS \\+ ('.*')\\)" m something)
+ (string-append "list(link_element.iter(NS + " something "))"))
+ (("loc_element.getiterator\\(NS \\+ ('.*')\\)" m something)
+ (string-append "list(loc_element.iter(NS + " something "))"))
+ (("element.getiterator\\(NS \\+ ('.*')\\)" m something)
+ (string-append "list(element.iter(NS + " something "))")))))
+ (add-after 'unpack 'numpy-compatibility
+ (lambda _
+ (substitute* '("Bio/Statistics/lowess.py"
+ "Tests/test_Cluster.py")
+ (("numpy.float32") "float")
+ (("numpy.float") "float"))))
+ (add-before 'check 'set-home
+ ;; Some tests require a home directory to be set.
+ (lambda _ (setenv "HOME" "/tmp")))
+ (add-before 'check 'build-extensions
+ (lambda _
+ ;; Cython extensions have to be built before running the tests.
+ (invoke "python3" "setup.py" "build_ext" "--inplace")))
+ (add-after 'unpack 'patch-tests
+ (lambda _
+ (substitute* "Tests/run_tests.py"
+ ;; Do not run doctests.
+ (("self.tests.append\\(\"doctest\"\\)") "")
+ (("opt == \"--offline\"") "True")))))))))
(define-public python-fastalite
(package
@@ 5266,16 5524,16 @@ off-target reads for a capture method that targets CpG-rich region.")
(define-public python-bx-python
(package
(name "python-bx-python")
- (version "0.9.0")
+ (version "0.13.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/bxlab/bx-python")
- (commit "4f4a48d3f227ae390c1b22072867ba86e347bdef")))
+ (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
- "1c914rw8phiw7zwzngz9i9hdciz5lq53drwdbpl2bd2sf5bj2biy"))))
+ "13318a3lydyg8fxawdb7anrny9a1j1sc1q4nd6pjg8ki5zr9r713"))))
(build-system pyproject-build-system)
(arguments
(list
@@ 5473,7 5731,7 @@ subgroups.")
(define-public python-pysam
(package
(name "python-pysam")
- (version "0.20.0")
+ (version "0.23.0")
(source (origin
(method git-fetch)
;; Test data is missing on PyPi.
@@ 5483,34 5741,39 @@ subgroups.")
(file-name (git-file-name name version))
(sha256
(base32
- "1dq6jwwm98lm30ijdgqc5xz5ppda4nj999y6qs78mhw8x0kij8gg"))
+ "0hk0ks6kqsm8252d0v1lw2d22x1awmxcr165nnhyacwbqh246skl"))
(modules '((guix build utils)))
(snippet '(begin
;; FIXME: Unbundle samtools and bcftools.
(delete-file-recursively "htslib")))))
(build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-before 'build 'set-flags
- (lambda* (#:key inputs #:allow-other-keys)
- (setenv "HTSLIB_MODE" "external")
- (setenv "HTSLIB_LIBRARY_DIR"
- (string-append (assoc-ref inputs "htslib") "/lib"))
- (setenv "HTSLIB_INCLUDE_DIR"
- (string-append (assoc-ref inputs "htslib") "/include"))
- (setenv "LDFLAGS" "-lncurses")
- (setenv "CFLAGS" "-D_CURSES_LIB=1")))
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- ;; Step out of source dir so python does not import from CWD.
- (with-directory-excursion "tests"
- (setenv "HOME" "/tmp")
- (invoke "make" "-C" "pysam_data")
- (invoke "make" "-C" "cbcf_data")
- ;; The FileHTTP test requires network access.
- (invoke "pytest" "-k" "not FileHTTP"))))))))
+ (list
+ #:test-flags
+ ;; This test requires network access.
+ '(list "-k" "not FileHTTP" "tests")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'patch-build-system
+ (lambda _
+ (substitute* "pyproject.toml"
+ ((":__legacy__") ""))))
+ (add-before 'build 'set-flags
+ (lambda* (#:key inputs #:allow-other-keys)
+ (setenv "HTSLIB_MODE" "external")
+ (setenv "HTSLIB_LIBRARY_DIR"
+ (string-append (assoc-ref inputs "htslib") "/lib"))
+ (setenv "HTSLIB_INCLUDE_DIR"
+ (string-append (assoc-ref inputs "htslib") "/include"))
+ (setenv "LDFLAGS" "-lncurses")
+ (setenv "CFLAGS" "-D_CURSES_LIB=1")))
+ (add-before 'check 'pre-check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (with-directory-excursion "tests"
+ (setenv "HOME" "/tmp")
+ (invoke "make" "-C" "pysam_data")
+ (invoke "make" "-C" "cbcf_data"))))))))
(propagated-inputs
(list htslib)) ; Included from installed header files.
(inputs
@@ 5918,7 6181,7 @@ time.")
(list python-bx-python python-numpy python-pybigwig python-pysam
zlib))
(native-inputs
- (list python-cython python-nose))
+ (list python-cython python-nose python-pyparsing))
(home-page "https://crossmap.sourceforge.net/")
(synopsis "Convert genome coordinates between assemblies")
(description
@@ 6305,78 6568,6 @@ gkm-SVM.")
accessing bigWig files.")
(license license:expat)))
-(define-public python-pyfasta
- ;; The release on pypi does not contain the test data files.
- (let ((commit "c2f0611c5311f1b1466f2d56560447898b4a8b03")
- (revision "1"))
- (package
- (name "python-pyfasta")
- (version (git-version "0.5.2" revision commit))
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/brentp/pyfasta")
- (commit commit)))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0a189id3fbv88gssyk6adbmz2ll1mqpmyw8vxmx3fi955gvaq9j7"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- #:phases
- '(modify-phases %standard-phases
- (add-after 'unpack 'python3.10-compat
- (lambda _
- (substitute* "pyfasta/__init__.py"
- (("from fasta import")
- "from pyfasta.fasta import")
- (("from records import")
- "from pyfasta.records import")
- (("from split_fasta import")
- "from pyfasta.split_fasta import")
- (("in f.iteritems")
- "in f.items"))
- (substitute* "pyfasta/fasta.py"
- (("from collections import Mapping")
- "from collections.abc import Mapping")
- (("from records import")
- "from pyfasta.records import"))
- (substitute* "pyfasta/records.py"
- (("cPickle") "pickle")
- (("\\(int, long\\)")
- "(int, int)")
- ;; XXX: it's not clear if this is really correct.
- (("buffer\\(self\\)")
- "memoryview(bytes(str(self), encoding='utf-8'))")
- (("sys.maxint") "sys.maxsize"))
- (substitute* "pyfasta/split_fasta.py"
- (("from cStringIO import")
- "from io import")
- (("in lens.iteritems") "in lens.items"))
- (substitute* "tests/test_all.py"
- (("f.keys\\(\\)\\) == \\['a-extra'")
- "list(f.keys())) == ['a-extra'")
- (("f.iterkeys\\(\\)") "iter(f.keys())")
- (("tests/data/" m)
- (string-append (getcwd) "/" m))))))))
- (propagated-inputs (list python-numpy))
- (native-inputs (list python-nose python-setuptools python-wheel))
- (home-page "https://github.com/brentp/pyfasta/")
- (synopsis "Pythonic access to fasta sequence files")
- (description
- "This library provides fast, memory-efficient, pythonic (and
-command-line) access to fasta sequence files. It stores a flattened version
-of a fasta sequence file without spaces or headers and uses either a
-@code{mmap} in numpy binary format or @code{fseek}/@code{fread} so the
-sequence data is never read into memory. It saves a pickle (@code{.gdx}) of
-the start and stop (for @code{fseek}/@code{mmap}) locations of each header in
-the fasta file for internal use.
-
-Note that this package has been deprecated in favor of @code{pyfaidx}.")
- (license license:expat))))
-
(define-public python-schema-salad
(package
(name "python-schema-salad")
@@ 9202,7 9393,7 @@ performance.")
(define-public htscodecs
(package
(name "htscodecs")
- (version "1.6.0")
+ (version "1.6.1")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/samtools/htscodecs/"
@@ 9210,7 9401,7 @@ performance.")
version "/htscodecs-" version ".tar.gz"))
(sha256
(base32
- "1h0827g9svil9jnjbpdlxjbl44rai5b95m61hs9ifbqrz9nvnjjb"))))
+ "0n962938clim15d5mmggsm7ki2ycyjwqvjgddihjlpdsr5qv28aq"))))
(build-system gnu-build-system)
(inputs (list bzip2 zlib))
(home-page "https://github.com/samtools/htscodecs")
@@ 9228,6 9419,48 @@ name/ID compression and quality score compression derived from fqzcomp.")
(define-public htslib
(package
(name "htslib")
+ (version "1.21")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/samtools/htslib/releases/download/"
+ version "/htslib-" version ".tar.bz2"))
+ (sha256
+ (base32
+ "08qq1yn6lqqnww532s11nr6gz0gfpn58rn3gy90kd5pl6pki1dc4"))
+ (snippet
+ #~(begin
+ (use-modules (guix build utils))
+ (delete-file-recursively "htscodecs")))))
+ (build-system gnu-build-system)
+ ;; Let htslib translate "gs://" and "s3://" to regular https links with
+ ;; "--enable-gcs" and "--enable-s3". For these options to work, we also
+ ;; need to set "--enable-libcurl".
+ (arguments
+ `(#:configure-flags '("--enable-gcs"
+ "--enable-libcurl"
+ "--enable-s3"
+ "--with-external-htscodecs")))
+ (inputs
+ (list bzip2 curl openssl xz))
+ ;; This is referred to in the pkg-config file as a required library.
+ (propagated-inputs
+ (list htscodecs zlib))
+ (native-inputs
+ (list perl))
+ (home-page "https://www.htslib.org")
+ (synopsis "C library for reading/writing high-throughput sequencing data")
+ (description
+ "HTSlib is a C library for reading/writing high-throughput sequencing
+data. It also provides the @command{bgzip}, @command{htsfile}, and
+@command{tabix} utilities.")
+ ;; Files under cram/ are released under the modified BSD license;
+ ;; the rest is released under the Expat license
+ (license (list license:expat license:bsd-3))))
+
+(define-public htslib-1.19
+ (package
+ (inherit htslib)
(version "1.19")
(source (origin
(method url-fetch)
@@ 9914,6 10147,8 @@ sequences).")
(with-directory-excursion (string-append "demo/" dir)
(invoke "bash" script))))
tests))))))))
+ (native-inputs
+ (list python-wheel))
(inputs
(list python-numpy
python-scipy
@@ 10695,13 10930,16 @@ BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.")
(sha256
(base32
"0gbb9iyb7swiv5455fm5rg98r7l6qn27v564yllqjd574hncpx6m"))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
(inputs
- (list python-cython
- python-bx-python
+ (list python-bx-python
+ python-cython
+ python-numpy
python-pybigwig
+ python-pyparsing
python-pysam
- python-numpy
+ python-setuptools
+ python-wheel
zlib))
(native-inputs
(list python-nose))
@@ 11925,30 12163,34 @@ bioinformatics file formats, sequence alignment, and more.")
("bzip2" ,bzip2)))))
(define-public seqmagick
- (package
- (name "seqmagick")
- (version "0.8.4")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "seqmagick" version))
- (sha256
- (base32
- "0c6skyig8fyylnbj4597pjj9h0dn36rkxrhwd34yrsc6k6f7r8a0"))))
- (build-system pyproject-build-system)
- (inputs
- (list python-biopython python-pygtrie))
- (native-inputs
- (list python-pytest python-setuptools python-wheel))
- (home-page "https://github.com/fhcrc/seqmagick")
- (synopsis "Tools for converting and modifying sequence files")
- (description
- "Bioinformaticians often have to convert sequence files between formats
+ (let ((commit "dee6ab9839cff317142e55678bb12c4c9ab2150f")
+ (revision "0"))
+ (package
+ (name "seqmagick")
+ (version (git-version "0.8.6" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/fhcrc/seqmagick")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0syipb7m44s5bqrhs17bwr28svy2s83j8d93kbazav92jzszzsw4"))))
+ (build-system pyproject-build-system)
+ (inputs
+ (list python-biopython python-pygtrie))
+ (native-inputs
+ (list python-nose python-setuptools python-wheel))
+ (home-page "https://github.com/fhcrc/seqmagick")
+ (synopsis "Tools for converting and modifying sequence files")
+ (description
+ "Bioinformaticians often have to convert sequence files between formats
and do little manipulations on them, and it's not worth writing scripts for
that. Seqmagick is a utility to expose the file format conversion in
BioPython in a convenient way. Instead of having a big mess of scripts, there
is one that takes arguments.")
- (license license:gpl3)))
+ (license license:gpl3))))
(define-public seqtk
(package
@@ 12346,7 12588,7 @@ Cuffdiff or Ballgown programs.")
(define-public taxtastic
(package
(name "taxtastic")
- (version "0.9.2")
+ (version "0.11.1")
(source (origin
;; The Pypi version does not include tests.
(method git-fetch)
@@ 12356,42 12598,47 @@ Cuffdiff or Ballgown programs.")
(file-name (git-file-name name version))
(sha256
(base32
- "1k6wg9ych1j3srnhdny1y4470qlhfg730rb3rm3pq7l7gw62vmgb"))))
- (build-system python-build-system)
+ "18h3vlyx9qp7xymd8ra6jn5h0vzlpzgcd75kslqyv2qcg1a7scc4"))))
+ (build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'prepare-directory
- (lambda _
- ;; This test fails, but the error is not caught by the test
- ;; framework, so the tests fail...
- (substitute* "tests/test_taxit.py"
- (("self.cmd_fails\\(''\\)")
- "self.cmd_fails('nothing')"))
- ;; This version file is expected to be created with git describe.
- (mkdir-p "taxtastic/data")
- (with-output-to-file "taxtastic/data/ver"
- (lambda () (display ,version)))))
- (replace 'check
- ;; Note, this fails to run with "-v" as it tries to write to a
- ;; closed output stream.
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "python" "-m" "unittest"))))
- ;; This fails because it cannot find psycopg2 even though it is
- ;; available.
- (delete 'sanity-check))))
+ (list
+ #:test-flags #~(list "-k" "not test_new_nodes02")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'prepare-directory
+ (lambda _
+ ;; This package is unknown to pypi.
+ (substitute* '("requirements.txt" "setup.py")
+ ((".*psycopg-binary.*") ""))
+ ;; This test fails, but the error is not caught by the test
+ ;; framework, so the tests fail...
+ (substitute* "tests/test_taxit.py"
+ (("self.cmd_fails\\(''\\)")
+ "self.cmd_fails('nothing')"))
+ ;; This version file is expected to be created with git describe.
+ (mkdir-p "taxtastic/data")
+ (with-output-to-file "taxtastic/data/ver"
+ (lambda () (display #$version)))))
+ (replace 'check
+ ;; Note, this fails to run with "-v" as it tries to write to a
+ ;; closed output stream.
+ (lambda* (#:key tests? test-flags #:allow-other-keys)
+ (when tests?
+ (apply invoke "python" "-m" "unittest" test-flags)))))))
+ (native-inputs
+ (list python-setuptools python-wheel))
(propagated-inputs
- (list python-sqlalchemy
+ (list python-biopython
python-decorator
- python-biopython
- python-pandas
- python-psycopg2
+ python-dendropy
python-fastalite
- python-pyyaml
- python-six
python-jinja2
- python-dendropy))
+ python-pandas
+ python-psycopg
+ python-psycopg2-binary
+ python-pyyaml
+ python-sqlalchemy-2
+ python-sqlparse))
(home-page "https://github.com/fhcrc/taxtastic")
(synopsis "Tools for taxonomic naming and annotation")
(description
@@ 14308,6 14555,7 @@ Needleman-Wunsch).")
(lambda _ (chdir "pairadise")))
(add-before 'build '2to3
(lambda _ (invoke "2to3" "--write" "--nobackups" "."))))))
+ (native-inputs (list python-setuptools python-wheel))
(inputs (list star))
(propagated-inputs (list python-pysam))
(home-page "https://github.com/Xinglab/PAIRADISE")
@@ 17156,31 17404,21 @@ API services.")
(define-public python-mgatk
(package
(name "python-mgatk")
- (version "0.6.7")
+ (version "0.7.0")
(source
(origin
- (method git-fetch)
+ (method git-fetch) ; no tests in PyPI archive
(uri (git-reference
(url "https://github.com/caleblareau/mgatk")
- ;; There is no tag for 0.6.7, but this is the commit
- ;; corresponding to the version bump.
- (commit "2633903acb1fb406bb58c787f320c3641f446ee7")))
+ ;; There is no tag for 0.7.0, but this is the commit
+ ;; corresponding to the version bump, see
+ ;; <https://github.com/caleblareau/mgatk/issues/101>.
+ (commit "8ffeac8476564049ef51b4d4d40eed452ae2fc38")))
(file-name (git-file-name name version))
(sha256
(base32
- "19iklfv1brwsfg1l5lrs3z8m343nskkn1998c1fs7fdn0lgrki2p"))))
+ "1qspzglj487bpyg8wpc29fjr8mj993q8w3jrdhylggiqpjx4l607"))))
(build-system pyproject-build-system)
- (arguments
- (list
- #:phases
- #~(modify-phases %standard-phases
- ;; The md5 module has been removed in Python 3
- (add-after 'unpack 'python3-compatibility
- (lambda _
- (substitute* "tests/test_cli.py"
- (("import md5") "from hashlib import md5")
- (("md5.new") "md5")
- (("\\.digest") ".hexdigest")))))))
(propagated-inputs
(list python-biopython
python-click
@@ 19548,6 19786,8 @@ implementation differs in these ways:
(add-after 'unpack 'patch-version-check
(lambda _
(substitute* "src/scanpy/_utils/__init__.py"
+ (("Version\\(anndata_version\\) < Version\\(\"0.6.10\"\\):")
+ "False:")
(("Version\\(anndata_version\\) >= Version\\(\"0.10.0\"\\):")
"True:"))))
(add-after 'unpack 'pretend-version
@@ 20317,18 20557,24 @@ pyGenomeTracks can make plots with or without Hi-C data.")
(define-public python-iced
(package
(name "python-iced")
- (version "0.5.8")
+ (version "0.5.13")
(source
(origin
(method url-fetch)
(uri (pypi-uri "iced" version))
(sha256
(base32
- "1avcjmpyyvhgbj5qca4l70ipiz7j3xmcw9p6rd9c06j99faa0r71"))))
- (build-system python-build-system)
- (arguments `(#:tests? #false)) ; there are none
+ "1fg6fxg6qhymr5d8drlvaclxgsfay2qcfsvpxkyy0r6cchscnpj5"))))
+ (build-system pyproject-build-system)
+ (native-inputs
+ (list python-pytest
+ python-setuptools
+ python-wheel))
(propagated-inputs
- (list python-numpy python-pandas python-scipy python-scikit-learn))
+ (list python-numpy
+ python-pandas
+ python-scipy
+ python-scikit-learn))
(home-page "https://github.com/hiclib/iced")
(synopsis "ICE normalization")
(description "This is a package for normalizing Hi-C contact counts
@@ 20961,7 21207,7 @@ polymorphisms) and indels with respect to a reference genome and more.")
(define-public cnvkit
(package
(name "cnvkit")
- (version "0.9.10")
+ (version "0.9.12")
(source
(origin
(method git-fetch)
@@ 20970,7 21216,7 @@ polymorphisms) and indels with respect to a reference genome and more.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0r303pqjg70zpxa564bavbfj99c6di0dafgqqwx2vh4vfsiif94q"))))
+ (base32 "090yh17symcahddx399kcx0mcw4gdrcc2jil3p8lb92r8c8kglb5"))))
(build-system pyproject-build-system)
(propagated-inputs
(list python-biopython
@@ 20987,7 21233,7 @@ polymorphisms) and indels with respect to a reference genome and more.")
;; R packages
r-dnacopy))
(inputs (list r-minimal)) ;for tests
- (native-inputs (list python-setuptools python-wheel))
+ (native-inputs (list python-pytest python-setuptools python-wheel))
(home-page "https://cnvkit.readthedocs.org/")
(synopsis "Copy number variant detection from targeted DNA sequencing")
(description
@@ 21426,24 21672,28 @@ throughput chromatin profiles. Typical use cases include:
(define-public umi-tools
(package
(name "umi-tools")
- (version "1.0.0")
+ (version "1.1.6")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "umi_tools" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/CGATOxford/UMI-tools")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
- (base32
- "08y3vz1vcx09whmbsn722lcs6jl9wyrh9i4p3k8j4cb1i32bij4a"))))
- (build-system python-build-system)
+ (base32 "1liykfj4msvcgk8an5qq802jcxwlijqxrvijipqj1pwpxqzl9qnh"))))
+ (build-system pyproject-build-system)
(inputs
(list python-pandas
python-future
python-scipy
python-matplotlib
python-regex
+ python-pybktree
+ python-scipy
python-pysam))
(native-inputs
- (list python-cython))
+ (list python-setuptools python-wheel))
(home-page "https://github.com/CGATOxford/UMI-tools")
(synopsis "Tools for analyzing unique modular identifiers")
(description "This package provides tools for dealing with @dfn{Unique
@@ 22021,7 22271,7 @@ effective when applied to the signal dataset.")
(define-public python-ont-fast5-api
(package
(name "python-ont-fast5-api")
- (version "4.0.0")
+ (version "4.1.3")
(source
(origin
(method git-fetch)
@@ 22031,7 22281,7 @@ effective when applied to the signal dataset.")
(file-name (git-file-name name version))
(sha256
(base32
- "01hj4751j424lzic2sc4bz1f8w7i7fpkjpy3rgghdyl5lyfyb4s4"))
+ "05zwjgdnzdrqfifhgw9rp4s22g8ysvjfhlaq9nb6p68q6mijy098"))
(modules '((guix build utils)))
(snippet
'(delete-file-recursively "ont_fast5_api/vbz_plugin"))))
@@ 23107,7 23357,7 @@ alignments, trees and genomic annotations.")
(define-public python-gffutils
(package
(name "python-gffutils")
- (version "0.10.1")
+ (version "0.13")
(source
(origin
(method git-fetch)
@@ 23117,27 23367,28 @@ alignments, trees and genomic annotations.")
(file-name (git-file-name name version))
(sha256
(base32
- "1gkzk7ps6w3ai2r81js9s9bzpba0jmxychnd2da6n9ggdnf2xzqz"))))
- (build-system python-build-system)
+ "148i7bk5bawrz19jp3nl0z859wdlldgrw8f0aw9wsprj8s3d713a"))))
+ (build-system pyproject-build-system)
(arguments
- '(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- ;; Tests need to access the HOME directory
- (setenv "HOME" "/tmp")
- (invoke "nosetests" "-a" "!slow")))))))
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'build 'set-HOME
+ (lambda _
+ ;; FileNotFoundError: [Errno 2] No such file or directory:
+ ;; '/homeless-shelter/.gffutils.test'
+ (setenv "HOME" "/tmp"))))))
+ (native-inputs
+ (list python-pytest
+ python-setuptools
+ python-wheel))
(propagated-inputs
(list python-argcomplete
python-argh
python-biopython
python-pybedtools
python-pyfaidx
- python-simplejson
- python-six))
- (native-inputs
- (list python-nose))
+ python-simplejson))
(home-page "https://github.com/daler/gffutils")
(synopsis "Tool for manipulation of GFF and GTF files")
(description
@@ 23843,51 24094,33 @@ for the analysis and visualization of raw nanopore signal.")
;; Some parts may be BSD-3-licensed.
(license license:mpl2.0)))
-(define-public python-pyvcf
- (let ((commit "476169cd457ba0caa6b998b301a4d91e975251d9")
+;; This is a fork of the original unmaintained python-pyvcf.
+(define-public python-pyvcf3
+ (let ((commit "1fb3789153d1d8e28e2cedf121399f276b5f312a")
(revision "0"))
(package
- (name "python-pyvcf")
- (version (git-version "0.6.8" revision commit))
- ;; Use git, because the PyPI tarballs lack test data.
+ (name "python-pyvcf3")
+ (version (git-version "1.0.3" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/jamescasbon/PyVCF.git")
- ;; Latest release is not tagged.
+ (url "https://github.com/dridk/PyVCF3")
(commit commit)))
(file-name (git-file-name name version))
(sha256
- (base32
- "0qf9lwj7r2hjjp4bd4vc7nayrhblfm4qcqs4dbd43a6p4bj2jv5p"))))
- (build-system python-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'patch-sample-script
- (lambda _
- ;; Add Python 3 compatibility to this sample script.
- (substitute* "scripts/vcf_sample_filter.py"
- (("print (.*)\n" _ arg)
- (string-append "print(" arg ")\n")))))
- (add-after 'install 'remove-installed-tests
- ;; Do not install test files.
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (delete-file-recursively (string-append
- (site-packages inputs outputs)
- "/vcf/test")))))))
- (native-inputs
- ;; Older setuptools is needed for use_2to3.
- (list python-cython python-setuptools-57))
- (propagated-inputs
- (list python-pysam python-rpy2))
- (home-page "https://github.com/jamescasbon/PyVCF")
+ (base32 "0i4j5bq5q32q216ja7yvg0mpww5j0b9p8ky5bya4d31wqmygal8z"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs (list python-setuptools))
+ (native-inputs (list python-setuptools python-wheel))
+ (home-page "https://github.com/dridk/PyVCF3")
(synopsis "Variant Call Format parser for Python")
(description "This package provides a @acronym{VCF,Variant Call Format}
parser for Python.")
(license license:expat))))
+(define-deprecated/public-alias python-pyvcf python-pyvcf3)
+
(define-public nanosv
(package
(name "nanosv")
@@ 23900,7 24133,7 @@ parser for Python.")
"1wl2daj0bwrl8fx5xi8j8hfs3mp3vg3qycy66538n032v1qkc6xg"))))
(build-system python-build-system)
(inputs
- (list python-configparser python-pysam python-pyvcf))
+ (list python-configparser python-pysam python-pyvcf3))
(home-page "https://github.com/mroosmalen/nanosv")
(synopsis "Structural variation detection tool for Oxford Nanopore data")
(description "NanoSV is a software package that can be used to identify
@@ 24153,8 24386,10 @@ aligner.")
(arguments
(list
#:test-flags
- ;; XXX: these two tests fail for unknown reasons
- '(list "-k" "not test_perfect_fit and not test_perfect_fit_2d")
+ '(list "--pyargs" "scvelo/core"
+ ;; XXX: these two tests fail for unknown reasons
+ "-k"
+ "not test_perfect_fit and not test_perfect_fit_2d")
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'matplotlib-compatibility
@@ 24165,17 24400,7 @@ aligner.")
;; Numba needs a writable dir to cache functions.
(add-before 'check 'set-numba-cache-dir
(lambda _
- (setenv "NUMBA_CACHE_DIR" "/tmp")))
- (replace 'check
- (lambda* (#:key tests? test-flags #:allow-other-keys)
- (when tests?
- ;; The discovered test file names must match the names of the
- ;; compiled files, so we cannot run the tests from
- ;; /tmp/guix-build-*.
- (with-directory-excursion
- (string-append #$output
- "/lib/python3.10/site-packages/scvelo/core/tests/")
- (apply invoke "pytest" "-v" test-flags))))))))
+ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
(propagated-inputs
(list python-anndata
python-hnswlib
@@ 24249,7 24474,8 @@ populations.")
(substitute* "setup.py"
(("'sklearn',") "")))))))
(native-inputs
- (list python-cython))
+ (list python-cython
+ python-wheel))
(propagated-inputs
(list python-scikit-learn
python-scipy
M gnu/packages/build-tools.scm => gnu/packages/build-tools.scm +8 -4
@@ 70,6 70,7 @@
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
#:use-module (gnu packages python-build)
+ #:use-module (gnu packages python-check)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
@@ 79,6 80,7 @@
#:use-module (gnu packages tls)
#:use-module (gnu packages unicode)
#:use-module (gnu packages version-control)
+ #:use-module (gnu packages xml)
#:use-module (guix build-system gnu)
#:use-module (guix build-system pyproject)
#:use-module (guix build-system python))
@@ 436,7 438,7 @@ other lower-level build files.")))
(define-public scons
(package
(name "scons")
- (version "4.4.0")
+ (version "4.5.0")
(source (origin
(method git-fetch)
(uri (git-reference
@@ 446,7 448,7 @@ other lower-level build files.")))
(patches (search-patches "scons-test-environment.patch"))
(sha256
(base32
- "1czswx1fj2j48rspkrvarkr43k0vii9rsmz054c9yby1dq362fgr"))))
+ "1skz1kzhwsp54i71jrsg46rkxwicfici7pq6qmfhlqd5zhrg21zb"))))
(build-system python-build-system)
(arguments
(list
@@ 467,7 469,9 @@ other lower-level build files.")))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
- (invoke "python" "runtest.py" "--all" "--unit-only"))))
+ ;; remove these tests as they require a read/write filesystem
+ (delete-file "SCons/Variables/PathVariableTests.py")
+ (invoke "python" "runtest.py" "--all" "--unit-only" ))))
(add-after 'install 'move-manuals
(lambda _
;; XXX: For some reason manuals get installed to the top-level
@@ 483,7 487,7 @@ other lower-level build files.")))
stray-manuals))))))))
(native-inputs
;; TODO: Add 'fop' when available in Guix to generate manuals.
- (list python-wheel
+ (list python-setuptools python-lxml python-wheel
;;For tests.
python-psutil))
(home-page "https://scons.org/")
M gnu/packages/check.scm => gnu/packages/check.scm +93 -200
@@ 1027,40 1027,43 @@ definition language, a safe runtime engine for test suites and a powerful
report generation engine.")
(license license:bsd-3)))
-(define-public python-gixy
- ;; The 0.1.20 release is missing some important fixes.
- ;; XXX: Commit 'e9008dcbd11f43ccac109b0cf2bf98a94e76b449' breaks tests
- ;; since it improperly removes an import.
- (let ((commit "303eb6887ddecab18138b6e427b04ae77c41d2f1")
- (revision "0")
- (base-version "0.1.20"))
- (package
- (name "python-gixy")
- (version (git-version base-version revision commit))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/yandex/gixy")
- (commit commit)))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0gymjcnvjx9snyrzdbmjnk93ibb161q72xam29vnl3yyac4r1330"))))
- (build-system pyproject-build-system)
- (native-inputs (list python-nose python-setuptools python-wheel))
- (propagated-inputs
- (list python-cached-property python-configargparse
- python-jinja2 python-six
- ;; XXX: gixy is incompatible with pyparsing >= 3.x.
- ;; See <https://github.com/yandex/gixy/pull/132> and
- ;; <https://github.com/yandex/gixy/pull/122>.
- python-pyparsing-2.4.7))
- (home-page "https://github.com/yandex/gixy")
- (synopsis "Static NGINX configuration analyzer")
- (description "Gixy is a static analyzer whose main goal is to help
+(define-public python-gixy-ng
+ (package
+ (name "python-gixy-ng")
+ (version "0.2.7")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/dvershinin/gixy")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0dipvy8y1nlhpka0cdk6hyv1j2388y7isbajpwskjrgqc5vayqx8"))))
+ (build-system pyproject-build-system)
+ ;; This package currently doesn't test properly, but we can't add
+ ;; pytest because it propagates another version of python-pyparsing
+ ;; that takes precedence over the right one.
+ (propagated-inputs (list python-configargparse
+ python-jinja2
+ python-pyparsing-2.4.7
+ python-six))
+ (native-inputs (list python-cached-property
+ python-setuptools
+ python-wheel))
+ (home-page "https://github.com/dvershinin/gixy")
+ (synopsis "Static NGINX configuration analyzer")
+ (description "Gixy is a static analyzer whose main goal is to help
prevent common NGINX misconfigurations. It provides the @command{gixy}
-command.")
- (license license:mpl2.0))))
+command.
+
+Note: This is an actively maintained fork of the original @code{python-gixy}
+package.")
+ (license license:mpl2.0)))
+
+(define-deprecated/public python-gixy python-gixy-ng
+ (package/inherit python-gixy-ng
+ (name "python-gixy")))
(define-public googletest
(package
@@ 1413,24 1416,32 @@ syntax validation, ...
(define-public python-parameterized
(package
(name "python-parameterized")
- (version "0.8.1")
+ (version "0.9.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "parameterized" version))
(sha256
- (base32 "0p1vhfw552rgd7gb2vy4l4l4k8mnbdz7f3chgzvk0r0qsqvzzfs1"))))
- (build-system python-build-system)
+ (base32 "1c89vc40zj5aj2zvbvw875wqpyf0x6xrqhm3q5jg797g5hkhbjbz"))))
+ (build-system pyproject-build-system)
(arguments
- '(#:phases (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (if tests?
- (invoke "nosetests" "-v")
- (format #t "test suite not run~%"))
- #t)))))
+ (list
+ #:test-flags #~(list "parameterized/test.py")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'fix-tests
+ (lambda _
+ (substitute* "parameterized/test.py"
+ ;; It's taken from NixOS package definition.
+ ;; <https://github.com/wolever/parameterized/issues/167>,
+ ;; <https://github.com/wolever/parameterized/pull/162>.
+ (("assert_equal\\(missing, \\[\\])") "")
+ (("assertRaisesRegexp") "assertRaisesRegex")))))))
(native-inputs
- (list python-mock python-nose))
+ (list python-pytest
+ python-mock
+ python-setuptools
+ python-wheel))
(home-page "https://github.com/wolever/parameterized")
(synopsis "Parameterized testing with any Python test framework")
(description
@@ 1438,31 1449,6 @@ syntax validation, ...
for every Python test framework. It supports nose, py.test, and unittest.")
(license license:bsd-2)))
-(define-public python-parameterized-next
- (package
- (inherit python-parameterized)
- (version "0.9.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "parameterized" version))
- (sha256
- (base32 "1c89vc40zj5aj2zvbvw875wqpyf0x6xrqhm3q5jg797g5hkhbjbz"))))
- (build-system pyproject-build-system)
- (arguments
- '(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (substitute* "parameterized/test.py"
- (("import mock") "from unittest import mock"))
- (invoke "python3" "-m" "unittest")))))))
- (native-inputs
- (list python-jinja2
- python-setuptools
- python-wheel))))
-
(define-public python-minimock
(package
(name "python-minimock")
@@ 2004,35 1990,29 @@ Python's @code{random.seed}.")
(define-public python-pytest-runner
(package
(name "python-pytest-runner")
- (version "6.0.0")
+ (version "6.0.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pytest-runner" version))
(sha256
(base32
- "11dnhxnjmh4nf1j8rnvx944ha3wg8ggrgrwdcx4c7d19xmi57n5l"))))
+ "16zly218ij0n6fxzqsasia3vh9xkzl9w0cs9pwvqy057hnap7m3h"))))
(build-system pyproject-build-system)
(arguments
(list
;; FIXME: The test suite requires 'python-pytest-virtualenv',
;; but that introduces a circular dependency.
- #:tests? #f
- #:phases
- #~(modify-phases %standard-phases
- (replace 'build
- (lambda _
- (let ((circa-1980 (* 10 366 24 60 60)))
- (setenv "SOURCE_DATE_EPOCH" (number->string circa-1980))
- (invoke "python" "-m" "build" "--wheel" "--no-isolation" "."))))
- (replace 'install
- (lambda _
- (let ((whl (car (find-files "dist" "\\.whl$"))))
- (invoke "pip" "--no-cache-dir" "--no-input"
- "install" "--no-deps" "--prefix" #$output whl)))))))
+ #:tests? #f))
(native-inputs
- (list python-pip python-pypa-build python-pytest
- python-setuptools python-setuptools-scm python-wheel))
+ (list python-pytest
+ python-pytest-checkdocs
+ python-pytest-enabler
+ ;; python-pytest-virtualenv
+ python-setuptools
+ python-setuptools-scm
+ python-types-setuptools
+ python-wheel))
(home-page "https://github.com/pytest-dev/pytest-runner")
(synopsis "Invoke py.test as a distutils command")
(description
@@ 2825,13 2805,13 @@ instantly.")
(define-public python-crosshair
(package
(name "python-crosshair")
- (version "0.0.76")
+ (version "0.0.84")
(source
(origin
(method url-fetch)
(uri (pypi-uri "crosshair-tool" version))
(sha256
- (base32 "1yvbhzs7r85gn4d7drl7p7vi1f5cga1xyy3mzxy3fglyf8kxyakh"))))
+ (base32 "1j6icn5f206yld9871p7a3v45jg8d8v4bhxh09lq3kzi09gr7maz"))))
(build-system pyproject-build-system)
(arguments
(list
@@ 2853,7 2833,7 @@ instantly.")
(("typing-inspect>=0.7.1") "typing-inspect>=0.6.0")
;; 'sanity-check fails for z3-solver, although it is
;; included in 'propagated-inputs.
- (("z3-solver==4.13.0.0") ""))))
+ (("z3-solver>=4.13.0.0") ""))))
(add-before 'check 'set-test-env
(lambda _
(setenv "PYTHONHASHSEED" "0")))))) ;tests rely on this value
@@ 2863,10 2843,16 @@ instantly.")
python-mypy
python-numpy
python-pytest
- python-pytest-xdist))
+ python-pytest-xdist
+ python-setuptools
+ python-wheel))
(propagated-inputs
- (list python-typeshed-client
+ (list python-importlib-metadata
+ python-packaging
+ ;; python-pygls
+ python-typeshed-client
python-typing-inspect
+ python-typing-extensions
z3))
(home-page "https://crosshair.readthedocs.io")
(synopsis "Analysis tool for Python using symbolic execution")
@@ 3132,39 3118,6 @@ produces a given output. As mypy can be told to display the type of an
expression this allows you to check mypys type interference.")
(license (list license:expat license:asl2.0))))
-(define-public python-pytest-pep8
- (package
- (name "python-pytest-pep8")
- (version "1.0.6")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "pytest-pep8" version))
- (sha256
- (base32
- "06032agzhw1i9d9qlhfblnl3dw5hcyxhagn7b120zhrszbjzfbh3"))))
- (build-system python-build-system)
- (arguments
- `(#:tests? #f ; Fails with recent pytest and pep8. See upstream issues #8 and #12.
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'fix-dependencies
- (lambda _
- (substitute* "setup.py"
- (("'pytest-cache', ") "")))) ; Included in recent pytest
- (replace 'check
- (lambda* (#:key tests? inputs outputs #:allow-other-keys)
- (when tests?
- (add-installed-pythonpath inputs outputs)
- (invoke "pytest" "-v")))))))
- (native-inputs
- (list python-pytest))
- (propagated-inputs
- (list python-pep8))
- (home-page "https://bitbucket.org/pytest-dev/pytest-pep8")
- (synopsis "Py.test plugin to check PEP8 requirements")
- (description "Pytest plugin for checking PEP8 compliance.")
- (license license:expat)))
-
(define-public python-pytest-perf
(package
(name "python-pytest-perf")
@@ 3231,19 3184,13 @@ each of the environments.")
(sha256
(base32
"0959qfxb4ayvfxvmpargvh4zfhwdq5l77gczhzv33bhmfblk8ccm"))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (delete 'check)
- (add-after 'install 'check
- (lambda* (#:key outputs inputs #:allow-other-keys)
- ;; It's easier to run tests after install.
- ;; Make installed package available for running the tests
- (add-installed-pythonpath inputs outputs)
- (invoke "py.test" "-vv" "-k" "not test_syntax_error"))))))
+ (list
+ #:test-flags
+ '(list "-k" "not test_syntax_error")))
(native-inputs
- (list python-coverage python-pytest python-pytest-pep8))
+ (list python-coverage python-pytest python-setuptools python-wheel))
(propagated-inputs
(list python-pyflakes))
(home-page "https://github.com/fschulze/pytest-flakes")
@@ 3485,7 3432,6 @@ backported from Python 2.7 for Python 2.4+.")
(build-system pyproject-build-system)
(native-inputs
(list python-mock
- python-nose
python-assertpy
python-pathpy
python-pyhamcrest
@@ 3541,37 3487,6 @@ tests written in a natural language style, backed up by Python code.")
JSON APIs with Behave.")
(license license:expat)))
-(define-public python-rednose
- (package
- (name "python-rednose")
- (version "1.2.3")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "rednose" version))
- (sha256
- (base32
- "11x5nx5b4wdq04s7vj1gcdl07jvvkfb37p0r5lg773gr5rr8mj6h"))))
- (build-system python-build-system)
- (arguments
- `(#:phases (modify-phases %standard-phases
- (add-after 'unpack 'patch-setup.py
- (lambda _
- ;; Six is only required for tests and later versions
- ;; work fine.
- (substitute* "setup.py"
- (("six==1.10.0") "six"))
- #t)))))
- (propagated-inputs
- (list python-colorama python-termstyle))
- (native-inputs
- (list python-six python-nose))
- (home-page "https://github.com/JBKahn/rednose")
- (synopsis "Colored output for Python nosetests")
- (description "This package provides colored output for the
-@command{nosetests} command of the Python Nose unit test framework.")
- (license license:bsd-3)))
-
(define-public python-nose-exclude
(package
(name "python-nose-exclude")
@@ 3632,30 3547,6 @@ running your code against a large number of randomly generated input
scenarios.")
(license license:expat)))
-(define-public python-nose-randomly
- (package
- (name "python-nose-randomly")
- (version "1.2.6")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "nose-randomly" version))
- (sha256
- (base32 "0z662rqhfk4bjmg806mn4frb8nz4gbh7mrddsrhfffp1g4yklj3y"))))
- (build-system python-build-system)
- (native-inputs
- (list python-nose python-numpy))
- (home-page "https://github.com/adamchainz/nose-randomly")
- (synopsis
- "Nose plugin to randomly order tests and control random.seed")
- (description
- "This is a @code{Nose} plugin to randomly order tests which can be quite
-powerful in discovering hidden flaws in the tests themselves, while helping to
-reduce inter-test dependencies. It also helps in controlling @code{random.seed},
-by resetting it to a repeatable number for each test, enabling the tests to
-create data based on random numbers and yet remain repeatable.")
- (license license:bsd-3)))
-
(define-public python-nose-timer
(package
(name "python-nose-timer")
@@ 4398,23 4289,25 @@ directories and files.")
(define-public python-pytest-regressions
(package
(name "python-pytest-regressions")
- (version "2.5.0")
+ (version "2.7.0")
(source
(origin
(method url-fetch)
- (uri (pypi-uri "pytest-regressions" version))
+ (uri (pypi-uri "pytest_regressions" version))
(sha256
- (base32 "1nbg20m83jsj9p12fm4qn5b7hc3vqb5h5fzfi6zvmwygq627i341"))))
+ (base32 "0pph1935rq180ax0szwwf3c6zq2v40snypagr49914i31570cc2c"))))
(build-system pyproject-build-system)
+ (arguments
+ (list
+ ;; Do not fail on warning.
+ ;; DeprecationWarning: module 'sre_constants' is deprecated
+ #:test-flags #~(list "-W" "ignore::DeprecationWarning")))
(native-inputs
- (list python-matplotlib
- python-numpy
+ (list python-numpy
python-pandas
- python-pillow
- python-restructuredtext-lint
+ python-pytest
python-setuptools
- python-setuptools-scm
- python-pytest))
+ python-setuptools-scm))
(propagated-inputs
(list python-pytest-datadir
python-pyyaml))
M gnu/packages/cpp.scm => gnu/packages/cpp.scm +67 -5
@@ 8,7 8,7 @@
;;; Copyright © 2019 Jan Wielkiewicz <tona_kosmicznego_smiecia@interia.pl>
;;; Copyright © 2020, 2021 Nicolò Balzarotti <nicolo@nixo.xyz>
;;; Copyright © 2020 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2020, 2021, 2023, 2024 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2020, 2021, 2023, 2024, 2025 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
;;; Copyright © 2020, 2021, 2022, 2024 Vinicius Monego <monego@posteo.net>
;;; Copyright © 2020, 2022 Marius Bakke <marius@gnu.org>
@@ 45,6 45,7 @@
;;; Copyright © 2025 Sharlatan Hellseher <sharlatanus@gmail.com>
;;; Copyright © 2025 Sergio Pastor Pérez <sergio.pastorperez@gmail.com>
;;; Copyright © 2025 Ashish SHUKLA <ashish.is@lostca.se>
+;;; Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
;;;
;;; This file is part of GNU Guix.
;;;
@@ 1549,7 1550,7 @@ tools:
;; header
(package
(name "cpp-httplib")
- (version "0.18.5")
+ (version "0.20.0")
(source
(origin
(method git-fetch)
@@ 1557,7 1558,7 @@ tools:
(url "https://github.com/yhirose/cpp-httplib")
(commit (string-append "v" version))))
(sha256
- (base32 "1jc31n4xdrknal4i1dvf8j6j9kafpczi0w5gbbi89xlir9dgm5kp"))
+ (base32 "0w5klyfsaws793xb0cbkjxg7lwrdm6f3m4z4v7pzkwl957f9q70m"))
(file-name (git-file-name name version))))
(build-system cmake-build-system)
(arguments
@@ 1606,7 1607,7 @@ library.")
(define-public cpplint
(package
(name "cpplint")
- (version "1.5.5")
+ (version "2.0.0")
(source
(origin
(method git-fetch)
@@ 1616,7 1617,7 @@ library.")
(url "https://github.com/cpplint/cpplint")
(commit version)))
(sha256
- (base32 "13l86aq0h1jga949k79k9x3hw2xqchjc162sclg2f99vz98zcz15"))
+ (base32 "06km4wh4944az1hk61g5w8pjhbvbccpgarz1dy7vhwkhfvmvggnk"))
(file-name (git-file-name name version))))
(build-system pyproject-build-system)
(arguments
@@ 1625,6 1626,11 @@ library.")
,@%pyproject-build-system-modules)
#:phases
#~(modify-phases (@ (guix build pyproject-build-system) %standard-phases)
+ (add-after 'unpack 'patch-build-system
+ (lambda _
+ (substitute* "pyproject.toml"
+ (("setuptools\\.build_meta:__legacy__")
+ "setuptools.build_meta"))))
(add-before 'wrap 'reduce-GUIX_PYTHONPATH
(lambda _
;; Hide the transitive native inputs from GUIX_PYTHONPATH
@@ 1651,9 1657,11 @@ library.")
(getenv "TMP_PYTHONPATH")))))))
(native-inputs
(list python-coverage
+ python-parameterized
python-pytest
python-pytest-cov
python-pytest-runner
+ python-pytest-timeout
python-setuptools
python-testfixtures
python-wheel))
@@ 2614,6 2622,40 @@ union, difference & exclusive-or, and line & polygon offsetting.
The library is based on Vatti's clipping algorithm.")
(license license:boost1.0)))
+(define-public clipper2
+ (package
+ (inherit clipper)
+ (name "clipper2")
+ (version "1.5.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/AngusJohnson/Clipper2")
+ (commit (string-append "Clipper2_" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1w8cmx712k45cb8gh9dakmbmybiwdx8c0b45mwpcldywx2lwxi2j"))
+ (modules '((guix build utils)))
+ (snippet #~(for-each
+ delete-file-recursively
+ '("CSharp" "DLL" "Delphi")))))
+ (build-system cmake-build-system)
+ (arguments
+ (list
+ #:configure-flags
+ #~(list "-DUSE_EXTERNAL_GTEST=ON"
+ "-DCLIPPER2_EXAMPLES=OFF")
+ #:phases #~(modify-phases %standard-phases
+ (add-after 'unpack 'chdir
+ (lambda _
+ (chdir "CPP"))))))
+ (native-inputs (list googletest))
+ (home-page "https://github.com/AngusJohnson/Clipper2")
+ (description
+ (string-append (package-description clipper) "\
+Note: This package is a major update of the original clipper library."))))
+
(define-public pcg-cpp
(let ((commit "ffd522e7188bef30a00c74dc7eb9de5faff90092")
(revision "2"))
@@ 3754,6 3796,26 @@ file name and location, as well as filters with friendly names (such as
\"source files\" or \"image files\") where supported.")
(license license:zlib)))
+(define-public string-view-lite
+ (package
+ (name "string-view-lite")
+ (version "1.8.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/martinmoene/string-view-lite")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1mfp3lmqx7ac0545akxd2v05rrapa3byz8q4gb9rqy94pcqbfyc5"))))
+ (build-system cmake-build-system)
+ (home-page "https://github.com/martinmoene/string-view-lite")
+ (synopsis "C++17 string-view for older C++")
+ (description "This package provides a compatibility header-only library
+for C++17 string-view.")
+ (license license:boost1.0)))
+
(define-public tsl-hopscotch-map
(package
(name "tsl-hopscotch-map")
M gnu/packages/crates-io.scm => gnu/packages/crates-io.scm +61 -7
@@ 47545,8 47545,45 @@ without performing I/O.")
("rust-rustversion" ,rust-rustversion-1)
("rust-tempfile" ,rust-tempfile-3))))))
+(define-public rust-notify-7
+ (package
+ (name "rust-notify")
+ (version "7.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "notify" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "02a0a1n0raxqslwhfprwmz7w34v54r42006q0m8bmy89jz1v8cy5"))))
+ (build-system cargo-build-system)
+ (arguments
+ (list
+ #:cargo-inputs (list rust-bitflags-2
+ rust-crossbeam-channel-0.5
+ rust-filetime-0.2
+ rust-fsevent-sys-4
+ rust-inotify-0.10
+ rust-kqueue-1
+ rust-libc-0.2
+ rust-log-0.4
+ rust-mio-1
+ rust-notify-types-1
+ rust-walkdir-2
+ rust-windows-sys-0.52)
+ #:cargo-development-inputs (list rust-insta-1
+ rust-nix-0.27
+ rust-serde-json-1
+ rust-tempfile-3)))
+ (home-page "https://github.com/notify-rs/notify")
+ (synopsis "Cross-platform filesystem notification library")
+ (description "This package contains a cross-platform filesystem
+notification library.")
+ (license license:cc0)))
+
(define-public rust-notify-6
(package
+ (inherit rust-notify-7)
(name "rust-notify")
(version "6.1.1")
(source
@@ 47556,7 47593,6 @@ without performing I/O.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32 "0bad98r0ilkhhq2jg3zs11zcqasgbvxia8224wpasm74n65vs1b2"))))
- (build-system cargo-build-system)
(arguments
`(#:cargo-inputs (("rust-bitflags" ,rust-bitflags-2)
("rust-crossbeam-channel" ,rust-crossbeam-channel-0.5)
@@ 47572,12 47608,7 @@ without performing I/O.")
("rust-windows-sys" ,rust-windows-sys-0.48))
#:cargo-development-inputs (("rust-nix" ,rust-nix-0.23)
("rust-serde-json" ,rust-serde-json-1)
- ("rust-tempfile" ,rust-tempfile-3))))
- (home-page "https://github.com/notify-rs/notify")
- (synopsis "Cross-platform filesystem notification library")
- (description "This package contains a cross-platform filesystem
-notification library.")
- (license license:cc0)))
+ ("rust-tempfile" ,rust-tempfile-3))))))
(define-public rust-notify-5
(package
@@ 47740,6 47771,29 @@ client and server")
Rust dbus client and server.")
(license (list license:expat license:asl2.0))))
+(define-public rust-notify-types-1
+ (package
+ (name "rust-notify-types")
+ (version "1.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "notify-types" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0x5idrpxzf70ng88rz28dqmgx1jyddf0vxx1x3csw09fw6skqpaq"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs (("rust-instant" ,rust-instant-0.1)
+ ("rust-serde" ,rust-serde-1))
+ #:cargo-development-inputs (("rust-insta" ,rust-insta-1)
+ ("rust-rstest" ,rust-rstest-0.21)
+ ("rust-serde-json" ,rust-serde-json-1))))
+ (home-page "https://github.com/notify-rs/notify")
+ (synopsis "Types used by the notify crate")
+ (description "This package provides rust types used by the notify crate.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-notmuch-0.8
(package
(name "rust-notmuch")
M gnu/packages/cybersecurity.scm => gnu/packages/cybersecurity.scm +13 -3
@@ 3,6 3,7 @@
;;; Copyright © 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2021 c4droid <c4droid@foxmail.com>
;;; Copyright © 2021 Raghav Gururajan <rg@raghavgururajan.name>
+;;; Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
;;;
;;; This file is part of GNU Guix.
;;;
@@ 30,9 31,11 @@
#:use-module (gnu packages engineering)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
- #:use-module (gnu packages python-xyz)
+ #:use-module (gnu packages python-build)
+ #:use-module (gnu packages python-compression)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-web)
+ #:use-module (gnu packages python-xyz)
#:use-module (gnu packages time)
#:use-module (gnu packages bioinformatics) ;python-intervaltree
#:use-module (gnu packages emulators))
@@ 123,24 126,26 @@ chains of gadgets to execute system calls.")
(define-public pwntools
(package
(name "pwntools")
- (version "4.4.0")
+ (version "4.15.0b1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pwntools" version))
(sha256
(base32
- "1qw7j0wwm1878aia08gyw5xljjr26qsbp45w65n4qff672sha5n5"))))
+ "091fsk9rvbjkcsp8mmww0ka26dvznmj4pbqwaiygcw90g3v94zgd"))))
(build-system python-build-system)
(arguments
'(#:tests? #f)) ;XXX: needs a specific version of unicorn
(propagated-inputs
(list capstone
+ python-colored-traceback
python-dateutil
python-intervaltree
python-mako
python-packaging
python-paramiko
+ python-pathlib2
python-psutil
python-pyelftools
python-pygments
@@ 148,9 153,14 @@ chains of gadgets to execute system calls.")
python-pysocks
python-requests
ropgadget
+ python-rpyc
python-six
python-sortedcontainers
+ python-unix-ar
+ python-zstandard
unicorn))
+ (native-inputs
+ (list python-setuptools python-toml python-wheel))
(home-page "https://github.com/Gallopsled/pwntools")
(synopsis
"Capture-the-flag (CTF) framework and exploit development library")
M gnu/packages/databases.scm => gnu/packages/databases.scm +64 -48
@@ 3371,20 3371,24 @@ coroutine-specific markup.")
(define-public python-asyncpg
(package
(name "python-asyncpg")
- (version "0.25.0")
+ (version "0.30.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "asyncpg" version))
(sha256
- (base32 "0h1573lp4607nppflnnjrhn7yrfy6i54cm98gi4qbcikjykfdy33"))))
- (build-system python-build-system)
- (propagated-inputs (list python-typing-extensions))
+ (base32 "0lf8xbrsb2ycpqx1vzlb05p48g5sh9zq24a8yh17cw5nia9fjlf5"))))
+ (build-system pyproject-build-system)
(native-inputs
(list postgresql
python-cython
python-pytest
- python-uvloop))
+ python-uvloop
+ python-distro
+ python-setuptools
+ python-wheel))
+ (propagated-inputs
+ (list python-async-timeout))
(home-page "https://github.com/MagicStack/asyncpg")
(synopsis "Fast PostgreSQL database client library for Python")
(description "@code{asyncpg} is a database interface library designed
@@ 4574,7 4578,11 @@ reasonable substitute.")
"test_tfunction_load_delete"
"test_tfunction_list"
;; AssertionError: assert 3 == 2
- "test_acl_list")
+ "test_acl_list"
+ ;; XXX: This test occasionally fails on i686-linux
+ #$@(if (target-x86-32?)
+ '("test_geopos")
+ '()))
" and not "))
#:phases
#~(modify-phases %standard-phases
@@ 4608,7 4616,7 @@ reasonable substitute.")
(define-public python-rq
(package
(name "python-rq")
- (version "1.11.1")
+ (version "2.3.1")
(source
(origin
(method git-fetch)
@@ 4617,24 4625,20 @@ reasonable substitute.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0dnjm2s036l4j4ypq0h903vh132dp2wiwjrn8jicz1nw829dqpzf"))))
- (build-system python-build-system)
+ (base32 "1w9aqvbvh1mfpgng0mdcskxl5y3ybcqqai5dnwgvg18am0xxhya6"))))
+ (build-system pyproject-build-system)
(arguments
- '(#:phases (modify-phases %standard-phases
- (add-before 'check 'start-redis
- (lambda _
- (invoke "redis-server" "--daemonize" "yes")))
- (replace 'check
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- ;; Drop test that needs the SDK for Sentry.io.
- (delete-file "tests/test_sentry.py")
- ;; Ensure 'rq' and 'rqworker' ends up on PATH.
- (setenv "PATH" (string-append out "/bin:"
- (getenv "PATH")))
- (invoke "pytest" "-vv")))))))
+ (list
+ #:phases #~(modify-phases %standard-phases
+ (add-before 'check 'start-redis
+ (lambda _
+ (invoke "redis-server" "--daemonize" "yes"))))))
(native-inputs
- (list python-mock python-psutil python-pytest redis))
+ (list python-hatchling
+ python-mock
+ python-psutil
+ python-pytest
+ redis))
(propagated-inputs
(list python-click python-redis))
(home-page "https://python-rq.org/")
@@ 4648,7 4652,7 @@ is designed to have a low barrier to entry.")
(define-public python-rq-scheduler
(package
(name "python-rq-scheduler")
- (version "0.10.0")
+ (version "0.14")
(home-page "https://github.com/rq/rq-scheduler")
(source (origin
(method git-fetch)
@@ 4658,21 4662,30 @@ is designed to have a low barrier to entry.")
(file-name (git-file-name name version))
(sha256
(base32
- "0xg6yazqs5kbr2ayvhvljs1h5vgx5k5dds613fmhswln7gglf9hk"))))
- (build-system python-build-system)
+ "09fh9m2vcl1jndq35xp1x0j8ih009r71qmhn2pkl93fykrqfavyn"))))
+ (build-system pyproject-build-system)
(arguments
- '(#:phases (modify-phases %standard-phases
- (add-before 'check 'start-redis
- (lambda _
- (invoke "redis-server" "--daemonize" "yes")))
- (replace 'check
- (lambda _
- (substitute* "run_tests.py"
- (("/usr/bin/env")
- (which "env")))
- (invoke "./run_tests.py"))))))
+ (list
+ #:test-flags
+ #~(list "-k" (string-append "not test_cron"
+ " and not test_job_creation_with"
+ " and not test_job_with_crontab"))
+ #:phases #~(modify-phases %standard-phases
+ (add-before 'check 'start-redis
+ (lambda _
+ (invoke "redis-server" "--daemonize" "yes")))
+ (add-after 'unpack 'loosen-requirements
+ (lambda _
+ (substitute* "setup.py"
+ (("crontab>=[0-9.]*")
+ "python-crontab")))))))
(native-inputs
- (list redis which))
+ (list python-crontab
+ python-freezegun
+ python-pytest
+ python-setuptools
+ python-wheel
+ redis))
(propagated-inputs
(list python-croniter python-rq))
(synopsis "Job scheduling capabilities for RQ (Redis Queue)")
@@ 4724,14 4737,15 @@ provides support for parsing, splitting and formatting SQL statements.")
(define-public python-sql
(package
(name "python-sql")
- (version "1.3.0")
+ (version "1.5.2")
(source
(origin
(method url-fetch)
- (uri (pypi-uri "python-sql" version))
+ (uri (pypi-uri "python_sql" version))
(sha256
- (base32 "0xnimfzlxj1ddrb5xj3s4gaii278a0gpxrvwmdmrdxgjfdi3lq4x"))))
- (build-system python-build-system)
+ (base32 "0dnd0vai9z1fjkppv2xv2f4vlwwz0dqa137f39mrbjw744vm4pvk"))))
+ (build-system pyproject-build-system)
+ (native-inputs (list python-setuptools python-wheel))
(home-page "https://python-sql.tryton.org/")
(synopsis "Library to write SQL queries in a pythonic way")
(description "@code{python-sql} is a library to write SQL queries, that
@@ 5359,7 5373,7 @@ other traditional Python scientific computing packages.")
(define-public python-fastparquet
(package
(name "python-fastparquet")
- (version "2024.2.0")
+ (version "2024.11.0")
(source
(origin
;; Fastparquet uses setuptools-scm to find the current version. This
@@ 5372,7 5386,7 @@ other traditional Python scientific computing packages.")
(commit version)))
(file-name (git-file-name name version))
(sha256
- (base32 "0f32dj1xvd11l0siznqd33dpjlhg9siylcjcfkcdlqfcy45jfj3v"))))
+ (base32 "0dhmyag06d073g1q58npbcikr9hjd6jgf05721gkl6m1gsprv7hq"))))
(build-system pyproject-build-system)
(arguments
(list
@@ 5398,6 5412,13 @@ other traditional Python scientific computing packages.")
;; Cython extensions need to be built for the check phase.
(lambda _
(invoke "python" "setup.py" "build_ext" "--inplace"))))))
+ (native-inputs
+ (list python-cython
+ python-pytest
+ python-pytest-xdist
+ python-setuptools
+ python-setuptools-scm
+ python-wheel))
(propagated-inputs
(list python-cramjam
python-fsspec
@@ 5405,11 5426,6 @@ other traditional Python scientific computing packages.")
python-numpy
python-packaging
python-pandas))
- (native-inputs
- (list python-cython
- python-pytest-runner
- python-pytest-xdist
- python-setuptools-scm))
(home-page "https://github.com/dask/fastparquet")
(synopsis "Python implementation of the Parquet file format")
(description
M gnu/packages/django.scm => gnu/packages/django.scm +17 -31
@@ 148,26 148,10 @@ to the @dfn{don't repeat yourself} (DRY) principle.")
;; This CVE seems fixed since 4.2.1.
(lint-hidden-cve . ("CVE-2023-31047"))))))
-(define-public python-django-3.2
- (package
- (inherit python-django-4.2)
- (version "3.2.21")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "Django" version))
- (sha256
- (base32
- "0g3zm2glh76g31q06g6fwkwvkrphjj3mnap5sgk1hx3v9r44rpm5"))))
- (native-search-paths '()) ;no need for TZDIR
- (propagated-inputs
- (modify-inputs (package-propagated-inputs python-django-4.2)
- ;; Django 4.0 deprecated pytz in favor of Pythons built-in zoneinfo.
- (append python-pytz)))))
-
;; archivebox requires django>=3.1.3,<3.2
(define-public python-django-3.1.14
(package
- (inherit python-django-3.2)
+ (inherit python-django-4.2)
(version "3.1.14")
(source (origin
(method url-fetch)
@@ 176,7 160,7 @@ to the @dfn{don't repeat yourself} (DRY) principle.")
(base32
"0ix3v2wlnplv78zxjrlw8z3hiap2d5mxvk0ny2fc65526shsb93j"))))
(propagated-inputs
- (modify-inputs (package-propagated-inputs python-django-3.2)
+ (modify-inputs (package-propagated-inputs python-django-4.2)
;; Django 4.0 deprecated pytz in favor of Pythons built-in zoneinfo.
(append python-pytz)))))
@@ 1055,39 1039,41 @@ support, and optional data-URI image and font embedding.")
(define-public python-django-rq
(package
(name "python-django-rq")
- (version "2.7.0")
+ (version "3.0.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "django-rq" version))
(sha256
(base32
- "0aw0fi0lg80qgdp9fhjbnlhvfh2p09rgy1nj6hxpyhi37kihni2h"))))
+ "1b371w4cdjlz83i2sg4gpx0z3svl3bfrn6zfy661374hv62xpnkv"))))
(build-system pyproject-build-system)
(arguments
(list
+ #:test-flags
+ #~(list "-k" "not test_scheduled_jobs and not test_started_jobs")
#:phases
- '(modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "redis-server" "--daemonize" "yes")
- (invoke "django-admin" "test" "django_rq"
- "--settings=django_rq.tests.settings"
- "--pythonpath=.")))))))
+ #~(modify-phases %standard-phases
+ (add-before 'check 'pre-check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "redis-server" "--daemonize" "yes")
+ (setenv "DJANGO_SETTINGS_MODULE" "django_rq.tests.settings")
+ (setenv "PYTHONPATH" (getcwd))))))))
(native-inputs
(list python-django-redis
- python-mock
+ python-pytest
+ python-pytest-django
python-rq-scheduler
python-setuptools
python-wheel
redis
tzdata-for-tests))
(propagated-inputs
- (list python-django python-rq))
+ (list python-django python-redis python-rq python-pyaml))
(home-page "https://github.com/ui/django-rq")
(synopsis "Django integration with RQ")
(description
- "Django integration with RQ, a Redis based Python queuing library.
+ "Django integration with RQ, a Redis based Python queuing library.
Django-RQ is a simple app that allows you to configure your queues in django's
settings.py and easily use them in your project.")
(license license:expat)))
M gnu/packages/documentation.scm => gnu/packages/documentation.scm +9 -8
@@ 41,6 41,7 @@
#:use-module (guix build-system copy)
#:use-module (guix build-system perl)
#:use-module (guix build-system python)
+ #:use-module (guix build-system pyproject)
#:use-module (guix build-system qt)
#:use-module (guix deprecation)
#:use-module (guix utils)
@@ 51,6 52,7 @@
#:use-module (gnu packages bash)
#:use-module (gnu packages check)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-build)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages bison)
#:use-module (gnu packages kde-frameworks)
@@ 315,6 317,8 @@ format, and supports the file types JPG, GIF, TIFF, PNG, and PNM for embedded
objects.")
(license license:artistic2.0)))
+;; XXX: This project looks not maintained, and some tests fail to pass, see
+;; <https://github.com/spyder-ide/docrepr/issues/49>.
(define-public python-docrepr
(package
(name "python-docrepr")
@@ 329,9 333,10 @@ objects.")
(base32
"1ma5gwy93m1djd3zdlnqfrwhgr8ic1qbsz5kkrb9f987ax40lfkd"))
(patches (search-patches "python-docrepr-fix-tests.patch"))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
(arguments
(list
+ #:tests? #f ; all tests fail
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'patch-sources
@@ 344,17 349,13 @@ objects.")
;; https://github.com/spyder-ide/docrepr/issues/54).
(substitute* "docrepr/utils.py"
(("except TypeError")
- "except (TypeError, shutil.Error)"))))
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "pytest" "-p" "no:warnings" "-vv")))))))
+ "except (TypeError, shutil.Error)")))))))
(native-inputs
(list python-ipython
python-matplotlib
python-numpy
- python-pytest
- python-pytest-asyncio))
+ python-setuptools
+ python-wheel))
(propagated-inputs
(list python-docutils
python-jinja2
M gnu/packages/ebook.scm => gnu/packages/ebook.scm +1 -1
@@ 249,7 249,7 @@ tags = [\"WS_X11\"]")
(string-append "[tool.sip.project]
sip-include-dirs = [\""
#$(this-package-input "python-pyqt")
- "/lib/python3.10/site-packages/PyQt5/bindings\"]")))
+ "/lib/python3.11/site-packages/PyQt5/bindings\"]")))
(substitute* "src/calibre/ebooks/pdf/pdftohtml.py"
(("PDFTOHTML = 'pdftohtml'")
(string-append "PDFTOHTML = \""
M gnu/packages/engineering.scm => gnu/packages/engineering.scm +17 -14
@@ 3138,7 3138,9 @@ Microwave engineering.")
python-scipy
python-sympy
python-wheel))
- (native-inputs (list python-pytest))
+ (native-inputs (list python-pytest
+ python-setuptools
+ python-wheel))
(home-page "https://github.com/mph-/lcapy")
(synopsis "Symbolic linear circuit analysis")
(description "Lcapy is a Python package for linear circuit analysis. It
@@ 5188,22 5190,23 @@ more.")
(package
(name "python-asyncua")
(version "1.1.5")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/FreeOpcUa/opcua-asyncio.git")
- (commit (string-append "v" version))
- (recursive? #t)))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0aisj8cpfhq50h4pv2p0c9iw5cqy3hxhn5adp8wd01c46dhg6y2x"))))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/FreeOpcUa/opcua-asyncio.git")
+ (commit (string-append "v" version))
+ ;; XXX: It clones <https://github.com/OPCFoundation/UA-Nodeset>
+ ;; submodule, check if it may be unbundled.
+ (recursive? #t)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0aisj8cpfhq50h4pv2p0c9iw5cqy3hxhn5adp8wd01c46dhg6y2x"))))
(build-system pyproject-build-system)
(native-inputs
- (list python-asynctest
+ (list python-pytest
python-pytest-asyncio-0.21
python-pytest-mock
- python-pytest-runner
python-setuptools
python-wheel))
(propagated-inputs
@@ 5342,7 5345,7 @@ and mogan.")
(("'\" [+] python_path [+]")
(string-append "'\" + std::string(\""
(assoc-ref outputs "out")
- "/lib/python3.10/site-packages"
+ "/lib/python3.11/site-packages"
"\") +")))))
(add-before 'check 'prepare-checks
(lambda _
M gnu/packages/file-systems.scm => gnu/packages/file-systems.scm +0 -27
@@ 2035,33 2035,6 @@ compatible directories.")
(home-page "https://github.com/trapexit/mergerfs-tools")
(license license:isc))))
-(define-public python-dropbox
- (package
- (name "python-dropbox")
- (version "12.0.2")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "dropbox" version))
- (sha256
- (base32 "0qlrc2ykl7zmv808apqv5ycfzrwnm13ngz1daizh9kszmpapy1ah"))
- (snippet
- '(begin
- (use-modules (guix build utils))
- (substitute* "setup.py"
- (("pytest-runner==5\\.2\\.0") "pytest-runner"))))))
- (build-system python-build-system)
- (arguments '(#:tests? #f)) ; Tests not included in the release tarball.
- (native-inputs
- (list python-pytest python-pytest-runner))
- (propagated-inputs
- (list python-requests python-six python-stone))
- (home-page "https://www.dropbox.com/developers")
- (synopsis "Official Dropbox API Client")
- (description "This package provides a Python SDK for integrating with the
-Dropbox API v2.")
- (license license:expat)))
-
(define-public dbxfs
(package
(name "dbxfs")
M gnu/packages/finance.scm => gnu/packages/finance.scm +57 -63
@@ 1039,15 1039,23 @@ of Bitcoin BIP-0039.")
(package
(name "python-u2flib-host")
(version "3.0.3")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "python-u2flib-host" version))
- (sha256
- (base32
- "02pwafd5kyjpc310ys0pgnd0adff1laz18naxxwsfrllqafqnrxb"))))
- (build-system python-build-system)
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "python-u2flib-host" version))
+ (sha256
+ (base32 "02pwafd5kyjpc310ys0pgnd0adff1laz18naxxwsfrllqafqnrxb"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ #~(list
+ "--deselect=test/test_soft.py::TestSoftU2FDevice::test_registeration"
+ "--deselect=test/test_reg_auth.py::TestRegister::test_register" "-k"
+ "not test_forget")))
(propagated-inputs (list python-hidapi python-requests))
- (native-inputs (list python-cryptography))
+ (native-inputs (list python-cryptography python-pytest python-setuptools
+ python-wheel))
(home-page "https://github.com/Yubico/python-u2flib-host")
(synopsis "Python based U2F host library")
(description
@@ 1059,32 1067,36 @@ of Bitcoin BIP-0039.")
(name "python-ledgerblue")
(version "0.1.54")
(source
- (origin
- (method url-fetch)
- (uri (pypi-uri "ledgerblue" version))
- (sha256
- (base32
- "0ghpvxgih1zarp788qi1xh5xmprv6yhaxglfbix4974i7r4pszqy"))))
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "ledgerblue" version))
+ (sha256
+ (base32 "0ghpvxgih1zarp788qi1xh5xmprv6yhaxglfbix4974i7r4pszqy"))))
(build-system pyproject-build-system)
(arguments
- `(#:tests? #f)) ; no tests
- (native-inputs
- (list python-setuptools python-wheel))
- (propagated-inputs
- (list python-bleak
- python-pyelftools
- python-pycryptodome
- python-ecpy
- python-future
- python-gnupg
- python-hidapi
- python-nfcpy
- python-pillow
- python-protobuf
- python-pycryptodomex
- python-pyscard
- python-u2flib-host
- python-websocket-client))
+ (list
+ #:tests? #f
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'build 'pretend-version
+ (lambda _
+ (setenv "SETUPTOOLS_SCM_PRETEND_VERSION"
+ #$version))))))
+ (native-inputs (list python-setuptools python-setuptools-scm python-wheel))
+ (propagated-inputs (list python-bleak
+ python-pyelftools
+ python-pycryptodome
+ python-ecpy
+ python-future
+ python-gnupg
+ python-hidapi
+ python-nfcpy
+ python-pillow
+ python-protobuf
+ python-pycryptodomex
+ python-pyscard
+ python-u2flib-host
+ python-websocket-client))
(home-page "https://github.com/LedgerHQ/blue-loader-python")
(synopsis "Python library to communicate with Ledger Blue/Nano S")
(description "@code{ledgerblue} is a Python library to communicate with
@@ 1216,9 1228,11 @@ the KeepKey Hardware Wallet.")
(sha256
(base32
"03zj602m2rln9yvr08dswy56vzkbldp8b074ixwzz525dafblr92"))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
(inputs
(list python-ledgerblue python-trezor-agent))
+ (native-inputs
+ (list python-setuptools python-wheel))
(home-page "https://github.com/romanz/trezor-agent")
(synopsis "Ledger as hardware SSH/GPG agent")
(description "This package allows using Ledger as hardware SSH/GPG agent.")
@@ 1414,42 1428,22 @@ Luhn and family of ISO/IEC 7064 check digit algorithms.")
(define-public python-duniterpy
(package
(name "python-duniterpy")
- (version "1.1.1")
+ (version "1.2.1")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "duniterpy" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://git.duniter.org/clients/python/duniterpy")
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
- (base32 "0h0fsawsrjd50lb1bkysb21ph39qlhmiymd3r5vs695qxvbwaqaa"))))
+ (base32 "1ysh9b5lzg053hv4iw3zbn7hid05qssiwmrl8sir8qlk958r8x60"))))
(build-system pyproject-build-system)
- (arguments
- ;; FIXME: Tests fail with: "TypeError: block_uid() missing 1 required
- ;; positional argument: 'value'".
- `(#:tests? #f
- #:phases (modify-phases %standard-phases
- (add-after 'unpack 'loosen-requirements
- (lambda _
- (substitute* "pyproject.toml"
- (("mnemonic = \"\\^0\\.19")
- "mnemonic = \">=0.19")
- (("jsonschema = \"\\^3\\.2")
- "jsonschema = \">=3.2"))))
- (add-after 'unpack 'adjust-for-new-libnacl
- (lambda _
- ;; Mimic upstream commit ad8f6a26e9e7067; remove
- ;; for newer versions of duniterpy.
- (substitute* "pyproject.toml"
- (("libnacl = \"1\\.8")
- "libnacl = \">=1.9"))
- (substitute* "duniterpy/key/ascii_armor.py"
- (("from libnacl\\.version import version as libnacl_version")
- "import importlib.metadata
-libnacl_version = importlib.metadata.version('libnacl')")))))))
(native-inputs
- (list python-poetry-core))
+ (list python-poetry-core-next
+ python-pytest))
(propagated-inputs
- (list python-attrs
- python-base58
+ (list python-base58
python-graphql-core
python-jsonschema
python-libnacl
M gnu/packages/fontutils.scm => gnu/packages/fontutils.scm +6 -1
@@ 505,14 505,19 @@ subroutinizer for fontTools.")
(uri (pypi-uri "cu2qu" version ".zip"))
(sha256
(base32 "1x762r7bf39g6aivfvrmq00h6f07abvs9x1xm0fz8l81vq8jz64c"))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
+ (arguments
+ ;; XXX: Try to remove it when updating python-fonttools.
+ (list #:test-flags #~(list "-k" "not test_ignore_single_points")))
(propagated-inputs (list python-fonttools))
(native-inputs
(list python-cython
python-defcon
python-pytest
python-pytest-runner
+ python-setuptools
python-setuptools-scm
+ python-wheel
unzip))
(home-page "https://github.com/googlefonts/cu2qu")
(synopsis "Cubic-to-quadratic bezier curve conversion")
M gnu/packages/freedesktop.scm => gnu/packages/freedesktop.scm +12 -7
@@ 68,6 68,7 @@
#:use-module (guix build-system gnu)
#:use-module (guix build-system meson)
#:use-module (guix build-system perl)
+ #:use-module (guix build-system pyproject)
#:use-module (guix build-system python)
#:use-module (guix build-system glib-or-gtk)
#:use-module (guix build-system qt)
@@ 128,6 129,7 @@
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages polkit)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-build)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages qt)
@@ 789,7 791,7 @@ other applications that need to directly deal with input devices.")
(define-public libei
(package
(name "libei")
- (version "1.3.0")
+ (version "1.4.0")
(source (origin
(method git-fetch)
(uri (git-reference
@@ 797,7 799,7 @@ other applications that need to directly deal with input devices.")
(commit version)))
(sha256
(base32
- "0idbl20ax060s7m435rszfv7c0bvpinjvq45qbqwvcvp0hg8r9y8"))
+ "04ll43616pyfm7c835azdggx9x3vfykpcg3pzmsfz4f2vl5whalm"))
(snippet
#~(begin
(use-modules (guix build utils))
@@ 819,17 821,18 @@ other applications that need to directly deal with input devices.")
;; liboeffis-1.0.pc requires.private libelogind
(list elogind))
(native-inputs
- (list doxygen
+ (list dbus
+ doxygen
libxml2
munit
pkg-config
python
python-attrs
- python-black
python-dbusmock
python-jinja2
python-pytest
python-structlog
+ python-pyaml
valgrind/interactive))
(home-page "https://libinput.pages.freedesktop.org/libei/")
(synopsis "Emulated Input protocol implementation")
@@ 2872,17 2875,19 @@ encoding names are iconv-compatible.")
(define-public python-cchardet
(package
(name "python-cchardet")
- (version "2.1.7")
+ (version "2.2.0a2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "cchardet" version))
(sha256
(base32
- "1bqfz85cd51sw0bvhvdq9ikccxi2ld7g5jpni4jkq1a5clrvca64"))))
- (build-system python-build-system)
+ "08wq5yfaafbjipabfc6kpyvivkk2394w7isv0mwx5agcf8cbnwnx"))))
+ (build-system pyproject-build-system)
(inputs
(list uchardet))
+ (native-inputs
+ (list python-setuptools python-wheel))
(home-page "https://github.com/PyYoshi/cChardet")
(synopsis "High-performance character encoding detection for Python")
(description "cChardet is a character encoding detector, written in
M gnu/packages/gnome-xyz.scm => gnu/packages/gnome-xyz.scm +1 -1
@@ 67,10 67,10 @@
#:use-module (gnu packages ibus)
#:use-module (gnu packages inkscape)
#:use-module (gnu packages image)
+ #:use-module (gnu packages maths)
#:use-module (gnu packages pcre)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
- #:use-module (gnu packages python-science)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages ssh)
#:use-module (gnu packages tls)
M gnu/packages/gnome.scm => gnu/packages/gnome.scm +3 -54
@@ 7479,60 7479,6 @@ almost all of them.")
principles are simplicity and standards compliance.")
(license license:gpl2+)))
-(define-public d-feet
- (package
- (name "d-feet")
- (version "0.3.16")
- (source (origin
- (method url-fetch)
- (uri (string-append "mirror://gnome/sources/" name "/"
- (version-major+minor version) "/"
- name "-" version ".tar.xz"))
- (sha256
- (base32
- "1jqw5ndpgyb0zxh0g21ai1911lfrm56vz18xbccfqm4sk95wwcw7"))
- (patches
- (search-patches "d-feet-drop-unused-meson-argument.patch"))))
- (build-system meson-build-system)
- (arguments
- (list
- #:glib-or-gtk? #t
- #:phases
- #~(modify-phases %standard-phases
- (add-before 'check 'pre-check
- (lambda _
- ;; The test suite requires a running X server.
- (system "Xvfb :1 &")
- (setenv "DISPLAY" ":1")))
- (add-before 'install 'disable-gtk-update-icon-cache
- (lambda _
- (setenv "DESTDIR" "/")))
- (add-after 'install 'wrap-program
- (lambda* (#:key outputs #:allow-other-keys)
- (wrap-program (search-input-file outputs "bin/d-feet")
- `("GUIX_PYTHONPATH" = (,(getenv "GUIX_PYTHONPATH")))
- `("GI_TYPELIB_PATH" = (,(getenv "GI_TYPELIB_PATH")))))))))
- (native-inputs
- (list `(,glib "bin")
- intltool
- itstool
- libxml2
- pkg-config
- python-pep8
- xorg-server-for-tests))
- (inputs
- (list bash-minimal
- gobject-introspection
- gtk+
- python-wrapper
- python-pygobject))
- (home-page "https://wiki.gnome.org/Apps/DFeet")
- (synopsis "D-Bus debugger")
- (description
- "D-Feet is a D-Bus debugger, which can be used to inspect D-Bus interfaces
-of running programs and invoke methods on those interfaces.")
- (license license:gpl2+)))
-
(define-public d-spy
(package
(name "d-spy")
@@ 7574,6 7520,9 @@ programs via D-Bus. It also ships a library for integration into development
environments.")
(license license:gpl2+)))
+(define-public d-feet
+ (deprecated-package "d-feet" d-spy))
+
(define-public yelp-xsl
(package
(name "yelp-xsl")
M gnu/packages/gnupg.scm => gnu/packages/gnupg.scm +9 -2
@@ 5,7 5,7 @@
;;; Copyright © 2014, 2015, 2016, 2020 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
;;; Copyright © 2015-2021, 2024 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2015, 2016, 2017, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2019, 2025 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016 Christine Lemmer-Webber <cwebber@dustycloud.org>
;;; Copyright © 2016, 2017 Nikita <nikita@n0.is>
;;; Copyright © 2016 Christopher Baines <mail@cbaines.net>
@@ 585,10 585,17 @@ interface (FFI) of Guile.")
"1ji3ynhp36m1ccx7bmaq75dhij9frpn19v9mpi4aajn8csl194il"))))
(build-system python-build-system)
(arguments
- '(#:phases
+ `(#:phases
(modify-phases %standard-phases
(add-before 'build 'set-environment
(lambda _
+ ;; GPGME is built with large file support, so we need to set
+ ;; _FILE_OFFSET_BITS to 64 in all users of the GPGME library.
+ ,@(if (or (target-x86-32?) (target-arm32?))
+ `((substitute* "setup.py"
+ (("extra_macros = dict\\(\\)")
+ "extra_macros = { \"_FILE_OFFSET_BITS\": 64 }")))
+ '())
(substitute* "setup.py"
(("cc") (which "gcc")))
#t)))
M gnu/packages/gnuzilla.scm => gnu/packages/gnuzilla.scm +19 -2
@@ 8,7 8,7 @@
;;; Copyright © 2017, 2023 Clément Lassieur <clement@lassieur.org>
;;; Copyright © 2017, 2018 Nikita <nikita@n0.is>
;;; Copyright © 2017, 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2018, 2020 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2018, 2020, 2025 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2019 Ivan Petkov <ivanppetkov@gmail.com>
;;; Copyright © 2020, 2024 Oleg Pykhalov <go.wigust@gmail.com>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
@@ 142,6 142,14 @@
"--with-intl-api")
#:phases
#~(modify-phases %standard-phases
+ (add-after 'unpack 'python-3.11-compatibility
+ (lambda _
+ (substitute* '("python/mozbuild/mozpack/files.py"
+ "python/mozbuild/mozbuild/util.py"
+ "python/mozbuild/mozbuild/action/process_define_files.py"
+ "python/mozbuild/mozbuild/backend/base.py"
+ "python/mozbuild/mozbuild/preprocessor.py")
+ (("\"rU\"") "\"r\""))))
(add-after 'patch-source-shebangs 'patch-cargo-checksums
(lambda _
(let ((null-hash
@@ 278,6 286,15 @@ in C/C++.")
(substitute-keyword-arguments (package-arguments mozjs)
((#:phases phases)
#~(modify-phases #$phases
+ (add-after 'unpack 'python-3.11-compatibility
+ (lambda _
+ (substitute* '("python/mozbuild/mozpack/files.py"
+ "python/mozbuild/mozbuild/util.py"
+ "python/mozbuild/mozbuild/action/process_define_files.py"
+ "python/mozbuild/mozbuild/backend/base.py"
+ "python/mozbuild/mozbuild/preprocessor.py"
+ "python/mozbuild/mozbuild/virtualenv.py")
+ (("'rU'") "'r'"))))
(add-after 'unpack 'patch-for-python-3.10
(lambda _
;; Some classes were moved from collections to collections.abc
@@ 1650,7 1667,7 @@ their corresponding VERSION, SOURCE and LOCALES variables."
(setenv "MACH_BUILD_PYTHON_NATIVE_PACKAGE_SOURCE" "system")
(setenv "GUIX_PYTHONPATH"
(string-append (getcwd)
- "/obj/_virtualenvs/build/lib/python3.10/site-packages"))
+ "/obj/_virtualenvs/build/lib/python3.11/site-packages"))
(setenv "BUILD_BACKENDS" "FasterMake,RecursiveMake")))
(replace 'build ;build and install data files
(lambda* (#:key outputs #:allow-other-keys)
M gnu/packages/graph.scm => gnu/packages/graph.scm +2 -2
@@ 389,9 389,9 @@ subplots, multiple-axes, polar charts, and bubble charts.")
(patches (search-patches "python-louvain-fix-test.patch"))
(sha256
(base32 "0sx53l555rwq0z7if8agirjgw4ddp8r9b949wwz8vlig03sjvfmp"))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
(native-inputs
- (list python-setuptools-57)) ;for use_2to3 support
+ (list python-setuptools python-wheel))
(propagated-inputs
(list python-networkx python-numpy))
(home-page "https://github.com/taynaud/python-louvain")
M gnu/packages/graphviz.scm => gnu/packages/graphviz.scm +10 -14
@@ 209,7 209,7 @@ structure and layout algorithms.")
(define-public python-uqbar
(package
(name "python-uqbar")
- (version "0.6.9")
+ (version "0.7.2")
(source
(origin
(method git-fetch)
@@ 218,27 218,23 @@ structure and layout algorithms.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "037qj3rymm6xzdpklddfhmfp2p1bq9fi3jrvxj6gmharphd5z869"))))
+ (base32 "1limp2m2smg0l3v6vn2fwhjcw1d8gakw5v0q7krb03q539qiql87"))))
(build-system pyproject-build-system)
- (arguments ; XXX: Disable failing tests.
- (list #:test-flags '(list "tests" "-k" "not test_find_executable \
-and not test_sphinx_book_text_broken_strict")))
+ (arguments
+ (list
+ #:test-flags #~(list "--pyargs" "uqbar")))
(native-inputs
(list graphviz
- python-flake8
- python-isort
- python-mypy
+ python-defusedxml
python-pytest
python-pytest-cov
python-setuptools
+ python-typing-extensions
python-wheel))
(propagated-inputs
- (list python-black python-sphinx-5 python-unidecode
- (package/inherit python-sphinx-rtd-theme
- (propagated-inputs
- (modify-inputs
- (package-propagated-inputs python-sphinx-rtd-theme)
- (replace "python-sphinx" python-sphinx-5))))))
+ (list python-black
+ python-sphinx
+ python-unidecode))
(home-page "https://github.com/josiah-wolf-oberholtzer/uqbar")
(synopsis "Tools for building documentation with Sphinx, Graphviz and LaTeX")
(description
M gnu/packages/image-processing.scm => gnu/packages/image-processing.scm +37 -45
@@ 1812,63 1812,55 @@ processing pipelines.")
(define-public labelme
(package
(name "labelme")
- (version "4.5.13")
+ ;; It's the latest available version which does not require not packaged
+ ;; <https://github.com/wkentaro/osam>.
+ (version "5.2.1")
(source
(origin
;; PyPi tarball lacks tests.
(method git-fetch)
(uri (git-reference
- (url "https://github.com/wkentaro/labelme.git")
+ (url "https://github.com/wkentaro/labelme")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0cmi2xb4dgh7738l259rgwhn9l134f0vnaaqc2gflc5yr3lqhrv2"))))
- (build-system python-build-system)
+ (base32 "1xpyad6rlkxyx51jaai4xhdy15k1gvm62xnkjn152hc1vj1c77sr"))))
+ (build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'loosen-requirements
- (lambda _
- ;; Don't require an outdated version of matplotlib.
- (substitute* "setup.py"
- (("matplotlib<3\\.3")
- "matplotlib"))))
- (add-before 'check 'start-xserver
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((xorg-server (assoc-ref inputs "xorg-server")))
- ;; Options taken from CI workflow.
- (system (string-append xorg-server "/bin/Xvfb :99 -screen 0 "
- "1920x1200x24 -ac +extension GLX +render "
- "-noreset &"))
- (setenv "DISPLAY" ":99.0"))))
- (replace 'check
- (lambda* (#:key inputs outputs tests? #:allow-other-keys)
- (when tests?
- (add-installed-pythonpath inputs outputs)
- ;; Fails when invoking help2man for unknown reason.
- (delete-file "tests/docs_tests/man_tests/test_labelme_1.py")
- ;; One test hangs.
- (delete-file "tests/labelme_tests/widgets_tests/test_label_dialog.py")
- ;; Calls incompatible function signatures.
- (delete-file "tests/labelme_tests/widgets_tests/test_label_list_widget.py")
- (setenv "MPLBACKEND" "agg")
- (invoke "pytest" "-v" "tests" "-m" "not gpu")))))))
- (propagated-inputs
- (list python-imgviz
- python-matplotlib
- python-numpy
- python-pillow
- python-pyyaml
- python-qtpy
- python-termcolor))
+ (list
+ #:test-flags
+ #~(list "-m" "not gpu"
+ ;; Fails when invoking help2man for unknown reason.
+ "--ignore=tests/docs_tests/man_tests/test_labelme_1.py")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'check 'start-xserver
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((xorg-server #$(this-package-native-input "xorg-server")))
+ ;; Options taken from CI workflow.
+ (system (string-append xorg-server "/bin/Xvfb :99 -screen 0 "
+ "1920x1200x24 -ac +extension GLX +render "
+ "-noreset &"))
+ (setenv "DISPLAY" ":99.0")))))))
(native-inputs
- (list python-pytest python-pytest-qt xorg-server-for-tests))
+ (list python-pytest
+ python-pytest-qt
+ xorg-server-for-tests
+ python-wheel))
+ (propagated-inputs
+ (list python-imgviz
+ python-matplotlib
+ python-natsort
+ python-numpy
+ python-pillow
+ python-pyyaml
+ python-qtpy
+ python-termcolor))
(home-page "https://github.com/wkentaro/labelme")
- (synopsis
- "Image Polygonal Annotation")
+ (synopsis "Image Polygonal Annotation")
(description
- "Image and video labeling tool supporting different shapes like
-polygons, rectangles, circles, lines, points and VOC/COCO export.")
+ "Image and video labeling tool supporting different shapes like polygons,
+rectangles, circles, lines, points and VOC/COCO export.")
(license license:gpl3+)))
(define-public charls
M gnu/packages/image.scm => gnu/packages/image.scm +4 -0
@@ 2761,6 2761,10 @@ GIF, TIFF, WEBP, BMP, PNG, XPM formats.")
(guix build utils))
#:phases
(modify-phases %standard-phases
+ (add-after 'unpack 'python3.11-compatibility
+ (lambda _
+ (substitute* "setup.py"
+ (("\"rU\"") "\"r\""))))
(add-after 'install 'glib-or-gtk-wrap
(assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap))
(add-after 'install 'wrap-program
M gnu/packages/irc.scm => gnu/packages/irc.scm +1 -1
@@ 919,7 919,7 @@ parsers")
;; unmaintained clone of <https://github.com/ircdocs/parser-tests>
;; which is packed in Guix as python-irc-parser-tests. Tests data
;; (YAML files) are distributed as Python package and located in
- ;; <lib/python3.10/site-packages/parser_tests/data/>.
+ ;; <lib/python3.11/site-packages/parser_tests/data/>.
(add-before 'check 'install-testcases-data
(lambda* (#:key import-path #:allow-other-keys)
(with-directory-excursion (string-append "src/" import-path)
M gnu/packages/iso-codes.scm => gnu/packages/iso-codes.scm +2 -1
@@ 122,7 122,8 @@ information.")
(build-system pyproject-build-system)
(native-inputs
(list python-pytest
- python-setuptools))
+ python-setuptools
+ python-wheel))
(propagated-inputs
(list python-pandas))
(home-page "https://github.com/IndEcol/country_converter")
M gnu/packages/jupyter.scm => gnu/packages/jupyter.scm +5 -12
@@ 64,13 64,6 @@
(sha256
(base32 "1qrhzazq10dz64y9mawr3ns595fsdhrj1wvbb42xhmcl66r1xq8a"))))
(build-system pyproject-build-system)
- (arguments
- (list
- #:phases
- ;; Because python-jsonschema has an old python-webcolor. Remove this
- ;; when python-team branch is merged.
- '(modify-phases %standard-phases
- (delete 'sanity-check))))
(propagated-inputs (list python-argon2-cffi
python-ipykernel
python-ipython-genutils
@@ 96,7 89,7 @@
python-pytest-jupyter
python-pytest-tornasync
python-requests
- python-requests-unixsocket
+ python-requests-unixsocket2
python-testpath))
(home-page "https://github.com/jupyter/nbclassic")
(synopsis "Jupyter Notebook as a Jupyter Server extension")
@@ 601,7 594,7 @@ JavaScript build steps.")
(setenv "PATH"
(string-append #$output "/bin:" (getenv "PATH"))))))))
(propagated-inputs
- (list python-anyio/without-dataclasses
+ (list python-anyio
python-argon2-cffi
python-jinja2
python-jupyter-client
@@ 1062,13 1055,13 @@ a notebook.")
(define-public python-ipympl
(package
(name "python-ipympl")
- (version "0.9.1")
+ (version "0.9.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "ipympl" version))
(sha256
- (base32 "11rppjdqzgs4pfiq8gww5xkpbk21fp86vvv839v56b9rqq06j2b4"))))
+ (base32 "12qgiy08klqb5gipm23yzh09p5g2k8ihcq2bprprdya84acw2rf8"))))
(build-system python-build-system)
(propagated-inputs
(list python-ipython
@@ 1079,7 1072,7 @@ a notebook.")
python-pillow
python-traitlets))
(native-inputs
- (list python-jupyter-packaging))
+ (list python-hatchling python-jupyter-packaging))
(home-page "https://matplotlib.org/ipympl/")
(synopsis "Matplotlib Jupyter Extension")
(description "Leveraging the Jupyter interactive widgets framework, ipympl
M gnu/packages/llvm.scm => gnu/packages/llvm.scm +1 -1
@@ 663,7 663,7 @@ output), and Binutils.")
(rename-file (string-append #$output "/share/opt-viewer")
opt-viewer-share))))
;; The build daemon goes OOM on i686-linux on this phase.
- #$@(if (and (version>=? version "16.0")
+ #$@(if (and (version>=? version "15.0")
(target-x86-32?))
#~((delete 'make-dynamic-linker-cache))
#~()))))
M gnu/packages/machine-learning.scm => gnu/packages/machine-learning.scm +140 -101
@@ 234,8 234,16 @@ family of functions.")
(sha256
(base32 "0cgysij0dix0fikyz2x4f8jvaskm5s5a04s07chzaz2dw1fpxdq8"))))
(build-system pyproject-build-system)
- (arguments ; disable flaky test
- (list #:test-flags '(list "-k" "not test_integrate_variable[x23-i]")))
+ (arguments
+ (list
+ #:test-flags
+ '(list "-k"
+ (string-append
+ ;; Disable flaky test
+ "not test_integrate_variable[x23-i]"
+ ;; XXX This test fails because the length of arguments
+ ;; is longer than the length of inputs.
+ " and not test_function_of_numeric_array"))))
(propagated-inputs (list python-makefun python-multipledispatch
python-numpy python-opt-einsum
python-typing-extensions))
@@ 423,33 431,25 @@ machine learning algorithms based on GPs.")
(define-public python-ml-collections
(package
(name "python-ml-collections")
- (version "0.1.1")
+ (version "1.0.0")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "ml_collections" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/google/ml_collections")
+ (commit (string-append "v" version))))
(sha256
- (base32 "1k38psfzqsqnl99fl578bd07zdmvfkja61r3sgjs2fj3xircrvrz"))))
+ (base32 "1f3rwbgnnvgh2jgnkwxfjdw18yly41hlx9fy56h0x36zyy8p0j21"))))
(build-system pyproject-build-system)
(arguments
(list
- #:phases
- #~(modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- ;; TODO: we can't seem to run the config_flags tests, because
- ;; the installed Python files conflict with those from the
- ;; source directory, resulting in constants to be defined more
- ;; than once.
- (invoke "pytest" "ml_collections/config_dict/tests"
- ;; This one fails because we're testing the __main__
- ;; class, not config_dict_test.
- "-k" "not testJSONConversionBestEffort")))))))
+ #:test-flags '(list "--pyargs" "ml_collections/config_dict/tests")))
(propagated-inputs
- (list python-absl-py python-contextlib2 python-pyyaml python-six))
- (native-inputs (list python-mock python-pytest python-setuptools
- python-wheel))
+ (list python-absl-py python-pyyaml))
+ (native-inputs (list python-pylint
+ python-pytest
+ python-pytest-xdist
+ python-flit-core))
(home-page "https://github.com/google/ml_collections")
(synopsis "Python collections designed for Machine Learning usecases")
(description
@@ 1843,7 1843,7 @@ in terms of new algorithms.")
pybind11
python-coverage
python-fb-re2
- python-parameterized-next
+ python-parameterized
python-pytest
python-pytest-runner
python-setuptools
@@ 2553,7 2553,7 @@ standard feature selection algorithms.")
(define-public python-cleanlab
(package
(name "python-cleanlab")
- (version "2.7.0")
+ (version "2.7.1")
;; The version on pypi does not come with tests.
(source (origin
(method git-fetch)
@@ 2563,7 2563,7 @@ standard feature selection algorithms.")
(file-name (git-file-name name version))
(sha256
(base32
- "0f8v5246nzy22r7zswv9vbpxc7wxaqjwry9iq0fqjp2ffch88h6j"))))
+ "073w45azq496x4bhrh8mdywcrg3gk33n13w1pqh1kiykw826ld9b"))))
(build-system pyproject-build-system)
(arguments
(list
@@ 2681,37 2681,37 @@ Covariance Matrix Adaptation Evolution Strategy (CMA-ES) for Python.")
(license license:expat)))
(define-public python-autograd
- (let* ((commit "c6d81ce7eede6db801d4e9a92b27ec5d409d0eab")
- (revision "0")
- (version (git-version "1.5" revision commit)))
- (package
- (name "python-autograd")
- (home-page "https://github.com/HIPS/autograd")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url home-page)
- (commit commit)))
- (sha256
- (base32
- "04kljgydng42xlg044h6nbzxpban1ivd6jzb8ydkngfq88ppipfk"))
- (file-name (git-file-name name version))))
- (version version)
- (build-system pyproject-build-system)
- (native-inputs
- (list python-nose python-pytest python-setuptools python-wheel))
- (propagated-inputs
- (list python-future python-numpy))
- (synopsis "Efficiently computes derivatives of NumPy code")
- (description "Autograd can automatically differentiate native Python and
-NumPy code. It can handle a large subset of Python's features, including loops,
-ifs, recursion and closures, and it can even take derivatives of derivatives
-of derivatives. It supports reverse-mode differentiation
+ (package
+ (name "python-autograd")
+ (version "1.7.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/HIPS/autograd")
+ (commit (string-append "v" version))))
+ (sha256
+ (base32 "1fpnmm3mzw355iq7w751j4mjfcr0yh324cxidba1l22652gg8r8m"))
+ (file-name (git-file-name name version))))
+ (build-system pyproject-build-system)
+ (native-inputs
+ (list python-hatchling
+ python-pytest))
+ (propagated-inputs
+ (list python-future
+ python-numpy))
+ (home-page "https://github.com/HIPS/autograd")
+ (synopsis "Efficiently computes derivatives of NumPy code")
+ (description
+ "Autograd can automatically differentiate native Python and NumPy code.
+It can handle a large subset of Python's features, including loops, ifs,
+recursion and closures, and it can even take derivatives of derivatives of
+derivatives. It supports reverse-mode differentiation
(a.k.a. backpropagation), which means it can efficiently take gradients of
scalar-valued functions with respect to array-valued arguments, as well as
forward-mode differentiation, and the two can be composed arbitrarily. The
main intended application of Autograd is gradient-based optimization.")
- (license license:expat))))
+ (license license:expat)))
(define-public lightgbm
(package
@@ 3370,8 3370,14 @@ Python.")
;; SOURCE_DATE_EPOCH is respected, which we set to some time in
;; 1980.
(lambda _ (setenv "SOURCE_DATE_EPOCH" "315532800")))
- (add-after 'unpack 'python3.10-compatibility
+ (add-after 'unpack 'python3.11-compatibility
(lambda _
+ ;; Py_TYPE was changed to an inline static function in Python
+ ;; 3.11, so it cannot be used on the left-hand side.
+ (substitute* "tensorflow/python/lib/core/bfloat16.cc"
+ (("Py_TYPE\\(&NPyBfloat16_Descr\\) = &PyArrayDescr_Type;")
+ "Py_SET_TYPE(&NPyBfloat16_Descr, &PyArrayDescr_Type);"))
+
;; See https://github.com/tensorflow/tensorflow/issues/20517#issuecomment-406373913
(substitute* '("tensorflow/python/eager/pywrap_tfe_src.cc"
"tensorflow/python/lib/core/ndarray_tensor.cc"
@@ 3421,6 3427,16 @@ Python.")
(string-append m
" and not isinstance(existing, type(object.__or__))")))
+ ;; ArgSpec has been replaced with FullArgSpec.
+ (substitute* "tensorflow/python/util/tf_inspect.py"
+ (("ArgSpec = _inspect.ArgSpec") "\
+ArgSpec = namedtuple('ArgSpec', [ 'args', 'varargs', 'keywords', 'defaults' ])
+def makeargspec(s):
+ return ArgSpec(args=s.args, varargs=s.varargs, keywords=s.varkw, defaults=s.defaults)
+")
+ (("_inspect.getargspec\\((.*)\\)" m target)
+ (string-append "makeargspec(_inspect.getfullargspec(" target "))")))
+
;; Fix the build with numpy >= 1.19.
;; Suggested in https://github.com/tensorflow/tensorflow/issues/41086#issuecomment-656833081
(substitute* "tensorflow/python/lib/core/bfloat16.cc"
@@ 3441,7 3457,22 @@ Python.")
(substitute* '("tensorflow/python/framework/fast_tensor_util.pyx"
"tensorflow/python/estimator/canned/linear_testing_utils.py")
(("np.asscalar") "np.ndarray.item"))))
- (add-after 'python3.10-compatibility 'chdir
+ (add-after 'python3.11-compatibility 'numpy-compatibility
+ (lambda _
+ (substitute* (cons* "tensorflow/compiler/xla/python/xla_client.py"
+ "tensorflow/contrib/layers/python/ops/sparse_ops_test.py"
+ (find-files "tensorflow/python/" "\\.py$"))
+ (("np.object") "object"))
+ (substitute* (append
+ '("tensorflow/compiler/tests/unary_ops_test.py"
+ "tensorflow/compiler/xla/python/xla_client.py"
+ "tensorflow/compiler/xla/python/xla_client_test.py")
+ (find-files "tensorflow/python/" "\\.py$")
+ (find-files "tensorflow/contrib/" "\\.py$"))
+ (("np.bool,") "bool,")
+ (("np.bool\\)") "bool)")
+ (("np.bool:") "bool:"))))
+ (add-after 'numpy-compatibility 'chdir
(lambda _ (chdir "tensorflow/contrib/cmake")))
(add-after 'chdir 'disable-downloads
(lambda* (#:key inputs #:allow-other-keys)
@@ 4169,7 4200,7 @@ project, and it will potentially also do the same for the Lime project.")
(propagated-inputs
(list python-h5py python-numpy))
(native-inputs
- (list python-pytest python-pytest-cov python-pytest-pep8
+ (list python-pytest python-pytest-cov
python-pytest-xdist))
(home-page "https://github.com/keras-team/keras-applications")
(synopsis "Reference implementations of popular deep learning models")
@@ 4339,7 4370,6 @@ with image data, text data, and sequence data.")
python-pandas
python-pytest
python-pytest-cov
- python-pytest-pep8
python-pytest-timeout
python-pytest-xdist
python-pyux
@@ 5558,7 5588,10 @@ Note: currently this package does not provide GPU support.")
;; These refuse to be run on CPU and really want a GPU
" and not test_add_random_walk_pe"
" and not test_asap"
- " and not test_two_hop"))
+ " and not test_two_hop"
+ ;; Failed when switched to python@3.11
+ ;; typing module internals
+ " and not test_type_repr"))
#:phases
'(modify-phases %standard-phases
(add-after 'unpack 'delete-top-level-directories
@@ 6315,7 6348,7 @@ tokenizers, @code{rust-tokenizers}.")
python-tokenizers
python-tqdm))
(native-inputs
- (list python-parameterized-next
+ (list python-parameterized
python-pytest python-setuptools python-wheel))
(home-page "https://github.com/huggingface/transformers")
(synopsis "Machine Learning for PyTorch and TensorFlow")
@@ 6459,34 6492,33 @@ of Hidden Markov Models.")
(define-public python-lap
(package
(name "python-lap")
- (version "0.4.0")
+ (version "0.5.12")
(source (origin
(method url-fetch)
(uri (pypi-uri "lap" version))
(sha256
(base32
- "0fqfxpq4jg9h4wxjw540gjmvfg1ccc1nssk7i9njg7qfdybxknn4"))))
- (build-system python-build-system)
+ "1za4mf5nd7vzwd24sy2mfxrk8mnwq7d8rv6h96yh8v5flx7422sp"))))
+ (build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (replace 'build
- (lambda* (#:key inputs #:allow-other-keys)
- (invoke "python" "setup.py" "build"
- "--cpu-baseline=sse2")))
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- ;; The tests must be run from elsewhere.
- (mkdir-p "/tmp/test")
- (copy-recursively "lap/tests" "/tmp/test")
- (with-directory-excursion "/tmp/test"
- (invoke "pytest" "-vv"))))))))
+ (list
+ #:test-flags #~(list "-v" #$output)
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'check 'check-cleanup
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (for-each
+ delete-file-recursively
+ (find-files #$output
+ (lambda (file stat)
+ (or (member (basename file)
+ '("tests" ".pytest_cache"))))
+ #:directories? #t))))))))
(propagated-inputs
- (list python-numpy
- python-scipy))
+ (list python-numpy))
(native-inputs
- (list python-cython python-pytest))
+ (list python-cython python-pytest python-setuptools python-wheel))
(home-page "https://github.com/gatagat/lap")
(synopsis "Linear Assignment Problem solver (LAPJV/LAPMOD)")
(description "Lap is a linear assignment problem solver using Jonker-Volgenant
@@ 6581,24 6613,23 @@ inference.")
(define-public python-linear-operator
(package
(name "python-linear-operator")
- (version "0.5.2")
+ (version "0.6")
(source (origin
(method url-fetch)
(uri (pypi-uri "linear_operator" version))
(sha256
(base32
- "03drb4hn9nn8jrqd9vbalihhahgpdm956hbs05bix7svradhknaw"))))
+ "0m56f3zrm8xh1bpwh4g7jfc79rf4j94g6zmz663b58pig4w6dqm9"))))
(build-system pyproject-build-system)
(propagated-inputs (list python-jaxtyping
+ python-mpmath
python-pytorch
- python-scipy
- python-typeguard))
- (native-inputs (list python-flake8
- python-flake8-print
- python-pytest
+ python-scipy))
+ (native-inputs (list python-pytest
python-setuptools
python-setuptools-scm
- python-twine))
+ python-typeguard
+ python-wheel))
(home-page "https://github.com/cornellius-gp/linear_operator/")
(synopsis "Linear operator implementation")
(description "LinearOperator is a PyTorch package for abstracting away the
@@ 6608,29 6639,34 @@ linear algebra routines needed for structured matrices (or operators).")
(define-public python-gpytorch
(package
(name "python-gpytorch")
- (version "1.12")
+ (version "1.14")
(source (origin
(method url-fetch)
(uri (pypi-uri "gpytorch" version))
(sha256
(base32
- "1pwsccll1hrgkifdmlxzcn6cvnwvyq2cimqzbfgihr13yw51cb6w"))))
+ "13cs6dx8qa5j4ygji9w5xbmaqc68ihqyzz33fyyf9qa6d8gc2b03"))))
(build-system pyproject-build-system)
(arguments
(list #:test-flags
- ;; test_deprecated_methods fails with an AssertionError.
- #~(list "-k" (string-append "not test_deprecated_methods"))))
- (propagated-inputs (list python-linear-operator
+ #~(list "-k" (string-append
+ ;; test_deprecated_methods fails with an AssertionError.
+ "not test_deprecated_methods"
+ ;; This test is flaky: Expects gradients of 0 exactly,
+ ;; can get negligible ones (e-10 to e-16).
+ " and not test_optimization_optimal_error")
+ ;; Ignore lenghty tests of little relevance.
+ "--ignore=test/examples/")))
+ (propagated-inputs (list python-jaxtyping
+ python-linear-operator
python-mpmath
python-scikit-learn
python-scipy))
- (native-inputs (list python-coverage
- python-flake8
- python-flake8-print
- python-nbval
+ (native-inputs (list python-nbval
python-pytest
python-setuptools
- python-twine))
+ python-setuptools-scm
+ python-wheel))
(home-page "https://gpytorch.ai")
(synopsis "Implementation of Gaussian Processes in PyTorch")
(description
@@ 6640,7 6676,7 @@ linear algebra routines needed for structured matrices (or operators).")
(define-public python-botorch
(package
(name "python-botorch")
- (version "0.11.3")
+ (version "0.13.0")
(source (origin
(method git-fetch) ;no tests in PyPI
(uri (git-reference
@@ 6649,7 6685,7 @@ linear algebra routines needed for structured matrices (or operators).")
(file-name (git-file-name name version))
(sha256
(base32
- "0nf9zrg1khvckb8kdpffqc3bnlhc0x03jd1560qmjamwl3j59m02"))))
+ "1sxgxdq892vg5xj30kb86003b9rwsipc95c7p1zdv865y4f38a8y"))))
(build-system pyproject-build-system)
(arguments
(list #:test-flags #~(list "-k" "not test_all_cases_covered")
@@ 6668,9 6704,12 @@ linear algebra routines needed for structured matrices (or operators).")
python-pyro-ppl
python-pytorch
python-scipy))
- (native-inputs (list python-pytest
+ (native-inputs (list python-pyre-extensions
+ python-pytest
python-pytest-cov
- python-setuptools-scm))
+ python-setuptools
+ python-setuptools-scm
+ python-wheel))
(home-page "https://botorch.org")
(synopsis "Bayesian Optimization in PyTorch")
(description
@@ 6779,7 6818,7 @@ simple speech recognition.")
"library_dirs=["
"'" #$vosk-api "/lib'"
"],\n\t"
- "libraries=['vosk', 'python3.10'],\n\t"
+ "libraries=['vosk', 'python3.11'],\n\t"
"include_dirs=["
"'" #$vosk-api "/src'" "])")))
(substitute* "vosk/__init__.py"
M gnu/packages/mail.scm => gnu/packages/mail.scm +34 -36
@@ 3588,14 3588,17 @@ an SMTP transaction before a message is committed to queue.")
(define-public mailman
(package
(name "mailman")
- (version "3.3.2")
+ (version "3.3.10")
(source
(origin
(method url-fetch)
(uri (pypi-uri "mailman" version))
(sha256
- (base32 "0a5ckbf8hc3y28b7p5psp0d4bxk601jlr5pd3hhh545xd8d9f0dg"))))
- (build-system python-build-system)
+ (base32 "0cjn8karkgrapgiv3ra6ddcngkf5c5779hrq369mvwi6ygy7ir0d"))))
+ (build-system pyproject-build-system)
+ (arguments
+ ;; XXX: Too much failing tests to try and isolate them.
+ (list #:tests? #f))
(propagated-inputs
(list gunicorn
python-aiosmtpd
@@ 3620,7 3623,7 @@ an SMTP transaction before a message is committed to queue.")
python-zope-event
python-zope-interface))
(native-inputs
- (list python-nose))
+ (list python-pytest python-pdm-backend))
(home-page "https://www.list.org")
(synopsis "Mailing list manager")
(description
@@ 3755,21 3758,17 @@ interfaces interacting with Mailman.")
(define-public python-mailman-hyperkitty
(package
(name "python-mailman-hyperkitty")
- (version "1.2.0")
+ (version "1.2.1")
(source
- (origin
- (method url-fetch)
- (uri (pypi-uri "mailman-hyperkitty" version))
- (sha256
- (base32
- "1ni6vf1yi14c0l895fk278x4na7ymhpkl1q0vnpzbkzplpa7200i"))))
- (build-system python-build-system)
- (propagated-inputs
- (list python-requests python-zope-interface))
- (inputs
- (list mailman))
- (native-inputs
- (list python-mock python-nose python-nose2))
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "mailman-hyperkitty" version))
+ (sha256
+ (base32 "0f6c1fs28w3r9k9mbg7gsv6pa45aayaadaa0dn4q5dfcqvxrvmpq"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs (list python-requests python-zope-interface))
+ (inputs (list mailman))
+ (native-inputs (list python-nose2 python-setuptools python-wheel))
(home-page "https://gitlab.com/mailman/mailman-hyperkitty/")
(synopsis "Mailman archiver plugin for HyperKitty")
(description
@@ 4681,18 4680,20 @@ the RFC 8617 Authenticated Received Chain (ARC) protocol.")
(define-public python-authheaders
(package
(name "python-authheaders")
- (version "0.13.0")
+ (version "0.16.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "authheaders" version))
(sha256
(base32
- "14k6i72k5f8dyvps8vc0aq0cczc8lvqpgjfjzsy6qqychjvjcmwk"))))
- (build-system python-build-system)
+ "12hl93336w64iyqalpv4rma2ijigav68qy1xmgziibdi7inxr3hi"))))
+ (build-system pyproject-build-system)
(propagated-inputs
(list python-authres python-dkimpy python-dnspython
python-publicsuffix2))
+ (native-inputs
+ (list python-setuptools python-wheel))
(home-page "https://github.com/ValiMail/authentication-headers")
(synopsis "Library wrapping email authentication header verification and generation")
(description
@@ 4707,30 4708,27 @@ DKIM and ARC sign messages and output the corresponding signature headers.")
(define-public python-aiosmtpd
(package
(name "python-aiosmtpd")
- (version "1.2.2")
+ (version "1.4.6")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/aio-libs/aiosmtpd")
- (commit version)))
+ (commit (string-append "v" version))))
(sha256
- (base32 "0083d6nf75xv8nq1il6jabz36v6c452svy4p402csxwwih5pw6sk"))
+ (base32 "0b5y94zc8pq75sjwsifblzgjnliyclkwypi68b2zffrxcdnz27r2"))
(file-name (git-file-name name version))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
(arguments
- '(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'delete-failing-tests
- (lambda _
- ;; This test uses an expired certificate.
- (delete-file "aiosmtpd/tests/test_smtps.py")
- #t))
- (replace 'check
- (lambda _
- (invoke "python" "-m" "nose2" "-v"))))))
+ ;; This QA test requires git.
+ (list #:test-flags ''("-k" "not test_ge_master")))
(native-inputs
- (list python-flufl-testing python-nose2))
+ (list python-pytest
+ python-pytest-asyncio
+ python-pytest-cov
+ python-pytest-mock
+ python-setuptools
+ python-wheel))
(propagated-inputs
(list python-atpublic))
(home-page "https://aiosmtpd.readthedocs.io/")
M gnu/packages/maths.scm => gnu/packages/maths.scm +108 -69
@@ 108,6 108,7 @@
#:use-module (guix build-system python)
#:use-module (guix build-system ruby)
#:use-module (gnu packages algebra)
+ #:use-module (gnu packages astronomy)
#:use-module (gnu packages audio)
#:use-module (gnu packages autotools)
#:use-module (gnu packages backup)
@@ 3551,46 3552,51 @@ ASCII text files using Gmsh's own scripting language.")
(define-public veusz
(package
(name "veusz")
- (version "3.3.1")
+ (version "3.6.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "veusz" version))
(sha256
- (base32 "1q7hi1qwwg4pgiz62isvv1pia85m13bspdpp1q3mrnwl11in0ag0"))))
- (build-system python-build-system)
+ (base32 "1lcmcfr0dcam8g1fp5qip8jnxglxx7i62ln3ix6l4c2bbv21l5y2"))))
+ (build-system pyproject-build-system)
(arguments
- `(;; Tests will fail because they depend on optional packages like
- ;; python-astropy, which is not packaged.
- #:tests? #f
- #:phases
- (modify-phases %standard-phases
- ;; Veusz will append 'PyQt5' to sip_dir by default. That is not how
- ;; the path is defined in Guix, therefore we have to change it.
- (add-after 'unpack 'fix-sip-dir
- (lambda _
- (substitute* "pyqtdistutils.py"
- (("os.path.join\\(sip_dir, 'PyQt5'\\)") "sip_dir"))))
- ;; Now we have to pass the correct sip_dir to setup.py.
- (replace 'build
- (lambda* (#:key inputs #:allow-other-keys)
- ;; We need to tell setup.py where to locate QtCoremod.sip
- ((@@ (guix build python-build-system) call-setuppy)
- "build_ext"
- (list (string-append "--sip-dir="
- (search-input-directory inputs "share/sip"))))))
- ;; Ensure that icons are found at runtime.
- (add-after 'install 'wrap-executable
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (wrap-program (string-append out "/bin/veusz")
- `("QT_PLUGIN_PATH" prefix
- ,(list (string-append (assoc-ref inputs "qtsvg")
- "/lib/qt5/plugins/"))))))))))
+ (list
+ ;; Tests currently fail with exception TypeError:
+ ;; calling <function version ...> returned 3.6.2, not a test
+ #:tests? #f
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; Veusz uses python's site-packages to look for pyqt5_include_dir.
+ (add-after 'unpack 'fix-pyqt5-include-dir
+ (lambda _
+ (substitute* "pyqt_setuptools.py"
+ (("get_path\\('platlib'\\)")
+ (format #f "~s"
+ (string-append
+ #$(this-package-input "python-pyqt")
+ "/lib/python"
+ #$(version-major+minor
+ (package-version python-wrapper))
+ "/site-packages"))))))
+ ;; Ensure that icons are found at runtime.
+ (add-after 'wrap 'wrap-executable
+ (lambda* (#:key inputs #:allow-other-keys)
+ (wrap-program (string-append #$output "/bin/veusz")
+ `("QT_PLUGIN_PATH" prefix
+ ,(list (string-append
+ (string-join
+ (list #$(this-package-input "qtbase")
+ #$(this-package-input "qtsvg")
+ #$(this-package-input "qtwayland"))
+ "/lib/qt5/plugins:")
+ "/lib/qt5/plugins")))))))))
(native-inputs
(list pkg-config
- ;;("python-astropy" ,python-astropy) ;; FIXME: Package this.
- qttools-5 python-sip-4))
+ python-astropy
+ python-setuptools
+ python-wheel
+ qttools-5))
(inputs
(list bash-minimal
ghostscript ;optional, for EPS/PS output
@@ 3598,7 3604,8 @@ ASCII text files using Gmsh's own scripting language.")
python-h5py ;optional, for HDF5 data
python-pyqt
qtbase-5
- qtsvg-5))
+ qtsvg-5
+ qtwayland-5))
(propagated-inputs
(list python-numpy))
(home-page "https://veusz.github.io/")
@@ 4346,7 4353,15 @@ recurrence relations.")
;; These tests fails with unexpected keyword arguments
;; in calls to cplot.
#~(list "--deselect" "tests/test_u3.py::test_write_single"
- "--deselect" "tests/test_u3.py::test_write_tree")))
+ "--deselect" "tests/test_u3.py::test_write_tree"
+ "-k" (string-join
+ ;; Tests fail in arrays comprising.
+ (list "not test_chebyshev1_p11[2-y2]"
+ "test_chebyshev1_p11[4-y4]"
+ "test_eval[1-ref1]"
+ "test_eval[t2-ref2]"
+ "test_eval[t3-ref3]")
+ " and not "))))
(native-inputs
(list python-matplotx
python-meshio
@@ 4437,6 4452,35 @@ bindings to almost all functions of PETSc.")
;; <https://github.com/dimpase/primecountpy/issues/16>.
(license license:gpl2+)))
+(define-public python-pyglm
+ (package
+ (name "python-pyglm")
+ (version "2.8.1")
+ (source
+ (origin
+ ;; Test files are not included in the archive in pypi.
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/Zuzu-Typ/PyGLM")
+ (commit version)
+ ;; XXX: Attempt to use Guix's glm@1.0.1 failed, try to figure out
+ ;; how to fix it.
+ (recursive? #t)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1ra54m0pb5aca7q6ymappjsyxdzdy17yz8rrhlql04k0p9lnf1v8"))))
+ (build-system pyproject-build-system)
+ (native-inputs
+ (list python-pytest
+ python-setuptools
+ python-wheel))
+ (home-page "https://github.com/Zuzu-Typ/PyGLM")
+ (synopsis "OpenGL Mathematics library for Python")
+ (description "PyGLM is a Python extension library which brings the OpenGL
+Mathematics (GLM) library to Python.")
+ (license license:zlib)))
+
(define-public python-quadpy
(package
(name "python-quadpy")
@@ 4454,6 4498,12 @@ bindings to almost all functions of PETSc.")
(base32
"1f989dipv7lqxvalfrvvlmhlxyl67a87lavyyqrr1mh88glhl592"))))
(build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ ;; AssertionError: Lebedev(047) -- observed: 41, expected: 47 (max err:
+ ;; 4.910e-15).
+ #~(list "--deselect=tests/test_u3.py::test_scheme_spherical[lebedev_047]")))
(native-inputs
(list python-accupy
python-pytest
@@ 7171,50 7221,39 @@ with C89.")
(define-public glm
(package
(name "glm")
- (version "0.9.9.8")
+ (version "1.0.1")
(source
(origin
- (method url-fetch)
- (uri (string-append "https://github.com/g-truc/glm/releases/download/"
- version "/glm-" version ".zip"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/g-truc/glm")
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
- (base32 "0k6yk9v46h690rshdx49x98y5qspkzibld1wb51jwcm35vba7qip"))))
+ (base32 "0890rvv3czi3nqj11dc2m3wcdfv0dm0nr63wfcpfikk9sk6b4w8s"))))
(build-system cmake-build-system)
(arguments
- `(#:phases (modify-phases %standard-phases
- (add-before 'configure 'set-environment
- (lambda _
- ;; Pass "-fno-ipa-modref" flag to the compiler to work
- ;; around a test failure with GCC 11. This is a
- ;; header-only library so these flags only affect tests.
- ;; See <https://github.com/g-truc/glm/pull/1087>.
- (setenv "CXXFLAGS" "-O2 -g -fno-ipa-modref")))
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- ;; Since version 0.9.9.6, 'make install' is not supported
- ;; and we have to do it "manually". Upstream discussion:
- ;; <https://github.com/g-truc/glm/pull/968>.
- (let* ((source (string-append "../glm"))
- (out (assoc-ref outputs "out"))
- (inc (string-append out "/include"))
- (lib (string-append out "/lib"))
- (pkgconfig (string-append lib "/pkgconfig")))
- (with-directory-excursion source
- (mkdir-p inc)
- (mkdir-p pkgconfig)
- (copy-recursively "glm" (string-append inc "/glm"))
- (copy-recursively "cmake" (string-append lib "/cmake"))
- (call-with-output-file (string-append pkgconfig "/glm.pc")
- (lambda (port)
- (format port
- "prefix=~a
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'install 'post-install
+ (lambda _
+ (let* ((doc (string-append #$output "/share/doc/glm"))
+ (pkgconfig (string-append #$output "/lib/pkgconfig")))
+ (mkdir-p doc)
+ (mkdir-p pkgconfig)
+ (copy-recursively "../source/doc/api" (string-append doc "/html"))
+ (install-file "../source/doc/manual.pdf" doc)
+ (call-with-output-file (string-append pkgconfig "/glm.pc")
+ (lambda (port)
+ (format port
+ "prefix=~a
includedir=${prefix}/include
Name: GLM
Description: OpenGL Mathematics
Version: ~a
-Cflags: -I${includedir}~%" out ,(version-prefix version 3)))))
- #t))))))
+Cflags: -I${includedir}~%" #$output #$version)))))))))
(native-inputs
(list unzip))
(home-page "https://glm.g-truc.net/")
@@ 11079,7 11118,7 @@ Mathics3.")
(propagated-inputs (list python-django-4.2
python-mathics-scanner
python-mathics-core
- python-networkx-next
+ python-networkx
python-pygments
python-requests))
(native-inputs (list python-pytest python-setuptools python-wheel))
M gnu/packages/medical.scm => gnu/packages/medical.scm +21 -11
@@ 19,6 19,7 @@
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages medical)
+ #:use-module (guix build-system pyproject)
#:use-module (guix build-system python)
#:use-module (guix build-system qt)
#:use-module (guix download)
@@ 29,6 30,7 @@
#:use-module (gnu packages databases)
#:use-module (gnu packages kde-frameworks) ; kirigami
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-build)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
@@ 93,18 95,26 @@ Health Federation.")
".tar.gz"))
(sha256
(base32 "09vrfqn511vswnj2q9m7srlwdgz066qvqpmja6sg1yl1ibh3cbpr"))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
(arguments
- `(#:use-setuptools? #f
- #:phases (modify-phases %standard-phases
- (add-after 'unpack 'patch-/usr
- (lambda* (#:key outputs #:allow-other-keys)
- (substitute* '("setup.py"
- "src/openmolar/settings/localsettings.py")
- (("/usr")
- (assoc-ref outputs "out"))) #t)))))
- (inputs (list python-pyqtwebengine python-pyqt+qscintilla
- python-mysqlclient qscintilla))
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'patch-/usr
+ (lambda* (#:key outputs #:allow-other-keys)
+ (substitute* '("setup.py"
+ "src/openmolar/settings/localsettings.py")
+ (("/usr") #$output))))
+ (add-after 'unpack 'set-acceptable-version
+ (lambda _
+ (substitute* "src/openmolar/settings/version.py"
+ ((#$version) "1.1.6")))))))
+ (native-inputs
+ (list python-setuptools python-wheel))
+ (inputs (list python-pyqtwebengine
+ python-pyqt+qscintilla
+ python-mysqlclient
+ qscintilla))
(propagated-inputs (list qtwebengine-5))
(home-page "https://openmolar.com/om1")
(synopsis "Dental practice management software")
M gnu/packages/monitoring.scm => gnu/packages/monitoring.scm +87 -41
@@ 14,6 14,7 @@
;;; Copyright © 2022 Hartmut Goebel <h.goebel@crazy-compilers.com>
;;; Copyright © 2022 ( <paren@disroot.org>
;;; Copyright © 2022 Mathieu Laparie <mlaparie@disr.it>
+;;; Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
;;;
;;; This file is part of GNU Guix.
;;;
@@ 68,6 69,7 @@
#:use-module (gnu packages prometheus)
#:use-module (gnu packages python)
#:use-module (gnu packages python-build)
+ #:use-module (gnu packages python-science)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages rrdtool)
@@ 433,23 435,24 @@ historical data.")
(define-public python-carbon
(package
(name "python-carbon")
- (version "1.1.8")
+ (version "1.1.10")
(source
(origin
(method url-fetch)
(uri (pypi-uri "carbon" version))
(sha256
(base32
- "1wb91fipk1niciffq5xwqbh8g7rl7ghdam4m97cjbig12i5qr4cm"))))
- (build-system python-build-system)
+ "0p6yjxif5ly5wkllnaw41w2zy9y0nffgfk91v861fn6c26lmnfy1"))))
+ (build-system pyproject-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
;; Don't install to /opt
(add-after 'unpack 'do-not-install-to-/opt
(lambda _ (setenv "GRAPHITE_NO_PREFIX" "1") #t)))))
+ (native-inputs (list python-setuptools python-wheel))
(propagated-inputs
- (list python-cachetools python-txamqp python-urllib3 python-whisper))
+ (list python-cachetools python-twisted python-txamqp python-urllib3))
(home-page "https://graphiteapp.org/")
(synopsis "Backend data caching and persistence daemon for Graphite")
(description "Carbon is a backend data caching and persistence daemon for
@@ 459,45 462,69 @@ and persisting them to disk using the Whisper time-series library.")
(license license:asl2.0)))
(define-public graphite-web
- (package
- (name "graphite-web")
- (version "1.1.10")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "graphite-web" version))
- (sha256
- (base32
- "0nnk3kwn0b6bq9xnmv9bac6hpcbdgpgwf283c1ck5nm80panh61z"))))
- (build-system python-build-system)
- (arguments
- `(#:tests? #f ;XXX: not in PyPI release & requires database
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'relax-requirements
- (lambda _
- (substitute* "setup.py"
- ;; Allow newer versions of django-tagging.
- (("django-tagging==") "django-tagging>=")
- ;; And Django.
- (("Django>=1\\.8,<3\\.1") "Django>=1.8,<4"))))
- ;; Don't install to /opt
- (add-after 'unpack 'do-not-install-to-/opt
- (lambda _ (setenv "GRAPHITE_NO_PREFIX" "1") #t)))))
- (propagated-inputs
- (list python-cairocffi
- python-django-3.2
- python-django-tagging
- python-pyparsing
- python-pytz
- python-six
- python-urllib3))
- (home-page "https://graphiteapp.org/")
- (synopsis "Scalable realtime graphing system")
- (description "Graphite is a scalable real-time graphing system that does
+ (let ((commit "49c28e2015d605ad9ec93524f7076dd924a4731a")
+ (revision "2"))
+ (package
+ (name "graphite-web")
+ (version (git-version "1.1.10" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/graphite-project/graphite-web")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0bcc6jh7gyp8f54dzy4zza1z46gk3530r952pi86irf834z106sg"))))
+ (build-system pyproject-build-system)
+ (arguments
+ `(#:tests? #f ;XXX: Requires database, unable to run now
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'relax-requirements
+ (lambda _
+ (substitute* "setup.py"
+ ;; Allow newer versions of django-tagging.
+ (("django-tagging==") "django-tagging>=")
+ ;; And Django.
+ (("Django>=3\\.2,<4") "Django>=4,<5"))))
+ ;; Don't install to /opt
+ (add-after 'unpack 'do-not-install-to-/opt
+ (lambda _ (setenv "GRAPHITE_NO_PREFIX" "1")))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (mkdir-p "storage/log/webapp")
+ (with-directory-excursion "webapp"
+ (invoke "./manage.py" "test" "--pythonpath=." "tests"
+ "-k" (string-join
+ (list
+ "not test_dashboard_save_temporary_xss_key"
+ "test_dashboard_save_temporary_xss_name")
+ " and not ")))))))))
+ (native-inputs
+ (list python-carbon
+ python-mock
+ python-pytest
+ python-rrdtool
+ python-setuptools
+ python-tzdata
+ python-wheel
+ python-whisper))
+ (propagated-inputs
+ (list python-cairocffi
+ python-django-4.2
+ python-django-tagging
+ python-pyparsing
+ python-pytz
+ python-six
+ python-urllib3))
+ (home-page "https://graphiteapp.org/")
+ (synopsis "Scalable realtime graphing system")
+ (description "Graphite is a scalable real-time graphing system that does
two things: store numeric time-series data, and render graphs of this data on
demand.")
- (license license:asl2.0)))
+ (license license:asl2.0))))
(define-public python-prometheus-client
(package
@@ 838,6 865,25 @@ display resumes.
@end itemize")
(license license:bsd-2)))
+(define-public python-rrdtool
+ (package
+ (name "python-rrdtool")
+ (version "0.1.16")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "rrdtool" version))
+ (sha256
+ (base32 "0l8lbarzfwbwnq9jm9gv4mmrxgjlb9hbz27sa8b703qa7s5zy2jz"))))
+ (build-system pyproject-build-system)
+ (arguments (list #:tests? #f)) ; No tests in pypi archive
+ (inputs (list rrdtool))
+ (native-inputs (list python-setuptools python-wheel))
+ (home-page "https://github.com/commx/python-rrdtool")
+ (synopsis "Python bindings for rrdtool")
+ (description "This package provides Python bindings for rrdtool.")
+ (license license:lgpl2.1)))
+
(define-public python-statsd
(package
(name "python-statsd")
M gnu/packages/music.scm => gnu/packages/music.scm +18 -7
@@ 1858,7 1858,11 @@ typographic detail of symbols on the page.")
(base32 "1y8s55b4mlsigm0xkk6qjpp08c75rv0swvjp0lj3cs6lgqdjxdjl"))))
(build-system pyproject-build-system)
(native-inputs
- (list lilypond python-pytest python-setuptools python-wheel))
+ (list lilypond
+ python-pytest
+ python-pytest-cov
+ python-setuptools
+ python-wheel))
(propagated-inputs
(list abjad))
(home-page "https://abjad.github.io")
@@ 3809,8 3813,14 @@ follows a traditional multi-track tape recorder control paradigm.")
(base32 "1lz2mvk4gqsyf92yxd3aaldx0d0qi28h4rnnvsaz4ls0ccqm80nk"))))
(build-system waf-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'python3.11-compatibility
+ (lambda _
+ (substitute* '("waflib/Context.py"
+ "waflib/ConfigSet.py")
+ (("'rU'") "'r'"))))
(add-after 'unpack 'remove-sse-flags
(lambda* (#:key system #:allow-other-keys)
(unless (or (string-prefix? "x86_64" system)
@@ 4617,8 4627,8 @@ standard MIDI file with the csvmidi program.")
(license license:public-domain)))
(define-public mididings
- (let ((commit "d98265be8afe7da20a5c7cfd0515f0d5fae5c53a")
- (revision "1"))
+ (let ((commit "bc71ea9c86bdc0b02364b11ab7331e8b3a86bb4f")
+ (revision "2"))
(package
(name "mididings")
(version (git-version "0" revision commit))
@@ 4630,8 4640,8 @@ standard MIDI file with the csvmidi program.")
(file-name (git-file-name name version))
(sha256
(base32
- "1a8i4yac5jjkq0vh73nwkv0j7vnvfwbzzagam4xdl1gpnc26n5xi"))))
- (build-system pyproject-build-system)
+ "1f0f8bpqbc1av0ggv6wjicymc2klliwdl1m5blmjcvy39q3cwd59"))))
+ (build-system meson-build-system)
(arguments
(list
#:phases
@@ 4647,6 4657,7 @@ standard MIDI file with the csvmidi program.")
(list alsa-lib
boost
jack-2
+ python
`(,python "tk")
python-dbus
python-decorator
M gnu/packages/networking.scm => gnu/packages/networking.scm +65 -65
@@ 1,6 1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2017, 2018, 2021 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2015, 2016, 2017, 2018, 2020, 2024 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018, 2020, 2024, 2025 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015, 2016, 2017, 2021 Stefan Reichör <stefan@xsteve.at>
;;; Copyright © 2016 Raimon Grau <raimonster@gmail.com>
@@ 911,80 911,80 @@ systems with no further dependencies.")
(define-public blueman
(package
(name "blueman")
- (version "2.3.4")
+ (version "2.4.4")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/blueman-project/blueman/releases"
"/download/" version "/blueman-" version ".tar.xz"))
(sha256
- (base32 "0lh1aqpdq6vi4agrgmm7fifjbxz2s5qcs3hr7nfjrwrp2j1361n2"))))
+ (base32 "1w45dr2cmy32cvxwqaybf5m2ziraj929f4lxcwapv266r1a92kyk"))))
(build-system glib-or-gtk-build-system)
(arguments
- `(#:configure-flags (list "--enable-polkit"
+ (list
+ #:configure-flags '(list "--enable-polkit"
"--without-systemdsystemunitdir" ; Not required
"--without-systemduserunitdir") ; Not required
- #:phases
- (modify-phases %standard-phases
- ;; Python references are not being patched in patch-phase of build,
- ;; despite using python-wrapper as input. So we patch them manually.
- (add-after 'unpack 'patch-python-references
- (lambda* (#:key inputs #:allow-other-keys)
- (with-directory-excursion "apps"
- (substitute* '("blueman-adapters.in" "blueman-applet.in"
- "blueman-manager.in" "blueman-mechanism.in"
- "blueman-rfcomm-watcher.in" "blueman-sendto.in"
- "blueman-services.in" "blueman-tray.in")
- (("@PYTHON@")
- (search-input-file inputs
- (string-append
- "/bin/python"
- ,(version-major+minor
- (package-version python)))))))))
- ;; Fix loading of external programs.
- (add-after 'unpack 'patch-external-programs
- (lambda* (#:key inputs #:allow-other-keys)
- (substitute* '("blueman/main/NetConf.py"
- "blueman/main/PPPConnection.py")
- (("/usr/sbin/bluetoothd")
- (search-input-directory inputs
- "/libexec/bluetooth/bluetoothd"))
- (("/sbin/iptables")
- (search-input-file inputs "/sbin/iptables"))
- (("/usr/sbin/pppd")
- (search-input-file inputs "/sbin/pppd")))))
- ;; Fix loading of pulseaudio libraries.
- (add-after 'unpack 'patch-pulseaudio-libraries
- (lambda* (#:key inputs #:allow-other-keys)
- (let* ((pulseaudio (assoc-ref inputs "pulseaudio"))
- (pulse (string-append pulseaudio "/lib/libpulse.so.0"))
- (pulse-glib (string-append pulseaudio
- "/lib/libpulse-mainloop-glib.so.0")))
- (with-directory-excursion "blueman/main"
- (substitute* "PulseAudioUtils.py"
- (("libpulse.so.0") pulse)
- (("libpulse-mainloop-glib.so.0") pulse-glib))))))
- ;; Fix running of blueman programs.
- (add-after 'glib-or-gtk-wrap 'wrap-blueman-progs
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (bin (string-append out "/bin/blueman-"))
- (libexec (string-append out "/libexec/blueman-"))
- (lib (string-append out "/lib/python"
- ,(version-major+minor
- (package-version python))
- "/site-packages")))
- (for-each
- (lambda (program)
- (wrap-program program
- `("GUIX_PYTHONPATH" = (,(getenv "GUIX_PYTHONPATH") ,lib))
- `("GI_TYPELIB_PATH" = (,(getenv "GI_TYPELIB_PATH")))))
- (append
- (map (lambda (prog) (string-append bin prog))
- '("adapters" "applet" "manager"
- "sendto" "services" "tray"))
- (map (lambda (prog) (string-append libexec prog))
- '("mechanism" "rfcomm-watcher"))))))))))
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; Python references are not being patched in patch-phase of build,
+ ;; despite using python-wrapper as input. So we patch them manually.
+ (add-after 'unpack 'patch-python-references
+ (lambda* (#:key inputs #:allow-other-keys)
+ (with-directory-excursion "apps"
+ (substitute* '("blueman-adapters.in" "blueman-applet.in"
+ "blueman-manager.in" "blueman-mechanism.in"
+ "blueman-rfcomm-watcher.in" "blueman-sendto.in"
+ "blueman-services.in" "blueman-tray.in")
+ (("@PYTHON@")
+ (search-input-file inputs
+ (string-append
+ "/bin/python"
+ #$(version-major+minor
+ (package-version (this-package-input "python-wrapper"))))))))))
+ ;; Fix loading of external programs.
+ (add-after 'unpack 'patch-external-programs
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* '("blueman/main/NetConf.py"
+ "blueman/main/PPPConnection.py")
+ (("/usr/sbin/bluetoothd")
+ (search-input-directory inputs
+ "/libexec/bluetooth/bluetoothd"))
+ (("/sbin/iptables")
+ (search-input-file inputs "/sbin/iptables"))
+ (("/usr/sbin/pppd")
+ (search-input-file inputs "/sbin/pppd")))))
+ ;; Fix loading of pulseaudio libraries.
+ (add-after 'unpack 'patch-pulseaudio-libraries
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let* ((pulseaudio #$(this-package-input "pulseaudio"))
+ (pulse (string-append pulseaudio "/lib/libpulse.so.0"))
+ (pulse-glib (string-append pulseaudio
+ "/lib/libpulse-mainloop-glib.so.0")))
+ (with-directory-excursion "blueman/main"
+ (substitute* "PulseAudioUtils.py"
+ (("libpulse.so.0") pulse)
+ (("libpulse-mainloop-glib.so.0") pulse-glib))))))
+ ;; Fix running of blueman programs.
+ (add-after 'glib-or-gtk-wrap 'wrap-blueman-progs
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((bin (string-append #$output "/bin/blueman-"))
+ (libexec (string-append #$output "/libexec/blueman-"))
+ (lib (string-append #$output "/lib/python"
+ #$(version-major+minor
+ (package-version (this-package-input "python-wrapper")))
+ "/site-packages")))
+ (for-each
+ (lambda (program)
+ (wrap-program program
+ `("GUIX_PYTHONPATH" = (,(getenv "GUIX_PYTHONPATH") ,lib))
+ `("GI_TYPELIB_PATH" = (,(getenv "GI_TYPELIB_PATH")))))
+ (append
+ (map (lambda (prog) (string-append bin prog))
+ '("adapters" "applet" "manager"
+ "sendto" "services" "tray"))
+ (map (lambda (prog) (string-append libexec prog))
+ '("mechanism" "rfcomm-watcher"))))))))))
(native-inputs
(list python-cython
`(,glib "bin")
M gnu/packages/openstack.scm => gnu/packages/openstack.scm +55 -45
@@ 115,20 115,30 @@ formatters, and other extensions.")
(define-public python-debtcollector
(package
(name "python-debtcollector")
- (version "1.19.0")
+ (version "3.0.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "debtcollector" version))
(sha256
- (base32
- "06c7vyn184y9f0lsrwaz13aq63hdz5fjrd191b8nifx6acsni42f"))))
- (build-system python-build-system)
+ (base32 "0vzarkvjclci98d8lvkix6qj59f7rxp1qg2x6q6is7qfbg91g29a"))
+ (modules '((guix build utils)))
+ (snippet #~(begin
+ (substitute* "test-requirements.txt"
+ (("^(coverage|hacking|pre-commit).*")
+ ""))))))
+ (build-system pyproject-build-system)
(propagated-inputs
- (list python-pbr python-six python-wrapt))
+ (list python-pbr python-wrapt))
(native-inputs
- (list ;; Tests.
- python-subunit python-testrepository python-testtools))
+ (list python-doc8
+ python-fixtures
+ python-openstackdocstheme
+ python-reno
+ python-setuptools
+ python-stestr
+ python-testtools
+ python-wheel))
(home-page "https://www.openstack.org/")
(synopsis
"Find deprecated patterns and strategies in Python code")
@@ 386,11 396,11 @@ extensions.")
python-fixtures
python-jsonschema
python-netaddr
- python-oslo.concurrency
- python-oslo.config
- python-oslo.log
- python-oslo.serialization
- python-oslo.utils
+ python-oslo-concurrency
+ python-oslo-config
+ python-oslo-log
+ python-oslo-serialization
+ python-oslo-utils
python-paramiko
python-prettytable
python-pyyaml
@@ 437,7 447,7 @@ OpenStack deployment.")
python-httplib2
python-iso8601
python-jsonschema
- python-oslo.log
+ python-oslo-log
python-paramiko
python-six))
(native-inputs
@@ 455,9 465,9 @@ common features used in Tempest.")
;;; Packages from the Oslo library
;;;
-(define-public python-oslo.concurrency
+(define-public python-oslo-concurrency
(package
- (name "python-oslo.concurrency")
+ (name "python-oslo-concurrency")
(version "5.0.0")
(source (origin
(method url-fetch)
@@ 490,8 500,8 @@ common features used in Tempest.")
python-fixtures
python-stestr
python-eventlet))
- (propagated-inputs (list python-fasteners python-oslo.config
- python-oslo.i18n python-oslo.utils))
+ (propagated-inputs (list python-fasteners python-oslo-config
+ python-oslo-i18n python-oslo-utils))
(home-page "https://docs.openstack.org/oslo.concurrency/latest/")
(synopsis "Oslo Concurrency library")
(description "The Oslo Concurrency Library provides utilities for safely
@@ 499,9 509,9 @@ running multi-thread, multi-process applications using locking mechanisms and
for running external processes.")
(license asl2.0)))
-(define-public python-oslo.config
+(define-public python-oslo-config
(package
- (name "python-oslo.config")
+ (name "python-oslo-config")
(version "8.7.1")
(source
(origin
@@ 515,7 525,7 @@ for running external processes.")
(propagated-inputs
(list python-debtcollector
python-netaddr
- python-oslo.i18n
+ python-oslo-i18n
python-rfc3986
python-requests
python-stevedore
@@ 527,9 537,9 @@ for running external processes.")
.ini style configuration files.")
(license asl2.0)))
-(define-public python-oslo.context
+(define-public python-oslo-context
(package
- (name "python-oslo.context")
+ (name "python-oslo-context")
(version "5.0.0")
(source
(origin
@@ 566,9 576,9 @@ about a request context. The request context is usually populated in the WSGI
pipeline and used by various modules such as logging.")
(license asl2.0)))
-(define-public python-oslo.i18n
+(define-public python-oslo-i18n
(package
- (name "python-oslo.i18n")
+ (name "python-oslo-i18n")
(version "3.20.0")
(source
(origin
@@ 592,9 602,9 @@ internationalization (i18n) features, especially translation for text strings
in an application or library.")
(license asl2.0)))
-(define-public python-oslo.log
+(define-public python-oslo-log
(package
- (name "python-oslo.log")
+ (name "python-oslo-log")
(version "5.0.0")
(source
(origin
@@ 612,11 622,11 @@ in an application or library.")
(propagated-inputs
(list python-dateutil
python-debtcollector
- python-oslo.config
- python-oslo.context
- python-oslo.i18n
- python-oslo.utils
- python-oslo.serialization
+ python-oslo-config
+ python-oslo-context
+ python-oslo-i18n
+ python-oslo-utils
+ python-oslo-serialization
python-pyinotify))
(native-inputs
(list python-fixtures python-oslotest python-stestr python-testtools
@@ 629,9 639,9 @@ configuration for all OpenStack projects. It also provides custom formatters,
handlers and support for context specific logging (like resource id’s etc).")
(license asl2.0)))
-(define-public python-oslo.serialization
+(define-public python-oslo-serialization
(package
- (name "python-oslo.serialization")
+ (name "python-oslo-serialization")
(version "4.2.0")
(source
(origin
@@ 647,10 657,10 @@ handlers and support for context specific logging (like resource id’s etc).")
(lambda* (#:key tests? #:allow-other-keys)
(when tests? (invoke "stestr" "run")))))))
(propagated-inputs
- (list python-msgpack python-oslo.utils python-pbr python-pytz))
+ (list python-msgpack python-oslo-utils python-pbr python-pytz))
(native-inputs
;; For tests.
- (list python-netaddr python-oslo.i18n python-oslotest python-stestr))
+ (list python-netaddr python-oslo-i18n python-oslotest python-stestr))
(home-page "https://launchpad.net/oslo")
(synopsis "Oslo serialization library")
(description
@@ 757,9 767,9 @@ documentation from the OpenStack project.")
for debugging, and better support for mocking results.")
(license asl2.0)))
-(define-public python-oslo.utils
+(define-public python-oslo-utils
(package
- (name "python-oslo.utils")
+ (name "python-oslo-utils")
(version "4.12.0")
(source
(origin
@@ 776,7 786,7 @@ for debugging, and better support for mocking results.")
(when tests? (invoke "stestr" "run")))))))
(propagated-inputs
(list python-debtcollector
- python-oslo.i18n
+ python-oslo-i18n
python-iso8601
python-netaddr
python-netifaces
@@ 843,8 853,8 @@ handling.")
python-hacking
python-lxml
python-oauthlib
- python-oslo.config
- python-oslo.utils
+ python-oslo-config
+ python-oslo-utils
python-oslotest
python-pbr
python-pyyaml
@@ 907,10 917,10 @@ process of writing new clients.")
python-iso8601
python-keystoneauth1
python-netaddr
- python-oslo.config
- python-oslo.i18n
- python-oslo.serialization
- python-oslo.utils
+ python-oslo-config
+ python-oslo-i18n
+ python-oslo-serialization
+ python-oslo-utils
python-prettytable
python-requests
python-six
@@ 1071,7 1081,7 @@ regardless of whether they are bundled or not.")
python-statsd
python-stestr
python-testscenarios
- python-oslo.config
+ python-oslo-config
python-oslotest))
(propagated-inputs (list python-appdirs
python-cryptography
M gnu/packages/orange.scm => gnu/packages/orange.scm +25 -6
@@ 31,6 31,7 @@
#:use-module (gnu packages graph)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages python-build)
+ #:use-module (gnu packages python-check)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-science)
#:use-module (gnu packages python-web)
@@ 59,24 60,42 @@
"test_copy_cut_paste"
;; AttributeError: 'NoneType' object has no attribute
;; 'isEnabled'
- "test_item_context_menu")
+ "test_item_context_menu"
+ ;; Tests fail with error: Failed: CALL ERROR: Exceptions
+ ;; caught in Qt event loop.
+ "test_create_new_window"
+ "test_new_window"
+ "test_dont_load_swp_on_new_window"
+ "test_toolbox"
+ "test_widgettoolgrid"
+ "test_editlinksnode"
+ "test_links_edit"
+ "test_links_edit_widget"
+ "test_flattened"
+ "test_tooltree_registry")
" and not "))
#:phases
#~(modify-phases %standard-phases
- (add-after 'unpack 'relax-requirements
- (lambda _
- (substitute* "setup.py"
- ;; Relax hard requirment of PIP.
- ((".*pip>=18.0.*") ""))))
+ (add-after 'unpack 'relax-requirements
+ (lambda _
+ (substitute* "setup.py"
+ ;; Relax hard requirment of PIP.
+ ((".*pip>=18.0.*") ""))))
(add-before 'check 'pre-check
(lambda _
(setenv "HOME" "/tmp")
+ (setenv "QT_PLUGIN_PATH"
+ (string-append #$(this-package-input "qtbase") "/lib/qt6/plugins:"
+ (getenv "QT_PLUGIN_PATH")))
(setenv "QT_QPA_PLATFORM" "offscreen"))))))
(native-inputs
(list python-pytest
+ python-pytest-qt
python-setuptools
python-trubar
python-wheel))
+ (inputs
+ (list qtbase))
(propagated-inputs
(list python-anyqt
python-cachecontrol
M gnu/packages/package-management.scm => gnu/packages/package-management.scm +105 -62
@@ 1123,6 1123,34 @@ Anaconda Cloud. Anaconda Cloud is useful for sharing packages, notebooks and
environments.")
(license license:bsd-3)))
+(define-public python-conda-inject
+ (package
+ (name "python-conda-inject")
+ (version "1.3.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/koesterlab/conda-inject")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1aig9l676wc2sjb20y7rdqf0hfcfjhh92yfiy82mf7kfnv7rp3rk"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:tests? #f)) ; tests require setting up Conda
+ (native-inputs
+ (list python-poetry-core))
+ (propagated-inputs
+ (list python-pyyaml))
+ (home-page "https://github.com/koesterlab/conda-inject")
+ (synopsis "Inject a conda environment into the current python environment")
+ (description
+ "This package provides helper functions for injecting a conda
+environment into the current python environment (by modifying @code{sys.path},
+without actually changing the current python environment).")
+ (license license:expat)))
+
(define-public python-conda-package-handling
(package
(name "python-conda-package-handling")
@@ 1315,7 1343,7 @@ written entirely in Python.")
(define-public conan
(package
(name "conan")
- (version "2.0.9")
+ (version "2.7.1")
(source
(origin
(method git-fetch) ; no tests in PyPI archive
@@ 1324,13 1352,74 @@ written entirely in Python.")
(commit version)))
(file-name (git-file-name name version))
(sha256
- (base32 "1ykfj7c3i0b57s7ql3p2lawxdzd2cn36f3k8p64lyzla8rwv4xdx"))))
- (build-system python-build-system)
+ (base32 "00mrx1ighvf6r6fy2iqxr286w3jfd0gwlzcqsw15cm9axblx5av9"))))
+ (build-system pyproject-build-system)
(arguments
(list
- #:modules '((guix build python-build-system)
+ #:modules '((guix build pyproject-build-system)
(guix build utils)
(ice-9 format))
+ #:test-flags
+ (let ((system (or (%current-target-system)
+ (%current-system))))
+ #~(list "-n" (number->string (parallel-job-count))
+ "-m" "not slow"
+ "--ignore=test/performance/"
+ ;; E ModuleNotFoundError: No module named 'docker'
+ "--ignore=test/functional/command/runner_test.py"
+ ;; Disable problematic tests.
+ "-k"
+ (string-append
+ ;; These tests rely on networking.
+ "not download_retries_errors "
+ "and not ftp "
+ ;; These tests are for old versions of cmake.
+ "and not test_custom_cmake_3_16 "
+ "and not test_custom_cmake_3_17 "
+ "and not test_custom_cmake_3_19 "
+ ;; Guix sets PKG_CONFIG_PATH itself, which is not
+ ;; expected by the following test.
+ "and not pkg_config_path "
+ "and not compare " ;caused by newer node-semver?
+ ;; This test hard-codes a compiler version.
+ "and not test_toolchain "
+ ;; The 'test_list' tests may fail
+ ;; non-deterministically (see:
+ ;; https://github.com/conan-io/conan/issues/13583).
+ "and not test_list "
+ ;; These tests fail when Autoconf attempt to load a
+ ;; shared library in the same directory (see:
+ ;; https://github.com/conan-io/conan/issues/13577).
+ "and not test_other_client_can_link_autotools "
+ "and not test_autotools_lib_template "
+ ;; Sometimes fail: https://github.com/conan-io/conan/issues/15936
+ "and not test_basic_parallel_install "
+ ;; These tests require additional build tools
+ "and not test_premake "
+ "and not test_sconsdeps "
+ ;; Unclear why libc is not found properly
+ "and not test_profile_detect_libc "
+ #$(if (not (string-prefix? "x86_64" system))
+ ;; These tests either assume the machine is
+ ;; x86_64, or require a cross-compiler to target
+ ;; it.
+ (string-append
+ "and not cpp_package "
+ "and not exclude_code_analysis "
+ "and not cmakedeps_multi "
+ "and not locally_build_linux "
+ "and not custom_configuration "
+ "and not package_from_system "
+ "and not cross_build_command "
+ "and not test_package "
+ "and not test_same ")
+ "")
+ #$(if (not (or (string-prefix? "x86_64" system)
+ (string-prefix? "i686" system)))
+ ;; This test only works with default arch "x86",
+ ;; "x86_64", "sparc" or "sparcv9".
+ "and not settings_as_a_dict_conanfile "
+ ""))))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'patch-paths
@@ 1345,21 1434,22 @@ written entirely in Python.")
;; The test suite expects GCC 9 to be used (see:
;; https://github.com/conan-io/conan/issues/13575). Render the
;; check version agnostic.
- (substitute* "conans/test/functional/toolchains/meson/_base.py"
+ (substitute* "test/functional/toolchains/meson/_base.py"
(("__GNUC__9")
"__GNUC__"))))
(add-after 'unpack 'use-current-cmake-for-tests
(lambda _
- (substitute* (find-files "conans/test" "\\.py$")
- (("@pytest.mark.tool\\(\"cmake\", \"3.23\")")
+ (substitute* (find-files "test" "\\.py$")
+ (("@pytest.mark.tool\\(\"cmake\", \".*\")")
"@pytest.mark.tool(\"cmake\")"))))
(add-before 'check 'configure-tests
(lambda _
(let* ((cmake-version #$(version-major+minor
- (package-version cmake)))
+ (package-version
+ (this-package-native-input "cmake"))))
(pkg-config-version #$(version-major+minor
(package-version pkg-config))))
- (call-with-output-file "conans/test/conftest_user.py"
+ (call-with-output-file "test/conftest_user.py"
(lambda (port)
(format port "\
tools_locations = {
@@ 1378,61 1468,12 @@ tools_locations = {
(add-before 'check 'set-home
(lambda _
(setenv "HOME" "/tmp")))
- (replace 'check
- (lambda* (#:key tests? outputs #:allow-other-keys)
- (define system #$(or (%current-target-system)
- (%current-system)))
+ (add-before 'check 'configure-tests
+ (lambda* (#:key tests? #:allow-other-keys)
(when tests?
(setenv "CONFIG_SHELL" (which "sh"))
(setenv "PATH" (string-append (getenv "PATH") ":"
- #$output "/bin"))
- (invoke "python" "-m" "pytest" "-vv"
- "-n" (number->string (parallel-job-count))
- "-m" "not slow"
- ;; Disable problematic tests.
- "-k"
- (string-append
- ;; These tests rely on networking.
- "not download_retries_errors "
- "and not ftp "
- ;; Guix sets PKG_CONFIG_PATH itself, which is not
- ;; expected by the following test.
- "and not pkg_config_path "
- "and not compare " ;caused by newer node-semver?
- ;; This test hard-codes a compiler version.
- "and not test_toolchain "
- ;; The 'test_list' tests may fail
- ;; non-deterministically (see:
- ;; https://github.com/conan-io/conan/issues/13583).
- "and not test_list "
- ;; These tests fail when Autoconf attempt to load a
- ;; shared library in the same directory (see:
- ;; https://github.com/conan-io/conan/issues/13577).
- "and not test_other_client_can_link_autotools "
- "and not test_autotools_lib_template "
- ;; Sometimes fail: https://github.com/conan-io/conan/issues/15936
- "and not test_basic_parallel_install "
- (if (not (string-prefix? "x86_64" system))
- ;; These tests either assume the machine is
- ;; x86_64, or require a cross-compiler to target
- ;; it.
- (string-append
- "and not cpp_package "
- "and not exclude_code_analysis "
- "and not cmakedeps_multi "
- "and not locally_build_linux "
- "and not custom_configuration "
- "and not package_from_system "
- "and not cross_build_command "
- "and not test_package "
- "and not test_same ")
- "")
- (if (not (or (string-prefix? "x86_64" system)
- (string-prefix? "i686" system)))
- ;; This test only works with default arch "x86",
- ;; "x86_64", "sparc" or "sparcv9".
- "and not settings_as_a_dict_conanfile "
- "")))))))))
+ #$output "/bin"))))))))
(propagated-inputs
(list python-bottle
python-colorama
@@ 1450,7 1491,7 @@ tools_locations = {
python-requests
python-six
python-tqdm
- python-urllib3))
+ python-urllib3-1.26))
(inputs
(list coreutils)) ;for printenv
(native-inputs
@@ 1467,7 1508,9 @@ tools_locations = {
python-parameterized
python-pytest
python-pytest-xdist
+ python-setuptools
python-webtest
+ python-wheel
which))
(home-page "https://conan.io")
(synopsis "Decentralized C/C++ package manager")
D gnu/packages/patches/onionshare-cli-async-mode.patch => gnu/packages/patches/onionshare-cli-async-mode.patch +0 -25
@@ 1,25 0,0 @@
-Specifying the `async_mode` parameter seems to have been a workaround for
-packaging on Windows and macOS. If not given, flask_socketio.SocketIO will
-probe for an available asynchronous model, e.g. `eventlet`, and otherwise gets
-stuck if `gevent-socketio` is not available.
-
-c.f. https://github.com/onionshare/onionshare/commit/ec7fa4ef16c9e1ba6028ee927c23f76c399a17a6
-and https://github.com/onionshare/onionshare/issues/1510
-
-diff --git a/cli/onionshare_cli/web/web.py b/cli/onionshare_cli/web/web.py
-index 64844b5..7e1b095 100644
---- a/cli/onionshare_cli/web/web.py
-+++ b/cli/onionshare_cli/web/web.py
-@@ -164,10 +164,10 @@ class Web:
- elif self.mode == "chat":
- if self.common.verbose:
- self.socketio = SocketIO(
-- async_mode="gevent", logger=True, engineio_logger=True
-+ logger=True, engineio_logger=True
- )
- else:
-- self.socketio = SocketIO(async_mode="gevent")
-+ self.socketio = SocketIO()
- self.socketio.init_app(self.app)
- self.chat_mode = ChatModeWeb(self.common, self)
-
A gnu/packages/patches/python-3.11-fix-tests.patch => gnu/packages/patches/python-3.11-fix-tests.patch +430 -0
@@ 0,0 1,430 @@
+From f0698133e7d6c353a3e6ae0fc62e57ba558a9bc0 Mon Sep 17 00:00:00 2001
+From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
+Date: Wed, 28 Oct 2020 22:55:05 -0400
+Subject: [PATCH] Skip problematic Python 3 tests in Guix.
+
+A subset of the hunks in this patch is tracked upstream at
+https://bugs.python.org/issue38845, which was contributed by Tanguy Le
+Carrour <tanguy@bioneland.org>.
+---
+ Lib/ctypes/test/test_callbacks.py | 3 +++
+ Lib/ctypes/test/test_find.py | 1 +
+ Lib/ctypes/test/test_libc.py | 3 +++
+ Lib/distutils/tests/test_archive_util.py | 2 ++
+ Lib/distutils/tests/test_sdist.py | 1 +
+ Lib/test/_test_multiprocessing.py | 2 ++
+ Lib/test/test_asyncio/test_base_events.py | 2 ++
+ Lib/test/test_generators.py | 1 +
+ Lib/test/test_pathlib.py | 3 +--
+ Lib/test/test_pdb.py | 4 ++--
+ Lib/test/test_regrtest.py | 2 ++
+ Lib/test/test_resource.py | 1 +
+ Lib/test/test_shutil.py | 2 ++
+ Lib/test/test_signal.py | 4 ++++
+ Lib/test/test_socket.py | 8 ++++++++
+ Lib/test/test_spwd.py | 6 ++----
+ Lib/test/test_tarfile.py | 9 ++++++---
+ Lib/test/test_threading.py | 3 +++
+ Lib/test/test_unicodedata.py | 1 +
+ Tools/scripts/run_tests.py | 2 +-
+ 20 files changed, 48 insertions(+), 12 deletions(-)
+
+diff --git a/Lib/ctypes/test/test_callbacks.py b/Lib/ctypes/test/test_callbacks.py
+index d8e9c5a760..94fc5929c9 100644
+--- a/Lib/ctypes/test/test_callbacks.py
++++ b/Lib/ctypes/test/test_callbacks.py
+@@ -5,6 +5,7 @@ from test import support
+ from ctypes import *
+ from ctypes.test import need_symbol
+ import _ctypes_test
++import platform
+
+ class Callbacks(unittest.TestCase):
+ functype = CFUNCTYPE
+@@ -178,6 +179,8 @@ class SampleCallbacksTestCase(unittest.TestCase):
+
+ self.assertLess(diff, 0.01, "%s not less than 0.01" % diff)
+
++ @unittest.skipIf(platform.machine() in ['mips64'],
++ "This test fails on this platform")
+ def test_issue_8959_a(self):
+ from ctypes.util import find_library
+ libc_path = find_library("c")
+diff --git a/Lib/ctypes/test/test_find.py b/Lib/ctypes/test/test_find.py
+index 92ac1840ad..c8eb75dedd 100644
+--- a/Lib/ctypes/test/test_find.py
++++ b/Lib/ctypes/test/test_find.py
+@@ -116,6 +116,7 @@ class FindLibraryLinux(unittest.TestCase):
+ with unittest.mock.patch("ctypes.util._findSoname_ldconfig", lambda *args: None):
+ self.assertNotEqual(find_library('c'), None)
+
++ @unittest.skipIf(True, "ldconfig is not used on Guix")
+ def test_find_library_with_ld(self):
+ with unittest.mock.patch("ctypes.util._findSoname_ldconfig", lambda *args: None), \
+ unittest.mock.patch("ctypes.util._findLib_gcc", lambda *args: None):
+diff --git a/Lib/ctypes/test/test_libc.py b/Lib/ctypes/test/test_libc.py
+index 56285b5ff8..c088ab3db8 100644
+--- a/Lib/ctypes/test/test_libc.py
++++ b/Lib/ctypes/test/test_libc.py
+@@ -2,6 +2,7 @@ import unittest
+
+ from ctypes import *
+ import _ctypes_test
++import platform
+
+ lib = CDLL(_ctypes_test.__file__)
+
+@@ -17,6 +18,8 @@ class LibTest(unittest.TestCase):
+ import math
+ self.assertEqual(lib.my_sqrt(2.0), math.sqrt(2.0))
+
++ @unittest.skipIf(platform.machine() in ['mips64'],
++ "This test fails on this platform")
+ def test_qsort(self):
+ comparefunc = CFUNCTYPE(c_int, POINTER(c_char), POINTER(c_char))
+ lib.my_qsort.argtypes = c_void_p, c_size_t, c_size_t, comparefunc
+diff --git a/Lib/distutils/tests/test_archive_util.py b/Lib/distutils/tests/test_archive_util.py
+index e9aad0e40f..8bbaa51ee5 100644
+--- a/Lib/distutils/tests/test_archive_util.py
++++ b/Lib/distutils/tests/test_archive_util.py
+@@ -333,6 +333,7 @@ class ArchiveUtilTestCase(support.TempdirManager,
+ self.assertEqual(os.path.basename(res), 'archive.tar.xz')
+ self.assertEqual(self._tarinfo(res), self._created_files)
+
++ @unittest.skipIf(True, "getgrgid(0)[0] raises a KeyError on Guix")
+ def test_make_archive_owner_group(self):
+ # testing make_archive with owner and group, with various combinations
+ # this works even if there's not gid/uid support
+@@ -362,6 +363,7 @@ class ArchiveUtilTestCase(support.TempdirManager,
+
+ @unittest.skipUnless(ZLIB_SUPPORT, "Requires zlib")
+ @unittest.skipUnless(UID_GID_SUPPORT, "Requires grp and pwd support")
++ @unittest.skipIf(True, "getgrgid(0)[0] raises a KeyError on Guix")
+ def test_tarfile_root_owner(self):
+ tmpdir = self._create_files()
+ base_name = os.path.join(self.mkdtemp(), 'archive')
+diff --git a/Lib/distutils/tests/test_sdist.py b/Lib/distutils/tests/test_sdist.py
+index 23db126959..6e2329df7d 100644
+--- a/Lib/distutils/tests/test_sdist.py
++++ b/Lib/distutils/tests/test_sdist.py
+@@ -443,6 +443,7 @@ class SDistTestCase(BasePyPIRCCommandTestCase):
+ "The tar command is not found")
+ @unittest.skipIf(find_executable('gzip') is None,
+ "The gzip command is not found")
++ @unittest.skipIf(True, "getgrgid(0)[0] raises a KeyError on Guix")
+ def test_make_distribution_owner_group(self):
+ # now building a sdist
+ dist, cmd = self.get_cmd()
+diff --git a/Lib/test/_test_multiprocessing.py b/Lib/test/_test_multiprocessing.py
+index e47905c863..31a5a9c308 100644
+--- a/Lib/test/_test_multiprocessing.py
++++ b/Lib/test/_test_multiprocessing.py
+@@ -1577,6 +1577,7 @@ class _TestCondition(BaseTestCase):
+ if pid is not None:
+ os.kill(pid, signal.SIGINT)
+
++ @unittest.skipIf(True, "This fails for unknown reasons on Guix")
+ def test_wait_result(self):
+ if isinstance(self, ProcessesMixin) and sys.platform != 'win32':
+ pid = os.getpid()
+@@ -3905,6 +3906,7 @@ class _TestSharedMemory(BaseTestCase):
+ sms.close()
+
+ @unittest.skipIf(os.name != "posix", "not feasible in non-posix platforms")
++ @unittest.skipUnless(sys.stdin.isatty(), "KeyboardInterrupts require a TTY device")
+ def test_shared_memory_SharedMemoryServer_ignores_sigint(self):
+ # bpo-36368: protect SharedMemoryManager server process from
+ # KeyboardInterrupt signals.
+diff --git a/Lib/test/test_asyncio/test_base_events.py b/Lib/test/test_asyncio/test_base_events.py
+index 533d5cc7f5..c4f860cc3b 100644
+--- a/Lib/test/test_asyncio/test_base_events.py
++++ b/Lib/test/test_asyncio/test_base_events.py
+@@ -1341,6 +1341,8 @@ class BaseEventLoopWithSelectorTests(test_utils.TestCase):
+ self._test_create_connection_ip_addr(m_socket, False)
+
+ @patch_socket
++ @unittest.skipUnless(support.is_resource_enabled('network'),
++ 'network is not enabled')
+ def test_create_connection_service_name(self, m_socket):
+ m_socket.getaddrinfo = socket.getaddrinfo
+ sock = m_socket.socket.return_value
+diff --git a/Lib/test/test_generators.py b/Lib/test/test_generators.py
+index 3bf1522808..04bac8a7db 100644
+--- a/Lib/test/test_generators.py
++++ b/Lib/test/test_generators.py
+@@ -33,6 +33,7 @@ class SignalAndYieldFromTest(unittest.TestCase):
+ else:
+ return "FAILED"
+
++ @unittest.skipIf(True, 'Keyboard interrupts do not work in the Guix build environment')
+ def test_raise_and_yield_from(self):
+ gen = self.generator1()
+ gen.send(None)
+diff --git a/Lib/test/test_pathlib.py b/Lib/test/test_pathlib.py
+index 3da35710b9..5404f9193d 100644
+--- a/Lib/test/test_pathlib.py
++++ b/Lib/test/test_pathlib.py
+@@ -2408,10 +2408,7 @@ class PosixPathTest(_BasePathTest, unittest.TestCase):
+ self.assertEqual(given, expect)
+ self.assertEqual(set(p.rglob("FILEd*")), set())
+
+- @unittest.skipUnless(hasattr(pwd, 'getpwall'),
+- 'pwd module does not expose getpwall()')
+- @unittest.skipIf(sys.platform == "vxworks",
+- "no home directory on VxWorks")
++ @unittest.skipIf(True, "Guix builder home is '/' which causes trouble for these tests")
+ def test_expanduser(self):
+ P = self.cls
+ support.import_module('pwd')
+diff --git a/Lib/test/test_pdb.py b/Lib/test/test_pdb.py
+index 8016f81e5a..10190486b4 100644
+--- a/Lib/test/test_pdb.py
++++ b/Lib/test/test_pdb.py
+@@ -1219,11 +1219,11 @@ def test_pdb_issue_20766():
+ > <doctest test.test_pdb.test_pdb_issue_20766[0]>(6)test_function()
+ -> print('pdb %d: %s' % (i, sess._previous_sigint_handler))
+ (Pdb) continue
+- pdb 1: <built-in function default_int_handler>
++ pdb 1: 1
+ > <doctest test.test_pdb.test_pdb_issue_20766[0]>(6)test_function()
+ -> print('pdb %d: %s' % (i, sess._previous_sigint_handler))
+ (Pdb) continue
+- pdb 2: <built-in function default_int_handler>
++ pdb 2: 1
+ """
+
+
+diff --git a/Lib/test/test_regrtest.py b/Lib/test/test_regrtest.py
+index a77638b10a..2069b349a8 100644
+--- a/Lib/test/test_regrtest.py
++++ b/Lib/test/test_regrtest.py
+@@ -811,6 +811,7 @@ class ArgsTestCase(BaseTestCase):
+ output = self.run_tests('--fromfile', filename)
+ self.check_executed_tests(output, tests)
+
++ @unittest.skipIf(True, 'Keyboard interrupts do not work in the Guix build environment.')
+ def test_interrupted(self):
+ code = TEST_INTERRUPTED
+ test = self.create_test('sigint', code=code)
+@@ -828,6 +829,7 @@ class ArgsTestCase(BaseTestCase):
+ % (self.TESTNAME_REGEX, len(tests)))
+ self.check_line(output, regex)
+
++ @unittest.skipIf(True, 'Keyboard interrupts do not work in the Guix build environment.')
+ def test_slowest_interrupted(self):
+ # Issue #25373: test --slowest with an interrupted test
+ code = TEST_INTERRUPTED
+diff --git a/Lib/test/test_resource.py b/Lib/test/test_resource.py
+index e5ece5284c..5299e54507 100644
+--- a/Lib/test/test_resource.py
++++ b/Lib/test/test_resource.py
+@@ -148,6 +148,7 @@ class ResourceTest(unittest.TestCase):
+
+ @unittest.skipUnless(hasattr(resource, 'prlimit'), 'no prlimit')
+ @support.requires_linux_version(2, 6, 36)
++ @unittest.skipIf(True, "Bug: the PermissionError is not raised")
+ def test_prlimit(self):
+ self.assertRaises(TypeError, resource.prlimit)
+ self.assertRaises(ProcessLookupError, resource.prlimit,
+diff --git a/Lib/test/test_shutil.py b/Lib/test/test_shutil.py
+index e19af64be0..1b893df6fa 100644
+--- a/Lib/test/test_shutil.py
++++ b/Lib/test/test_shutil.py
+@@ -1427,6 +1427,7 @@ class TestArchives(BaseTest, unittest.TestCase):
+ base_name = os.path.join(tmpdir, 'archive')
+ self.assertRaises(ValueError, make_archive, base_name, 'xxx')
+
++ @unittest.skipIf(True, "The Guix build container has no root user")
+ @support.requires_zlib()
+ def test_make_archive_owner_group(self):
+ # testing make_archive with owner and group, with various combinations
+@@ -1455,6 +1456,7 @@ class TestArchives(BaseTest, unittest.TestCase):
+ self.assertTrue(os.path.isfile(res))
+
+
++ @unittest.skipIf(True, "The Guix build container has no root user")
+ @support.requires_zlib()
+ @unittest.skipUnless(UID_GID_SUPPORT, "Requires grp and pwd support")
+ def test_tarfile_root_owner(self):
+diff --git a/Lib/test/test_signal.py b/Lib/test/test_signal.py
+index 45553a6a42..55623f01a3 100644
+--- a/Lib/test/test_signal.py
++++ b/Lib/test/test_signal.py
+@@ -78,7 +78,8 @@ class PosixTests(unittest.TestCase):
+ self.assertLess(len(s), signal.NSIG)
+
+ @unittest.skipUnless(sys.executable, "sys.executable required.")
+ @support.requires_subprocess()
++ @unittest.skipUnless(sys.stdin.isatty(), "KeyboardInterrupts require a TTY device")
+ def test_keyboard_interrupt_exit_code(self):
+ """KeyboardInterrupt triggers exit via SIGINT."""
+ process = subprocess.run(
+@@ -128,7 +129,8 @@ class WindowsSignalTests(unittest.TestCase):
+ signal.signal(7, handler)
+
+ @unittest.skipUnless(sys.executable, "sys.executable required.")
+ @support.requires_subprocess()
++ @unittest.skipUnless(sys.stdin.isatty(), "KeyboardInterrupts require a TTY device")
+ def test_keyboard_interrupt_exit_code(self):
+ """KeyboardInterrupt triggers an exit using STATUS_CONTROL_C_EXIT."""
+ # We don't test via os.kill(os.getpid(), signal.CTRL_C_EVENT) here
+@@ -1245,6 +1247,7 @@ class StressTest(unittest.TestCase):
+
+ class RaiseSignalTest(unittest.TestCase):
+
++ @unittest.skipUnless(sys.stdin.isatty(), "KeyboardInterrupts require a TTY device")
+ def test_sigint(self):
+ with self.assertRaises(KeyboardInterrupt):
+ signal.raise_signal(signal.SIGINT)
+@@ -1275,6 +1278,7 @@ class RaiseSignalTest(unittest.TestCase):
+
+ class PidfdSignalTest(unittest.TestCase):
+
++ @unittest.skipUnless(sys.stdin.isatty(), "KeyboardInterrupts require a TTY device")
+ @unittest.skipUnless(
+ hasattr(signal, "pidfd_send_signal"),
+ "pidfd support not built in",
+diff --git a/Lib/test/test_socket.py b/Lib/test/test_socket.py
+index aefba4f397..6c89f558d5 100755
+--- a/Lib/test/test_socket.py
++++ b/Lib/test/test_socket.py
+@@ -1009,6 +1009,8 @@ class GeneralModuleTests(unittest.TestCase):
+ if not fqhn in all_host_names:
+ self.fail("Error testing host resolution mechanisms. (fqdn: %s, all: %s)" % (fqhn, repr(all_host_names)))
+
++ @unittest.skipUnless(support.is_resource_enabled('network'),
++ 'network is not enabled')
+ def test_host_resolution(self):
+ for addr in [socket_helper.HOSTv4, '10.0.0.1', '255.255.255.255']:
+ self.assertEqual(socket.gethostbyname(addr), addr)
+@@ -1140,6 +1142,8 @@ class GeneralModuleTests(unittest.TestCase):
+ self.assertWarns(DeprecationWarning, socket.ntohs, k)
+ self.assertWarns(DeprecationWarning, socket.htons, k)
+
++ @unittest.skipUnless(os.path.exists("/etc/services"),
++ "getservbyname uses /etc/services, which is not in the chroot")
+ def testGetServBy(self):
+ eq = self.assertEqual
+ # Find one service that exists, then check all the related interfaces.
+@@ -1489,6 +1493,8 @@ class GeneralModuleTests(unittest.TestCase):
+ raise
+ self.assertRaises(TypeError, s.ioctl, socket.SIO_LOOPBACK_FAST_PATH, None)
+
++ @unittest.skipUnless(os.path.exists("/etc/gai.conf"),
++ "getaddrinfo() will fail")
+ def testGetaddrinfo(self):
+ try:
+ socket.getaddrinfo('localhost', 80)
+@@ -1571,6 +1577,8 @@ class GeneralModuleTests(unittest.TestCase):
+ # only IP addresses are allowed
+ self.assertRaises(OSError, socket.getnameinfo, ('mail.python.org',0), 0)
+
++ @unittest.skipUnless(os.path.exists("/etc/gai.conf"),
++ "getaddrinfo() will fail")
+ @unittest.skipUnless(support.is_resource_enabled('network'),
+ 'network is not enabled')
+ def test_idna(self):
+diff --git a/Lib/test/test_spwd.py b/Lib/test/test_spwd.py
+index 07793c84c8..fec672bcbe 100644
+--- a/Lib/test/test_spwd.py
++++ b/Lib/test/test_spwd.py
+@@ -5,8 +5,7 @@ from test import support
+ spwd = support.import_module('spwd')
+
+
+-@unittest.skipUnless(hasattr(os, 'geteuid') and os.geteuid() == 0,
+- 'root privileges required')
++@unittest.skipUnless(os.path.exists("/etc/shadow"), 'spwd tests require /etc/shadow')
+ class TestSpwdRoot(unittest.TestCase):
+
+ def test_getspall(self):
+@@ -56,8 +55,7 @@ class TestSpwdRoot(unittest.TestCase):
+ self.assertRaises(TypeError, spwd.getspnam, bytes_name)
+
+
+-@unittest.skipUnless(hasattr(os, 'geteuid') and os.geteuid() != 0,
+- 'non-root user required')
++@unittest.skipUnless(os.path.exists("/etc/shadow"), 'spwd tests require /etc/shadow')
+ class TestSpwdNonRoot(unittest.TestCase):
+
+ def test_getspnam_exception(self):
+diff --git a/Lib/test/test_tarfile.py b/Lib/test/test_tarfile.py
+index 29cde91bf7..8d0f20e8bf 100644
+--- a/Lib/test/test_tarfile.py
++++ b/Lib/test/test_tarfile.py
+@@ -2607,9 +2607,12 @@ def root_is_uid_gid_0():
+ import pwd, grp
+ except ImportError:
+ return False
+- if pwd.getpwuid(0)[0] != 'root':
+- return False
+- if grp.getgrgid(0)[0] != 'root':
++ try:
++ if pwd.getpwuid(0)[0] != 'root':
++ return False
++ if grp.getgrgid(0)[0] != 'root':
++ return False
++ except KeyError:
+ return False
+ return True
+
+diff --git a/Lib/test/test_tools/test_freeze.py b/Lib/test/test_tools/test_freeze.py
+index 0e7ed67de7..6539a2983b 100644
+--- a/Lib/test/test_tools/test_freeze.py
++++ b/Lib/test/test_tools/test_freeze.py
+@@ -23,6 +23,7 @@
+ 'test is too slow with PGO')
+ class TestFreeze(unittest.TestCase):
+
++ @unittest.skipIf(True, 'Fails on Guix.')
+ @support.requires_resource('cpu') # Building Python is slow
+ def test_freeze_simple_script(self):
+ script = textwrap.dedent("""
+diff --git a/Lib/test/test_threading.py b/Lib/test/test_threading.py
+index c21cdf8eb7..6c9d575032 100644
+--- a/Lib/test/test_threading.py
++++ b/Lib/test/test_threading.py
+@@ -1398,5 +1398,6 @@ class MiscTestCase(unittest.TestCase):
+ signal.signal(signum, handler)
+
++ @unittest.skipIf(True, 'Keyboard interrupts do not work in the Guix build container.')
+ def test_interrupt_main_subthread(self):
+ # Calling start_new_thread with a function that executes interrupt_main
+ # should raise KeyboardInterrupt upon completion.
+@@ -1409,6 +1410,8 @@ class InterruptMainTests(unittest.TestCase):
+ t.join()
+ t.join()
+
++
++ @unittest.skipIf(True, 'Keyboard interrupts do not work in the Guix build container.')
+ def test_interrupt_main_mainthread(self):
+ # Make sure that if interrupt_main is called in main thread that
+ # KeyboardInterrupt is raised instantly.
+diff --git a/Lib/test/test_unicodedata.py b/Lib/test/test_unicodedata.py
+index b552d2bd17..28b1144e15 100644
+--- a/Lib/test/test_unicodedata.py
++++ b/Lib/test/test_unicodedata.py
+@@ -309,6 +309,7 @@ class UnicodeMiscTest(UnicodeDatabaseTest):
+ self.assertEqual(len(lines), 1,
+ r"\u%.4x should not be a linebreak" % i)
+
++@requires_resource('network')
+ class NormalizationTest(unittest.TestCase):
+ @staticmethod
+ def check_version(testfile):
+diff --git a/Tools/scripts/run_tests.py b/Tools/scripts/run_tests.py
+index bcfa5e943b..1f2484971b 100644
+--- a/Tools/scripts/run_tests.py
++++ b/Tools/scripts/run_tests.py
+@@ -41,7 +41,7 @@ def main(regrtest_args):
+ else:
+ args.extend(['-j', '0']) # Use all CPU cores
+ if not any(is_resource_use_flag(arg) for arg in regrtest_args):
+- args.extend(['-u', 'all,-largefile,-audio,-gui'])
++ args.extend(['-u', 'all,-largefile,-audio,-gui,-network'])
+
+ if cross_compile and hostrunner:
+ # If HOSTRUNNER is set and -p/--python option is not given, then
+--
+2.29.2
+
A gnu/packages/patches/python-bed-reader-use-store-samples.patch => gnu/packages/patches/python-bed-reader-use-store-samples.patch +147 -0
@@ 0,0 1,147 @@
+From 7e6bcdfeed54500ca533d2f0eb12078248c43c77 Mon Sep 17 00:00:00 2001
+Message-ID: <7e6bcdfeed54500ca533d2f0eb12078248c43c77.1743682382.git.ngraves@ngraves.fr>
+From: Nicolas Graves <ngraves@ngraves.fr>
+Date: Thu, 3 Apr 2025 11:33:58 +0200
+Subject: [PATCH] samples: Use deterministic samples in Guix.
+
+---
+ bed_reader/_sample_data.py | 86 +++++++++-----------------------------
+ 1 file changed, 19 insertions(+), 67 deletions(-)
+
+diff --git a/bed_reader/_sample_data.py b/bed_reader/_sample_data.py
+index 6ca4cc0..6a1146e 100644
+--- a/bed_reader/_sample_data.py
++++ b/bed_reader/_sample_data.py
+@@ -1,33 +1,8 @@
++import os
+ import tempfile
+ from pathlib import Path, PurePath
+ from typing import Union
+
+-try:
+- import pooch
+-
+- """
+- Load sample data.
+- """
+-
+- POOCH = pooch.create(
+- # Use the default cache folder for the OS
+- path=pooch.os_cache("bed_reader"),
+- # The remote data is on Github
+- base_url="https://raw.githubusercontent.com/"
+- + "fastlmm/bed-sample-files/main/",
+- # If this is a development version, get the data from the master branch
+- version_dev="main",
+- # The registry specifies the files that can be fetched
+- env="BED_READER_DATA_DIR",
+- )
+-
+- # Get registry file from package_data
+- registry_file = Path(__file__).parent / "tests/registry.txt"
+- # Load this registry file
+- POOCH.load_registry(registry_file)
+-except ImportError:
+- pooch = None
+-
+
+ def sample_file(filepath: Union[str, Path]) -> str:
+ """Retrieve a sample .bed file. (Also retrieves associated .fam and .bim files).
+@@ -40,50 +15,41 @@ def sample_file(filepath: Union[str, Path]) -> str:
+ Returns
+ -------
+ str
+- Local name of sample .bed file.
+-
+-
+- .. note::
+- This function requires the :mod:`pooch` package. Install `pooch` with:
+-
+- .. code-block:: bash
+-
+- pip install --upgrade bed-reader[samples]
+-
+-
+- By default this function puts files under the user's cache directory.
+- Override this by setting
+- the `BED_READER_DATA_DIR` environment variable.
++ Local path of sample .bed file.
+
+ Example
+ --------
+
+ .. doctest::
+
+- >>> # pip install bed-reader[samples] # if needed
+ >>> from bed_reader import sample_file
+ >>>
+ >>> file_name = sample_file("small.bed")
+ >>> print(f"The local file name is '{file_name}'")
+ The local file name is '...small.bed'
+-
+ """
+- if pooch is None:
+- raise ImportError(
+- "The function sample_file() requires pooch. "
+- + "Install it with 'pip install --upgrade bed-reader[samples]'.",
++ filepath = Path(filepath)
++ sample_dir = os.environ.get("BED_READER_DATA_DIR")
++ if sample_dir is None:
++ raise EnvironmentError(
++ "BED_READER_DATA_DIR environment variable is not set. "
++ "This should point to the directory containing the sample files."
+ )
+
+- filepath = Path(filepath)
+- file_string = str(filepath)
+- if file_string.lower().endswith(".bed"):
+- POOCH.fetch(file_string[:-4] + ".fam")
+- POOCH.fetch(file_string[:-4] + ".bim")
+- return POOCH.fetch(file_string)
++ file_path = Path(sample_dir) / filepath
++
++ # Check if file exists
++ if not file_path.exists():
++ raise FileNotFoundError(
++ f"Sample file '{filepath}' not found in {sample_dir}. "
++ f"Make sure you're using the latest samples in BED_READER_DATA_DIR."
++ )
++
++ return str(file_path)
+
+
+ def sample_url(filepath: Union[str, Path]) -> str:
+- """Retrieve a URL to a sample .bed file. (Also makes ready associated .fam and .bim files).
++ """Retrieve a URL to a sample .bed file.
+
+ Parameters
+ ----------
+@@ -95,25 +61,11 @@ def sample_url(filepath: Union[str, Path]) -> str:
+ str
+ URL to sample .bed file.
+
+-
+- .. note::
+- This function requires the :mod:`pooch` package. Install `pooch` with:
+-
+- .. code-block:: bash
+-
+- pip install --upgrade bed-reader[samples]
+-
+-
+- By default this function puts files under the user's cache directory.
+- Override this by setting
+- the `BED_READER_DATA_DIR` environment variable.
+-
+ Example
+ --------
+
+ .. doctest::
+
+- >>> # pip install bed-reader[samples] # if needed
+ >>> from bed_reader import sample_url
+ >>>
+ >>> url = sample_url("small.bed")
+--
+2.49.0
+
A gnu/packages/patches/python-property-cached-asyncio-3_11.patch => gnu/packages/patches/python-property-cached-asyncio-3_11.patch +201 -0
@@ 0,0 1,201 @@
+From d89186b47dc25c5ef5907c146edf3f792d50774b Mon Sep 17 00:00:00 2001
+Message-ID: <d89186b47dc25c5ef5907c146edf3f792d50774b.1743608515.git.ngraves@ngraves.fr>
+From: Nicolas Graves <ngraves@ngraves.fr>
+Date: Wed, 2 Apr 2025 17:29:45 +0200
+Subject: [PATCH] Update to python 3.11
+
+---
+ property_cached/__init__.py | 21 +++-------
+ tests/test_async_cached_property.py | 3 +-
+ tests/test_coroutine_cached_property.py | 51 ++++++++++---------------
+ 3 files changed, 27 insertions(+), 48 deletions(-)
+
+diff --git a/property_cached/__init__.py b/property_cached/__init__.py
+index 3353048..c033542 100644
+--- a/property_cached/__init__.py
++++ b/property_cached/__init__.py
+@@ -3,6 +3,7 @@ import functools
+ import pkg_resources
+ import threading
+ import weakref
++from inspect import iscoroutinefunction
+ from time import time
+
+
+@@ -31,12 +32,12 @@ class cached_property(property):
+ if obj is None:
+ return self
+
+- if asyncio and asyncio.iscoroutinefunction(self.func):
+- return self._wrap_in_coroutine(obj)
+-
+ value = self.cache.get(obj, self._sentinel)
+ if value is self._sentinel:
+- value = self.cache[obj] = self.func(obj)
++ if iscoroutinefunction(self.func):
++ self.cache[obj] = value = asyncio.ensure_future(self.func(obj))
++ else:
++ self.cache[obj] = value = self.func(obj)
+
+ return value
+
+@@ -49,18 +50,6 @@ class cached_property(property):
+ def __delete__(self, obj):
+ del self.cache[obj]
+
+- def _wrap_in_coroutine(self, obj):
+-
+- @functools.wraps(obj)
+- @asyncio.coroutine
+- def wrapper():
+- value = self.cache.get(obj, self._sentinel)
+- if value is self._sentinel:
+- self.cache[obj] = value = asyncio.ensure_future(self.func(obj))
+- return value
+-
+- return wrapper()
+-
+
+ class threaded_cached_property(cached_property):
+ """
+diff --git a/tests/test_async_cached_property.py b/tests/test_async_cached_property.py
+index 1af139d..32b3410 100644
+--- a/tests/test_async_cached_property.py
++++ b/tests/test_async_cached_property.py
+@@ -9,8 +9,7 @@ import property_cached as cached_property
+
+ def unittest_run_loop(f):
+ def wrapper(*args, **kwargs):
+- coro = asyncio.coroutine(f)
+- future = coro(*args, **kwargs)
++ future = f(*args, **kwargs)
+ loop = asyncio.get_event_loop()
+ loop.run_until_complete(future)
+
+diff --git a/tests/test_coroutine_cached_property.py b/tests/test_coroutine_cached_property.py
+index 40e443b..5864301 100644
+--- a/tests/test_coroutine_cached_property.py
++++ b/tests/test_coroutine_cached_property.py
+@@ -14,8 +14,7 @@ import property_cached as cached_property
+
+ def unittest_run_loop(f):
+ def wrapper(*args, **kwargs):
+- coro = asyncio.coroutine(f)
+- future = coro(*args, **kwargs)
++ future = f(*args, **kwargs)
+ loop = asyncio.get_event_loop()
+ loop.run_until_complete(future)
+
+@@ -33,14 +32,12 @@ def CheckFactory(cached_property_decorator):
+ self.control_total = 0
+ self.cached_total = 0
+
+- @asyncio.coroutine
+- def add_control(self):
++ async def add_control(self):
+ self.control_total += 1
+ return self.control_total
+
+ @cached_property_decorator
+- @asyncio.coroutine
+- def add_cached(self):
++ async def add_cached(self):
+ self.cached_total += 1
+ return self.cached_total
+
+@@ -52,74 +49,68 @@ class TestCachedProperty(unittest.TestCase):
+
+ cached_property_factory = cached_property.cached_property
+
+- @asyncio.coroutine
+- def assert_control(self, check, expected):
++ async def assert_control(self, check, expected):
+ """
+ Assert that both `add_control` and 'control_total` equal `expected`
+ """
+- value = yield from check.add_control()
++ value = await check.add_control()
+ self.assertEqual(value, expected)
+ self.assertEqual(check.control_total, expected)
+
+- @asyncio.coroutine
+- def assert_cached(self, check, expected):
++ async def assert_cached(self, check, expected):
+ """
+ Assert that both `add_cached` and 'cached_total` equal `expected`
+ """
+ print("assert_cached", check.add_cached)
+- value = yield from check.add_cached
++ value = await check.add_cached
+ self.assertEqual(value, expected)
+ self.assertEqual(check.cached_total, expected)
+
+ @unittest_run_loop
+- @asyncio.coroutine
+- def test_cached_property(self):
++ async def test_cached_property(self):
+ Check = CheckFactory(self.cached_property_factory)
+ check = Check()
+
+ # The control shows that we can continue to add 1
+- yield from self.assert_control(check, 1)
+- yield from self.assert_control(check, 2)
++ await self.assert_control(check, 1)
++ await self.assert_control(check, 2)
+
+ # The cached version demonstrates how nothing is added after the first
+- yield from self.assert_cached(check, 1)
+- yield from self.assert_cached(check, 1)
++ await self.assert_cached(check, 1)
++ await self.assert_cached(check, 1)
+
+ # The cache does not expire
+ with freeze_time("9999-01-01"):
+- yield from self.assert_cached(check, 1)
++ await self.assert_cached(check, 1)
+
+ # Typically descriptors return themselves if accessed though the class
+ # rather than through an instance.
+ self.assertTrue(isinstance(Check.add_cached, self.cached_property_factory))
+
+ @unittest_run_loop
+- @asyncio.coroutine
+- def test_reset_cached_property(self):
++ async def test_reset_cached_property(self):
+ Check = CheckFactory(self.cached_property_factory)
+ check = Check()
+
+ # Run standard cache assertion
+- yield from self.assert_cached(check, 1)
+- yield from self.assert_cached(check, 1)
++ await self.assert_cached(check, 1)
++ await self.assert_cached(check, 1)
+
+ # Clear the cache
+ del check.add_cached
+
+ # Value is cached again after the next access
+- yield from self.assert_cached(check, 2)
+- yield from self.assert_cached(check, 2)
++ await self.assert_cached(check, 2)
++ await self.assert_cached(check, 2)
+
+ @unittest_run_loop
+- @asyncio.coroutine
+- def test_none_cached_property(self):
++ async def test_none_cached_property(self):
+ class Check(object):
+ def __init__(self):
+ self.cached_total = None
+
+ @self.cached_property_factory
+- @asyncio.coroutine
+- def add_cached(self):
++ async def add_cached(self):
+ return self.cached_total
+
+- yield from self.assert_cached(Check(), None)
++ await self.assert_cached(Check(), None)
+--
+2.49.0
+
M gnu/packages/patches/python-sip-include-dirs.patch => gnu/packages/patches/python-sip-include-dirs.patch +8 -9
@@ 5,16 5,15 @@ It seems that we cannot easily change the destination folder of these
files though, so this variable must be set on a per-package basis (and
non through search-path).
---- sip/sipbuild/builder.py 2023-03-22 09:06:37.588792878 +0100
-+++ sip/sipbuild/builder.py 2023-03-22 09:10:35.830181134 +0100
-@@ -254,6 +254,10 @@
+--- sip/sipbuild/builder.py
++++ sip/sipbuild/builder.py
+@@ -227,5 +227,9 @@
os.path.join(project.target_dir,
project.get_bindings_dir()))
-+ # Add extra bindings from environment for GNU Guix.
-+ if 'SIP_INCLUDE_DIRS' in os.environ:
-+ sip_include_dirs.extend(os.environ['SIP_INCLUDE_DIRS'].split(os.pathsep))
++ # Add extra bindings from environment for GNU Guix
++ if 'SIP_INCLUDE_DIRS' in os.environ:
++ sip_include_dirs.extend(os.environ['SIP_INCLUDE_DIRS'].split(os.pathsep))
+
- # Generate the sip.h file for the shared sip module.
- copy_sip_h(abi_major_version, project.build_dir,
- project.sip_module, version_info=project.version_info)
+ # Generate the code for each set of bindings.
+ api_files = []
A gnu/packages/patches/python-vaex-core-fix-tsl-use.patch => gnu/packages/patches/python-vaex-core-fix-tsl-use.patch +67 -0
@@ 0,0 1,67 @@
+From 8cb8808b3ceccf4ab3ac542739ef490abe7e76b3 Mon Sep 17 00:00:00 2001
+Message-ID: <8cb8808b3ceccf4ab3ac542739ef490abe7e76b3.1743597010.git.ngraves@ngraves.fr>
+From: Nicolas Graves <ngraves@ngraves.fr>
+Date: Wed, 2 Apr 2025 14:29:40 +0200
+Subject: [PATCH] Fix tsl map use
+
+---
+ packages/vaex-core/src/hash_string.hpp | 25 ++++++++++++++++---------
+ 1 file changed, 16 insertions(+), 9 deletions(-)
+
+diff --git a/packages/vaex-core/src/hash_string.hpp b/packages/vaex-core/src/hash_string.hpp
+index d3b60199..0ed69d1c 100644
+--- a/packages/vaex-core/src/hash_string.hpp
++++ b/packages/vaex-core/src/hash_string.hpp
+@@ -39,13 +39,15 @@ class hash_base : public hash_common<Derived, T, hashmap<T, int64_t>> {
+ for (int i = 0; i < nmaps; i++) {
+ string_arrays.emplace_back(std::make_shared<StringList64>());
+ StringList64 *strings = string_arrays[i].get();
+- // equal_to<string_ref>& eq = this->maps[i].key_eq();
+- this->maps[i].m_ht.strings_equals = strings;
+- this->maps[i].m_ht.strings_hash = strings;
++ equal_to<key_type> eq;
++ eq.strings_equals = strings;
++ hash<key_type> h;
++ h.strings_hash = strings;
++ this->maps[i] = hashmap_type(8, h, eq);
+ }
+ };
+
+- virtual std::string _get(hashmap_type &map, typename hashmap_type::key_type key) override { return map.m_ht.strings_equals->get(key.index); };
++ virtual std::string _get(hashmap_type &map, typename hashmap_type::key_type key) override { return string_arrays[0]->get(key.index); };
+
+ size_t bytes_used() const {
+ int64_t buffer_size = 0; // collect buffer size
+@@ -391,9 +393,12 @@ class ordered_set : public hash_base<ordered_set<T>, T, T, V> {
+ template <class SL>
+ static ordered_set *create(std::shared_ptr<SL> keys, int64_t null_value, int64_t nan_count, int64_t null_count, std::string *fingerprint) {
+ ordered_set *set = new ordered_set(1);
+- set->maps[0].m_ht.strings_equals = keys.get();
+- set->maps[0].m_ht.strings_hash = keys.get();
+ set->string_arrays[0] = keys;
++ equal_to<key_type> eq;
++ eq.strings_equals = keys.get();
++ hash<key_type> h;
++ h.strings_hash = keys.get();
++ set->maps[0] = hashmap_type(keys->length, h, eq);
+ {
+ size_t size = keys->length;
+ set->maps[0].reserve(size);
+@@ -701,9 +706,11 @@ class index_hash : public hash_base<index_hash<T>, T, T, V> {
+ // string_arrays_overflow.emplace_back(std::make_shared<StringList64>());
+ // for each key in overflow, it should be present in the main string array
+ StringList64 *strings = this->string_arrays[i].get();
+- // equal_to<string_ref>& eq = this->maps[i].key_eq();
+- overflows[i].m_ht.strings_equals = strings;
+- overflows[i].m_ht.strings_hash = strings;
++ equal_to<key_type> eq;
++ eq.strings_equals = strings;
++ hash<key_type> h;
++ h.strings_hash = strings;
++ overflows[i] = overflow_type(8, h, eq);
+ }
+ }
+
+--
+2.49.0
+
D gnu/packages/patches/python-wxwidgets-type-errors.patch => gnu/packages/patches/python-wxwidgets-type-errors.patch +0 -42
@@ 1,42 0,0 @@
-Merged upstream but not yet released (see:
-https://github.com/wxWidgets/Phoenix/pull/2387/commits/5d9f7aa185cd18da3e93ae1d0033fb9172d7a714).
-
-From 5d9f7aa185cd18da3e93ae1d0033fb9172d7a714 Mon Sep 17 00:00:00 2001
-From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
-Date: Mon, 1 May 2023 13:53:55 -0400
-Subject: [PATCH] agw: Fix TypeError caused by floats with Python 3.10
- extensions.
-
-This fixes the following error:
-
- File "/lib/python3.10/site-packages/wx/lib/agw/pygauge.py", line 380, in OnPaint
- dc.DrawText(drawString, textXPos, textYPos)
- TypeError: DC.DrawText(): arguments did not match any overloaded call:
- overload 1: argument 2 has unexpected type 'float'
- overload 2: argument 2 has unexpected type 'float'
- TimeLeft: 3.0
-
-Visible when using Python 3.10 or newer.
----
- wx/lib/agw/pygauge.py | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/wx/lib/agw/pygauge.py b/wx/lib/agw/pygauge.py
-index b8654436a..da42e6f61 100644
---- a/wx/lib/agw/pygauge.py
-+++ b/wx/lib/agw/pygauge.py
-@@ -367,12 +367,12 @@ def OnPaint(self, event):
- drawString = self._drawIndicatorText_formatString.format(drawValue)
- rect = self.GetClientRect()
- (textWidth, textHeight, descent, extraLeading) = dc.GetFullTextExtent(drawString)
-- textYPos = (rect.height-textHeight)/2
-+ textYPos = (rect.height-textHeight)//2
-
- if textHeight > rect.height:
- textYPos = 0-descent+extraLeading
-
-- textXPos = (rect.width-textWidth)/2
-+ textXPos = (rect.width-textWidth)//2
-
- if textWidth>rect.width:
- textXPos = 0
D gnu/packages/patches/trytond-add-egg-modules-to-path.patch => gnu/packages/patches/trytond-add-egg-modules-to-path.patch +0 -22
@@ 1,22 0,0 @@
-Work around trytond.module not being a real namespace module.
-
-Solution is to add all trytond module's locations to
-trytond.modules._path__. This will make trytond.module behave much
-like a namespace module.
-Adding to __path__ is done in update_egg_modules() to ensure __path__
-is updated whenever the list of egg modules is updated.
-
-*** a/trytond/modules/__init__.py 1970-01-01 01:00:01.000000000 +0100
---- b/trytond/modules/__init__.py 2021-12-02 18:12:15.385101986 +0100
-***************
-*** 38,43 ****
---- 38,46 ----
- import pkg_resources
- for ep in pkg_resources.iter_entry_points('trytond.modules'):
- EGG_MODULES[ep.name] = ep
-+ path = os.path.join(ep.dist.location, 'trytond', 'modules')
-+ if not path in __path__ and os.path.isdir(path):
-+ __path__.append(path)
- except ImportError:
- pass
-
M gnu/packages/patchutils.scm => gnu/packages/patchutils.scm +3 -3
@@ 366,7 366,7 @@ you to figure out what is going on in that merge you keep avoiding.")
(define-public patchwork
(package
(name "patchwork")
- (version "3.1.1")
+ (version "3.2.1")
(source (origin
(method git-fetch)
(uri (git-reference
@@ 375,7 375,7 @@ you to figure out what is going on in that merge you keep avoiding.")
(file-name (git-file-name name version))
(sha256
(base32
- "0is9d4gf93jcbyshyj2k3kjyrjnvimrm6bai6dbcx630md222j5w"))))
+ "04ikawdyhjwspxvhazbp5f5vym672y0jcw8rd2m75h9ipcpnyxim"))))
(build-system python-build-system)
(arguments
`(;; TODO: Tests require a running database
@@ 499,7 499,7 @@ if __name__ == \"__main__\":
(inputs
(list python-wrapper))
(propagated-inputs
- (list python-django-3.2
+ (list python-django
;; TODO: Make this configurable
python-psycopg2
python-mysqlclient
M gnu/packages/protobuf.scm => gnu/packages/protobuf.scm +8 -11
@@ 2,7 2,7 @@
;;; Copyright © 2014, 2022 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016 Daniel Pimentel <d4n1@d4n1.org>
;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
-;;; Copyright © 2017, 2018, 2019, 2022, 2023 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017-2019, 2022-2025 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2020, 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
@@ 175,7 175,7 @@ internal RPC protocols and file formats.")
(package
(inherit protobuf)
(name "protobuf")
- (version "3.20.2")
+ (version "3.20.3")
(source (origin
(method url-fetch)
(uri (string-append
@@ 186,7 186,7 @@ internal RPC protocols and file formats.")
(snippet '(delete-file-recursively "third_party"))
(sha256
(base32
- "1hsscx9jm8qv3afgwc764rx9sx1ylkrr54xw1wc0mfjbl8mpw5m0"))))
+ "0ggyfrfal7wms4n8pba224jwpjxn19rigd5y90m3x2bg97ych775"))))
(build-system gnu-build-system)
(arguments (substitute-keyword-arguments (package-arguments protobuf)
;; XXX: insists on using bundled googletest
@@ 467,21 467,18 @@ mechanism for serializing structured data.")
(define-public python-protobuf
(package
(name "python-protobuf")
- (version "3.20.2")
+ (version "3.20.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "protobuf" version))
(sha256
(base32
- "0l0p2lczs5iahgkhzm3298pjl49bk9iiwngkglg7ll7fkqqwlbbi"))))
+ "1wh5f4rnzbv46xy1rx62cprhg5hqf2py06s9b7rfpzwwki12fd1f"))))
(build-system python-build-system)
- (inputs (list protobuf))
- (arguments
- `(;; Favor C++ implementation from protobuf over the native Python
- ;; implementation. The additional dependency yields significant
- ;; performance improvements for some workloads.
- #:configure-flags '("--cpp_implementation")))
+ ;; The C++ implementation is not compatible with Python 3.11, so we cannot
+ ;; pass --cpp_implementation any more.
+ (inputs (list protobuf-3.20))
(home-page "https://github.com/google/protobuf")
(synopsis "Protocol buffers is a data interchange format")
(description
M gnu/packages/python-build.scm => gnu/packages/python-build.scm +16 -16
@@ 344,18 344,6 @@ facilitate packaging Python projects, where packaging includes:
license:asl2.0 ;packaging is dual ASL2/BSD-2
license:bsd-2))))
-;; This is the last version with use_2to3 support.
-(define-public python-setuptools-57
- (package
- (inherit python-setuptools)
- (version "57.5.0")
- (source (origin
- (inherit (package-source python-setuptools))
- (uri (pypi-uri "setuptools" version))
- (sha256
- (base32
- "091sp8lrin7qllrhhx7y0iiv5gdb1d3l8a1ip5knk77ma1njdlyr"))))))
-
(define-public python-wheel
(package
(name "python-wheel")
@@ 412,14 400,14 @@ installed with a newer @code{pip} or with wheel's own command line utility.")
(define-public python-pyparsing
(package
(name "python-pyparsing")
- (version "3.0.6")
+ (version "3.2.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pyparsing" version))
(sha256
- (base32 "109b9r802wb472hgmxclljprh5cid0w3p6mk9alba7pg2c0frgfr"))))
- (build-system python-build-system)
+ (base32 "02jz5rv3vx46xvjszda467l269jz9narlrwd0a83mpk6zma0i631"))))
+ (build-system pyproject-build-system)
(outputs '("out" "doc"))
(arguments
`(#:tests? #f ;no test target
@@ 440,6 428,7 @@ installed with a newer @code{pip} or with wheel's own command line utility.")
(find-files dir ".*")))
(list "docs" "htmldoc" "examples")
(list doc html-doc examples))))))))
+ (native-inputs (list python-flit-core))
(home-page "https://github.com/pyparsing/pyparsing")
(synopsis "Python parsing class library")
(description
@@ 459,7 448,8 @@ that client code uses to construct the grammar directly in Python code.")
(method url-fetch)
(uri (pypi-uri "pyparsing" version))
(sha256
- (base32 "1hgc8qrbq1ymxbwfbjghv01fm3fbpjwpjwi0bcailxxzhf3yq0y2"))))))
+ (base32 "1hgc8qrbq1ymxbwfbjghv01fm3fbpjwpjwi0bcailxxzhf3yq0y2"))))
+ (native-inputs (list python-setuptools python-wheel))))
(define-public python-packaging-bootstrap
(package
@@ 569,6 559,16 @@ a light weight, fully compliant, self-contained package allowing PEP 517
compatible build front-ends to build Poetry managed projects.")
(license license:expat)))
+(define-public python-poetry-core-next
+ (package/inherit python-poetry-core
+ (version "2.1.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "poetry_core" version))
+ (sha256
+ (base32 "015a0802radb2x5wsbywm4fggv4s1srh8zyml5v58xgrxg8bpnzr"))))))
+
;;; This package exists to bootstrap python-tomli.
(define-public python-flit-core-bootstrap
(package
M gnu/packages/python-check.scm => gnu/packages/python-check.scm +79 -52
@@ 288,27 288,70 @@ Avocado machine readable outputs this one is streamlined (per test results).
@end table")
(license license:gpl2))) ;some files are under GPLv2 only
+(define-public python-pytest-black
+ (package
+ (name "python-pytest-black")
+ (version "0.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "pytest_black" version))
+ (sha256
+ (base32
+ "04dmhv8dzh356qdxz6hrwfz3nk3mlc9shicgpns5r03rydap9dzc"))))
+ (build-system pyproject-build-system)
+ (native-inputs
+ (list python-setuptools
+ python-wheel))
+ (propagated-inputs
+ (list python-black
+ python-pytest
+ python-toml))
+ ;; Project maintenance has been changed, see
+ ;; <https://github.com/shopkeep/pytest-black/issues/70>.
+ (home-page "https://github.com/coherent-oss/pytest-black")
+ (synopsis "Pytest plugin to enable format checking with black")
+ (description
+ "This package provides a pytest plugin to enable format checking with the
+Python code formatter \"black\".")
+ (license license:expat)))
+
+(define-public python-pytest-freezer
+ (package
+ (name "python-pytest-freezer")
+ (version "0.4.9")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "pytest_freezer" version))
+ (sha256
+ (base32 "0an8y6ri3bhij4137gphdw2yg6rq7if4nb1qjj7zjsy4kjy1dgr1"))))
+ (build-system pyproject-build-system)
+ (native-inputs
+ (list python-flit-core))
+ (propagated-inputs
+ (list python-freezegun
+ python-pytest))
+ (home-page "https://github.com/pytest-dev/pytest-freezer/")
+ (synopsis "Pytest plugin providing a fixture interface for spulec/freezegun")
+ (description
+ "Pytest plugin providing a fixture interface for
+@url{https://github.com/spulec/freezegun, freezegun}.")
+ (license license:expat)))
+
(define-public python-beartype
(package
(name "python-beartype")
- (version "0.10.4")
+ (version "0.19.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "beartype" version))
(sha256
- (base32 "0amzckgw9c93bl4jf0q6322j9wyyf3i8vl03yixfkrpllzv6kv14"))))
+ (base32 "0wv598iv9c2s6ivfiara9pnkdlnas8xjw063wvyi0dswpb0xyhny"))))
(build-system pyproject-build-system)
- (arguments
- (list
- #:test-flags
- #~(list
- "beartype_test"
- ;; These tests rely on git through the "get_main_readme_file" helper.
- "-k" (string-append "not test_doc_readme "
- "and not test_sphinx "
- "and not test_pep561_mypy"))))
- (native-inputs (list python-pytest python-setuptools python-wheel))
+ (native-inputs
+ (list python-hatchling python-numpy python-pygments python-pytest))
(home-page "https://github.com/beartype/beartype")
(synopsis "Fast runtime type checking for Python")
(description "Beartype aims to be a very fast runtime type checking tool
@@ 2628,6 2671,8 @@ them using any Python VM with basically no runtime overhead.")
(list
#:test-flags
#~(list
+ ;; This one started failing with the last update of Numpy.
+ "--ignore=tests/test_beartype.py"
;; Multiple failures due to undefined names (typing package must be
;; too outdated, or perhaps they use a newer pandas).
"--ignore=tests/test_mypy.py"
@@ 2846,7 2891,7 @@ help in debugging failures and optimizing the scheduler to improve speed.")
(define-public python-pytest-subprocess
(package
(name "python-pytest-subprocess")
- (version "1.5.2")
+ (version "1.5.3")
(source
(origin
(method git-fetch) ;no tests in PyPI archive
@@ 2856,17 2901,17 @@ help in debugging failures and optimizing the scheduler to improve speed.")
(file-name (git-file-name name version))
(sha256
(base32
- "1mncfyn0vkbf7d03zc8wmv7nl354ck5i9gfblp9220ihc52whhy0"))))
+ "1yb5y6dqzf6k5a07yzdpw8w50bm7zbsdvv06ii7c7vyg9wx5iw6y"))))
(build-system pyproject-build-system)
- (native-inputs (list python-anyio
- python-coverage
- python-docutils
- python-nox
- python-pygments
- python-pytest
- python-pytest-asyncio
- python-pytest-rerunfailures
- python-wheel))
+ (native-inputs
+ (list python-anyio
+ python-docutils
+ python-pygments
+ python-pytest
+ python-pytest-asyncio
+ python-pytest-rerunfailures
+ python-setuptools
+ python-wheel))
(home-page "https://github.com/aklajnert/pytest-subprocess")
(synopsis "Fake subprocess for Pytest")
(description
@@ 2950,25 2995,6 @@ __version_tuple__ = version_tuple = (~a)~%" version version-tuple)))))))))
in an opinionated way.")
(license license:expat)))
-(define-public python-parameterizedtestcase
- (package
- (name "python-parameterizedtestcase")
- (version "0.1.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "parameterizedtestcase" version))
- (sha256
- (base32 "0zhjmsd16xacg4vd7zb75kw8q9khn52wvad634v1bvz7swaivk2c"))))
- (build-system python-build-system)
- (native-inputs (list python-setuptools-57)) ;for use_2to3
- (home-page
- "https://github.com/msabramo/python_unittest_parameterized_test_case")
- (synopsis "Parameterized tests for Python's unittest module")
- (description "This package provides parameterized tests for Python's
-@code{unittest} module taking inspiration from pytest.")
- (license license:expat)))
-
(define-public python-pytest-rerunfailures
(package
(name "python-pytest-rerunfailures")
@@ 3271,13 3297,13 @@ attachments).
(define-public python-vcrpy
(package
(name "python-vcrpy")
- (version "6.0.2")
+ (version "7.0.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "vcrpy" version))
(sha256
- (base32 "02fwmmc33qqybzbj1lvdz458g1fffm5cgnqihj4larw4268kvqc8"))))
+ (base32 "0l1sdfc51024jclqv9104nagpirxx8w0gcn5h0bdxv950jnr2qqp"))))
(build-system pyproject-build-system)
(arguments
(list
@@ 3290,22 3316,23 @@ attachments).
"test_testcase_playback")
" and not "))))
(native-inputs
- (list nss-certs-for-test
- python-flask
+ (list python-aiohttp
+ python-boto3
python-httplib2
- python-ipaddress
- python-mock
+ python-httpx
python-pytest
python-pytest-cov
+ python-pytest-aiohttp
+ python-pytest-asyncio
python-pytest-httpbin
+ python-requests
python-setuptools
+ python-tornado
python-urllib3
+ python-werkzeug
python-wheel))
(propagated-inputs
- (list python-pyyaml
- python-six
- python-wrapt
- python-yarl))
+ (list python-pyyaml python-wrapt python-yarl))
(home-page "https://github.com/kevin1024/vcrpy")
(synopsis "Automatically mock your HTTP interactions")
(description
M gnu/packages/python-compression.scm => gnu/packages/python-compression.scm +28 -0
@@ 11,6 11,7 @@
;;; Copyright © 2024 TakeV <takev@disroot.org>
;;; Copyright © 2023 Ivan Vilata i Balaguer <ivan@selidor.net>
;;; Copyright © 2024 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
;;;
;;; This file is part of GNU Guix.
;;;
@@ 764,6 765,33 @@ install: libbitshuffle.so
(inputs '())
(native-inputs '())))
+(define-public python-unix-ar
+ (package
+ (name "python-unix-ar")
+ (version "0.2.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "unix_ar" version))
+ (sha256
+ (base32 "0kicwxsh28x8r34a7cgzv2i65gsd4qjw2vf29pwq4fpsf3n2i4xz"))))
+ (build-system pyproject-build-system)
+ (arguments
+ ;; These tests have timestamp-related issues.
+ (list #:test-flags
+ #~(list "-m" "unittest" "-k" "not test_add and not test_addfile")
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? test-flags #:allow-other-keys)
+ (apply invoke "python" test-flags))))))
+ (native-inputs (list python-pytest python-setuptools python-wheel))
+ (home-page "https://github.com/getninjas/unix_ar")
+ (synopsis "AR file handling in Python")
+ (description "This package provides utilities to handle AR files in
+Python.")
+ (license license:bsd-3)))
+
(define-public python-zipp
(package
(name "python-zipp")
M gnu/packages/python-crypto.scm => gnu/packages/python-crypto.scm +28 -54
@@ 11,7 11,7 @@
;;; Copyright © 2016, 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2016, 2017 Nikita <nikita@n0.is>
;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2015, 2016, 2017, 2019, 2022, 2024 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2019, 2022, 2024, 2025 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016 Danny Milosavljevic <dannym+a@scratchpost.org>
;;; Copyright © 2016, 2017, 2020 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2017 Carlo Zancanaro <carlo@zancanaro.id.au>
@@ 57,6 57,7 @@
#:use-module (guix build-system python)
#:use-module (guix utils)
#:use-module (gnu packages)
+ #:use-module (gnu packages certs)
#:use-module (gnu packages check)
#:use-module (gnu packages crates-io)
#:use-module (gnu packages crates-tls)
@@ 141,17 142,19 @@ Password Scheme\"} by Niels Provos and David Mazieres.")
(uri (pypi-uri "passlib" version))
(sha256
(base32 "015y5qaw9qnxr29lg60dml1g5rbqd4586wy5n8m41ib55gvm1zfy"))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'check 'set-PYTHON_EGG_CACHE
+ ;; Some tests require access to "$HOME/.cython".
+ (lambda _
+ (setenv "PYTHON_EGG_CACHE" "/tmp"))))))
(native-inputs
- (list python-nose))
+ (list python-nose python-setuptools python-wheel))
(propagated-inputs
- (list python-bcrypt))
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-before 'check 'set-PYTHON_EGG_CACHE
- ;; Some tests require access to "$HOME/.cython".
- (lambda _ (setenv "PYTHON_EGG_CACHE" "/tmp"))))))
+ (list python-argon2-cffi python-bcrypt python-cryptography))
(home-page "https://bitbucket.org/ecollins/passlib")
(synopsis "Comprehensive password hashing framework")
(description
@@ 162,32 165,6 @@ useful for a wide range of tasks, from verifying a hash found in /etc/shadow,
to providing full-strength password hashing for multi-user application.")
(license license:bsd-3)))
-(define-public python-pyblake2
- (package
- (name "python-pyblake2")
- (version "1.1.2")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "pyblake2" version))
- (sha256
- (base32
- "0gz9hgznv5zw4qjq43xa56y0yikimx30gffvibxzm0nv5sq7xk2w"))))
- (build-system python-build-system)
- (home-page "https://github.com/dchest/pyblake2")
- (synopsis "BLAKE2 hash function for Python")
- (description "BLAKE2 is a cryptographic hash function, which offers
-stronger security while being as fast as MD5 or SHA-1, and comes in two
-flavors: @code{BLAKE2b}, optimized for 64-bit platforms and produces digests
-of any size between 1 and 64 bytes, and @code{BLAKE2s}, optimized for 8- to
-32-bit platforms and produces digests of any size between 1 and 32 bytes.
-
-This package provides a Python interface for BLAKE2.")
- ;; The COPYING file declares it as public domain, with the option to
- ;; alternatively use and redistribute it under a variety of permissive
- ;; licenses. cc0 is explicitly mentioned in setup.py and pyblake2module.c.
- (license (list license:public-domain license:cc0))))
-
(define-public python-paramiko
(package
(name "python-paramiko")
@@ 455,13 432,7 @@ blake3, a cryptographic hash function.")
;; Those tests uses PKCS12, which has been removed in
;; pyopenssl 23.3.0:
"not test_custom_not_before_not_after"
- "test_ca_cert_in_mem"
- ;; Those tests try to download certificates:
- "test_file_wildcard"
- "test_file_wildcard_subdomains"
- "test_in_mem_parent_wildcard_cert"
- "test_in_mem_parent_wildcard_cert_at_tld"
- "test_in_mem_parent_wildcard_cert_2")
+ "test_ca_cert_in_mem")
" and not "))
#:phases
#~(modify-phases %standard-phases
@@ 474,7 445,7 @@ blake3, a cryptographic hash function.")
(propagated-inputs
(list python-pyopenssl python-tldextract))
(native-inputs
- (list python-pytest-cov python-setuptools python-wheel))
+ (list nss-certs-for-test python-pytest-cov python-setuptools python-wheel))
(home-page "https://github.com/ikreymer/certauth")
(synopsis "Certificate authority creation tool")
(description "This package provides a small library, built on top of
@@ 658,7 629,13 @@ ciphers, message digests and key derivation functions.")
;; PyOpenSSL runs tests against a certificate with a fixed
;; expiry time. To ensure successful builds in the future,
;; set the time to roughly the release date.
- (invoke "faketime" "2024-07-20" "pytest" "-vv" "-k"
+ (invoke "faketime" "2024-07-20" "pytest" "-vv"
+ "--deselect"
+ ;; This test seems to fail when using faketime, at
+ ;; least on aarch64-linux with OSError: [Errno 22]
+ ;; Invalid argument
+ "tests/test_ssl.py::TestDTLS::test_timeout"
+ "-k"
;; This test tries to look up certificates from
;; the compiled-in default path in OpenSSL, which
;; does not exist in the build environment.
@@ 1657,17 1634,14 @@ signatures.")
(uri (pypi-uri "PGPy" version))
(sha256
(base32 "10w3h934fi1ijx72ppn67a50yhkf8n1db6xx02gk2fjc7wsjx717"))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "pytest")))))))
+ (list #:test-flags
+ ;; All broken tests are in this file.
+ ;; They fail with ValueError: key_size must be at least 1024-bits.
+ #~(list "--ignore" "tests/test_10_exceptions.py")))
(native-inputs
- (list python-pytest
- python-wheel))
+ (list python-pytest python-setuptools python-wheel))
(propagated-inputs (list python-cryptography python-pyasn1))
(home-page "https://github.com/SecurityInnovation/PGPy")
(synopsis "Python implementation of OpenPGP")
M gnu/packages/python-science.scm => gnu/packages/python-science.scm +420 -95
@@ 27,6 27,7 @@
;;; Copyright © 2024 Marco Baggio <marco.baggio@mdc-berlin.de>
;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr>
;;; Copyright © 2024 Rick Huijzer <ikbenrickhuyzer@gmail.com>
+;;; Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
;;;
;;; This file is part of GNU Guix.
;;;
@@ 67,6 68,7 @@
#:use-module (gnu packages maths)
#:use-module (gnu packages mpi)
#:use-module (gnu packages pcre)
+ #:use-module (gnu packages package-management)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
@@ 82,6 84,7 @@
#:use-module (gnu packages ssh)
#:use-module (gnu packages statistics)
#:use-module (gnu packages time)
+ #:use-module (gnu packages version-control)
#:use-module (gnu packages xdisorg)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
@@ 372,7 375,21 @@ Features:
(build-system pyproject-build-system)
(arguments
(list
- #:test-flags #~(list "--pyargs" "numdifftools")
+ #:test-flags
+ #~(list "--pyargs" "numdifftools"
+ "-k" (string-join
+ ;; Tests failing with error: TypeError: a must be an array
+ ;; of real numbers, see
+ ;; <https://github.com/pbrod/numdifftools/issues/72>.
+ (list "not test_high_order_derivative"
+ "test_low_order_derivative_on_example_functions"
+ "test_sinx_div_x"
+ "test_complex_hessian_issue_35"
+
+ "numdifftools.fornberg.Taylor"
+ "numdifftools.fornberg.derivative"
+ "numdifftools.fornberg.taylor")
+ " and not "))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'relax-requirements
@@ 1052,6 1069,172 @@ utilizing the power of scikit-learn, e.g., for pre-processing or doing
cross-validation.")
(license license:gpl3+))))
+(define-public python-snakemake-interface-common
+ (package
+ (name "python-snakemake-interface-common")
+ (version "1.17.4")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/snakemake/snakemake-interface-common")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "19fyqs048zdvrmq5sdayzch850kwsyv2x6xn57cjjzcm4zpjrh9w"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:phases
+ #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "python3" "tests/tests.py")))))))
+ (native-inputs (list python-poetry-core python-pytest))
+ (propagated-inputs (list python-argparse-dataclass python-configargparse))
+ (home-page "https://github.com/snakemake/snakemake-interface-common")
+ (synopsis "Common functions and classes for Snakemake and its plugins")
+ (description "This package provides common functions and classes
+for Snakemake and its plugins.")
+ (license license:expat)))
+
+(define-public python-snakemake-interface-executor-plugins
+ (package
+ (name "python-snakemake-interface-executor-plugins")
+ (version "9.3.3")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url (string-append "https://github.com/snakemake/"
+ "snakemake-interface-executor-plugins"))
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1kjjcgkk1rbavb687x5ayw35ayhsnhpg9262k317x911wqpsj2fm"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "python3" "tests/tests.py")))))))
+ (propagated-inputs (list python-argparse-dataclass
+ python-snakemake-interface-common
+ python-throttler))
+ (native-inputs (list python-poetry-core python-pytest))
+ (home-page (string-append "https://github.com/snakemake/"
+ "python-snakemake-interface-executor-plugins"))
+ (synopsis "Interface for Snakemake executor plugins")
+ (description
+ "This package provides a stable interface for interactions between Snakemake and
+its executor plugins.")
+ (license license:expat)))
+
+(define-public python-snakemake-interface-report-plugins
+ (package
+ (name "python-snakemake-interface-report-plugins")
+ (version "1.1.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url (string-append "https://github.com/snakemake/"
+ "snakemake-interface-report-plugins"))
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0i6z9vk6nv2m3jsym0glrb7h9isdlfza2yq14vbqcslybdi9ykfa"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:tests? #f ;circular dependency on snakemake
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "python3" "tests/tests.py")))))))
+ (propagated-inputs (list python-snakemake-interface-common python-pytest))
+ (native-inputs (list python-poetry-core))
+ (home-page (string-append "https://github.com/snakemake/"
+ "python-snakemake-interface-report-plugins"))
+ (synopsis "Interface for Snakemake report plugins")
+ (description "This package provides a stable interface for interactions
+between Snakemake and its report plugins.")
+ (license license:expat)))
+
+(define-public python-snakemake-interface-software-deployment-plugins
+ (package
+ (name "python-snakemake-interface-software-deployment-plugins")
+ (version "0.6.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url (string-append "https://github.com/snakemake/"
+ "snakemake-interface-software-deployment-plugins"))
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0b4kkznfyfck9f92pkimhyl13ljisfn67rsilm1a5inq2ywpmxba"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "python3" "tests/tests.py")))))))
+ (propagated-inputs (list python-argparse-dataclass
+ python-snakemake-interface-common))
+ (native-inputs (list python-poetry-core))
+ (home-page (string-append "https://github.com/snakemake/"
+ "snakemake-interface-software-deployment-plugins"))
+ (synopsis "Interface for Snakemake software deployment plugins")
+ (description
+ "This package provides a stable interface for interactions between Snakemake and
+its software deployment plugins.")
+ (license license:expat)))
+
+(define-public python-snakemake-interface-storage-plugins
+ (package
+ (name "python-snakemake-interface-storage-plugins")
+ (version "3.3.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url (string-append "https://github.com/snakemake/"
+ "snakemake-interface-storage-plugins"))
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "05n5xgwagb01nyzi8xfvp0nvdfl24lxidgksm7k86p68n1rijd5a"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:tests? #f ;circular dependency on snakemake
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "python3" "tests/tests.py")))))))
+ (propagated-inputs (list python-reretry python-snakemake-interface-common
+ python-throttler python-wrapt))
+ (native-inputs (list python-poetry-core python-pytest))
+ (home-page (string-append "https://github.com/snakemake/"
+ "snakemake-interface-storage-plugins"))
+ (synopsis "Interface for Snakemake storage plugins")
+ (description
+ "This package provides a stable interface for interactions between
+Snakemake and its storage plugins.")
+ (license license:expat)))
+
(define-public python-tdda
(package
(name "python-tdda")
@@ 1643,7 1826,7 @@ doing practical, real world data analysis in Python.")
(lambda _
(copy-recursively
(string-append #$output
- "/lib/python3.10/site-packages/pandas/_libs")
+ "/lib/python3.11/site-packages/pandas/_libs")
"pandas/_libs"))))))
(propagated-inputs
(list python-dateutil
@@ 2465,7 2648,7 @@ objects.")
(define-public python-pytensor
(package
(name "python-pytensor")
- (version "2.18.1")
+ (version "2.28.3") ; the minimal version supporting SciPy 1.12.0
(source (origin
(method git-fetch)
(uri (git-reference
@@ 2474,52 2657,65 @@ objects.")
(file-name (git-file-name name version))
(sha256
(base32
- "0qa0y13xfm6w7ry7gp0lv84c8blyg34a9ns7ynwqyhf9majq08s5"))))
+ "1yz1yslms6kdmy4sgnvbnghhclcpkc80z3vaw9c2y3b3j1fs9b4v"))))
(build-system pyproject-build-system)
(arguments
(list
+ #:test-flags
+ ;; XXX: Full test suite takes about 20-30min to complete in single
+ ;; thread, attempt to run tests in parallel with pytest-xdist fails even
+ ;; so upstream provides a support for that, try to figure out how to
+ ;; improve it.
+ ;;
+ ;; Upstream implements a script, showing slow tests which may be used to
+ ;; exclude even more hanging/slow ones, see
+ ;; <scripts/slowest_tests/extract-slow-tests.py>.
+ ;;
+ ;; Skip computationally intensive tests.
+ #~(list "--ignore" "tests/scan/"
+ "--ignore" "tests/tensor/"
+ "--ignore" "tests/sandbox/"
+ "--ignore" "tests/sparse/sandbox/"
+ ;; Tests hang while running from these files.
+ "--ignore" "tests/compile/test_compilelock.py"
+ "--ignore" "tests/link/jax/test_tensor_basic.py"
+ ;; XXX: Tests finish with error in these files, check why.
+ "--ignore" "tests/compile/function/test_types.py"
+ "--ignore" "tests/link/numba/test_basic.py"
+ "--ignore" "tests/link/numba/test_blockwise.py"
+ "--ignore" "tests/link/numba/test_elemwise.py"
+ "-k" (string-join
+ ;; Skip benchmark tests.
+ (list "not test_elemwise_speed"
+ "test_logsumexp_benchmark"
+ "test_fused_elemwise_benchmark"
+ "test_scan_multiple_output"
+ "test_vector_taps_benchmark"
+ "test_cython_performance"
+ ;; Assertion fails in tests.
+ "test_choose_signature"
+ "test_fgraph_to_python_names")
+ " and not ")
+ ;; Tests collection selects pytensor, which does not contain
+ ;; tests and fails to pass; manually provide a test directory
+ ;; instead.
+ "tests")
#:phases
#~(modify-phases %standard-phases
;; Replace version manually because pytensor uses
;; versioneer, which requires git metadata.
(add-after 'unpack 'versioneer
(lambda _
- (with-output-to-file "setup.cfg"
- (lambda ()
- (display "\
-[versioneer]
-VCS = git
-style = pep440
-versionfile_source = pytensor/_version.py
-versionfile_build = pytensor/_version.py
-tag_prefix =
-parentdir_prefix = pytensor-
-")))
(invoke "versioneer" "install")
(substitute* "setup.py"
- (("versioneer.get_version\\(\\)")
- (string-append "\"" #$version "\"")))))
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (setenv "HOME" "/tmp") ; required for most tests
- ;; Test discovery fails, have to call pytest by hand.
- ;; test_tensor_basic.py file requires JAX.
- (invoke "python" "-m" "pytest" "-vv"
- "--ignore" "tests/link/jax/test_tensor_basic.py"
- ;; Skip benchmark tests.
- "-k" (string-append
- "not test_elemwise_speed"
- " and not test_logsumexp_benchmark"
- " and not test_fused_elemwise_benchmark"
- " and not test_scan_multiple_output"
- " and not test_vector_taps_benchmark"
- " and not test_cython_performance")
- ;; Skip computationally intensive tests.
- "--ignore" "tests/scan/"
- "--ignore" "tests/tensor/"
- "--ignore" "tests/sandbox/"
- "--ignore" "tests/sparse/sandbox/")))))))
+ (("version=versioneer.get_version\\(),")
+ (format #f "version=~s," #$version)))))
+ (add-before 'check 'pre-check
+ (lambda _
+ ;; It is required for most tests.
+ (setenv "HOME" "/tmp")
+ ;; Cython extensions have to be built before running the tests.
+ (invoke "python" "setup.py" "build_ext" "--inplace"))))))
(native-inputs (list python-cython
python-pytest
python-pytest-mock
@@ 2663,6 2859,9 @@ annotations on an existing boxplots and barplots generated by seaborn.")
(sha256
(base32 "0jrq2vhan2h280h6cw1sm5hys2nzmf19w4py64k3nrkc320z9mni"))))
(build-system pyproject-build-system)
+ (arguments
+ ;; This is a Numpy DeprecationWarning, remove it on next update.
+ (list #:test-flags ''("-k" "not test_h5_io")))
;; Pint is optional, but we do not propagate it due to its size.
(native-inputs
(list python-pint
@@ 2878,32 3077,6 @@ and more
@end itemize")
(license license:gpl3)))
-(define-public python-pyglm
- (package
- (name "python-pyglm")
- (version "2.5.7")
- (source
- (origin
- ;; Test files are not included in the archive in pypi.
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/Zuzu-Typ/PyGLM")
- (commit version)
- ;; Checkout the bundled `glm` submodule. PyGLM uses the
- ;; currently unreleased GLM_EXT_matrix_integer feature. Can
- ;; maybe unbundle once glm@0.9.9.9 is released.
- (recursive? #t)))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "08v0cgkwsf8rxscx5g9c5p1dy38rvak2fy3q6hg985if1nj6d9ks"))))
- (build-system python-build-system)
- (home-page "https://github.com/Zuzu-Typ/PyGLM")
- (synopsis "OpenGL Mathematics library for Python")
- (description "PyGLM is a Python extension library which brings the OpenGL
-Mathematics (GLM) library to Python.")
- (license license:zlib)))
-
(define-public python-dask-expr
(package
(name "python-dask-expr")
@@ 3794,18 3967,37 @@ it can be used for displaying many qualitatively different samples.")
(package
(name "python-paramz")
(version "0.9.6")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/sods/paramz")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "1ywc2jzj40m6wmq227j3snxvp4434s0m1xk1abg6v6mr87pv2sa9"))))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/sods/paramz")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1ywc2jzj40m6wmq227j3snxvp4434s0m1xk1abg6v6mr87pv2sa9"))))
(build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ #~(list "-k"
+ ;; Two tests fail with error: TypeError: arrays to stack must be
+ ;; passed as a "sequence" type such as list or tuple.
+ (string-append "not test_raveled_index"
+ " and not test_regular_expression_misc")
+ "paramz/tests/array_core_tests.py"
+ "paramz/tests/cacher_tests.py"
+ "paramz/tests/examples_tests.py"
+ "paramz/tests/index_operations_tests.py"
+ "paramz/tests/init_tests.py"
+ "paramz/tests/lists_and_dicts_tests.py"
+ "paramz/tests/model_tests.py"
+ "paramz/tests/observable_tests.py"
+ "paramz/tests/parameterized_tests.py"
+ "paramz/tests/pickle_tests.py"
+ "paramz/tests/verbose_optimize_tests.py")))
(native-inputs
- (list python-nose
+ (list python-pytest
python-setuptools
python-wheel))
(propagated-inputs
@@ 4055,16 4247,10 @@ numerical computation.")
(sha256
(base32
"0jb5lia0q742d1713jk33vlj41y61sf52j6pgk7pvhxvfxglgxjr"))))
- (build-system python-build-system)
- (arguments
- '(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "pytest" "-vv")))))))
+ (build-system pyproject-build-system)
(propagated-inputs (list python-numpy))
- (native-inputs (list python-pytest python-pytest-cov python-pytest-pep8))
+ (native-inputs
+ (list python-pytest python-pytest-cov python-setuptools python-wheel))
(home-page "https://github.com/dgasmith/opt_einsum")
(synopsis "Optimizing numpys einsum function")
(description
@@ 4080,24 4266,44 @@ documentation for more information.")
(define-public python-vaex-core
(package
(name "python-vaex-core")
- (version "4.17.1")
+ (version "4.18.1")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "vaex-core" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://www.github.com/maartenbreddels/vaex")
+ (commit (string-append "core-v" version))))
+ (file-name (git-file-name name version))
(sha256
- (base32 "1rzx5px3fwi5mh1z8y91brvffk7dkhj287lnmqp8zp6836kkqhya"))
- (modules '((guix build utils)))
+ (base32 "1sp096msbzgjlwi8c1ink2bp4pjff9pvikqz1y1li8d3in4gpgdr"))
+ (patches
+ (search-patches "python-vaex-core-fix-tsl-use.patch"))
+ (modules '((guix build utils)
+ (ice-9 ftw)))
(snippet
- ;; Remove bundled libraries
- '(for-each delete-file-recursively
- (list "vendor/boost"
- "vendor/pcre"
- "vendor/pybind11")))))
+ #~(begin
+ ;; Delete everything except for vaex-core itself:
+ (define (delete-except exception)
+ (lambda (file)
+ (unless (member file `("." ".." ,exception))
+ (delete-file-recursively file))))
+ (for-each (delete-except "packages") (scandir "."))
+ (with-directory-excursion "packages"
+ (for-each (delete-except "vaex-core") (scandir ".")))
+ (for-each (lambda (file)
+ (unless (member file '("." ".."))
+ (rename-file
+ (string-append "packages/vaex-core/" file)
+ file)))
+ (scandir "packages/vaex-core"))
+ (delete-file-recursively "packages")
+ (delete-file-recursively "vendor")))))
(build-system pyproject-build-system)
- (arguments (list #:tests? #false)) ;require vaex.server and others, which require vaex-core.
+ (arguments
+ ;; require vaex.server and others, which require vaex-core.
+ (list #:tests? #false))
(inputs
- (list boost pcre pybind11-2.3))
+ (list boost pcre pybind11 string-view-lite tsl-hopscotch-map))
(propagated-inputs
(list python-aplus
python-blake3
@@ 4321,6 4527,125 @@ compagnies.")
neuronal models")
(license license:bsd-3)))
+(define-public snakemake
+ (package
+ (name "snakemake")
+ (version "8.29.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "snakemake" version))
+ (sha256
+ (base32 "1ilpmrjmnc529p4gw2x23ik1d8b5pm6k1dhq08dknvfjsf3vgyjr"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ #~(list
+ ;; XXX: Unclear why these tests fail.
+ "--ignore=tests/test_report_href/test_script.py"
+ "--ignore=tests/test_script_py/scripts/test_explicit_import.py"
+ "--ignore=tests/test_output_index.py"
+ ;; We don't care about testing old python@3.7 on Guix.
+ "--ignore=tests/test_conda_python_3_7_script/test_script.py"
+ ;; Those require additional snakemake plugins.
+ "--ignore=tests/test_api.py"
+ "--ignore=tests/test_executor_test_suite.py"
+ ;; We don't care about lints.
+ "--ignore=tests/test_linting.py"
+ ;; These tests attempt to change S3 buckets on AWS and fail
+ ;; because there are no AWS credentials.
+ "--ignore=tests/test_tibanna"
+ ;; It's a similar story with this test, which requires access
+ ;; to the Google Storage service.
+ "--ignore=tests/test_google_lifesciences")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'avoid-assets-download
+ (lambda _
+ (substitute* "setup.py"
+ (("^from assets import Assets") "")
+ (("^Assets\\.deploy\\(\\)") ""))))
+ ;; For cluster execution Snakemake will call Python. Since there is
+ ;; no suitable GUIX_PYTHONPATH set, cluster execution will fail. We
+ ;; fix this by calling the snakemake wrapper instead.
+ (add-after 'unpack 'call-wrapper-not-wrapped-snakemake
+ (lambda _
+ (substitute* "snakemake/executors/__init__.py"
+ (("self\\.get_python_executable\\(\\),")
+ "")
+ (("\"-m snakemake\"")
+ (string-append "\"" #$output
+ "/bin/snakemake" "\""))
+ ;; The snakemake command produced by format_job_exec contains
+ ;; references to /gnu/store. Prior to patching above that's
+ ;; just a reference to Python; after patching it's a reference
+ ;; to the snakemake executable.
+ ;;
+ ;; In Tibanna execution mode Snakemake arranges for a certain
+ ;; Docker image to be deployed to AWS. It then passes its own
+ ;; command line to Tibanna. This is misguided because it only
+ ;; ever works if the local Snakemake command was run inside
+ ;; the same Docker image. In the case of using Guix this is
+ ;; never correct, so we need to replace the store reference.
+ (("tibanna_args.command = command")
+ (string-append
+ "tibanna_args.command = command.replace('"
+ #$output "/bin/snakemake', 'python3 -m snakemake')")))))
+ (add-after 'unpack 'patch-version
+ (lambda _
+ (substitute* "setup.py"
+ (("version=versioneer.get_version\\(\\)")
+ (format #f "version=~s" #$version)))
+ (substitute* '("snakemake/_version.py"
+ "versioneer.py")
+ (("0\\+unknown") #$version))))
+ (add-before 'check 'pre-check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (setenv "HOME" "/tmp")))))))
+ (propagated-inputs
+ (list python-appdirs
+ python-conda-inject
+ python-configargparse
+ python-connection-pool
+ python-dpath
+ python-gitpython
+ python-humanfriendly
+ python-immutables
+ python-jinja2
+ python-jsonschema
+ python-nbformat
+ python-packaging
+ python-psutil
+ python-pulp
+ python-pyyaml
+ python-requests
+ python-reretry
+ python-smart-open
+ python-snakemake-interface-common
+ python-snakemake-interface-executor-plugins
+ python-snakemake-interface-report-plugins
+ python-snakemake-interface-storage-plugins
+ python-tabulate
+ python-throttler
+ python-wrapt
+ python-yte))
+ (native-inputs
+ (list python-docutils
+ python-numpy
+ python-pandas
+ python-setuptools
+ python-tomli
+ python-wheel))
+ (home-page "https://snakemake.readthedocs.io")
+ (synopsis "Python-based execution environment for make-like workflows")
+ (description
+ "Snakemake aims to reduce the complexity of creating workflows by
+providing a clean and modern domain specific specification language (DSL) in
+Python style, together with a fast and comfortable execution environment.")
+ (license license:expat)))
+
;;;
;;; Avoid adding new packages to the end of this file. To reduce the chances
;;; of a merge conflict, place them above by existing packages with similar
M gnu/packages/python-web.scm => gnu/packages/python-web.scm +510 -404
@@ 54,7 54,7 @@
;;; Copyright © 2022 Peter Polidoro <peter@polidoro.io>
;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
;;; Copyright © 2022 Luis Henrique Gomes Higino <luishenriquegh2701@gmail.com>
-;;; Copyright © 2022 Nicolas Graves <ngraves@ngraves.fr>
+;;; Copyright © 2022, 2025 Nicolas Graves <ngraves@ngraves.fr>
;;; Copyright © 2022 Tomasz Jeneralczyk <tj@schwi.pl>
;;; Copyright © 2022 msimonin <matthieu.simonin@inria.fr>
;;; Copyright © 2022 Michael Rohleder <mike@rohleder.de>
@@ 392,17 392,88 @@ Async mode for @url{https://domainconnect.org/, Domain Connect protocol}.")
@url{https://www.domainconnect.org/, Domain Connect} protocol.")
(license license:expat)))
+(define-public python-dropbox
+ (package
+ (name "python-dropbox")
+ (version "12.0.2")
+ (source
+ (origin
+ (method git-fetch) ; no tests in PyPI release
+ (uri (git-reference
+ (url "https://github.com/dropbox/dropbox-sdk-python")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0pyvi2mbibah42kq8804d98ghypm46wr8swqr34apnvnlp9j2nzl"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ #~(list "-k" (string-join
+ ;; Network access is required.
+ (list "not test_bad_auth"
+ "test_app_auth"
+ "test_bad_pins"
+ "test_bad_pins_session"
+ "test_downscope"
+ "test_multi_auth"
+ "test_path_root"
+ "test_path_root_err"
+ "test_refresh"
+ "test_rpc"
+ "test_team"
+ "test_upload_download"
+ "test_versioned_route")
+ " and not "))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'relax-requirements
+ (lambda _
+ (substitute* "setup.py"
+ ;; 'stone>=2,<3.3.3',
+ ((">=2,<3.3.3") ">=2,<3.4.0"))))
+ (add-before 'check 'pre-check
+ (lambda _
+ ;; Otherwise tests setup erroring.
+ (setenv "LEGACY_USER_DROPBOX_TOKEN" "guix")
+ (setenv "LEGACY_USER_CLIENT_ID" "guix")
+ (setenv "LEGACY_USER_CLIENT_SECRET" "guix")
+ (setenv "LEGACY_USER_REFRESH_TOKEN" "guix")
+ (setenv "SCOPED_USER_DROPBOX_TOKEN" "guix")
+ (setenv "SCOPED_USER_CLIENT_ID" "guix")
+ (setenv "SCOPED_USER_CLIENT_SECRET" "guix")
+ (setenv "SCOPED_USER_REFRESH_TOKEN" "guix")
+ (setenv "SCOPED_TEAM_DROPBOX_TOKEN" "guix")
+ (setenv "SCOPED_TEAM_CLIENT_ID" "guix")
+ (setenv "SCOPED_TEAM_CLIENT_SECRET" "guix")
+ (setenv "SCOPED_TEAM_REFRESH_TOKEN" "guix")
+ (setenv "DROPBOX_SHARED_LINK" "guix"))))))
+ (native-inputs
+ (list nss-certs-for-test
+ python-mock
+ python-pytest
+ python-pytest-mock
+ python-setuptools
+ python-wheel))
+ (propagated-inputs
+ (list python-requests python-six python-stone))
+ (home-page "https://www.dropbox.com/developers")
+ (synopsis "Official Dropbox API Client")
+ (description "This package provides a Python SDK for integrating with the
+Dropbox API v2.")
+ (license license:expat)))
+
(define-public python-eventlet
(package
(name "python-eventlet")
- (version "0.38.2")
+ (version "0.39.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "eventlet" version))
(sha256
(base32
- "1b7dhy3pyp3nfv0zzjrs7i3kam40cl1nh3acy2fd59ywy4x84ika"))))
+ "04051hmlq49kvdymf56hp08vjc6251937fh6vvnj2h1d51sn92ja"))))
(build-system pyproject-build-system)
(arguments
(list
@@ 794,22 865,19 @@ API rules.")
(define-public python-frozenlist
(package
(name "python-frozenlist")
- (version "1.2.0")
+ ;; XXX: Any newer versions fail to build, check why.
+ (version "1.3.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "frozenlist" version))
(sha256
- (base32 "1pkr23by7pk9lsmsh0wiqirpkq3f1f08b0615nbzysn51bk1n838"))))
- (build-system python-build-system)
- (arguments
- '(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "pytest" "tests")))))))
- (native-inputs (list python-pytest))
+ (base32 "0sispcpras096fxrd0i35qs25fqy4r0x8v1d6f40pag845bwbg2q"))))
+ (build-system pyproject-build-system)
+ (native-inputs
+ (list python-pytest
+ python-setuptools
+ python-wheel))
(home-page "https://github.com/aio-libs/frozenlist")
(synopsis "List-like data structure for Python")
(description "@code{frozenlist.FrozenList} is a list-like structure which
@@ 1663,7 1731,7 @@ decode and default on encode.
(define-public python-cfn-lint
(package
(name "python-cfn-lint")
- (version "1.22.1")
+ (version "1.28.0")
(source (origin
(method git-fetch)
(uri (git-reference
@@ 1672,7 1740,7 @@ decode and default on encode.
(file-name (git-file-name name version))
(sha256
(base32
- "1zz121r9yv1irwdbk07s7958fh43h3r3q39qcj0gv4kpgb0vdf32"))))
+ "0n1v05516s0zy64v1a7f7pj5h9lscvbkkwnlgmys7g8lydlgf0v4"))))
(build-system pyproject-build-system)
(arguments
(list
@@ 1945,19 2013,23 @@ over a different origin than that of the web application.")
(define-public python-furl
(package
(name "python-furl")
- (version "2.1.3")
+ (version "2.1.4")
(source
(origin
(method url-fetch)
(uri (pypi-uri "furl" version))
(sha256
- (base32
- "0knc76pm8pzigs3bpx9fccfsfxqrgblqphar46hq9i364vz8hqas"))))
- (build-system python-build-system)
+ (base32 "05b058xisv8kghvcpaxvssml2jjkh1cmzyrrjwk2kjb62985fxl7"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:test-flags
+ #~(list "-k" (string-append "not test_hosts"
+ " and not test_netloc"
+ " and not test_odd_urls"))))
(propagated-inputs
- (list python-six python-orderedmultidict))
+ (list python-orderedmultidict python-six))
(native-inputs
- (list python-flake8))
+ (list python-flake8 python-pytest python-setuptools python-wheel))
(home-page "https://github.com/gruns/furl")
(synopsis "URL manipulation in Python")
(description "Furl provides an easy-to-use alternative to the
@@ 2055,7 2127,7 @@ other HTTP libraries.")
python-pytest-mock
python-requests
python-requests-toolbelt
- python-requests-unixsocket
+ python-requests-unixsocket2
python-setuptools
python-setuptools-scm
python-trustme
@@ 2476,23 2548,39 @@ and that could be anything you want.")
(uri (pypi-uri "h2" version))
(sha256
(base32 "1fraip114fm1ha5w37pdc0sk8dn9pb0ck267zrwwpap7zc4clfm8"))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? inputs outputs #:allow-other-keys)
- (when tests?
- (add-installed-pythonpath inputs outputs)
- (invoke "python" "-m" "pytest" "-vv" "test"
- ;; This test exceededs the Hypothesis deadline.
- ,@(if (target-riscv64?)
- `("-k" "not test_changing_max_frame_size")
- '()))))))))
+ (list
+ ;; AssertionError: assert '<RemoteSettingsChanged
+ ;; changed_settings:{ChangedSetting(setting=4, original_value=65536,
+ ;; new_value=32768)}>' == '<RemoteSettingsChanged
+ ;; changed_settings:{ChangedSetting(setting=SettingCodes.INITIAL_WINDOW_SIZE,
+ ;; original_value=65536, new_value=32768)}>'
+ #:test-flags
+ #~(list "-k"
+ (string-join
+ (list "not test_remotesettingschanged_repr"
+ ;; This test exceededs the Hypothesis deadline.
+ #$@(if (target-riscv64?)
+ #~("test_changing_max_frame_size")
+ #~())
+ "test_streamreset_repr"
+ "test_settingsacknowledged_repr"
+ "test_connectionterminated_repr[None-None]"
+ "test_connectionterminated_repr[some"
+ "test_remotesettingschanged_repr"
+ "test_streamreset_repr"
+ "test_settingsacknowledged_repr"
+ "test_connectionterminated_repr[None-None]"
+ "test_connectionterminated_repr[some")
+ " and not "))))
(native-inputs
- (list python-hypothesis python-pytest))
+ (list python-pytest
+ python-setuptools
+ python-wheel))
(propagated-inputs
- (list python-hpack python-hyperframe))
+ (list python-hpack
+ python-hyperframe))
(home-page "https://github.com/python-hyper/h2")
(synopsis "HTTP/2 State-Machine based protocol implementation")
(description
@@ 3206,7 3294,6 @@ compliance with the specification.")
(propagated-inputs
(list python-attrs
python-aiohttp
- python-dictpath
python-isodate
python-jsonschema
python-lazy-object-proxy
@@ 3305,13 3392,13 @@ options.")
(package
(inherit python-cssutils)
(name "python-css-parser")
- (version "1.0.7")
+ (version "1.0.10")
(source
(origin
(method url-fetch)
- (uri (pypi-uri "css-parser" version ".tar.gz"))
+ (uri (pypi-uri "css-parser" version))
(sha256
- (base32 "1ldv9s3an4pgk7b5x6z07rw9b5fdrasdldnf22829pb26b39dq15"))))
+ (base32 "0qs375slcwqd7slizh6hzkwxx7cdj36v8kwn0qrfji1kscm9f7mz"))))
(home-page "https://github.com/ebook-utils/css-parser")
(synopsis "Fork of cssutils modified for parsing ebooks")
(description
@@ 3351,7 3438,7 @@ another XPath engine to find the matching elements in an XML or HTML document.")
(define-public python-databricks-cli
(package
(name "python-databricks-cli")
- (version "0.17.0")
+ (version "0.18.0")
(home-page "https://github.com/databricks/databricks-cli")
(source (origin
(method git-fetch)
@@ 3359,19 3446,21 @@ another XPath engine to find the matching elements in an XML or HTML document.")
(file-name (git-file-name name version))
(sha256
(base32
- "1qwbxnx64kw7lrzlyx3hfbnjxpc19cqvvj0gcrkqpyjsgd08vja0"))))
- (build-system python-build-system)
+ "1avag4kwqk2f24r5i0vcmhm6s1gsw6maykhlyj2ixz0qc05pjzvl"))))
+ (build-system pyproject-build-system)
(arguments
- '(#:phases (modify-phases %standard-phases
- (replace 'check
- (lambda _
- (invoke "pytest" "tests" "-vv"))))))
+ (list #:phases #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (invoke "pytest" "tests" "-vv"))))))
(native-inputs
;; For tests.
(list python-decorator
python-mock
python-pytest
- python-requests-mock))
+ python-requests-mock
+ python-setuptools
+ python-wheel))
(propagated-inputs
(list python-click
python-oauthlib
@@ 3981,19 4070,22 @@ that have uses outside of the Zope framework.")
(define-public python-zope-testing
(package
(name "python-zope-testing")
- (version "4.7")
+ (version "5.0.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "zope.testing" version))
(sha256
- (base32
- "1sh3c3i0m8n8fnhqiry0bk3rr356i56ry7calmn57s1pvv8yhsyn"))))
- (build-system python-build-system)
- (home-page "https://pypi.org/project/zope.testing/")
+ (base32 "0jfnycp9kzmmkk0rard8chd81v5yp6vnm09ky7d3qmv6svcd0z78"))))
+ (build-system pyproject-build-system)
+ (native-inputs
+ (list python-setuptools
+ python-wheel))
+ (home-page "https://zopetesting.readthedocs.io/")
(synopsis "Zope testing helpers")
- (description "Zope.testing provides a number of testing utilities for HTML
-forms, HTTP servers, regular expressions, and more.")
+ (description
+ "Zope.testing provides a number of testing utilities for HTML forms, HTTP
+servers, regular expressions, and more.")
(license license:zpl2.1)))
(define-public python-zope-testrunner
@@ 4382,6 4474,28 @@ verification of the SSL peer.")
(home-page "https://github.com/cedadev/ndg_httpsclient/")
(license license:bsd-3)))
+(define-public python-netaddr
+ (package
+ (name "python-netaddr")
+ (version "1.3.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "netaddr" version))
+ (sha256
+ (base32 "12p4ysgawhgkka0sz1dkwgwc2za80dxdp9wvfxivfldmjnc3sg2w"))))
+ (build-system pyproject-build-system)
+ (native-inputs (list python-poetry-core
+ python-pytest
+ python-setuptools
+ python-wheel))
+ (home-page "https://netaddr.readthedocs.io")
+ (synopsis "Pythonic manipulation of network addresses")
+ (description
+ "A Python library for representing and manipulating IPv4, IPv6, CIDR, EUI
+and MAC network addresses.")
+ (license license:bsd-3)))
+
(define-public python-nh3
(package
(name "python-nh3")
@@ 4628,58 4742,33 @@ than Python’s urllib2 library.")
python-requests.")
(license license:isc)))
-(define-public python-requests-unixsocket
+(define-public python-requests-unixsocket2
(package
- (name "python-requests-unixsocket")
- (version "0.2.0")
+ (name "python-requests-unixsocket2")
+ (version "0.4.2")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "requests-unixsocket" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.com/thelabnyc/requests-unixsocket2")
+ (commit (string-append "v" version))))
(sha256
- (base32 "1sn12y4fw1qki5gxy9wg45gmdrxhrndwfndfjxhpiky3mwh1lp4y"))))
+ (base32 "0vy0c1xwwmm6xqabhl2j7zqgsldvcs8ar547nk5r9l2yb7gngzjk"))))
(build-system pyproject-build-system)
- (arguments
- (list
- #:test-flags
- ;; TypeError: HTTPConnection.request() got an unexpected keyword
- ;; argument 'chunked'
- #~(list "-k" (string-append "not test_unix_domain_adapter_ok"
- " and not test_unix_domain_adapter_url_with_query_params"
- " and not test_unix_domain_adapter_connection_error"
- " and not test_unix_domain_adapter_monkeypatch"))
- #:phases
- #~(modify-phases %standard-phases
- (add-before 'check 'skip-pep8
- (lambda _
- (substitute* "pytest.ini"
- (("--pep8") "")))))))
(native-inputs
- (list python-apipkg
- python-appdirs
- python-execnet
- python-packaging
- python-pep8
- python-py
- python-pyparsing
- python-pytest
- python-pytest-cache
- python-pytest-pep8
- python-setuptools
- python-six
- python-waitress
- python-wheel))
+ (list python-poetry-core python-pytest python-waitress))
(propagated-inputs
- (list python-pbr
- python-requests
- python-urllib3))
- (home-page "https://github.com/msabramo/requests-unixsocket")
+ (list python-pbr python-requests))
+ (home-page "https://gitlab.com/thelabnyc/requests-unixsocket2")
(synopsis "Talk HTTP via a UNIX domain socket")
(description
"This Python package lets you use the @code{requests} library to talk
HTTP via a UNIX domain socket.")
(license license:asl2.0)))
+(define-public python-requests-unixsocket
+ (deprecated-package "python-requests-unixsocket" python-requests-unixsocket2))
+
(define-public python-requests_ntlm
(package
(name "python-requests_ntlm")
@@ 5037,7 5126,22 @@ supports url redirection and retries, and also gzip and deflate decoding.")
(define-public python-urllib3-next
(package
- (name "python-urllib3")
+ (inherit python-urllib3)
+ (version "2.3.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "urllib3" version))
+ (sha256
+ (base32
+ "0k90y2bbmw87b9wx7lf0ps0wjpjbnk3h61byrrwid1ph7jdl9igq"))))
+ (native-inputs
+ (list python-hatchling
+ python-hatch-vcs))))
+
+(define-public python-urllib3-1.26
+ (package
+ (inherit python-urllib3)
(version "1.26.17")
(source
(origin
@@ 5046,29 5150,9 @@ supports url redirection and retries, and also gzip and deflate decoding.")
(sha256
(base32
"08fzhaf77kbjj5abpl9xag6fpfxkdp1k5s7sqd3ayacdq91a5mi4"))))
- (build-system python-build-system)
- (arguments `(#:tests? #f))
- (propagated-inputs
- (append
- ;; These 5 inputs are used to build urrlib3[secure]
- (list python-certifi)
- (if (member (%current-system)
- (package-transitive-supported-systems python-cryptography))
- (list python-cryptography)
- '())
- (list python-idna)
- (if (member (%current-system)
- (package-transitive-supported-systems python-pyopenssl))
- (list python-pyopenssl)
- '())
- (list python-pysocks)))
- (home-page "https://urllib3.readthedocs.io/")
- (synopsis "HTTP library with thread-safe connection pooling")
- (description
- "Urllib3 supports features left out of urllib and urllib2 libraries. It
-can reuse the same socket connection for multiple requests, it can POST files,
-supports url redirection and retries, and also gzip and deflate decoding.")
- (license license:expat)))
+ (native-inputs
+ (list python-setuptools
+ python-wheel))))
(define-public python-awscrt
(package
@@ 5212,7 5296,7 @@ opt.override_default_trust_store_from_path(None, os.getenv('SSL_CERT_FILE')) if
(list groff-minimal
python-botocore
python-colorama
- python-docutils-0.15
+ python-docutils-0.16
python-pyyaml
python-rsa
python-s3transfer))
@@ 5450,13 5534,13 @@ headers required for a compressed response and compresses the response data.")
(define-public python-flask-seasurf
(package
(name "python-flask-seasurf")
- (version "1.1.1")
+ (version "2.0.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "Flask-SeaSurf" version))
(sha256
(base32
- "1aaib4n27q0f2alp87mhv3f79vg7qckp71rphbd0mb39qw470lsl"))))
+ "0g5dsm2ikv8q4qcrb2446pbs972l5wkxyfmxsriqdsl02nz06h4f"))))
(build-system pyproject-build-system)
(arguments
(list #:tests? #false)) ;there are none
@@ 5513,28 5597,6 @@ upload, and reCAPTCHA.")
for overriding static files.")
(license license:gpl3+)))
-(define-public python-cookies
- (package
- (name "python-cookies")
- (version "2.2.1")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "cookies" version))
- (sha256
- (base32
- "13pfndz8vbk4p2a44cfbjsypjarkrall71pgc97glk5fiiw9idnn"))))
- (build-system python-build-system)
- (arguments
- `(;; test are broken: https://gitlab.com/sashahart/cookies/issues/3
- #:tests? #f))
- (native-inputs
- (list python-pytest))
- (synopsis "HTTP cookie parser and renderer")
- (description "A RFC 6265-compliant HTTP cookie parser and renderer in
-Python.")
- (home-page "https://gitlab.com/sashahart/cookies")
- (license license:expat)))
-
(define-public python-responses
(package
(name "python-responses")
@@ 5668,6 5730,39 @@ for the basic TCP/IP protocols.")
concurrent HTTP client library for python using @code{gevent}.")
(license license:expat)))
+(define-public python-gevent-websocket
+ (package
+ (name "python-gevent-websocket")
+ (version "0.10.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "gevent-websocket" version))
+ (sha256
+ (base32 "1c2zv2rahp1gil3cj66hfsqgy0n35hz9fny3ywhr2319d0lz7bky"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:tests? #f)) ; no tests in PyPI or git
+ (native-inputs
+ (list python-setuptools
+ python-wheel))
+ (propagated-inputs
+ (list python-gevent))
+ (home-page "https://gitlab.com/noppo/gevent-websocket")
+ (synopsis "Websocket handler for the gevent pywsgi server")
+ (description
+ "Websocket handler for the gevent pywsgi server, a Python network
+library.
+
+Features include:
+@itemize
+@item integration on both socket level or using an abstract interface
+@item RPC and PubSub framework using @acronym{WebSocket Application Messaging
+Protocol, WAMP}
+@item easily extendible using a simple WebSocket protocol plugin API
+@end itemize")
+ (license license:asl2.0)))
+
(define-public python-requests-oauthlib
(package
(name "python-requests-oauthlib")
@@ 6114,30 6209,56 @@ users' sessions over extended periods of time.")
library for Python")
(license license:asl2.0)))
+(define-public python-authlib
+ (package
+ (name "python-authlib")
+ (version "1.5.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "authlib" version))
+ (sha256
+ (base32 "0blpvz2v2r8yvsgm1yr3n61mhwxvh1b0kyf2rp0i4wv6n3n8bg2w"))))
+ (build-system pyproject-build-system)
+ ;; No tests target.
+ (arguments (list #:tests? #false))
+ (propagated-inputs
+ (list python-cryptography
+ python-django
+ python-flask
+ python-httpx
+ python-requests
+ python-sqlalchemy-2
+ python-starlette
+ python-werkzeug))
+ (native-inputs (list python-pytest python-setuptools python-wheel))
+ (home-page "https://pypi.org/project/Authlib/1")
+ (synopsis "Build OAuth and OpenID Connect servers and clients")
+ (description
+ "This is a Python library for building OAuth and OpenID Connect servers
+and clients.")
+ (license license:bsd-3)))
+
(define-public python-flask-oidc
(package
(name "python-flask-oidc")
- (version "1.4.0")
+ (version "2.3.1")
(source
(origin
(method url-fetch)
- (uri (pypi-uri "flask-oidc" version))
+ (uri (pypi-uri "flask_oidc" version))
(sha256
(base32
- "0klgwpn2iy5y7011xh2c8zkryxdwkpxh7qjs3hp5cynl748ia4hc"))))
- (build-system python-build-system)
- (arguments
- (list #:phases
- #~(modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "nosetests")))))))
+ "1200xhqiqlqfmrq54v2p6cf3nny86njjw8r7sk5j59hlk9a683zk"))))
+ (build-system pyproject-build-system)
(propagated-inputs
- (list python-flask python-itsdangerous python-oauth2client
- python-six))
+ (list python-authlib
+ python-blinker
+ python-flask
+ python-requests
+ python-responses))
(native-inputs
- (list python-nose python-mock))
+ (list python-pytest python-poetry-core))
(home-page "https://github.com/puiterwijk/flask-oidc")
(synopsis "OpenID Connect extension for Flask")
(description "@code{python-flask-oidc} provides an OpenID Connect extension
@@ 6237,7 6358,7 @@ CSS tidy. Also supports URL rewriting in CSS files.")
python-wheel))
(propagated-inputs
(list python-certifi
- python-urllib3-next))
+ python-urllib3-1.26))
(home-page "https://github.com/elastic/elasticsearch-py")
(synopsis "Low-level client for Elasticsearch")
(description "Official low-level client for Elasticsearch. Its goal is to
@@ 6521,13 6642,13 @@ addon modules.")
"0z74sa1xw5h20yin9faj0vvdbq713cgbj84klc72jr9nmpjv303c"))
(patches (search-patches "python-werkzeug-tests.patch"))))
(arguments
- '(#:phases
- (modify-phases %standard-phases
- (delete 'check)
- (add-after 'install 'check
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (add-installed-pythonpath inputs outputs)
- (invoke "python" "-m" "pytest"))))))
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'ignore-warnings
+ (lambda _
+ (substitute* "setup.cfg"
+ ((" error.*") "")))))))
(propagated-inputs
(list python-requests))
(native-inputs
@@ 6765,7 6886,7 @@ for URL parsing and changing.")
(propagated-inputs (list python-arrow python-pytz python-requests))
(native-inputs (list python-requests-mock
python-setuptools
- python-urllib3-next
+ python-urllib3-1.26
python-wheel))
(home-page "https://github.com/ucfopen/canvasapi")
(synopsis "API wrapper for the Canvas LMS")
@@ 7275,61 7396,65 @@ hard or impossible to fix in cssselect.")
(sha256
(base32 "1qq46ym3ymzfn4j6fnykfmr1f4qnb7x7p15dlw37hi38v87jpw9v"))
(modules '((guix build utils)))
- (snippet
- '(begin (delete-file-recursively "vendor")
- (delete-file "uvloop/loop.c")))))
+ (snippet
+ '(begin (delete-file-recursively "vendor")
+ (delete-file "uvloop/loop.c")))))
(build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'preparations
- (lambda _
- ;; Use packaged libuv.
- (substitute* "setup.py" (("self.use_system_libuv = False")
- "self.use_system_libuv = True"))
- ;; Replace hardcoded shell command.
- (substitute* "uvloop/loop.pyx"
- (("b'/bin/sh'") (string-append "b'" (which "sh") "'")))
- #t))
- ,@(if (target-riscv64?)
- `((add-after 'unpack 'adjust-test-timeouts
- (lambda _
- (substitute* '("tests/test_tcp.py"
- "tests/test_unix.py")
- (("SSL_HANDSHAKE_TIMEOUT = 15\\.0")
- "SSL_HANDSHAKE_TIMEOUT = 30.0")))))
- '())
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- ;; Remove Python module, which conflicts with the installed version,
- ;; but lacks the built C module.
- (delete-file-recursively "uvloop")
- ;; The tests are prone to get stuck. Use pytest-timeout’s --timeout
- ;; flag to get a meaningful idea about where.
- (invoke "pytest" "-vv" "--timeout=300"
- "--timeout-method=thread"
- "-k" (string-append
- ;; Timeout, because SIGINT cannot be sent to child.
- "not test_signals_sigint_pycode_continue "
- "and not test_signals_sigint_pycode_stop "
- "and not test_signals_sigint_uvcode "
- "and not test_signals_sigint_uvcode_two_loop_runs "
- ;; This test is racy and prone to get stuck on
- ;; various platforms, possibly a aiohttp issue:
- ;; https://github.com/MagicStack/uvloop/issues/412
- "and not test_remote_shutdown_receives_trailing_data "
- ;; It looks like pytest is preventing
- ;; custom stdout/stderr redirection,
- ;; even with -s.
- "and not test_process_streams_redirect "
- ;; FileNotFoundError: [Errno 2] No such file or
- ;; directory
- "and not test_process_env_2"
- ,@(if (target-riscv64?)
- `(" and not test_renegotiation"
- " and not test_getaddrinfo_21")
- `())))))))))
+ (list
+ #:test-flags
+ ;; The tests are prone to get stuck. Use pytest-timeout’s --timeout flag
+ ;; to get a meaningful idea about where.
+ #~(list "--timeout=300"
+ "--timeout-method=thread"
+ "-k" (string-join
+ (list
+ ;; Timeout, because SIGINT cannot be sent to child.
+ "not test_signals_sigint_pycode_continue"
+ "test_signals_sigint_pycode_stop"
+ "test_signals_sigint_uvcode"
+ "test_signals_sigint_uvcode_two_loop_runs"
+ ;; This test is racy and prone to get stuck on
+ ;; various platforms, possibly a aiohttp issue:
+ ;; https://github.com/MagicStack/uvloop/issues/412
+ "test_remote_shutdown_receives_trailing_data"
+ ;; It looks like pytest is preventing
+ ;; custom stdout/stderr redirection,
+ ;; even with -s.
+ "test_process_streams_redirect"
+ ;; FileNotFoundError: [Errno 2] No such file or
+ ;; directory
+ "test_process_env_2"
+ ;; socket.gaierror: [Errno -2] Name or service not known
+ "test_getaddrinfo_21"
+ #$@(if (target-riscv64?)
+ `("test_renegotiation")
+ `()))
+ " and not "))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'preparations
+ (lambda _
+ ;; Use packaged libuv.
+ (substitute* "setup.py" (("self.use_system_libuv = False")
+ "self.use_system_libuv = True"))
+ ;; Replace hardcoded shell command.
+ (substitute* "uvloop/loop.pyx"
+ (("b'/bin/sh'") (string-append "b'" (which "sh") "'")))))
+ #$@(if (target-riscv64?)
+ `((add-after 'unpack 'adjust-test-timeouts
+ (lambda _
+ (substitute* '("tests/test_tcp.py"
+ "tests/test_unix.py")
+ (("SSL_HANDSHAKE_TIMEOUT = 15\\.0")
+ "SSL_HANDSHAKE_TIMEOUT = 30.0")))))
+ '())
+ (add-before 'check 'pre-check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ ;; Remove Python module, which conflicts with the installed
+ ;; version, but lacks the built C module.
+ (delete-file-recursively "uvloop")))))))
(native-inputs
(list python-aiohttp
python-cython-3
@@ 7361,72 7486,75 @@ event loop. It is implemented in Cython and uses libuv under the hood.")
(outputs '("out" "doc"))
(build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'build 'build-doc
- (lambda _
- (invoke "make" "-C" "docs" "PAPER=a4" "html" "info")
- (delete-file "docs/build/texinfo/Makefile")
- (delete-file "docs/build/texinfo/Gunicorn.texi")))
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (if tests?
- (begin
- (invoke "pytest" "-vv"
- ;; Disable the geventlet tests because eventlet uses
- ;; dnspython, which does not work in the build
- ;; container due to lack of /etc/resolv.conf, etc.
- "--ignore=tests/workers/test_geventlet.py"))
- (format #t "test suite not run~%"))))
- (add-after 'install 'install-doc
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((doc (string-append (assoc-ref outputs "doc")
- "/share/doc/" ,name "-" ,version))
- (html (string-append doc "/html"))
- (info (string-append doc "/info"))
- (examples (string-append doc "/examples")))
- (mkdir-p html)
- (mkdir-p info)
- (mkdir-p examples)
- (copy-recursively "docs/build/html" html)
- (copy-recursively "docs/build/texinfo" info)
- (copy-recursively "examples" examples)
- (for-each (lambda (file)
- (copy-file file (string-append doc "/" file)))
- '("README.rst" "NOTICE" "LICENSE" "THANKS")))))
- ;; XXX: The wrap phase includes native inputs on PYTHONPATH, (see
- ;; <https://bugs.gnu.org/25235>), leading to an inflated closure
- ;; size. Override it to only add the essential entries.
- (replace 'wrap
- (lambda* (#:key native-inputs inputs outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (python (assoc-ref (or native-inputs inputs) "python"))
- (sitedir (string-append "/lib/python"
- (python-version python)
- "/site-packages")))
- (wrap-program (string-append out "/bin/gunicorn")
- `("PYTHONPATH" ":" prefix
- ,(map (lambda (output)
- (string-append output sitedir))
- (list python out))))))))))
+ `(#:test-flags
+ ;; Disable the geventlet tests because eventlet uses dnspython, which
+ ;; does not work in the build container due to lack of /etc/resolv.conf
+ '("--ignore=tests/workers/test_geventlet.py")
+ #:phases (modify-phases %standard-phases
+ (add-after 'build 'build-doc
+ (lambda _
+ (invoke "make"
+ "-C"
+ "docs"
+ "PAPER=a4"
+ "html"
+ "info")
+ (delete-file "docs/build/texinfo/Makefile")
+ (delete-file "docs/build/texinfo/Gunicorn.texi")))
+ (add-after 'install 'install-doc
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((doc (string-append (assoc-ref outputs "doc")
+ "/share/doc/"
+ ,name "-"
+ ,version))
+ (html (string-append doc "/html"))
+ (info (string-append doc "/info"))
+ (examples (string-append doc "/examples")))
+ (mkdir-p html)
+ (mkdir-p info)
+ (mkdir-p examples)
+ (copy-recursively "docs/build/html" html)
+ (copy-recursively "docs/build/texinfo" info)
+ (copy-recursively "examples" examples)
+ (for-each (lambda (file)
+ (copy-file file
+ (string-append doc "/" file)))
+ '("README.rst" "NOTICE" "LICENSE" "THANKS")))))
+ ;; XXX: The wrap phase includes native inputs on PYTHONPATH, (see
+ ;; <https://bugs.gnu.org/25235>), leading to an inflated closure
+ ;; size. Override it to only add the essential entries.
+ (replace 'wrap
+ (lambda* (#:key native-inputs inputs outputs
+ #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (python (assoc-ref (or native-inputs inputs)
+ "python"))
+ (sitedir (string-append "/lib/python"
+ (python-version python)
+ "/site-packages")))
+ (wrap-program (string-append out "/bin/gunicorn")
+ `("PYTHONPATH" ":" prefix
+ ,(map (lambda (output)
+ (string-append output sitedir))
+ (list python out))))))))))
(inputs (list bash-minimal))
- (native-inputs
- (list binutils ;; for ctypes.util.find_library()
- python-aiohttp
- python-gevent
- python-pytest
- python-pytest-cov
- python-sphinx
- texinfo))
+ (native-inputs (list binutils ;for ctypes.util.find_library()
+ python-aiohttp
+ python-gevent
+ python-pytest
+ python-pytest-cov
+ python-sphinx
+ texinfo))
(propagated-inputs (list python-packaging python-setuptools python-wheel))
(home-page "https://gunicorn.org/")
(synopsis "Python WSGI HTTP Server for UNIX")
- (description "Gunicorn ‘Green Unicorn’ is a Python WSGI HTTP
+ (description
+ "Gunicorn ‘Green Unicorn’ is a Python WSGI HTTP
Server for UNIX. It’s a pre-fork worker model ported from Ruby’s
Unicorn project. The Gunicorn server is broadly compatible with
various web frameworks, simply implemented, light on server resources,
and fairly speedy.")
- (license license:expat)))
+ (license license:expat)))
(define-public gunicorn-next
(package
@@ 7544,13 7672,14 @@ and fairly speedy.")
python-trustme
python-wsproto))
(propagated-inputs
- (list python-click
+ (list python-a2wsgi
+ python-click
python-dotenv
python-h11
python-httptools
python-pyyaml
python-uvloop
- python-watchgod
+ python-watchfiles
python-websockets))
(home-page "https://github.com/encode/uvicorn")
(synopsis "Fast ASGI server implementation")
@@ 7642,71 7771,76 @@ with GitLab instances through their API.")
interfaces, inferring which argument is the path, and which is the address.")
(license license:expat)))
+;; XXX: This project missed maintainer upstream, see
+;; <https://github.com/joeyespo/grip/issues/387>.
+;; Consider to remove if it keeps failing to build.
(define-public grip
(package
(name "grip")
(version "4.6.1")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/joeyespo/grip")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0vhimd99zw7s1fihwr6yfij6ywahv9gdrfcf5qljvzh75mvzcwh8"))))
- (build-system python-build-system)
- (propagated-inputs (list python-docopt
- python-flask
- python-markdown
- python-path-and-address
- python-pygments
- python-requests))
- (native-inputs (list python-pytest python-responses))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/joeyespo/grip")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0vhimd99zw7s1fihwr6yfij6ywahv9gdrfcf5qljvzh75mvzcwh8"))))
+ (build-system pyproject-build-system)
(arguments
- (list #:phases
- #~(modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key inputs outputs tests? #:allow-other-keys)
- (when tests?
- (add-installed-pythonpath inputs outputs)
- (setenv "PATH"
- (string-append (getenv "PATH") ":"
- #$output "/bin"))
- (invoke "py.test" "-m" "not assumption")))))))
+ (list
+ #:test-flags
+ ;; All tests fail requiring network access, ignore the whole file.
+ #~(list "--ignore=tests/test_github.py")
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; This fixes the removal of `charset` attribute of requests from
+ ;; Werkzeug 2.3.0.
+ ;; Fixed in grip's commit <2784eb2c1515f1cdb1554d049d48b3bff0f42085>.
+ (add-after 'unpack 'fix-response-encoding
+ (lambda _
+ (substitute* "grip/app.py"
+ (("response.charset")
+ "getattr(response, 'charset', 'utf-8')")))))))
+ (native-inputs
+ (list nss-certs-for-test
+ python-pytest
+ python-responses
+ python-setuptools
+ python-wheel))
+ (propagated-inputs
+ (list python-docopt
+ python-flask
+ python-markdown
+ python-path-and-address
+ python-pygments
+ python-requests))
(home-page "https://github.com/joeyespo/grip")
(synopsis "Preview Markdown files using the GitHub API")
(description
- "Grip is a command-line server application written in Python
-that uses the GitHub Markdown API to render a local Markdown file. The styles
-and rendering come directly from GitHub, so you'll know exactly how it will
-appear. Changes you make to the file will be instantly reflected in the browser
-without requiring a page refresh.")
+ "Grip is a command-line server application written in Python that uses
+the GitHub Markdown API to render a local Markdown file. The styles and
+rendering come directly from GitHub, so you'll know exactly how it will
+appear. Changes you make to the file will be instantly reflected in the
+browser without requiring a page refresh.")
(license license:expat)))
(define-public python-port-for
(package
(name "python-port-for")
- (version "0.4")
+ (version "0.7.4")
(source
(origin
(method url-fetch)
- (uri (pypi-uri "port-for" version))
+ (uri (pypi-uri "port_for" version))
(sha256
- (base32
- "1pncxlj25ggw99r0ijfbkq70gd7cbhqdx5ivsxy4jdp0z14cpda7"))))
- (build-system python-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'use-urllib3
- (lambda _
- (substitute* "port_for/_download_ranges.py"
- (("urllib2") "urllib3")))))))
+ (base32 "13826s2d4hzzmv69wws6a7ryhminclv2bqaw6cpl929gnbki6xzw"))))
+ (build-system pyproject-build-system)
(propagated-inputs
(list python-urllib3))
(native-inputs
- (list python-mock))
+ (list python-pytest python-setuptools python-wheel))
(home-page "https://github.com/kmike/port-for/")
(synopsis "TCP localhost port finder and association manager")
(description
@@ 8423,19 8557,19 @@ Swagger.")
(define-public python-manuel
(package
(name "python-manuel")
- (version "1.10.1")
+ (version "1.13.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "manuel" version))
(sha256
(base32
- "1bdzay7j70fly5fy6wbdi8fbrxjrrlxnxnw226rwry1c8a351rpy"))))
- (build-system python-build-system)
+ "0nl8psji3fizbxw34gdg22dndlg9lf5f56mnh1vr4vgsx06i4qsx"))))
+ (build-system pyproject-build-system)
(propagated-inputs
- (list python-six))
+ (list python-setuptools))
(native-inputs
- (list python-zope-testing))
+ (list python-setuptools python-wheel python-zope-testing))
(home-page "https://pypi.org/project/manuel/")
(synopsis "Build tested documentation")
(description
@@ 8445,7 8579,7 @@ Swagger.")
(define-public python-pecan
(package
(name "python-pecan")
- (version "1.4.1")
+ (version "1.6.1")
(source
(origin
(method git-fetch) ;no tests in pypi release
@@ 8455,28 8589,17 @@ Swagger.")
(file-name (git-file-name name version))
(sha256
(base32
- "10lz0cqafx3j24m52vv9ph0bxrzyx6wv2dgz7g9kfm60lhaskqkh"))))
- (build-system python-build-system)
+ "1ybjvpws741bvxd7aq5hh8gv5sk9836hb9afgalqsm0lxsq0li3a"))))
+ (build-system pyproject-build-system)
(arguments
(list
- #:phases
- #~(modify-phases %standard-phases
- (add-after 'unpack 'relax-requirements
- (lambda _
- (substitute* "test-requirements.txt"
- ;; Drop extraneous virtualenv requirement.
- ((".*virtualenv.*") ""))))
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "pytest" "-vv" "pecan")))))))
+ #:test-flags '(list "--pyargs" "pecan")))
(native-inputs
(list gunicorn
python-genshi
python-jinja2
python-pytest
- python-sqlalchemy
- uwsgi))
+ python-sqlalchemy))
(propagated-inputs
(list python-logutils
python-mako
@@ 8656,17 8779,24 @@ esprima.js)")
(define-public python-js2py
(package
(name "python-js2py")
- (version "0.71")
+ (version "0.74")
(source
(origin
(method url-fetch)
(uri (pypi-uri "Js2Py" version))
(sha256
- (base32 "1kkzkys6dfcbdv51vqxr9cmak350ab4mmykb8dysx60lvl4i06x4"))))
- (build-system python-build-system)
- (arguments '(#:tests? #false)) ; none included
+ (base32 "0bwpp23qpx9amzqisiqvzlr17hr7vxqp4ry8lgxhw639hjmadwrr"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:tests? #f)) ; tests require Node
+ (native-inputs
+ (list python-pytest
+ python-setuptools
+ python-wheel))
(propagated-inputs
- (list python-pyjsparser python-six python-tzlocal))
+ (list python-numpy
+ python-pyjsparser
+ python-tzlocal))
(home-page "https://github.com/PiotrDabkowski/Js2Py")
(synopsis "JavaScript to Python translator")
(description
@@ 8970,19 9100,29 @@ applications.")
(define-public python-sanic
(package
(name "python-sanic")
- (version "23.12.1")
+ (version "25.3.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "sanic" version))
(sha256
- (base32
- "115vnir4qijv89139g5h0i4l0n4w3bgh1ickgnk8xidxsa0wla15"))))
+ (base32 "1fv9wgsj54scbr7qhmwdgc4zqnqpwacpakcfxhsg10gc04h54pbp"))
+ ;; Loosen requirements for both python-sanic and python-sanic-bootstrap.
+ (modules '((guix build utils)))
+ (snippet #~(substitute* "setup.py"
+ (("setuptools>=[0-9.]*")
+ "setuptools")))))
(build-system pyproject-build-system)
(arguments
- (list
- #:test-flags
- '(list "-k"
+ (list
+ #:test-flags
+ #~(list "--asyncio-mode=auto"
+ "--ignore=tests/benchmark/"
+ "--ignore=tests/typing/test_typing.py"
+ ;; Most tests hang or fail
+ "--ignore=tests/test_cli.py"
+ "--ignore=tests/worker/test_worker_serve.py"
+ "-k"
(string-append
;; PyPi sources lack examples module.
"not test_gunicorn_"
@@ 8994,6 9134,8 @@ applications.")
" and not test_listeners_triggered"
" and not test_keep_alive_connection_context"
" and not test_keep_alive_client_timeout"
+ " and not test_conflicting_body_methods_overload"
+ " and not test_unix_connection"
;; Unclear why they fail since core-updates merge.
" and not test_missing_sni"
" and not test_no_matching_cert"
@@ 9005,14 9147,9 @@ applications.")
" and not test_setup_and_teardown_unix"
" and not test_configure_socket"
;; Freezes
- " and not test_server_run_with_repl"))
- #:phases
- #~(modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? test-flags #:allow-other-keys)
- (when tests?
- (apply invoke "pytest" "-vv" "./tests"
- test-flags)))))))
+ " and not test_server_run_with_repl"
+ " and not test_server_run"
+ " and not test_no_workers"))))
(propagated-inputs
(list python-aiofiles
python-aioquic
@@ 9026,22 9163,20 @@ applications.")
python-uvloop
python-websockets))
(native-inputs
- (list python-bandit
- python-beautifulsoup4
+ (list python-beautifulsoup4
python-chardet
- python-coverage
python-cryptography
python-docutils
python-mypy
python-pygments
python-pytest
+ python-pytest-asyncio
python-pytest-benchmark
python-pytest-sanic
python-sanic-testing
python-setuptools
python-slotscheck
python-towncrier
- python-tox
python-types-ujson
python-uvicorn
python-wheel))
@@ 9712,38 9847,6 @@ Only the RGB colorspace is supported. Conversion to/from the HSL colorspace
can be handled by the @code{colorsys} module in the Python standard library.")
(license license:bsd-3)))
-(define-public python-webcolors-24
- (package
- (inherit python-webcolors)
- (name "python-webcolors")
- (version "24.11.1")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "webcolors" version))
- (sha256
- (base32 "1xl0vn4xa03vjwx6fj19q9kgb94g65gvdf3p0ivsy0i2ydldgczc"))))
- (build-system pyproject-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'fix-build-error
- (lambda _
- ;; pdm wants optional-dependencies instead of dependency-groups.
- ;; See <https://pdm-project.org/en/latest/usage/dependency/>.
- (substitute* "pyproject.toml"
- (("\\[dependency-groups\\]")
- "[project.optional-dependencies]"))))
- (replace 'check
- (lambda* (#:key tests? inputs outputs #:allow-other-keys)
- (when tests?
- (add-installed-pythonpath inputs outputs)
- ;; Our python-nox version is incompatible,
- ;; so use pytest instead.
- (invoke "pytest")))))))
- (native-inputs (list python-pdm-backend python-pytest))
- (license license:bsd-3)))
-
(define-public python-woob
(package
(name "python-woob")
@@ 10071,8 10174,9 @@ regular expressions.")
(build-system pyproject-build-system)
(arguments
(list #:test-flags
- ;; Tests requiring a display.
- #~(list "-k" (string-append
+ #~(list "--numprocesses" (number->string (parallel-job-count))
+ ;; Tests requiring a display.
+ "-k" (string-append
"not " (string-join
(list "test_pformat"
"test_pformat_old_windows"
@@ 10081,7 10185,9 @@ regular expressions.")
"test_persist")
" and not "))
;; Connection refused to some local FTP server.
- "--ignore=tests/test_feedexport.py")
+ "--ignore=tests/test_feedexport.py"
+ ;; Skip documentation testing.
+ "--ignore=docs")
#:phases
#~(modify-phases %standard-phases
(add-before 'check 'prepare-test-environment
M gnu/packages/python-xyz.scm => gnu/packages/python-xyz.scm +1066 -1009
@@ 185,7 185,6 @@
#:use-module (gnu packages adns)
#:use-module (gnu packages aidc)
#:use-module (gnu packages algebra)
- #:use-module (gnu packages astronomy)
#:use-module (gnu packages attr)
#:use-module (gnu packages audio)
#:use-module (gnu packages autotools)
@@ 232,6 231,7 @@
#:use-module (gnu packages gsasl)
#:use-module (gnu packages gstreamer)
#:use-module (gnu packages gtk)
+ #:use-module (gnu packages guile-xyz)
#:use-module (gnu packages haskell-xyz)
#:use-module (gnu packages icu4c)
#:use-module (gnu packages image)
@@ 309,6 309,7 @@
#:use-module (guix build-system meson)
#:use-module (guix build-system pyproject)
#:use-module (guix build-system python)
+ #:use-module (guix deprecation)
#:use-module (guix download)
#:use-module (guix hg-download)
#:use-module (guix git-download)
@@ 320,44 321,41 @@
(define-public python-apprise
(package
(name "python-apprise")
- (version "1.9.2")
+ (version "1.9.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "apprise" version))
(sha256
- (base32 "1a3kzpjdp29l4ryafd36gs8apg61f16ljw93h1051p98f0hv23i9"))))
+ (base32 "19k51ici58134m61f6di0m36mbqgdyr6r31i8v6rk22vldz6d0zm"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
#~(list "--numprocesses" (number->string (parallel-job-count))
"--ignore=test/test_plugin_macosx.py"
- "-k" (string-append "not test_plugin_mqtt_tls_connect_success"
- " and not test_plugin_mqtt_tls_no_verify_success"
- ;; AssertionError: assert False
- " and not test_plugin_wxpusher_edge_cases"))))
- (propagated-inputs (list python-certifi
- python-click
- python-markdown
- python-pyyaml
- python-requests
- python-requests-oauthlib))
+ ;; AssertionError
+ "--deselect=test/test_plugin_wxpusher.py::test_plugin_wxpusher_urls")))
(native-inputs
(list python-babel
python-pytest
- python-pytest-cov
python-pytest-mock
python-pytest-xdist
python-setuptools
python-wheel))
+ (propagated-inputs
+ (list python-certifi
+ python-click
+ python-markdown
+ python-pyyaml
+ python-requests
+ python-requests-oauthlib))
(home-page "https://github.com/caronc/apprise")
- (synopsis
- "Push notification Python library that works with many platforms")
+ (synopsis "Push notification library")
(description
- "Apprise is a Python library that allows sending push notifications to a broad
-range of notification services, such as Telegram, Discord, Slack, Amazon SNS,
-Gotify, etc.")
+ "Apprise is a Python library that allows sending push notifications to a
+broad range of notification services, such as Telegram, Discord, Slack, Amazon
+SNS, Gotify, etc.")
(license license:bsd-2)))
(define-public python-archspec
@@ 1863,6 1861,34 @@ formatting in the terminal. It comes with a collection of color codes and
names for 256 color terminal setups.")
(license license:expat)))
+(define-public python-colored-traceback
+ ;; No tags in upstream repository.
+ (let ((commit "98e6dea7111f7681db823c518f18026374a832b9")
+ (revision "0"))
+ (package
+ (name "python-colored-traceback")
+ (version (git-version "0.4.2" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/staticshock/colored-traceback.py")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "19d5mpwk7398b8fjh6abnr96wz70vf5vb4p207r8sny748rwx451"))))
+ (build-system pyproject-build-system)
+ (arguments
+ ;; Tests are incompatible with current python version.
+ (list #:tests? #f))
+ (propagated-inputs (list python-colorama python-pygments))
+ (native-inputs (list python-setuptools python-wheel))
+ (home-page "https://github.com/staticshock/colored-traceback.py")
+ (synopsis "Automatically color uncaught exception tracebacks")
+ (description "This package provides python utilities to automatically
+color uncaught exception tracebacks.")
+ (license license:isc))))
+
(define-public python-colorful
(package
(name "python-colorful")
@@ 3186,7 3212,9 @@ simple function calls.")
(native-inputs
(list python-pytest
python-pytest-cov
+ python-setuptools
python-setuptools-scm
+ python-wheel
xorg-server-for-tests))
(home-page "https://github.com/glue-viz/echo")
(synopsis "Callback Properties in Python")
@@ 3509,17 3537,17 @@ planar geometric objects. It is based on the @code{GEOS} library.")
(define-public python-shortuuid
(package
(name "python-shortuuid")
- (version "0.5.0")
+ (version "1.0.13")
(source
(origin
(method url-fetch)
(uri (pypi-uri "shortuuid" version))
(sha256
(base32
- "1f8i4zwj5vmpzbz6b17bljy4399gx5aq7vsyw63sz2qgyjcd73yh"))))
- (build-system python-build-system)
+ "0wjygiwk07irgqmr29bv7rvq9pc71ff3jinzn620a9h6yq3wzf9v"))))
+ (build-system pyproject-build-system)
(native-inputs
- (list python-pep8))
+ (list python-poetry-core python-pytest))
(home-page "https://github.com/skorokithakis/shortuuid")
(synopsis "Generator library for concise, unambiguous and URL-safe UUIDs")
(description
@@ 4013,23 4041,30 @@ Unicode-to-LaTeX conversion.")
(define-public python-cftime
(package
(name "python-cftime")
- (version "1.6.2")
+ (version "1.6.4")
(source
(origin
(method url-fetch)
(uri (pypi-uri "cftime" version))
(sha256
- (base32 "1lp6jrjjgl18csn4bcnphn0l16ag4aynvn7x0kins155p07w0546"))))
+ (base32 "1p5fw25hjqpzwxw3662f72ga30kpf8pbbph8fgb7x2kmjdhl09g3"))))
(build-system pyproject-build-system)
+ (arguments
+ (list #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'remove-unwanted-pytest-options
+ (lambda _
+ (substitute* "setup.cfg"
+ (("doctest_optionflags.*")
+ "")
+ (("--cov.*")
+ "")))))))
(propagated-inputs
(list python-numpy))
(native-inputs
- (list python-check-manifest
- python-coverage
- python-coveralls
- python-cython
- python-pytest-cov
- python-sphinx
+ (list python-cython
+ python-pytest
+ python-setuptools
python-twine
python-wheel))
(home-page "https://unidata.github.io/cftime/")
@@ 4112,14 4147,24 @@ protocol.")
(define-public python-ncls
(package
(name "python-ncls")
- (version "0.0.65")
+ (version "0.0.68")
(source (origin
(method url-fetch)
(uri (pypi-uri "ncls" version))
(sha256
(base32
- "1wx06xqknd2r98w8z93f47g5dpxzn92kamhj8vkq0nj569hf7cg1"))))
- (build-system python-build-system)
+ "14xsnzr34xa4rwfcdjry9aqjs8i03s9fzy6jgrwj3fr3n6msbal1"))))
+ (build-system pyproject-build-system)
+ (arguments
+ ;; Those tests fail with warnings (not errors) for the Numpy update.
+ ;; Remove it at next python-team iteration.
+ (list #:test-flags ''("--ignore=examples/test_all_overlaps_both.py"
+ "--ignore=examples/test_find_overlap_list.py")))
+ (native-inputs (list python-cython
+ python-pandas
+ python-pytest
+ python-setuptools
+ python-wheel))
(propagated-inputs (list python-numpy))
(home-page "https://github.com/endrebak/ncls")
(synopsis "Nested containment list data structure")
@@ 4332,16 4377,16 @@ version identifier.")
(define-public python-serpent
(package
(name "python-serpent")
- (version "1.28")
+ (version "1.41")
(source
(origin
(method url-fetch)
(uri (pypi-uri "serpent" version))
(sha256
- (base32 "1arnckykpkvv2qrp49l1k7q5mr5pisswl0rvdx98x8wsl1n361pk"))))
- (build-system python-build-system)
+ (base32 "15bhxpihxvbphsvp4wyh2kwfz7xasmki9zwcsj3l6r66wdgh61q4"))))
+ (build-system pyproject-build-system)
(native-inputs
- (list python-attrs python-pytz))
+ (list python-attrs python-pytz python-setuptools python-wheel))
(home-page "https://github.com/irmen/Serpent")
(synopsis "Serializer for literal Python expressions")
(description
@@ 4495,43 4540,55 @@ helpers.")
language. It aims to be fast.")
(license license:expat)))
+;; XXX: The project might be abandoned and this package has no users in Guix,
+;; consider to remove if it keeps failing.
+;; See: <https://github.com/ethanfurman/aenum/issues/45>,
+;; <https://github.com/ethanfurman/aenum/issues/44>,
+;; <https://github.com/ethanfurman/aenum/issues/27>.
(define-public python-aenum
(package
(name "python-aenum")
- (version "3.1.12")
+ (version "3.1.15")
(source
(origin
(method url-fetch)
(uri (pypi-uri "aenum" version))
(sha256
- (base32 "1w1ffkcxgnimi5w8802qk6w2qxz9k8hpvsg6yy2zi08ahs8iqlry"))
+ (base32 "0ncmbdblqhqyb2mg73d5663vx3q2xb9q8hmj77zp1y64336pdgcc"))
(modules '((guix build utils)))
(snippet
;; Delete the Python 2 specific files which won't compile
;; in Python 3.
'(for-each delete-file (find-files "." "_py2.py$")))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
(arguments
- `(#:phases (modify-phases %standard-phases
- (replace 'check
- (lambda _
- ;; We must run the test suite module directly, as it
- ;; fails to define the 'tempdir' variable in scope for
- ;; the tests otherwise
- ;; (see:https://bitbucket.org/stoneleaf/aenum/\
- ;; issues/32/running-tests-with-python-setuppy-test).
- (invoke "python3" "aenum/test.py")
- ;; This one fails with "NameError: name
- ;; 'test_pickle_dump_load' is not defined" (see:
- ;; https://bitbucket.org/stoneleaf/aenum/issues/33
- ;; /error-running-the-test_v3py-test-suite).
- ;; (invoke "python3" "aenum/test_v3.py")
- #t)))))
- (home-page "https://bitbucket.org/stoneleaf/aenum")
+ (list
+ #:test-flags
+ ;; These tests are defined in "aenum/test_v3.py" and require a function
+ ;; "test_pickle_dump_load" from "aenum/test.py" which is not imported
+ ;; into the module's scope.
+ #~(list "-k" (string-join
+ (list "not test_pickle_enum_function_with_qualname"
+ "test_class_nested_enum_and_pickle_protocol_four"
+ "test_subclasses_with_getnewargs_ex")
+ " and not "))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'fix-tests
+ (lambda _
+ (substitute* "aenum/test_v3.py"
+ ;; tempdir variable is not defined in the module.
+ (("import tempfile.*")
+ (format #f "import tempfile~%tempdir = tempfile.mkdtemp()~%"))))))))
+ (native-inputs
+ (list python-pytest
+ python-setuptools
+ python-wheel))
+ (home-page "https://github.com/ethanfurman/aenum")
(synopsis "Advanced enumerations, namedtuples and constants for Python")
- (description "The aenum library includes an @code{Enum} base class, a
-metaclass-based @code{NamedTuple} implementation and a @code{NamedConstant}
-class.")
+ (description
+ "The aenum library includes an @code{Enum} base class, a metaclass-based
+@code{NamedTuple} implementation and a @code{NamedConstant} class.")
(license license:bsd-3)))
(define-public python-calver
@@ 4667,43 4724,6 @@ Pythonic interface. It is mainly targeted for testing and automation
tasks rather than a standard compliant master implementation.")
(license license:expat)))
-(define-public python-caniusepython3
- (package
- (name "python-caniusepython3")
- (version "7.2.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "caniusepython3" version))
- (sha256
- (base32
- "0a755444ln38j8d7xb3yw0wzpd0mjrzfn6zqvsh06nw1vdaq4l28"))))
- (build-system python-build-system)
- (arguments
- `(#:phases (modify-phases %standard-phases
- (add-after 'unpack 'relax-requirements
- (lambda _
- (substitute* "setup.py"
- ;; These are for compatibility with Python 2.
- ((".*'argparse', 'backports.functools_lru_cache',.*")
- ""))
- (substitute* "dev_requirements.txt"
- ((".*pylint.*") "")) ;not actually required
- #t))
- (replace 'check
- (lambda _
- (invoke "py.test" "-k" "not NetworkTests"))))))
- (propagated-inputs
- (list python-distlib python-packaging python-requests))
- (native-inputs
- (list python-mock python-pytest))
- (home-page "https://github.com/brettcannon/caniusepython3")
- (synopsis "Check for Python 3-incompatible Python libraries")
- (description "The @command{caniusepython3} command scans your project and
-reports the Python 3-incompatible libraries it found. It can also be used as
-a library.")
- (license license:asl2.0)))
-
(define-public python-diskcache
(package
(name "python-diskcache")
@@ 5344,15 5364,33 @@ lossless but can be tweaked for more aggressive cleaning.")
(define-public python-mechanize
(package
(name "python-mechanize")
- (version "0.4.7")
+ (version "0.4.10")
(source
(origin
(method url-fetch)
(uri (pypi-uri "mechanize" version))
(sha256
- (base32
- "02b845y85ka5sl2cj93lll3v326d8bww07bq1q0y1643h7sshwqp"))))
- (build-system python-build-system)
+ (base32 "1pvxjnhqi6iq7nnjksnfvyzxcibbwfjc9fzp22v0msp7kdzr9shx"))))
+ (build-system pyproject-build-system)
+ (arguments
+ ;; XXX: Unclear why tests are failing.
+ (list #:tests? #f
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'check 'configure-tests
+ (lambda _
+ (setenv "GUIX_PYTHONPATH"
+ (string-append (getcwd) "/test-tools:"
+ (getenv "GUIX_PYTHONPATH"))))))))
+ (native-inputs
+ (list python-html5-parser
+ python-html5lib
+ python-lxml
+ python-service-identity
+ python-setuptools
+ python-six
+ python-twisted
+ python-wheel))
(propagated-inputs
(list python-html5lib))
(home-page "https://github.com/python-mechanize/mechanize")
@@ 5479,40 5517,26 @@ Python.")
(define-public python-jsonargparse
(package
(name "python-jsonargparse")
- (version "4.21.1")
+ (version "4.37.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "jsonargparse" version))
(sha256
(base32
- "1k3b60x0zf86fh50y2jyby30gksqriyvvpfnf5mqq0qn7jih01y7"))))
+ "1b9w9j27phj5j00pmhp11lzf53yc4dnwknhxacv2bfyiiaq0af2s"))))
(build-system pyproject-build-system)
(arguments
- (list
- #:test-flags
- '(list "-k" (string-append "not test_env_prefix"
- " and not test_basemodel"
- " and not test_field_default_factory"
- " and not test_field_description"
- " and not test_get_param_relative_import_from_init"
- ;; Strangely, the arguments are interpreted
- ;; as arguments to pytest.
- " and not test_pydantic_types"))))
+ (list #:test-flags
+ '(list "-k" "not test_env_prefix")))
(propagated-inputs
- (list python-contextvars
- python-docstring-parser
- python-pyyaml
- python-typeshed-client))
+ (list python-pyyaml))
(native-inputs
(list python-attrs
- python-coverage
- python-pycodestyle
+ python-pypa-build
python-pydantic
python-pytest
python-pytest-subtests
python-responses
- python-tox
- python-types-requests
python-setuptools
python-wheel))
(home-page "https://github.com/omni-us/jsonargparse/")
@@ 5884,15 5908,12 @@ a certain expected condition.")
;; Delete generated Cython C files.
(snippet
'(for-each delete-file (find-files "." "\\.c$")))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
(arguments
(list
- #:phases
- '(modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "python" "setup.py" "test")))))))
+ ;; XXX: Update to python@3.11 broke some python-nose functionality.
+ ;; Tests are broken but the package itself is most likely fine.
+ #:tests? #f))
(propagated-inputs
(list python-joblib
python-networkx
@@ 5901,8 5922,9 @@ a certain expected condition.")
python-scipy))
(native-inputs
(list python-cython
- python-nose
- python-pandas))
+ python-pandas
+ python-setuptools
+ python-wheel))
(home-page "https://pypi.python.org/pypi/pomegranate/")
(synopsis "Graphical models library for Python")
(description
@@ 6719,24 6741,38 @@ between Julian dates and Gregorian dates.")
(define-public python-jsondiff
(package
- (name "python-jsondiff")
- (version "1.2.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "jsondiff" version))
- (sha256
- (base32
- "00v3689175aqzdscrxpffm712ylp8jvcpqdg51ca22ni6721p51l"))))
- (build-system python-build-system)
- (native-inputs
- (list python-nose python-nose-random))
- (home-page
- "https://github.com/fzumstein/jsondiff")
- (synopsis "Compare JSON and JSON-like structures in Python")
- (description "@code{jsondiff} is a Python library which lets you
-compare, diff, and patch JSON and JSON-like structures in Python.")
- (license license:expat)))
+ (name "python-jsondiff")
+ (version "2.2.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "jsondiff" version))
+ (sha256
+ (base32
+ "1zpp8l2ii9ic1sk6kdcqxk0v5q9pgdmdhg1h4vg8dfl6i8n1d3b5"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'build 'set-version
+ (lambda _
+ (substitute* "pyproject.toml"
+ (("^version_file.*") "")
+ (("dynamic = \\[\"version\"\\]")
+ (string-append "version = \"" #$version "\""))))))))
+ (propagated-inputs (list python-pyyaml))
+ (native-inputs
+ (list python-hypothesis
+ python-pytest
+ python-setuptools
+ python-setuptools-scm
+ python-wheel))
+ (home-page "https://github.com/fzumstein/jsondiff")
+ (synopsis "Compare JSON and JSON-like structures in Python")
+ (description "@code{jsondiff} is a Python library which lets you compare,
+diff, and patch JSON and JSON-like structures in Python.")
+ (license license:expat)))
(define-public python-ddlparse
(package
@@ 6802,7 6838,7 @@ and convert DDL to BigQuery JSON schema.")
python-referencing-bootstrap
python-rpds-py
python-uri-template
- python-webcolors-24))
+ python-webcolors))
(home-page "https://github.com/Julian/jsonschema")
(synopsis "Implementation of JSON Schema for Python")
(description
@@ 7111,27 7147,25 @@ JavaScript-like message boxes. Types of dialog boxes include:
(define-public python-pympler
(package
(name "python-pympler")
- (home-page "https://pythonhosted.org/Pympler/")
- (version "1.0.1")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "Pympler" version))
- (sha256
- (base32
- "1ynkqpv2akldmvkll5vh5zhwj433s1d59iv0f76lygyak4silgwr"))))
- (build-system python-build-system)
+ (version "1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "pympler" version))
+ (sha256
+ (base32 "090403k1wvqyddjwbla4843dylysrkd8yw7i62222b4rp1y8dahy"))))
+ (build-system pyproject-build-system)
(arguments
(list
- #:phases
- #~(modify-phases %standard-phases
- (add-after 'unpack 'skip-broken-test
- (lambda _
- ;; FIXME: This test fails for no good reason:
- ;; https://github.com/pympler/pympler/issues/153
- (substitute* "test/muppy/test_tracker.py"
- (("^([[:blank:]]+)def test_stracker_create_summary" all indent)
- (string-append indent "@unittest.skipIf(True, \
-'Fails on Guix too for unknown reasons')\n" all))))))))
+ ;; One test fails with error: 'function (test.muppy.test_summary.func)'
+ ;; != 'function (muppy.test_summary.func)'.
+ ;; See <https://github.com/pympler/pympler/issues/134>.
+ #:test-flags #~(list "-k" "not test_repr_function")))
+ (native-inputs
+ (list python-pytest
+ python-setuptools
+ python-wheel))
+ (home-page "https://pythonhosted.org/Pympler/")
(synopsis "Measure, monitor and analyze memory behavior")
(description
"Pympler is a development tool to measure, monitor and analyze
@@ 7239,33 7273,44 @@ e.g. filters, callbacks and errbacks can all be promises.")
(define-public python-virtualenv
(package
(name "python-virtualenv")
- (version "20.28.0")
+ (version "20.29.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "virtualenv" version))
(sha256
(base32
- "1aj980vffl4mpq4j67f7a0j07rlm8jp5yw8xh3m8fywfpdi3571c"))))
+ "0dfwnn8i1y33kgxhi4xyhsj4yr5vsin7zf9c343bcbyk700rgf5q"))))
(build-system pyproject-build-system)
(arguments
- ;; These tests require Internet access.
- (list #:test-flags '(list "-k" "not test_seed_link_via_app_data")))
+ (list
+ #:test-flags
+ #~(list "-k" (string-join
+ (list
+ ;; These tests require Internet access.
+ "not test_seed_link_via_app_data"
+ ;; AssertionError: assert 'python' in ['python3',
+ ;; 'python3.11'].
+ ;;
+ ;; PythonInfo() returns: 'system_executable':
+ ;; '/gnu/store/...-python-wrapper-3.11.11/bin/python'
+ "test_fallback_existent_system_executable")
+ " and not "))))
(native-inputs
- (list python-covdefaults
- python-coverage
- python-flaky
+ (list python-flaky
python-hatch-vcs
python-hatchling
python-packaging
python-pytest
python-pytest-env
+ python-pytest-freezer
python-pytest-mock
python-pytest-timeout
python-setuptools
python-time-machine))
(propagated-inputs
- (list python-distlib python-filelock python-importlib-metadata
+ (list python-distlib
+ python-filelock
python-platformdirs))
(home-page "https://virtualenv.pypa.io/")
(synopsis "Virtual Python environment builder")
@@ 7875,7 7920,11 @@ structure for Python.")
(setenv "LANG" "")
;; required for tests/test_configmanager.py
(setenv "HOME" "/tmp"))))))
- (native-inputs (list python-pytest python-pytest-cov python-pyhamcrest))
+ (native-inputs
+ (list python-pytest
+ python-pytest-cov
+ python-pyhamcrest
+ python-wheel))
(inputs
(list bash-minimal ; for wrap-program
gtksourceview-3
@@ 8081,21 8130,21 @@ via commands such as @command{rst2man}, as well as supporting Python code.")
;; licensed under the PFSL, BSD 2-clause, and GPLv3+ licenses.
(license (list license:public-domain license:psfl license:bsd-2 license:gpl3+))))
-;; awscli refuses to be built with docutils < 0.16.
-(define-public python-docutils-0.15
+;; awscli refuses to be built with docutils < 0.17.
+(define-public python-docutils-0.16
(package
(inherit python-docutils)
- (version "0.15")
+ (version "0.16")
(source (origin
(method url-fetch)
(uri (pypi-uri "docutils" version))
(sha256
(base32
- "0ja8q6mdj6xv62jjw3phv8j5nfqi5x8hnfy4pqfcjcgz4b34k8sl"))))
+ "1z3qliszqca9m719q3qhdkh0ghh90g500avzdgi7pl77x5h3mpn2"))))
;; tests contain Python 2 syntax.
(arguments '(#:tests? #false))
(native-inputs
- (list python-setuptools-57))))
+ (list python-setuptools))))
(define-public python-docx
(package
@@ 8141,6 8190,26 @@ Microsoft Word (.docx) documents.")
"This package provides a tiny LRU cache implementation and decorator.")
(license license:bsd-4)))
+(define-public python-reretry
+ (package
+ (name "python-reretry")
+ (version "0.11.8")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "reretry" version))
+ (sha256
+ (base32 "1qrjsjzah8gw1bciqn8bhrj80fjjg13qg8jks7qs4bjipv71yygj"))))
+ (build-system pyproject-build-system)
+ (native-inputs (list python-setuptools python-wheel))
+ (home-page "https://github.com/leshchenko1979/reretry")
+ (synopsis "Functional decorator for retrying on exceptions")
+ (description
+ "This package is a fork from the retry package, but with some of added
+community-sourced features. It provides an easy to use, but functional
+decorator for retrying on exceptions.")
+ (license license:asl2.0)))
+
(define-public python-restructuredtext-lint
(package
(name "python-restructuredtext-lint")
@@ 8869,15 8938,31 @@ or for visual regression testing purposes.")
(define-public python-rstr
(package
(name "python-rstr")
- (version "2.2.6")
+ (version "3.2.2")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "rstr" version))
- (sha256
- (base32
- "197dw8mbq0pjjz1l6h1ksi62vgn7x55d373ch74y06744qiq5sjx"))))
- (build-system python-build-system)
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/leapfrogonline/rstr")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1z9d660jnv72jn8qzpa9hddpv5f953js8i75hfhkcw68vmdfndnr"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'build 'pretend-version
+ ;; The version string is usually derived via setuptools-scm, but
+ ;; without the git metadata available, the version string is set to
+ ;; '0.0.0'.
+ (lambda _
+ (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version))))))
+ (native-inputs (list python-pytest
+ python-setuptools
+ python-setuptools-scm
+ python-wheel))
(home-page "https://github.com/leapfrogonline/rstr")
(synopsis "Generate random strings in Python")
(description "This package provides a python module for generating
@@ 9713,11 9798,15 @@ writing C extensions for Python as easy as Python itself.")
(define-public python-numpy
(package
(name "python-numpy")
- ;; XXX: Any other versions up to 1.26.4 failed to build with error similar
- ;; to: 'fenv_t' has not been declared in '::' 58 | using ::fenv_t;
- ;; See <https://github.com/numpy/numpy/issues/21075#issuecomment-1047976197>,
- ;; <https://github.com/numpy/numpy/issues/24318>.
- (version "1.24.4")
+ ;; XXX: Starting from v1.26.0 the project includes a vendored-meson which
+ ;; is needed for SIMD and BLAS/LAPACK features that are not yet available
+ ;; in upstream Meson.
+ ;;
+ ;; See:
+ ;; - URL <https://raw.githubusercontent.com/numpy/numpy>
+ ;; - commit :: 2f3549c9d7c5048621568e431c86bc7530742723
+ ;; - file <doc/source/building/understanding_meson.rst>
+ (version "1.26.2")
(source
(origin
(method url-fetch)
@@ 9726,7 9815,7 @@ writing C extensions for Python as easy as Python itself.")
version "/numpy-" version ".tar.gz"))
(sha256
(base32
- "0qwldmkq5bns561ppkz7psphc4jqfj5j1x4dhq0i8r4qwjjf7xc0"))))
+ "1snknqb4hmv6b720nsaz21g7h6z1ikdvnsqyy5vmgavnfr23hmzn"))))
(build-system pyproject-build-system)
(arguments
(list
@@ 9735,6 9824,18 @@ writing C extensions for Python as easy as Python itself.")
(ice-9 format))
#:phases
#~(modify-phases %standard-phases
+ ;; XXX: It fails with an issue "'fenv_t' has not been declared..."
+ ;; when the gfortran header is used. Remove gfortran from
+ ;; CPLUS_INCLUDE_PATH as a workaround. Taken from
+ ;; <https://issues.guix.gnu.org/73439#45>.
+ (add-after 'set-paths 'hide-gfortran
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((gfortran (assoc-ref inputs "gfortran")))
+ (setenv "CPLUS_INCLUDE_PATH"
+ (string-join
+ (delete (string-append gfortran "/include/c++")
+ (string-split (getenv "CPLUS_INCLUDE_PATH") #\:))
+ ":")))))
(add-before 'build 'parallelize-build
(lambda _
(setenv "NPY_NUM_BUILD_JOBS"
@@ 9802,6 9903,12 @@ include_dirs = ~:*~a/include~%"
`(" and not test_identityless_reduction_huge_array"
" and not (TestKind and test_all)")
'())
+ ;; This test fails with a Fortran failure (16
+ ;; expected but got -1), due to the fact that it
+ ;; requires a 64-bit system.
+ #$@(if (or (target-x86-32?) (target-arm32?))
+ `(" and not test_int")
+ '())
;; These tests fail when building from aarch64-linux.
#$@(if (target-arm32?)
`(" and not test_features"
@@ 9818,7 9925,6 @@ include_dirs = ~:*~a/include~%"
(list gfortran
meson-python
pkg-config
- python-cython ;; overwrite Cython from meson-python
python-hypothesis
python-mypy
python-pytest
@@ 9916,6 10022,16 @@ include_dirs = ~:*~a/include~%" #$(this-package-input "openblas")))))))))
#:tests? #f ;we're only generating the documentation
#:phases
#~(modify-phases %standard-phases
+ (add-after 'unpack 'avoid-external-deps
+ (lambda _
+ ;; XXX: Avoid theme-switcher to avoid sphinx error
+ ;; TemplateNotFound('theme-switcher.html')
+ ;; XXX: Avoid version-switcher because it depends on the value
+ ;; of external https://numpy.org/doc/_static/versions.json
+ (substitute* "doc/source/conf.py"
+ (("\
+\"navbar_end\": \\[\"theme-switcher\", \"version-switcher\", ")
+ "\"navbar_end\": ["))))
(add-before 'build 'add-gnu-freefont-to-texmf
(lambda _
;; XXX: The Sphinx-generated tex output specifies the GNU
@@ 9961,6 10077,7 @@ include_dirs = ~:*~a/include~%" #$(this-package-input "openblas")))))))))
(("\"contents\"") "'index'")
;; Disable Sphinx extensions that produce broken Texinfo.
((".*'numpydoc'.*") "")
+ ((".*'sphinx.ext.autodoc'.*") "")
((".*'sphinx.ext.autosummary'.*") ""))
(invoke "make" "info" sphinxopts)
;; Install the HTML documentation.
@@ 9984,13 10101,15 @@ include_dirs = ~:*~a/include~%" #$(this-package-input "openblas")))))))))
python-pandas
python-pydata-sphinx-theme
python-scipy ;used by matplotlib
- python-sphinx-4
+ python-sphinx
+ python-sphinx-design
python-sphinx-panels
texinfo
(texlive-updmap.cfg
(list texlive-cbfonts
texlive-cm-super
texlive-expdlist
+ texlive-fandol
texlive-greek-fontenc
texlive-latexmk
texlive-polyglossia
@@ 10478,7 10597,7 @@ semantic version parser for Node.js.")
(define-public python-patch-ng
(package
(name "python-patch-ng")
- (version "1.17.4")
+ (version "1.18.1")
(source
(origin
(method git-fetch) ;no tests in PyPI archive
@@ 10488,7 10607,7 @@ semantic version parser for Node.js.")
(file-name (git-file-name name version))
(sha256
(base32
- "0qxn4ss2s54qy87xrpcybz26kp2fwlaq41x4k9jcmp6d7p0w569m"))))
+ "1kr3h0bkcr02zyfsmwmxfv5b4b9vf3bhsvrlwp6cwrfy3q3qnyq8"))))
(build-system python-build-system)
(arguments
`(#:phases (modify-phases %standard-phases
@@ 11108,16 11227,16 @@ the results.")
(define-public python-pykdtree
(package
(name "python-pykdtree")
- (version "1.3.4")
+ (version "1.3.9")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pykdtree" version))
(sha256
- (base32 "0p8n2ljdacfixkiw092974dmhy4s1c0h032ii1z9kwi9h5h5rgmy"))))
+ (base32 "0q4zrqdn8ad6f710yggkhvx4avf2h1hsbg9qa7ghly54v4vhpgd7"))))
(build-system python-build-system)
(native-inputs
- (list python-nose))
+ (list python-cython python-pytest python-setuptools python-wheel))
(propagated-inputs
(list python-numpy))
(home-page "https://github.com/storpipfugl/pykdtree")
@@ 11576,7 11695,9 @@ the OleFileIO module from PIL, the Python Image Library.")
(method url-fetch)
(uri (pypi-uri "property-cached" version ".zip"))
(sha256
- (base32 "0wxv5sdx1p7ils36j6j6hfscz8v2vzbq212i8y8r0lrnxpqlx71y"))))
+ (base32 "0wxv5sdx1p7ils36j6j6hfscz8v2vzbq212i8y8r0lrnxpqlx71y"))
+ (patches
+ (search-patches "python-property-cached-asyncio-3_11.patch"))))
(build-system pyproject-build-system)
(arguments
(list
@@ 11755,17 11876,10 @@ a general image processing tool.")
(arguments
(list
#:test-flags
- #~(list "-k" ; XXX: 10/12 bit tests fail
+ #~(list "-k"
(string-append
- "not test_save_bgr_16bit_to_10_12_bit"
- " and not test_save_bgra_16bit_to_10_12_bit"
- " and not test_open_heif_compare_non_standard_modes_data"
- " and not test_open_save_disable_16bit"
- " and not test_heif_read_images[image_path16]"
- " and not test_heif_read_images[image_path43]"
- " and not test_premultiplied_alpha"
- " and not test_hdr_save"
- " and not test_I_color_modes_to_10_12_bit"))))
+ "not test_heif_read_images[image_path25]"
+ " and not test_heif_read_images[image_path49]"))))
(inputs (list libheif))
(propagated-inputs (list python-pillow))
(native-inputs (list opencv ; for opencv-python
@@ 11774,7 11888,6 @@ a general image processing tool.")
python-numpy
python-packaging
python-pre-commit
- python-pylint
python-pympler
python-setuptools
python-pytest
@@ 12516,46 12629,36 @@ formulas and hyperlinks to multiple worksheets in an Excel 2007+ XLSX file.")
(define-public python-pywavelets
(package
(name "python-pywavelets")
- (version "1.2.0")
+ (version "1.8.0")
(home-page "https://github.com/PyWavelets/pywt")
(source (origin
(method url-fetch)
- (uri (pypi-uri "PyWavelets" version))
+ (uri (pypi-uri "pywavelets" version))
(sha256
(base32
- "13csbr6ls9q9ww53z2xwwsj0hpsz88rj2iwp623h0kmv8yq6kgbc"))
- (snippet
- #~(begin
- (use-modules ((guix build utils)))
- (for-each delete-file
- (list
- "pywt/_extensions/_cwt.c"
- "pywt/_extensions/_dwt.c"
- "pywt/_extensions/_pywt.c"
- "pywt/_extensions/_pywt.h"
- "pywt/_extensions/_swt.c"))))))
- (build-system python-build-system)
+ "1aimbjxvflmx4qrl17bfzy64pz5ql4s9bhnb8g0ssh28fm2h507k"))))
+ (build-system pyproject-build-system)
(arguments
- '(#:modules ((ice-9 ftw)
- (srfi srfi-1)
- (srfi srfi-26)
- (guix build utils)
- (guix build python-build-system))
- #:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda _
- (let ((cwd (getcwd))
- (libdir (find (cut string-prefix? "lib." <>)
- (scandir "build"))))
- (with-directory-excursion (string-append cwd "/build/" libdir)
- (invoke "pytest" "-vv"))))))))
+ (list
+ #:test-flags '(list "--pyargs" "pywt")
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; The compiled libraries are only in the output at this point,
+ ;; but they are needed to run tests.
+ ;; FIXME: This should be handled by the pyargs pytest argument,
+ ;; but is not for some reason.
+ (add-before 'check 'pre-check
+ (lambda _ (chdir #$output))))))
(native-inputs
- (list python-cython
- python-matplotlib ;for tests
+ (list meson
+ ninja
+ pkg-config
+ python-cython-3
+ python-meson-python
+ python-numpy
python-pytest))
(propagated-inputs
- (list python-numpy))
+ (list python-numpy python-scipy))
(synopsis "Wavelet transforms in Python")
(description
"PyWavelets is a library for wavelet transforms in Python. Wavelets are
@@ 13206,7 13309,7 @@ def get_requires_for_build_sdist(config_settings=None):
python-pytest-enabler
python-pytest-flake8
python-pytest-mypy
- python-setuptools-57
+ python-setuptools
python-setuptools-scm))
(propagated-inputs
(list python-zipp))
@@ 13891,7 13994,7 @@ without using the configuration machinery.")
python-setuptools
python-wheel
cmake-minimal
- pybind11-2.13))
+ pybind11))
(home-page "https://github.com/metaopt/optree")
(synopsis "Optimized PyTree Utilities")
(description "This package contains operations on PyTrees (a tree made of
@@ 14969,19 15072,6 @@ interfaces in an easy and portable manner.")
of the structure, dynamics, and functions of complex networks.")
(license license:bsd-3)))
-(define-public python-networkx-next
- (package
- (inherit python-networkx)
- (name "python-networkx")
- (version "3.4.2")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "networkx" version))
- (sha256
- (base32 "1qaks3c3h5qlw25z949q3plw8iwgm9h152kwnam64lwc89lkcz1h"))))
- (build-system pyproject-build-system)))
-
(define-public python-datrie
(package
(name "python-datrie")
@@ 15095,15 15185,23 @@ GA4GH Task Execution API.")
(define-public python-toposort
(package
(name "python-toposort")
- (version "1.6")
+ (version "1.10")
(source
(origin
(method url-fetch)
(uri (pypi-uri "toposort" version))
(sha256
(base32
- "1b2hppzjg3p006qya3yfdnp76dwq8frl97lypdam0kw4xxb8yhm7"))))
- (build-system python-build-system)
+ "1gd66z5dy6j7qs5qkj1pg0vb15rwd571yq02fkm9d9nhaff4gfxz"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (invoke "python3" "-m" "test.test_toposort"))))))
+ (native-inputs (list python-setuptools python-wheel))
(home-page "https://gitlab.com/ericvsmith/toposort")
(synopsis "Topological sort algorithm")
(description
@@ 15162,7 15260,34 @@ character level, as opposed to most VCS systems, which opt for a line-based
approach.")
(license license:expat)))
-(define-public snakemake
+(define-public python-throttler
+ (package
+ (name "python-throttler")
+ (version "1.2.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/uburuntu/throttler")
+ (commit (string-append "v" version))))
+ (sha256
+ (base32 "1gn21x0zkm7rr7qijlz7nvw7z0mm1j2r0r2lslg7wln1z36gjkbw"))))
+ (build-system pyproject-build-system)
+ (native-inputs (list python-aiohttp
+ python-codecov
+ python-flake8
+ python-pytest
+ python-pytest-asyncio
+ python-pytest-cov
+ python-setuptools
+ python-wheel))
+ (home-page "https://github.com/uburuntu/throttler")
+ (synopsis "Throttling with asyncio support")
+ (description
+ "This is a Python package for easy throttling with asyncio support.")
+ (license license:expat)))
+
+(define-public snakemake-5
(package
(name "snakemake")
(version "5.32.2")
@@ 15187,7 15312,9 @@ approach.")
"--ignore=tests/test_tibanna.py"
;; It's a similar story with this test, which requires access
;; to the Google Storage service.
- "--ignore=tests/test_google_lifesciences.py")
+ "--ignore=tests/test_google_lifesciences.py"
+ ;; Unclear failure.
+ "-k" "not test_lint[long_run-positive]")
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'tabulate-compatibility
@@ 15248,7 15375,7 @@ Python style, together with a fast and comfortable execution environment.")
(define-public snakemake-6
(package
- (inherit snakemake)
+ (inherit snakemake-5)
(name "snakemake")
(version "6.15.5")
(source
@@ 15263,6 15390,13 @@ Python style, together with a fast and comfortable execution environment.")
(build-system pyproject-build-system)
(arguments
(list
+ #:test-flags
+ '(list
+ ;; This test attempts to change S3 buckets on AWS and fails
+ ;; because there are no AWS credentials.
+ "--ignore=tests/test_tibanna.py"
+ ;; Unclear failure.
+ "-k" "not test_lint[long_run-positive]")
#:phases
#~(modify-phases %standard-phases
;; For cluster execution Snakemake will call Python. Since there is
@@ 15289,14 15423,8 @@ Python style, together with a fast and comfortable execution environment.")
(substitute* '("snakemake/_version.py"
"versioneer.py")
(("0\\+unknown") #$version))))
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (setenv "HOME" "/tmp")
- ;; This test attempts to change S3 buckets on AWS and fails
- ;; because there are no AWS credentials.
- (delete-file "tests/test_tibanna.py")
- (invoke "pytest")))))))
+ (add-before 'check 'pre-check
+ (lambda _ (setenv "HOME" "/tmp"))))))
(propagated-inputs
(list python-appdirs
python-configargparse
@@ 15333,7 15461,7 @@ Python style, together with a fast and comfortable execution environment.")
(package
(inherit snakemake-6)
(name "snakemake")
- (version "7.7.0")
+ (version "7.32.4")
(source
(origin
(method git-fetch)
@@ 15342,10 15470,20 @@ Python style, together with a fast and comfortable execution environment.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "1qrqbmx4cbis0wxr6dl2rdjv9v627sbirsz6v5c31vlbqwkvs04q"))))
+ (base32 "1d5hizai89k1glfqfkvf1ghj0l7wm8il6gl5pfwk2gkza87yka6d"))))
(build-system pyproject-build-system)
(arguments
(list
+ #:test-flags
+ ;; This test attempts to change S3 buckets on AWS and fails
+ ;; because there are no AWS credentials.
+ '(list "--ignore=tests/test_tibanna.py"
+ ;; It's a similar story with this test, which requires access to
+ ;; the Google Storage service.
+ "--ignore=tests/test_google_lifesciences.py"
+ "--ignore-glob=tests/test_conda_python_3_7_script/*"
+ ;; We don't have a slurm installation in the build environment
+ "--ignore=tests/test_slurm.py")
#:phases
#~(modify-phases %standard-phases
;; For cluster execution Snakemake will call Python. Since there is
@@ 15374,12 15512,6 @@ Python style, together with a fast and comfortable execution environment.")
(string-append
"tibanna_args.command = command.replace('"
#$output "/bin/snakemake', 'python3 -m snakemake')")))))
- ;; No longer needed with 7.15.2+
- (add-after 'unpack 'tabulate-compatibility
- (lambda _
- (substitute* "snakemake/dag.py"
- (("\"job\": rule,")
- "\"job\": rule.name,"))))
(add-after 'unpack 'patch-version
(lambda _
(substitute* "setup.py"
@@ 15388,17 15520,8 @@ Python style, together with a fast and comfortable execution environment.")
(substitute* '("snakemake/_version.py"
"versioneer.py")
(("0\\+unknown") #$version))))
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (setenv "HOME" "/tmp")
- ;; This test attempts to change S3 buckets on AWS and fails
- ;; because there are no AWS credentials.
- (delete-file "tests/test_tibanna.py")
- ;; It's a similar story with this test, which requires access
- ;; to the Google Storage service.
- (delete-file "tests/test_google_lifesciences.py")
- (invoke "pytest")))))))
+ (add-before 'check 'pre-check
+ (lambda _ (setenv "HOME" "/tmp"))))))
(propagated-inputs
(list python-appdirs
python-configargparse
@@ 15407,6 15530,7 @@ Python style, together with a fast and comfortable execution environment.")
python-docutils
python-filelock
python-gitpython
+ python-humanfriendly
python-jinja2
python-jsonschema
python-nbformat
@@ 15415,12 15539,13 @@ Python style, together with a fast and comfortable execution environment.")
python-pulp
python-pyyaml
python-py-tes
- python-ratelimiter
python-requests
python-retry
+ python-reretry
python-smart-open
python-stopit
python-tabulate
+ python-throttler
python-toposort
python-wrapt
python-yte))
@@ 15612,20 15737,29 @@ function signatures.")
(define-public python-yte
(package
(name "python-yte")
- (version "1.2.0")
+ (version "1.7.0")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "yte" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/koesterlab/yte")
+ (commit (string-append "v" version))))
(sha256
- (base32 "07hm1warpqi4ifqgkaz5sg887x4a44yhxafmpf835ywnpchg4s03"))))
- (build-system python-build-system)
+ (base32 "01hxl47bfb0jp2rh6qb6wrm6m8p5rfk21gksqb8qxxv9a037dnsv"))))
+ (build-system pyproject-build-system)
(arguments
- '(#:phases
- (modify-phases %standard-phases
+ (list
+ #:phases
+ '(modify-phases %standard-phases
(add-after 'unpack 'set-HOME
- (lambda _ (setenv "HOME" "/tmp"))))))
- (propagated-inputs (list python-plac python-pyyaml))
+ (lambda _ (setenv "HOME" "/tmp")))
+ (replace 'check
+ (lambda* (#:key tests? test-flags #:allow-other-keys)
+ (when tests?
+ (apply invoke "pytest"
+ (append test-flags (list "tests.py")))))))))
+ (propagated-inputs (list python-dpath python-plac python-pyyaml))
+ (native-inputs (list python-numpy python-poetry-core python-pytest))
(home-page "https://github.com/koesterlab/yte")
(synopsis "YAML template engine with Python expressions")
(description
@@ 16144,29 16278,6 @@ you do not want to store entirely on disk or on memory.")
application monitoring and error tracking software.")
(license license:bsd-2)))
-(define-public python-pep8
- ;; This package has been renamed to ‘pycodestyle’ and is no longer updated.
- ;; Its last release (1.7.1) adds only a scary warning to this effect, breaking
- ;; some dependents' test suites, and nothing more.
- (package
- (name "python-pep8")
- (version "1.7.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "pep8" version))
- (sha256
- (base32
- "002rkl4lsn6x2mxmf8ar00l0m8i3mzrc6pnzz77blyksmpsxa4x1"))
- (patches (search-patches "python-pep8-stdlib-tokenize-compat.patch"))))
- (build-system python-build-system)
- (home-page "https://pep8.readthedocs.org/")
- (synopsis "Python style guide checker")
- (description
- "This tools checks Python code against some of the style conventions in
-PEP 8.")
- (license license:expat)))
-
(define-public python-pep8-naming
(package
(name "python-pep8-naming")
@@ 16586,41 16697,6 @@ expressions after the entire file has been read. This enables support for
first-class forward references that stub files use.")
(license license:expat)))
-;; XXX: Deprecated in upstream: This repository has been archived by the owner
-;; on Nov 30, 2024. It is now read-only.
-;; Consider to remove when nothing is depend on it.
-(define-public python-flake8-pie
- (package
- (name "python-flake8-pie")
- (version "0.16.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "flake8-pie" version))
- (sha256
- (base32 "1fhmwm8blimnfmi1cj8q0kqd77vskgjb794jbp837yh64ywvgp5q"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- #:test-flags
- #~(list "-k" "not test_examples and not test_prefer_simple_any_all")
- #:phases
- #~(modify-phases %standard-phases
- (add-after 'unpack 'use-poetry-core
- (lambda _
- ;; Patch to use the core poetry API.
- (substitute* "pyproject.toml"
- (("poetry.masonry.api") "poetry.core.masonry.api")))))))
- (native-inputs
- (list python-poetry-core
- python-pytest))
- (home-page "https://github.com/sbdchd/flake8-pie")
- (synopsis "Flake8 extension that implements lints")
- (description
- "This package provides a flake8 extension that implements miscellaneous
-lints.")
- (license license:bsd-2)))
-
(define-public python-flake8-quotes
(package
(name "python-flake8-quotes")
@@ 17192,6 17268,7 @@ number of lines in the contained files easily.")
(license license:expat)))
;;; Tests are left out in the main package to avoid cycles.
+;; XXX: When updating, solve comment in python-cu2qu.
(define-public python-fonttools-minimal
(hidden-package
(package
@@ 17424,26 17501,6 @@ reading and writing MessagePack data.")
((".fromstring\\(") ".frombytes("))
#t))))))))
-(define-public python-netaddr
- (package
- (name "python-netaddr")
- (version "0.8.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "netaddr" version))
- (sha256
- (base32
- "0hx2npi0wnhwlcybilgwlddw6qffx1mb7a3sj4p9s7bvl33mgk6n"))))
- (build-system python-build-system)
- (arguments `(#:tests? #f)) ;; No tests.
- (home-page "https://github.com/drkjam/netaddr/")
- (synopsis "Pythonic manipulation of network addresses")
- (description
- "A Python library for representing and manipulating IPv4, IPv6, CIDR, EUI
-and MAC network addresses.")
- (license license:bsd-3)))
-
(define-public python-openstep-plist
(package
(name "python-openstep-plist")
@@ 17892,29 17949,6 @@ asyncio.")
(description "Snuggs are S-expressions for Numpy.")
(license license:expat)))
-(define-public python-pytest-black
- (package
- (name "python-pytest-black")
- (version "0.3.12")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "pytest-black" version))
- (sha256
- (base32
- "19bmbcnaq02md8nnj6pywri3vps8sxnhysbfy386qkbn9w09ncqx"))))
- (build-system python-build-system)
- (propagated-inputs
- (list python-pytest python-black python-toml))
- (native-inputs
- (list python-setuptools-scm))
- (home-page "https://github.com/shopkeep/pytest-black")
- (synopsis "Pytest plugin to enable format checking with black")
- (description
- "This package provides a pytest plugin to enable format checking with the
-Python code formatter \"black\".")
- (license license:expat)))
-
(define-public python-geojson
(package
(name "python-geojson")
@@ 18238,16 18272,37 @@ implementations of ASN.1-based codecs and protocols.")
(define-public python-asn1tools
(package
(name "python-asn1tools")
- (version "0.166.0")
+ (version "0.167.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "asn1tools" version))
(sha256
- (base32 "1hragm8dsm10rlyz67xslj01bycprlnimdmq1i2acns6kl6difpn"))))
- (build-system python-build-system)
+ (base32 "1cpm6m3znagc553bc5l0rhwg2fccrl0k8m1pbvn6x2kqdmpkzmfa"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ #~(list "-k" (string-join
+ ;; Tests fail with error: IndexError: string index out of
+ ;; range. It may be some incompatability wit pyparsing,
+ ;; see <https://github.com/eerimoq/asn1tools/issues/167>.
+ (list "not test_c_source"
+ "test_command_line_generate_c_source_oer"
+ "test_command_line_generate_c_source_uper"
+ "test_command_line_generate_rust_source_uper"
+ "test_missing_parameterized_value"
+ "test_c_source"
+ "test_parse_parameterization")
+ " and not "))))
+ (native-inputs
+ (list python-pytest
+ python-setuptools
+ python-wheel))
(propagated-inputs
- (list python-bitstruct python-diskcache python-prompt-toolkit
+ (list python-bitstruct
+ python-diskcache
+ python-prompt-toolkit
python-pyparsing))
(home-page "https://github.com/eerimoq/asn1tools")
(synopsis "ASN.1 parsing, encoding and decoding")
@@ 18748,20 18803,26 @@ libmagic.")))
#~(list "-n" (number->string (parallel-job-count))
"-m" "not flaky"
"-k"
- (string-append
- ;; The two "break_01" tests have been failing on
- ;; Python 3.10:
- ;; <https://github.com/fabioz/PyDev.Debugger/issues/222>.
- "not test_set_pydevd_break_01 "
- ;; the GUI event loop requires an X server.
- "and not test_gui_event_loop_custom "
- ;; This test validates that 'pydevd' is not in the
- ;; exception message, but it is due to being part
- ;; of the build file name present in the message.
- "and not test_evaluate_exception_trace "
- ;; This test fail with TimeoutError, no message on stderr.
- "and not test_soft_terminate "
- "and not test_debugger_case_deadlock_interrupt_thread"))
+ (string-join
+ (list
+ ;; The two "break_01" tests have been failing on
+ ;; Python 3.10:
+ ;; <https://github.com/fabioz/PyDev.Debugger/issues/222>.
+ "not test_set_pydevd_break_01 "
+ ;; the GUI event loop requires an X server.
+ "test_gui_event_loop_custom"
+ ;; This test validates that 'pydevd' is not in the
+ ;; exception message, but it is due to being part
+ ;; of the build file name present in the message.
+ "test_evaluate_exception_trace"
+ ;; This test fail with TimeoutError, no message on stderr.
+ "test_soft_terminate"
+ "test_debugger_case_deadlock_interrupt_thread"
+ ;; subprocess.CalledProcessError
+ ;; Python 3.11/3.12 specific issue:
+ ;; <https://github.com/fabioz/PyDev.Debugger/issues/284>.
+ "test_find_main_thread_id")
+ " and not "))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'fix-tests
@@ 19469,7 19530,7 @@ convert an @code{.ipynb} notebook file into various static formats including:
python-pytest
python-pytest-cov
python-requests
- python-requests-unixsocket
+ python-requests-unixsocket2
python-setuptools
python-wheel))
(home-page "https://jupyter.org/")
@@ 20021,6 20082,25 @@ be set via config files and/or environment variables.")
connection pool.")
(license license:expat)))
+(define-public python-argparse-dataclass
+ (package
+ (name "python-argparse-dataclass")
+ (version "2.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "argparse_dataclass" version))
+ (sha256
+ (base32 "0zr9r4n00x2wi5kyzw3bxvrdp5k113jw7f9p4f414bsaj4f69aq9"))))
+ (build-system pyproject-build-system)
+ (native-inputs (list python-setuptools python-wheel))
+ (home-page "https://github.com/mivade/argparse_dataclass")
+ (synopsis "Declarative command-line interfaces using argparse and dataclasses")
+ (description
+ "This package provides declarative command-line interfaces using argparse
+and dataclasses.")
+ (license license:expat)))
+
(define-public python-argparse-manpage
(package
(name "python-argparse-manpage")
@@ 20043,27 20123,6 @@ connection pool.")
@code{ArgumentParser} object.")
(license license:asl2.0)))
-(define-public python-contextlib2
- (package
- (name "python-contextlib2")
- (version "0.6.0.post1")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "contextlib2" version))
- (sha256
- (base32
- "0bhnr2ac7wy5l85ji909gyljyk85n92w8pdvslmrvc8qih4r1x01"))))
- (build-system python-build-system)
- (home-page "https://contextlib2.readthedocs.org/")
- (synopsis "Tools for decorators and context managers")
- (description "This module is primarily a backport of the Python
-3.2 contextlib to earlier Python versions. Like contextlib, it
-provides utilities for common tasks involving decorators and context
-managers. It also contains additional features that are not part of
-the standard library.")
- (license license:psfl)))
-
(define-public python-contexttimer
(package
(name "python-contexttimer")
@@ 21394,19 21453,28 @@ project template.")
(define-public python-pyquery
(package
(name "python-pyquery")
- (version "1.2.17")
+ (version "2.0.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pyquery" version))
(sha256
(base32
- "1xia20wm0vx5dk85kcwgh13bylz8qh47ffjxssd2586r60xi783a"))))
- (build-system python-build-system)
+ "1brg6aawb9m5mdfmc6g7v5r6pczbx67r4l9cn5yh6bdi0qkvp501"))))
+ (build-system pyproject-build-system)
+ (arguments
+ ;; This test requires network access.
+ (list #:test-flags #~(list "-k" "not test_get")))
(native-inputs
- (list python-webob python-webtest))
+ (list python-pytest
+ python-pytest-cov
+ python-requests
+ python-setuptools
+ python-webob
+ python-webtest
+ python-wheel))
(propagated-inputs
- (list python-lxml python-cssselect))
+ (list python-cssselect python-lxml))
(home-page "https://github.com/gawel/pyquery")
(synopsis "Make jQuery-like queries on xml documents")
(description "pyquery allows you to make jQuery queries on xml documents.
@@ 21414,34 21482,6 @@ The API is as much as possible the similar to jQuery. pyquery uses lxml for
fast xml and html manipulation.")
(license license:bsd-3)))
-(define-public python-anyjson
- (package
- (name "python-anyjson")
- (version "0.3.3")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "anyjson" version))
- (sha256
- (base32
- "1fjph4alvcscsl5d4b6qpv1yh31jy05jxi1l0xff7lws7j32v09p"))))
- (build-system python-build-system)
- (arguments
- `(;; We could possibly get tests working, but on Python 3 it's not so easy.
- ;; Very strangely, 2to3 is run *during setup.py install* (or bdist, or
- ;; whatever) so this transformation needs to be done before the tests
- ;; can be run. Maybe we could add a build step to transform beforehand
- ;; but it could be annoying/difficult.
- #:tests? #f))
- (native-inputs (list python-setuptools-57)) ;for use_2to3 support
- (home-page "https://bitbucket.org/runeh/anyjson/")
- (synopsis
- "Wraps best available JSON implementation in a common interface")
- (description
- "Anyjson loads whichever is the fastest JSON module installed
-and provides a uniform API regardless of which JSON implementation is used.")
- (license license:bsd-3)))
-
(define-public python-amqp
(package
(name "python-amqp")
@@ 21664,46 21704,6 @@ Eventlet, or gevent. Tasks can execute asynchronously (in the background) or
synchronously (wait until ready).")
(license license:bsd-3)))
-(define-public python-cesium
- (package
- (name "python-cesium")
- (version "0.12.1")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "cesium" version))
- (sha256
- (base32
- "0jr0ycqz9ns6mcskm4sxx92k40fj3v0x9knjaw5ac9f3mpqxsfbv"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- #:phases
- #~(modify-phases %standard-phases
- ;; The installed test files contain the /gnu/store location, not the
- ;; location of the discovered test files from the build directory.
- ;; The test framework doesn't like this. The easiest way around
- ;; this mismatch is to jump to the output directory.
- (add-before 'check 'check-chdir
- (lambda _ (chdir #$output))))))
- (propagated-inputs
- (list python-click ;XXX required by python-dask
- python-cloudpickle
- python-dask
- python-gatspy
- python-joblib
- python-numpy
- python-pandas
- python-scikit-learn
- python-scipy
- python-toolz))
- (native-inputs (list python-cython python-pytest python-setuptools-scm
- python-setuptools python-wheel))
- (home-page "https://pypi.org/project/cesium/")
- (synopsis "Library for time-series feature extraction and processing")
- (description
- "Cesium is a library for time-series feature extraction and processing.")
- (license license:bsd-3)))
-
(define-public python-translitcodec
(package
(name "python-translitcodec")
@@ 21805,7 21805,10 @@ applications.")
(base32 "0j6ksfnq9qfjdfppbkdz7jh6w0gnslwnckhafmlgim29b25g0z51"))))
(build-system pyproject-build-system)
(arguments
- (list #:phases
+ (list #:test-flags
+ ;; XXX: Added with python@3.11, not fixed upstream.
+ #~(list "-k" "not test_regression_bug13")
+ #:phases
#~(modify-phases %standard-phases
(add-before 'check 'set-qpa
(lambda _
@@ 22535,22 22538,18 @@ own code, responding to click events and updating clock every second.")
(define-public python-tblib
(package
(name "python-tblib")
- (version "1.6.0")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "tblib" version))
- (sha256
- (base32
- "0i136n5pydmd202254wzrdbspkw0br0c9mbxhfs9hpfbahvyx6r2"))))
- (build-system python-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda _
- (invoke "py.test" "-vv" "tests" "README.rst"))))))
+ (version "2.0.0") ; XXX: higher versions fail on 'check phase
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "tblib" version))
+ (sha256
+ (base32 "1mzcf0fp7267yya9ni5qlr8dj190hsnmyxz0cszgi2y0fbr31px6"))))
+ (build-system pyproject-build-system)
(native-inputs
- (list python-pytest python-six))
+ (list python-pytest
+ python-setuptools
+ python-wheel))
(home-page "https://github.com/ionelmc/python-tblib")
(synopsis "Traceback serialization library")
(description
@@ 22651,19 22650,28 @@ are synchronized with data exchanges on \"channels\".")
(define-public python-objgraph
(package
(name "python-objgraph")
- (version "3.4.1")
+ (version "3.6.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "objgraph" version))
(sha256
- (base32
- "19qmqsh984zq1rzzjy4vqnmviaqnymcyl8h7z99pnicbgwnm2adz"))))
- (build-system python-build-system)
+ (base32 "1n0swlq11w36r2p6x7b4y0zz10dgzpdc8qasyk3y68kl1zsg5f80"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ #~(list "tests.py"
+ ;; AssertionError: [0, 1, 2] not found in [[], [], [], [], [],
+ ;; [], [], [], [], [], [], [], ...
+ "-k" "not test_at_addrs")))
+ (native-inputs
+ (list graphviz
+ python-pytest
+ python-setuptools
+ python-wheel))
(propagated-inputs
(list python-graphviz))
- (native-inputs
- (list python-mock graphviz))
(home-page "https://mg.pov.lt/objgraph/")
(synopsis "Draw Python object reference graphs with graphviz")
(description
@@ 23039,14 23047,18 @@ are optionally backed by a C extension built on librdkafka.")
(define-public python-wcwidth
(package
(name "python-wcwidth")
- (version "0.1.8")
+ (version "0.2.13")
(source (origin
(method url-fetch)
(uri (pypi-uri "wcwidth" version))
(sha256
(base32
- "1a1pzds3xzfylm5mnc5f6c1p8kiig0daqjc9gygd9rc3cj53x2zj"))))
- (build-system python-build-system)
+ "1dbj74q1iz349sdkxrkc90f7xd4y7a9bdvgxg3cqdcly7430rskj"))))
+ (build-system pyproject-build-system)
+ (native-inputs (list python-pytest
+ python-pytest-cov
+ python-setuptools
+ python-wheel))
(home-page "https://github.com/jquast/wcwidth")
(synopsis "Measure number of terminal column cells of wide-character codes")
(description "Wcwidth measures the number of terminal column cells of
@@ 23404,6 23416,9 @@ strings require only one extra byte in addition to the strings themselves.")
"test_omit_default_roundtrip"
"test_optional_field_roundtrip"
"test_renaming"
+ ;; 'utf-8' codec can't encode character '\ud800' in
+ ;; position 0: surrogates not allowed
+ "test_simple_classes"
;; This test fails with an assertion error on the build
;; farm, but not on my laptop.
"test_nodefs_generated_unstructuring_cl"
@@ 24393,30 24408,23 @@ etc.")
(define-public python-stem
(package
(name "python-stem")
- (version "1.8.0")
+ (version "1.8.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "stem" version))
(sha256
(base32
- "1hk8alc0r4m669ggngdfvryndd0fbx0w62sclcmg55af4ak8xd50"))))
- (build-system python-build-system)
+ "10mm9qw4xv7d18086ivy38iaz04z72018186q03j5y69skzikyw3"))))
+ (build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'fix-tests
- ;; See https://github.com/torproject/stem/issues/56
- (lambda _
- (substitute* "run_tests.py"
- (("test\\.task\\.MOCK_VERSION,")
- ""))))
- (replace 'check
- (lambda _
- (invoke "./run_tests.py" "--unit")
- #t)))))
+ (list
+ #:phases #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (invoke "./run_tests.py" "--unit"))))))
(native-inputs
- (list python-mock python-pycodestyle python-pyflakes))
+ (list python-setuptools python-wheel))
(home-page "https://stem.torproject.org/")
(synopsis
"Python controller library that allows applications to interact with Tor")
@@ 24497,7 24505,7 @@ client.")
(define-public python-pymodbus
(package
(name "python-pymodbus")
- (version "2.5.3")
+ (version "3.8.6")
(source
(origin
(method git-fetch)
@@ 24506,46 24514,41 @@ client.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32
- "0kjjrx7xrlx0pf3y67hhr4xvqrly3xzmvf6ic5as61m6z19m7zd5"))))
- (build-system python-build-system)
+ (base32 "1sncllh01c6vqq4fh9k3yg9fchmmw661rcp0066l7fis6sp4yw82"))))
+ (build-system pyproject-build-system)
(arguments
- `(#:phases (modify-phases %standard-phases
- (add-after 'unpack 'disable-problematic-tests
- (lambda _
- ;; The following test modules rely on Python's own
- ;; 'test' module, which is not distributed in the Python
- ;; package of Guix.
- (delete-file "test/test_client_async_asyncio.py")
- (delete-file "test/test_client_sync_diag.py")
- ;; The following test module requires the asynctest
- ;; library, abandoned without support for Python 3.9+
- ;; (see:
- ;; https://github.com/riptideio/pymodbus/issues/681).
- (delete-file "test/test_server_asyncio.py")))
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "python" "-m" "pytest")))))))
- (native-inputs
- (list python-mock
- python-pytest
- python-redis
- python-sqlalchemy
- python-tornado
- python-twisted))
- (propagated-inputs
- (list python-pyserial
- python-six
- ;; For the REPL.
- python-aiohttp
- python-click
- python-prompt-toolkit
- python-pygments
- python-pyserial-asyncio))
+ (list
+ #:test-flags
+ #~(list "--ignore"
+ "test/server/test_simulator_api.py"
+ ;; These tests require the presence of a certificate.
+ "--ignore-glob"
+ "test/examples/*"
+ "--ignore"
+ "test/client/test_client.py")))
+ (native-inputs (list python-mock
+ python-pytest
+ python-pytest-asyncio
+ python-pytest-cov
+ python-pytest-xdist
+ python-redis
+ python-setuptools
+ python-sqlalchemy
+ python-tornado
+ python-twisted
+ python-wheel))
+ (propagated-inputs (list python-pyserial
+ python-six
+ ;; For the REPL.
+ python-aiohttp
+ python-click
+ python-prompt-toolkit
+ python-pygments
+ python-pyserial-asyncio))
(home-page "https://github.com/riptideio/pymodbus/")
(synopsis "Modbus protocol stack in Python")
- (description "Pymodbus is a full Modbus protocol implementation using
+ (description
+ "Pymodbus is a full Modbus protocol implementation using
@code{asyncio}, @code{tornado} or @code{twisted} for its asynchronous
communications core. It includes the following @emph{client} features:
@itemize
@@ 24843,35 24846,6 @@ callback-heavy mode of interaction typical in some Kivy applications.")
without requiring an event loop, useful for creative responsive GUIs.")
(license license:expat)))
-(define-public python-asynctest
- (package
- (name "python-asynctest")
- (version "0.13.0")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "asynctest" version))
- (sha256
- (base32
- "1b3zsy7p84gag6q8ai2ylyrhx213qdk2h2zb6im3xn0m5n264y62"))))
- (build-system python-build-system)
- (arguments
- ;; The test suite appears to be incompatible with Python 3.9+, completes
- ;; with 25 failures and 41 errors out of 220 tests (see:
- ;; https://github.com/Martiusweb/asynctest/issues/149).
- (list #:tests? #f
- #:phases #~(modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "python" "-m" "unittest" "test")))))))
- (home-page "https://github.com/Martiusweb/asynctest/")
- (synopsis "Unittest extensions for testing asyncio libraries")
- (description
- "The @code{asynctest} Python package is built on top of the standard
-@code{unittest} module and cuts down boilerplate code when testing libraries
-for @code{asyncio}.")
- (license license:asl2.0)))
-
(define-public python-binaryornot
(package
(name "python-binaryornot")
@@ 25453,6 25427,32 @@ working with Portable Executable (PE) files. It makes to most information
from the header, as well as section details and data available.")
(license license:expat)))
+(define-public python-pyemd
+ (package
+ (name "python-pyemd")
+ (version "1.0.0")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "pyemd" version))
+ (sha256
+ (base32
+ "1zh0v47lxa33xg04jyvblzl1g4m3k2khx0b3xr6isnyinbkmlaxl"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs (list python-numpy))
+ (native-inputs
+ (list python-cython-3
+ python-pytest
+ python-setuptools
+ python-setuptools-scm
+ python-wheel))
+ (home-page "https://github.com/wmayner/pyemd")
+ (synopsis
+ "Wrapper for Pele and Werman's implementation of the Earth Mover's Distance")
+ (description
+ "This package provides a Python wrapper for Ofir Pele and Michael
+Werman's implementation of the Earth Mover's Distance.")
+ (license license:expat)))
+
(define-public python-imagesize
(package
(name "python-imagesize")
@@ 25499,14 25499,14 @@ JPEG2000 and GIF files in pure Python.")
(define-public python-argcomplete
(package
(name "python-argcomplete")
- (version "3.2.2")
+ (version "3.5.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "argcomplete" version))
(sha256
(base32
- "18h023ma2m2gw8w8dm2pvv4k0vpli94293jl57p2ch4vln79xr7k"))))
+ "14jkqmc4nhp1vxkiha7mv7zlvqiyzyjsfzbvihlvpbnqvq7gaay1"))))
(build-system pyproject-build-system)
(arguments
(list
@@ 25521,11 25521,8 @@ JPEG2000 and GIF files in pure Python.")
"def __disable_test_console_script"))
(invoke "python3" "./test/test.py" "-v")))))))
(native-inputs
- (list python-coverage
- python-mypy
- python-pexpect
- python-setuptools
- python-setuptools-scm
+ (list python-pexpect
+ python-hatchling
python-wheel
tcsh
fish
@@ 25738,6 25735,8 @@ Mustache templating language renderer.")
"-k" (string-append
;; Don't install anything, thank you.
"not test_install_non_existent_extension"
+ ;; _pybind11_conduit_v1_ not found.
+ " and not test_wrap_coverage"
;; See <https://github.com/duckdb/duckdb/issues/11961>.
" and not test_fetchmany"
;; See <https://github.com/duckdb/duckdb/issues/10702>.
@@ 25907,29 25906,29 @@ creating a tag.")
(define-public python-qrcode
(package
(name "python-qrcode")
- (version "7.3.1")
+ (version "8.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "qrcode" version))
(sha256
- (base32 "0y35jlwfvkgn9341lzshyaqgpp61vysjh107vhdd96ya83r6ynip"))))
- (build-system python-build-system)
- (arguments
- ;; FIXME: Tests require packaging 'pymaging'.
- '(#:tests? #f))
+ (base32 "0iz3pj67b90k2racwzbf9yml6rjs8nnrpvhns6b45zppa2qy4p02"))))
+ (build-system pyproject-build-system)
+ (native-inputs
+ (list python-poetry-core
+ python-pytest))
(propagated-inputs
- (list python-lxml ; for SVG output
- python-pillow)) ; for PNG output
+ (list python-pillow
+ python-pypng))
(home-page "https://github.com/lincolnloop/python-qrcode")
(synopsis "QR Code image generator")
- (description "This package provides a pure Python QR Code generator
- module. It uses the Python Imaging Library (PIL) to allow for the generation
- of QR Codes.
+ (description
+ "This package provides a pure Python QR Code generator module. It uses
+the Python Imaging Library (PIL) to allow for the generation of QR Codes.
- In addition this package provides a command line tool to generate QR codes and
- either write these QR codes to a file or do the output as ascii art at the
- console.")
+In addition this package provides a command line tool to generate QR codes and
+either write these QR codes to a file or do the output as ascii art at the
+console.")
(license license:bsd-3)))
(define-public python-rst2ansi
@@ 26349,7 26348,7 @@ both as keys and as attributes.")
;; fails due to deprecation warnings, etc.
#:tests? #f))
(native-inputs
- (list python-coverage-test-runner python-pep8))
+ (list python-coverage-test-runner))
(propagated-inputs
(list python-pyaml))
(home-page "https://liw.fi/cliapp/")
@@ 26375,7 26374,7 @@ both as keys and as attributes.")
(file-name (git-file-name name version))))
(build-system python-build-system)
(native-inputs
- (list python-coverage-test-runner python-pep8))
+ (list python-coverage-test-runner))
(arguments
`(#:phases
(modify-phases %standard-phases
@@ 27022,16 27021,15 @@ functionality removed from @code{packaging}.")
(sha256
(base32
"09nhrz80dfm60nssbvjgz4czzy4yzfa8gxczcdlzbgcnnvm914vb"))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
(propagated-inputs
- (list python-lxml python-genshi))
- (native-inputs
- (list python-magic))
+ (list python-lxml python-magic python-genshi))
+ (native-inputs (list python-setuptools python-wheel))
(home-page "https://relatorio.tryton.org/")
(synopsis "Templating library able to output ODT and PDF files")
(description "Relatorio is a templating library which provides a way to
- easily output ODT, ODS, PNG, SVG and several other kinds of files. Support
- for more filetypes can be easily added by creating plugins for them.")
+easily output ODT, ODS, PNG, SVG and several other kinds of files. Support
+for more filetypes can be easily added by creating plugins for them.")
(license license:gpl3+)))
(define-public python-radon
@@ 27107,10 27105,20 @@ conversion: Gamut A, B, and C.")
(base32
"1jmrskj399idw1czx6dvy2zfaijnwi02b55vx979ixp7q2mnzz68"))))
(build-system python-build-system)
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'remove-rednose-dependency
+ (lambda _
+ (substitute* "setup.py"
+ (("'rednose'") ""))
+ (substitute* '("requirements.txt" "setup.cfg")
+ (("rednose.*") "")))))))
(propagated-inputs
(list python-mock python-six))
(native-inputs
- (list python-nose python-rednose))
+ (list python-nose))
(home-page "https://github.com/gabrielfalcao/sure")
(synopsis "Automated testing library in python for python")
(description
@@ 27955,25 27963,6 @@ pure Python module.")
version of @code{SocksiPy} with bug fixes and extra features.")
(license license:bsd-3)))
-(define-public python-pydiff
- (package
- (name "python-pydiff")
- (version "0.2")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "pydiff" version))
- (sha256
- (base32
- "1als83h9w0gab24ipyna6khm390qmpnpkc5jksmdbs2xc8hp2z44"))))
- (build-system python-build-system)
- (home-page "https://github.com/myint/pydiff")
- (synopsis "Library to diff two Python files at the bytecode level")
- (description
- "@code{pydiff} makes it easy to look for actual code changes while
-ignoring formatting changes.")
- (license license:expat)))
-
(define-public python-pydub
(package
(name "python-pydub")
@@ 28193,17 28182,30 @@ in human-readable HTML format.")
(define-public python-ratelimiter
(package
(name "python-ratelimiter")
- (version "1.2.0")
+ (version "1.2.0.post1")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "ratelimiter" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/RazerM/ratelimiter")
+ ;; From https://github.com/RazerM/ratelimiter/pull/11
+ (commit "59a0827c434706d62b89e16a220e4ae12e618858")))
(sha256
(base32
- "1dhz85mj5bqd2mij84ncs6pz32hgidr79hay4aqfmzaa4rbb497p"))))
- (build-system python-build-system)
+ "1v34w12f41j0l2gy9ji9ip01kj4idjfjx7a97wrlr1ibxi7hg3bs"))))
+ (build-system pyproject-build-system)
(arguments
- '(#:tests? #f)) ; There are no tests in the pypi archive.
+ (list #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'pytest-compatibility
+ (lambda _
+ (substitute* "tests/conftest.py"
+ (("pytest.collect.File") "pytest.File")))))))
+ (native-inputs
+ (list python-pytest
+ python-pytest-asyncio
+ python-setuptools
+ python-wheel))
(home-page "https://github.com/RazerM/ratelimiter")
(synopsis "Simple rate limiting object")
(description
@@ 28464,18 28466,53 @@ Time} values as well as an event scheduler.")
(define-public python-pyro4
(package
(name "python-pyro4")
- (version "4.77")
+ (version "4.82")
(source
(origin
(method url-fetch)
(uri (pypi-uri "Pyro4" version))
(sha256
- (base32 "0gsjg869y4gpy265s1gj1f2qy6jn5iz8r2bwwnq78r1r5yi15zib"))))
- (build-system python-build-system)
+ (base32 "1yr1rv2afmq55wb14sx9qplzkqw7fya9rprsqdyxfbg90h45n7si"))))
+ (build-system pyproject-build-system)
(arguments
- '(#:tests? #f)) ;FIXME: Some tests require network access.
+ (list #:test-flags
+ #~(list "-k"
+ (string-join
+ ;; Those tests require network.
+ (list "testBCstart"
+ "testAutoClean"
+ "testDaemonPyroObj"
+ "testLookupAndRegister"
+ "testLookupInvalidHmac"
+ "testLookupUnixsockParsing"
+ "testMulti"
+ "testRefuseDottedNames"
+ "testResolve"
+ "testBCLookup0000"
+ "testPyroname"
+ "testResolveAsymmetricHmacUsage"
+ "testResolveWrongHmac"
+ "testStartNSfunc"
+ "testCustomDictClass"
+ "testDictClassFail"
+ "testBroadcast"
+ "testGetIP"
+ ;; XXX: Unclear why this test fails.
+ "testCustomClassFail")
+ " and not "))
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? test-flags #:allow-other-keys)
+ (if tests?
+ (apply invoke "python" "-m" "unittest" test-flags)
+ (format #t "test suite not run.~%")))))))
(native-inputs
- (list python-cloudpickle python-dill python-msgpack))
+ (list python-cloudpickle
+ python-dill
+ python-msgpack
+ python-setuptools
+ python-wheel))
(propagated-inputs
(list python-serpent))
(home-page "https://pyro4.readthedocs.io")
@@ 29204,6 29241,25 @@ working with iterables.")
Python.")
(license license:expat)))
+(define-public python-pybktree
+ (package
+ (name "python-pybktree")
+ (version "1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "pybktree" version))
+ (sha256
+ (base32 "0asd2lw9c5l5wi4z24k7gkhlprpdkcvs8d94szk56x9xvmy07h7f"))))
+ (build-system pyproject-build-system)
+ (native-inputs (list python-setuptools python-wheel))
+ (home-page "https://github.com/Jetsetter/pybktree")
+ (synopsis "Pythonic BK-tree data structure")
+ (description
+ "This package provides a BK-tree data structure to allow fast querying of
+close matches in Python.")
+ (license license:expat)))
+
(define-public python-pybtex
(package
(name "python-pybtex")
@@ 29722,38 29778,21 @@ user-space file systems in Python.")
(define-public python-stone
(package
(name "python-stone")
- (version "3.2.1")
+ (version "3.3.9")
(source
- (origin
- (method url-fetch)
- (uri (pypi-uri "stone" version))
- (sha256
- (base32
- "0xby5mpsms7b2rv8j6mvxzmzz5i9ii01brb9ylxz6kiv2i08piwv"))))
- (build-system python-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'change-version-requirements
- (lambda _
- ;; Match the requirement in test/requirements.txt
- (substitute* "setup.py"
- (("pytest < 5") "pytest < 7"))
- ;; We don't care about a coverage report.
- (substitute* "test/requirements.txt"
- (("coverage.*") "coverage\n"))))
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- ;; These tests don't import correctly.
- (delete-file "test/test_js_client.py")
- (delete-file "test/test_tsd_types.py")
- (delete-file "test/test_python_gen.py")
- (invoke "pytest")))))))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/dropbox/stone")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1x0kj4jygssjn66lbkln95chhf85vzy1wnpziy9jvpf4kbc1bmfy"))))
+ (build-system pyproject-build-system)
(propagated-inputs
- (list python-ply python-six))
+ (list python-jinja2 python-packaging python-ply python-six))
(native-inputs
- (list python-coverage python-mock python-pytest python-pytest-runner))
+ (list python-pytest python-pytest-runner python-setuptools python-wheel))
(home-page "https://github.com/dropbox/stone")
(synopsis "Official Api Spec Language for Dropbox")
(description
@@ 29763,7 29802,7 @@ user-space file systems in Python.")
(define-public pybind11
(package
(name "pybind11")
- (version "2.8.1")
+ (version "2.13.6")
(source (origin
(method git-fetch)
(uri (git-reference
@@ 29771,7 29810,7 @@ user-space file systems in Python.")
(commit (string-append "v" version))))
(sha256
(base32
- "10hrkrh78sk7k0ydw1ghmp7gvpwmkby0l2s0kf2iaj9sz0vijkhs"))
+ "1dbnki0pnky39kr04afd9ks597bzjc530zbk33jjss53nfvdvlj8"))
(file-name (git-file-name name version))))
(build-system cmake-build-system)
(native-inputs
@@ 29809,22 29848,6 @@ library: to minimize boilerplate code in traditional extension modules by
inferring type information using compile-time introspection.")
(license license:bsd-3)))
-;; Needed for python-optree
-(define-public pybind11-2.13
- (package
- (inherit pybind11)
- (name "pybind11")
- (version "2.13.6")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/pybind/pybind11")
- (commit (string-append "v" version))))
- (sha256
- (base32
- "1dbnki0pnky39kr04afd9ks597bzjc530zbk33jjss53nfvdvlj8"))
- (file-name (git-file-name name version))))))
-
;; Needed for scipy
(define-public pybind11-2.10
(package
@@ 29841,26 29864,6 @@ inferring type information using compile-time introspection.")
"0rbcfvl7y472sykzdq3vrkw83kar0lpzhk3wq9yj9cdydl8cpfcz"))
(file-name (git-file-name name version))))))
-;; This is needed for python-vaex-core.
-(define-public pybind11-2.3
- (package
- (inherit pybind11)
- (name "pybind11")
- (version "2.3.0")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/pybind/pybind11")
- (commit (string-append "v" version))))
- (sha256
- (base32
- "11b6dniri8m05spfd2a19irz82shf4sdca73566bniggrf3zclnf"))
- (file-name (git-file-name name version))))
- (arguments
- (substitute-keyword-arguments (package-arguments pybind11)
- ((#:tests? tests? #false)
- #false)))))
-
(define-public python-pooch
(package
(name "python-pooch")
@@ 30485,9 30488,8 @@ codecs for use in data storage and communication applications.")
;; but occasionally fail. They fail pretty reliably on the
;; build farm.
"-k" (string-append "not test_lazy_loader and not open_array"
- ;; TODO: remove this on python-team branch.
- ;; This only fails on the master branch.
- " and not test_encode_decode_array_dtype_shape_v3"))
+ ;; File not found.
+ " and not test_filesystem_path"))
#:phases
#~(modify-phases %standard-phases
(add-before 'build 'set-version
@@ 30546,8 30548,12 @@ N-dimensional arrays for Python.")
(arguments
(list
#:test-flags
- ;; This one test seemingly freezes
- '(list "-k" "not test_read_lazy_h5_cluster")
+ #~(list "-k" #$(string-append
+ ;; This one test seemingly freezes
+ "not test_read_lazy_h5_cluster"
+ ;; Fails with a numpy deprecation warning
+ ;; but not an actual failure
+ " and not test_read_write_X"))
#:phases
#~(modify-phases %standard-phases
;; Doctests require scanpy from (gnu packages bioinformatics)
@@ 30606,24 30612,25 @@ object-oriented library such as @code{scikit-learn}.")
(define-public python-dill
(package
(name "python-dill")
- (version "0.3.6")
+ (version "0.3.9")
(source
(origin
(method url-fetch)
(uri (pypi-uri "dill" version))
(sha256
- (base32 "0wr37zwyiprrv29jcc1hl5cla72faiwfs0mhvbxxhmkqd3rmbnz5"))))
+ (base32 "0b2inivjahjlph54a70x6wi3pax4qsgclhlw0blbz37nvmyjdal1"))))
(build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (with-directory-excursion "/tmp"
- (invoke "nosetests" "-v"))))))))
+ (list
+ #:phases #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (if tests?
+ ;; Extracted from tox.ini
+ (invoke "python" "dill/tests/__main__.py")
+ (format #t "test suite not run~%")))))))
(native-inputs
- (list python-nose python-setuptools python-wheel))
+ (list python-setuptools python-wheel))
(home-page "https://pypi.org/project/dill/")
(synopsis "Serialize all of Python")
(description "Dill extends Python's @code{pickle} module for serializing
@@ 30640,39 30647,43 @@ the saved state of the original interpreter session.")
(define-public python-multiprocess
(package
(name "python-multiprocess")
- (version "0.70.14")
+ (version "0.70.17")
(source
(origin
(method url-fetch)
(uri (pypi-uri "multiprocess" version))
(sha256
(base32
- "0splzd9w9yi42vl7b6mm99vb82jp2adhdrizw1xd4q125z0szp9y"))))
+ "0ypm9yj1ng1s96hk2iwll190dkpc2j5zras8kay9x00n6hdg3qja"))))
(build-system pyproject-build-system)
(arguments
(list
#:phases
- '(modify-phases %standard-phases
- (add-after 'unpack 'disable-broken-tests
- (lambda _
- ;; The "wait_result" and "shared_memory..." tests are broken as
- ;; there is no keyboard interrupt.
- ;;
- ;; The "preload_resources" test fails as it cannot find
- ;; mp_preload.py.
- (substitute* "py3.10/multiprocess/tests/__init__.py"
- (("^(.*)def test_(\
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'disable-broken-tests
+ (lambda* (#:key inputs #:allow-other-keys)
+ ;; The "wait_result" and "shared_memory..." tests are broken as
+ ;; there is no keyboard interrupt.
+ ;;
+ ;; The "preload_resources" test fails as it cannot find
+ ;; mp_preload.py.
+ (substitute*
+ (string-append "py" (python-version
+ (assoc-ref inputs "python"))
+ "/multiprocess/tests/__init__.py")
+ (("^(.*)def test_(\
wait_result|\
shared_memory_SharedMemoryServer_ignores_sigint|\
preload_resources\
)" line indent)
- (string-append indent
- "@unittest.skip(\"Disabled by Guix\")\n"
- line)))))
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "python" "-m" "multiprocess.tests")))))))
+ (string-append indent
+ "@unittest.skip(\"Disabled by Guix\")\n"
+ line)))))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (if tests?
+ (invoke "python" "-m" "multiprocess.tests")
+ (format #t "test suite not run~%")))))))
(propagated-inputs
(list python-dill))
(native-inputs (list python-setuptools python-wheel))
@@ 30694,17 30705,9 @@ library's @code{threading} module.")
(sha256
(base32
"1rs5a3hx1fcpfsxxkl5kx6g06c82wqjqgdqyny5l1ggl1wq0rmfn"))))
- (build-system python-build-system)
- (arguments
- (list
- #:phases
- #~(modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "pytest" "-vv")))))))
+ (build-system pyproject-build-system)
(propagated-inputs (list python-dill))
- (native-inputs (list python-check-manifest python-pytest python-wheel))
+ (native-inputs (list python-pytest python-setuptools python-wheel))
(home-page "https://github.com/sixty-north/multiprocessing_on_dill")
(synopsis "Multiprocessing using dill instead of pickle")
(description
@@ 30750,26 30753,19 @@ functions and classes.")
(define-public python-toolz
(package
(name "python-toolz")
- (version "0.11.2")
+ (version "1.0.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "toolz" version))
(sha256
(base32
- "0cxwlh8dz8gq0l0bzchjnqqwhdp261nfd958ppqm518k2mg2scbb"))))
- (build-system python-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key inputs outputs tests? #:allow-other-keys)
- (when tests?
- (add-installed-pythonpath inputs outputs)
- (invoke "python" "-m" "pytest" "--doctest-modules"
- "--pyargs" "toolz")))))))
+ "00ks0jhl1jwm9576c5sh10pnla8ni21yvg4kcxasr627l3cy71ic"))))
+ (build-system pyproject-build-system)
(native-inputs
- (list python-pytest))
+ (list python-pytest
+ python-setuptools
+ python-wheel))
(home-page "https://github.com/pytoolz/toolz/")
(synopsis "List processing tools and functional utilities")
(description
@@ 31097,13 31093,13 @@ run on top of the dynamic task schedulers.")
(define-public python-dask-image
(package
(name "python-dask-image")
- (version "2023.8.1")
+ (version "2024.5.3")
(source
(origin
(method url-fetch)
- (uri (pypi-uri "dask-image" version))
+ (uri (pypi-uri "dask_image" version))
(sha256
- (base32 "1dh49lvirf5fbgq5hw1c4972czg5w12fg9y689cinyjjn22qk6jy"))))
+ (base32 "0g4293n1vjlpyxbvd1xz3pz9an9z4rnsw1m7lynhm00m0bgiz7qc"))))
(build-system pyproject-build-system)
(arguments
(list
@@ 31119,7 31115,15 @@ run on top of the dynamic task schedulers.")
"--ignore=tests/test_dask_image/test_ndfourier/test_core.py"
"--ignore=tests/test_dask_image/test_ndinterp/test_spline_filter.py"
"--ignore=tests/test_dask_image/test_ndmeasure/test_core.py"
- "--ignore=tests/test_dask_image/test_ndmeasure/test_find_objects.py")))
+ "--ignore=tests/test_dask_image/test_ndmeasure/test_find_objects.py")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'build 'set-version
+ (lambda _
+ (substitute* "pyproject.toml"
+ (("^version_file.*") "")
+ (("dynamic = \\[\"version\"\\]")
+ (string-append "version = \"" #$version "\""))))))))
(propagated-inputs (list python-dask
python-numpy
python-pandas-2
@@ 31127,7 31131,16 @@ run on top of the dynamic task schedulers.")
python-scipy
python-tifffile))
(native-inputs
- (list python-pytest-flake8 python-pytest))
+ (list python-coverage
+ python-flake8
+ python-pytest
+ python-pytest-cov
+ python-pytest-flake8
+ python-pytest-timeout
+ python-setuptools
+ python-setuptools-scm
+ python-twine
+ python-wheel))
(home-page "https://github.com/dask/dask-image")
(synopsis "Distributed image processing")
(description "This is a package for image processing with Dask arrays.
@@ 31246,15 31259,18 @@ Features:
(define-public python-precis-i18n
(package
(name "python-precis-i18n")
- (version "1.0.3")
+ (version "1.1.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "precis_i18n" version))
(sha256
- (base32
- "1qfb78zpx565vqkg0xhx75pna9sc35m370vpcz82982c8ix3ypyz"))))
- (build-system python-build-system)
+ (base32 "0cdv2vbn0kwfq0pxj4l52s2xiaqablb2cgk0nph6r9cyqayf77rn"))))
+ (build-system pyproject-build-system)
+ (native-inputs
+ (list python-pytest
+ python-setuptools
+ python-wheel))
(home-page "https://github.com/byllyfish/precis_i18n")
(synopsis "Implementation of the PRECIS framework")
(description
@@ 31390,15 31406,16 @@ in doctests.")
(define-public python-attr
(package
(name "python-attr")
- (version "0.3.1")
+ (version "0.3.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "attr" version))
(sha256
- (base32
- "0pbpskvxp5hzdvcaf766ljwpckshir8sf7z6jqji6zyib20594ch"))))
- (build-system python-build-system)
+ (base32 "1x2627x0n2rxx8wib4cksbjjnncff8finq97k37dq70qd2kvrvhw"))))
+ (build-system pyproject-build-system)
+ (native-inputs
+ (list python-setuptools python-wheel))
(home-page "https://github.com/denis-ryzhkov/attr")
(synopsis "Decorator for attributes of target function or class")
(description "Simple decorator to set attributes of target function or
@@ 31767,32 31784,29 @@ format.")
(define-public python-crontab
(package
(name "python-crontab")
- (version "3.0.0")
+ (version "3.2.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri name version))
(sha256
- (base32 "0yd3vdhl7z8lxa30czsry65srha51ppdcwnhjgxx9pwx0djp9yvr"))))
- (build-system python-build-system)
+ (base32 "0sy3qlki43n6qmhzzzyya4wcs50mcp3mg1ddn9h39plsscfps1j0"))))
+ (build-system pyproject-build-system)
(arguments
- (list
- #:phases
- #~(modify-phases %standard-phases
- (add-before 'check 'disable-failing-tests
- (lambda _
- (substitute* '("tests/test_compatibility.py"
- "tests/test_frequency.py")
- (("test_07_non_posix_shell")
- "__off_test_07_non_posix_shell")
- ;; Fails on leap years
- (("test_19_frequency_at_month")
- "__off_test_19_frequency_at_month")
- ;; AssertionError: 48 != 24
- (("test_20_frequency_at_year")
- "__off_test_20_frequency_at_year")))))))
+ (list #:test-flags
+ ;; This test is made for Windows.
+ #~(list "-k" "not test_07_non_posix_shell")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'defaults-to-mcron
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "crontab.py"
+ (("/usr/bin/crontab")
+ (search-input-file inputs "bin/crontab"))))))))
(inputs
- (list python-dateutil))
+ (list mcron python-dateutil))
+ (native-inputs
+ (list python-pytest python-setuptools python-wheel))
(home-page "https://gitlab.com/doctormo/python-crontab/")
(synopsis "Module for reading and writing crontab files")
(description "This Python module can read, write crontab files, and
@@ 31973,37 31987,25 @@ one-off scripts.")
(define-public python-cached-property
(package
(name "python-cached-property")
- (version "1.5.2")
+ (version "2.0.1")
(source
(origin
(method url-fetch)
- (uri (pypi-uri "cached-property" version))
+ (uri (pypi-uri "cached_property" version))
(sha256
- (base32
- "0c51i6yzg6dlq6zhk4c6nv33mg8gv05kkan36k9b5jzf71c7b9cz"))))
- (build-system python-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- ;; https://github.com/pydanny/cached-property/issues/131
- ;; recent versions of freezegun break one test
- (add-after 'unpack 'disable-broken-test
- (lambda _
- (substitute* "tests/test_cached_property.py"
- (("def test_threads_ttl_expiry\\(self\\)" m)
- (string-append "@unittest.skip(\"Disabled by Guix\")\n"
- " " m)))
- #t)))))
+ (base32 "0hbni4q15n8wspdj48j6xvg977pgm1r5wwjq3x7hxvp30mqn2ka8"))))
+ (build-system pyproject-build-system)
(native-inputs
- (list python-freezegun))
- (home-page
- "https://github.com/pydanny/cached-property")
- (synopsis
- "Decorator for caching properties in classes")
+ (list python-freezegun
+ python-pytest
+ python-setuptools
+ python-wheel))
+ (home-page "https://github.com/pydanny/cached-property")
+ (synopsis "Decorator for caching properties in classes")
(description
"This package provides a decorator which makes caching
-time-or-computationally-expensive properties quick and easy and works in Python
-2 or 3.")
+time-or-computationally-expensive properties quick and easy and works in
+Python 2 or 3.")
(license license:bsd-3)))
(define-public python-folium
@@ 32473,38 32475,38 @@ register custom encoders and decoders.")
(define-public python-ujson
(package
(name "python-ujson")
- (version "5.7.0")
+ (version "5.10.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "ujson" version))
(sha256
(base32
- "08vvyfyg4qvjy2vxrvc0qix5zmd0j6wd0icvmhc633xfvkayb277"))
+ "1habmn3bmmv2ym4ldiijcavdkdzp8h28h60hgwjkhxwcbly8zkdk"))
(modules '((guix build utils)))
(snippet
- '(begin (delete-file-recursively "deps") #t))))
- (build-system python-build-system)
+ #~(begin (delete-file-recursively "deps")))))
+ (build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'link-to-system-double-conversion
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((d-c (assoc-ref inputs "double-conversion")))
- (substitute* "setup.py"
- (("./deps/double-conversion/double-conversion\"")
- (string-append d-c "/include/double-conversion\""))
- (("-lstdc++" stdc)
- (string-append "-L" d-c "/lib\","
- " \"-ldouble-conversion\","
- " \"" stdc)))
- #t)))
- (replace 'check
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (add-installed-pythonpath inputs outputs)
- (invoke "pytest"))))))
- (native-inputs
- (list double-conversion python-setuptools-scm python-pytest))
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'link-to-system-double-conversion
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((d-c (assoc-ref inputs "double-conversion")))
+ (substitute* "setup.py"
+ (("./deps/double-conversion/double-conversion\"")
+ (string-append d-c "/include/double-conversion\""))
+ (("-lstdc++" stdc)
+ (string-append "-L" d-c "/lib\","
+ " \"-ldouble-conversion\","
+ " \"" stdc)))))))))
+ (native-inputs
+ (list double-conversion
+ python-pytest
+ python-setuptools
+ python-setuptools-scm
+ python-wheel))
(home-page "https://github.com/ultrajson/ultrajson")
(synopsis "Ultra fast JSON encoder and decoder for Python")
(description
@@ 32614,10 32616,7 @@ standard error channel (stderr) in your program.")
python-sniffio
python-typing-extensions))
(native-inputs
- (list python-contextlib2
- python-hypothesis
- python-mock
- python-psutil
+ (list python-psutil
python-pytest
python-pytest-mock
python-setuptools
@@ 32635,17 32634,6 @@ concurrency on top of asyncio, and works in harmony with the native SC of trio
itself.")
(license license:expat)))
-;; TODO: This will become the default on the python-team branch. Dataclasses
-;; is part of Python.
-(define-public python-anyio/without-dataclasses
- (package
- (inherit python-anyio)
- (propagated-inputs
- (list python-contextvars
- python-idna
- python-sniffio
- python-typing-extensions))))
-
(define-public python-argh
;; There are 21 commits since the latest release containing important
;; improvements.
@@ 33162,39 33150,58 @@ such as a file modification and trigger an action. This is similar to inotify,
but portable.")
(license license:asl2.0)))
-(define-public python-watchgod
+(define-public python-watchfiles
(package
- (name "python-watchgod")
- (version "0.8.1")
+ (name "python-watchfiles")
+ (version "1.0.4")
(source
(origin
;; There are no tests in the PyPI tarball.
(method git-fetch)
(uri (git-reference
- (url "https://github.com/samuelcolvin/watchgod")
+ (url "https://github.com/samuelcolvin/watchfiles")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0zm9xd2qf3d74l67yv8j3zhhhvi0vp25vhkg46l9d7flh9m04qrp"))))
- (build-system pyproject-build-system)
+ (base32 "1kaxq0drjwlvcsg4in25w1bhjjgm1zlz06rr2macyi6s5x96g46h"))))
+ (build-system cargo-build-system)
(arguments
- (list #:test-flags '(list "-o" "asyncio_mode=auto"
- ;; PytestUnraisableExceptionWarning
- "-k" "not test_watch_log and not test_awatch")
- #:phases #~(modify-phases %standard-phases
- (delete 'sanity-check))))
+ (list
+ #:install-source? #f
+ #:imported-modules `(,@%cargo-build-system-modules
+ ,@%pyproject-build-system-modules)
+ #:modules '((guix build cargo-build-system)
+ ((guix build pyproject-build-system) #:prefix py:)
+ (guix build utils))
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'build
+ (assoc-ref py:%standard-phases 'build))
+ (add-after 'build 'install-rust-library
+ (lambda _
+ (copy-file "target/release/lib_rust_notify.so"
+ "watchfiles/_rust_notify.so")))
+ (replace 'check
+ (lambda* (#:key tests? test-flags #:allow-other-keys)
+ (if tests?
+ ;; Missing file in source.
+ (invoke "pytest" "-vv" "-k" "not test_docs_examples")
+ (format #t "test suite not run~%"))))
+ (replace 'install
+ (assoc-ref py:%standard-phases 'install)))
+ #:cargo-inputs
+ (list rust-crossbeam-channel-0.5 rust-notify-7 rust-pyo3-0.23)))
(native-inputs
- (list python-anyio
+ (list maturin
+ python-anyio
python-coverage
- python-pygments
+ python-dirty-equals
python-pytest
- python-pytest-asyncio
python-pytest-cov
python-pytest-mock
- python-pytest-sugar
- python-setuptools
- python-wheel))
- (home-page "https://github.com/samuelcolvin/watchgod")
+ python-pytest-timeout
+ python-wrapper))
+ (home-page "https://github.com/samuelcolvin/watchfiles")
(synopsis "Simple, modern file watching and code reload in Python")
(description
"Simple, modern file watching and code reload in Python inspired by
@@ 33202,6 33209,9 @@ but portable.")
operating systems and an elegant approach to concurrency using threading.")
(license license:expat)))
+(define-deprecated/alias python-watchgod python-watchfiles)
+(export python-watchgod)
+
(define-public python-wget
(package
(name "python-wget")
@@ 33718,14 33728,18 @@ library. Only the high-level API is bound.")
(define-public python-frozendict
(package
(name "python-frozendict")
- (version "2.3.4")
+ (version "2.4.6")
(source
(origin
(method url-fetch)
(uri (pypi-uri "frozendict" version))
(sha256
- (base32 "0y3zn57i1q5192f7l4w2z2zsy3rrx50g563msaq954r58s1v3d0m"))))
- (build-system python-build-system)
+ (base32 "13ib358v66c9ykfz3plpxcs96ca6vkx8w84sjv26zlpvf1jd2z6z"))))
+ (build-system pyproject-build-system)
+ (native-inputs
+ (list python-pytest
+ python-setuptools
+ python-wheel))
(home-page "https://github.com/Marco-Sulla/python-frozendict")
(synopsis "Simple immutable mapping for Python")
(description
@@ 34234,25 34248,6 @@ cryptographically signed ones).")
dictionaries.")
(license license:expat)))
-(define-public python-dictpath
- (package
- (name "python-dictpath")
- (version "0.1.3")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "dictpath" version))
- (sha256
- (base32 "1n4hq4wbgaw59bbb16nhkgg5wk8sl4iw940vjrgx4xmifqxxw73m"))))
- (build-system python-build-system)
- (native-inputs (list python-pytest python-pytest-cov python-pytest-flake8))
- (home-page "https://github.com/p1c2u/pathable")
- (synopsis "Object-oriented path library for Python")
- (description "This object-oriented dictionary path Python library enables
-traversing resources like paths or accessing resources on demand with separate
-accessor layer.")
- (license license:asl2.0)))
-
(define-public pyzo
(package
(name "pyzo")
@@ 34342,24 34337,22 @@ intended for validating data coming into Python as JSON, YAML, etc.")
(define-public python-cmd2
(package
(name "python-cmd2")
- (version "2.3.3")
+ (version "2.5.11")
(source
(origin
(method url-fetch)
(uri (pypi-uri "cmd2" version))
(sha256
(base32
- "0h1naik558qh48gx2iyy0a0khvw5fz0in69y84mbrhsm9nq7w3bm"))))
+ "0abl9aalyfbncw39d41gd3mmdgjvd7jlaa372r0lmghz0a2x781h"))))
(build-system pyproject-build-system)
(arguments
(list #:test-flags '(list "-k" "not test_find_editor_not_specified \
and not test_transcript")))
(propagated-inputs
- (list python-attrs python-colorama python-pyperclip python-wcwidth))
+ (list python-pyperclip python-wcwidth))
(native-inputs
- (list python-invoke
- python-mock
- python-pytest
+ (list python-pytest
python-pytest-cov
python-pytest-mock
python-setuptools
@@ 34619,23 34612,31 @@ reStructuredText, and plain text.")
(define-public python-lazr-delegates
(package
(name "python-lazr-delegates")
- (version "2.0.4")
+ (version "2.1.1")
(source
(origin
(method url-fetch)
- (uri (pypi-uri "lazr.delegates" version))
+ (uri (pypi-uri "lazr_delegates" version))
(sha256
- (base32
- "1rdnl85j9ayp8n85l0ciip621j9dcziz5qnmv2m7krgwgcn31vfx"))))
- (build-system python-build-system)
+ (base32 "1p02diwzn58jhpvf9m8bhb5p0xkx5gnc84mzgwr3zdsidrhv5kmf"))))
+ (build-system pyproject-build-system)
(arguments
- '(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests? (invoke "nosetests")))))))
+ (list
+ #:test-flags #~(list "-v" #$output)
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'check 'check-cleanup
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (for-each
+ delete-file-recursively
+ (find-files #$output
+ (lambda (file stat)
+ (or (member (basename file)
+ '("tests" ".pytest_cache"))))
+ #:directories? #t))))))))
(native-inputs
- (list python-nose))
+ (list python-pytest python-setuptools python-wheel))
(propagated-inputs
(list python-zope-interface))
(home-page "https://launchpad.net/lazr.delegates")
@@ 34650,23 34651,31 @@ and delegating behavior.")
(define-public python-lazr-config
(package
(name "python-lazr-config")
- (version "2.2.3")
+ (version "3.1")
(source
(origin
(method url-fetch)
- (uri (pypi-uri "lazr.config" version))
+ (uri (pypi-uri "lazr_config" version))
(sha256
- (base32
- "1qdbrzl61q7cjhbnxvw9y3frcr935y7diwy15xrwcv9ynvw76jmp"))))
- (build-system python-build-system)
+ (base32 "02xb4fs9rm6bf3f00qkq8pihgqvrvn2wfnvydn2vg9p73ddhcmvw"))))
+ (build-system pyproject-build-system)
(arguments
- '(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda _
- (invoke "python" "-s" "-m" "nose" "-P" "lazr"))))))
+ (list
+ #:test-flags #~(list "-v" #$output)
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'check 'check-cleanup
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (for-each
+ delete-file-recursively
+ (find-files #$output
+ (lambda (file stat)
+ (or (member (basename file)
+ '("tests" ".pytest_cache"))))
+ #:directories? #t))))))))
(native-inputs
- (list python-nose))
+ (list python-pytest python-setuptools python-wheel))
(propagated-inputs
(list python-lazr-delegates python-zope-interface))
(home-page "https://launchpad.net/lazr.config")
@@ 34717,17 34726,41 @@ RFC 3464.")
(define-public python-flufl-i18n
(package
(name "python-flufl-i18n")
- (version "3.0")
+ (version "5.1.0")
(source
(origin
(method url-fetch)
- (uri (pypi-uri "flufl.i18n" version))
+ (uri (pypi-uri "flufl_i18n" version))
(sha256
(base32
- "1flwpn1xhgc957zj3zxw92dhdjh0lsy0hdvzq32dzqpsajfsvq1r"))))
- (build-system python-build-system)
+ "0bm4kmi04gm164y5nmadmrg79y1l1cs9iwxcv9y7gq0dgyr20xms"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:test-flags
+ #~(list "--no-cov" "--ignore-glob=docs/*")
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; This phase add a symlink of dist-info dir for packages
+ ;; expecting flufl.i18n rather than flufl_i18n (mailman).
+ (add-after 'install 'add-custom-dist-info
+ (lambda _
+ (for-each
+ (lambda (dir)
+ (with-directory-excursion (dirname dir)
+ (let ((base (basename dir)))
+ (symlink base
+ (string-join (string-split base #\_) ".")))))
+ (find-files #$output
+ (lambda (file stat)
+ (string-suffix? ".dist-info" file))
+ #:directories? #t)))))))
(propagated-inputs
(list python-atpublic))
+ (native-inputs
+ (list python-hatchling
+ python-pytest
+ python-pytest-cov
+ python-sybil))
(home-page "https://flufli18n.readthedocs.io")
(synopsis "API for Python internationalization")
(description
@@ 34743,15 34776,38 @@ different tasks.")
(define-public python-flufl-lock
(package
(name "python-flufl-lock")
- (version "4.0")
+ (version "8.1.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "flufl.lock" version))
(sha256
- (base32
- "055941zyma3wfx25jhm8wcsghpv3jc3iwi1gdrdjhzcnfhn62lxq"))))
- (build-system python-build-system)
+ (base32 "1jz7vipjga4x803gfsb9mvnfb6q8my7ib000nsc3v9ljaq0050yq"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:test-flags
+ #~(list "--no-cov" "--ignore-glob=docs/*")
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; This phase add a symlink of dist-info dir for packages
+ ;; expecting flufl.lock rather than flufl_lock (mailman).
+ (add-after 'install 'add-custom-dist-info
+ (lambda _
+ (for-each
+ (lambda (dir)
+ (with-directory-excursion (dirname dir)
+ (let ((base (basename dir)))
+ (symlink base
+ (string-join (string-split base #\_) ".")))))
+ (find-files #$output
+ (lambda (file stat)
+ (string-suffix? ".dist-info" file))
+ #:directories? #t)))))))
+ (native-inputs
+ (list python-hatchling
+ python-pytest
+ python-pytest-cov
+ python-sybil))
(propagated-inputs
(list python-atpublic python-psutil))
(home-page "https://flufllock.readthedocs.io")
@@ 34882,25 34938,17 @@ dates in almost any string formats commonly found on web pages.")
(define-public python-dpath
(package
(name "python-dpath")
- (version "2.0.1")
+ (version "2.2.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "dpath" version))
(sha256
(base32
- "1ymi9ssk7i0mx3mviplf4csfvzibdd6wyj4qzj6s487n9xgnp85y"))))
- (build-system python-build-system)
+ "0gkavmc44f9cj3kch68343r2ajsbvbsjcmsmkqhkzsjmvhqfdxrl"))))
+ (build-system pyproject-build-system)
(native-inputs
- (list python-hypothesis python-mock python-nose))
- (arguments
- '(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (add-installed-pythonpath inputs outputs)
- ;; This invocation is taken from tox.ini.
- (invoke "nosetests" "-d" "-v" "tests/"))))))
+ (list python-hypothesis python-nose2 python-setuptools python-wheel))
(home-page "https://github.com/akesterson/dpath-python")
(synopsis "File-system-like pathing and searching for dictionaries")
(description
@@ 37067,9 37115,9 @@ generation, and software testing purposes.")
(define-public python-peachpy
;; There is no tag in this repo.
- (let ((commit "913d74c35a6b1d330e90bfc055208ce5b06b35a0")
+ (let ((commit "349e8f836142b2ed0efeb6bb99b1b715d87202e9")
(version "0.2.0") ;from 'peachpy/__init__.py'
- (revision "2"))
+ (revision "3"))
(package
(name "python-peachpy")
(version (git-version version revision commit))
@@ 37080,17 37128,15 @@ generation, and software testing purposes.")
(file-name (git-file-name name version))
(sha256
(base32
- "1wnqxspxsacw4556q0b9fbw11nhrkgn6gs8g43jdnpa35f3z9kb6"))
+ "16pnkghmqjc7pbws0yhyrwlz43d5pffb5c6v2bb4jk0j537gwzbi"))
(patches (search-patches "python-peachpy-determinism.patch"))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
(arguments
- '(#:phases (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "nosetests")))))))
+ ;; The issue is known and the test will probably never be fixed.
+ ;; https://github.com/Maratyszcza/PeachPy/issues/131
+ (list #:test-flags ''("--ignore=tests/arm/test_arm.py")))
(native-inputs
- (list python-nose python-rednose python-setuptools))
+ (list python-pytest python-setuptools python-wheel))
(propagated-inputs
(list python-six python-opcodes))
(synopsis "Efficient assembly code generation in Python")
@@ 37677,7 37723,12 @@ statements in OFX files.")
;; The timestamp to local offset tests fail due to
;; missing timezone data (see:
;; https://github.com/danielrichman/strict-rfc3339/issues/9).
- "-k" "not LocalOffset")))))))
+ "-k"
+ #$@(if (or (target-x86-32?) (target-arm32?))
+ ;; On 32-bit platforms the size of time_t is
+ ;; too small for these tests.
+ '("not LocalOffset and not TestTimestampToRFC3339UTCOffset")
+ '("not LocalOffset")))))))))
(native-inputs (list python-pytest))
(home-page "https://github.com/danielrichman/strict-rfc3339")
(synopsis "RFC3339 procedures library")
@@ 38296,7 38347,9 @@ these linters: @code{pycodestlye}, @code{pyflakes}")
(arguments
(list
#:test-flags #~(list "--durations=10"
- "--ignore=tests/integration/test_dev_server.py")
+ "--ignore=tests/integration/test_dev_server.py"
+ ;; Assertion fails in diff of HTML template.
+ "-k" "not test_compiling_markdown")
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'fix-pytest-config
@@ 39156,17 39209,21 @@ implementing a pre-defined interface.")
(define-public python-itemloaders
(package
(name "python-itemloaders")
- (version "1.1.0")
+ (version "1.3.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "itemloaders" version))
(sha256
- (base32 "0j2aw4ipalj208594x80blpgkh1i63gqqa4nb67b823av9hirn11"))))
+ (base32 "0w37g31n06x6v6b4w7cz3nbq4wl6cv7rrzg3fr203gw3pqx5pbsg"))))
(build-system pyproject-build-system)
- (native-inputs (list python-pytest python-setuptools python-wheel))
+ (native-inputs
+ (list python-packaging
+ python-pytest
+ python-setuptools
+ python-wheel))
(propagated-inputs
- (list python-itemadapter python-jmespath python-parsel python-w3lib))
+ (list python-itemadapter python-jmespath python-parsel))
(home-page "https://github.com/scrapy/itemloaders")
(synopsis "Base library for scrapy's ItemLoader")
(description "Itemloaders is a library that helps you collect data
@@ 40466,13 40523,13 @@ read all zbar supported codes.")
(define-public python-zeroc-ice
(package
(name "python-zeroc-ice")
- (version "3.7.9")
+ (version "3.7.10.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "zeroc-ice" version))
(sha256
(base32
- "0bqkrjxp2fbz34x3wxkxji39kxinypzg8q2994sibiay29mpipxb"))))
+ "0r46q4hd7xbpvnidbra1prkg4xhmajxjjmclfqgp3pv0lgyslqxh"))))
(build-system pyproject-build-system)
(inputs (list openssl))
(native-inputs (list python-setuptools python-wheel))
M gnu/packages/python.scm => gnu/packages/python.scm +404 -5
@@ 660,6 660,405 @@ def contents() -> str:
(variable "PYTHONTZPATH")
(files (list "share/zoneinfo")))))))
+(define-public python-3.11
+ (package
+ (inherit python-3.10)
+ (name "python")
+ (version "3.11.11")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://www.python.org/ftp/python/"
+ version "/Python-" version ".tar.xz"))
+ (patches (search-patches
+ "python-3-deterministic-build-info.patch"
+ "python-3.11-fix-tests.patch"
+ "python-3-hurd-configure.patch"
+ "python-3-search-paths.patch"))
+ (sha256
+ (base32
+ "1qrvsxg5g0b0pgz2iigxic2j3g6b2c59iva46vins8ydl33j169a"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Delete the bundled copy of libexpat.
+ (delete-file-recursively "Modules/expat")
+ (substitute* "Modules/Setup"
+ ;; Link Expat instead of embedding the bundled one.
+ (("^#pyexpat.*") "pyexpat pyexpat.c -lexpat\n"))
+ ;; Delete windows binaries
+ (for-each delete-file
+ (find-files "Lib/distutils/command" "\\.exe$"))))))
+ (arguments
+ (list
+ #:test-target "test"
+ #:configure-flags
+ #~(list "--enable-shared" ;allow embedding
+ "--with-system-expat" ;for XML support
+ "--with-system-ffi" ;build ctypes
+ "--with-ensurepip=install" ;install pip and setuptools
+ "--with-computed-gotos" ;main interpreter loop optimization
+ "--enable-unicode=ucs4"
+ "--without-static-libpython"
+ "--enable-loadable-sqlite-extensions"
+
+ ;; FIXME: These flags makes Python significantly faster,
+ ;; but leads to non-reproducible binaries.
+ ;; "--with-lto" ;increase size by 20MB, but 15% speedup
+ ;; "--enable-optimizations"
+
+ ;; Prevent the installed _sysconfigdata.py from retaining
+ ;; a reference to coreutils.
+ "INSTALL=install -c"
+ "MKDIR_P=mkdir -p"
+
+ ;; Add a reference to libxcrypt in LIBS so that the
+ ;; sysconfigdata file records it and propagates it to programs
+ ;; linking against Python.
+ (let ((libxcrypt
+ (false-if-exception
+ (dirname
+ (search-input-file %build-inputs
+ "lib/libcrypt.so.1")))))
+ (string-append
+ "LIBS="
+ (if libxcrypt
+ (string-append "-L" libxcrypt)
+ "")))
+
+ ;; Disable runtime check failing if cross-compiling, see:
+ ;; https://lists.yoctoproject.org/pipermail/poky/2013-June/008997.html
+ #$@(if (%current-target-system)
+ '("ac_cv_buggy_getaddrinfo=no"
+ "ac_cv_file__dev_ptmx=no"
+ "ac_cv_file__dev_ptc=no")
+ '())
+ ;; -fno-semantic-interposition reinstates some
+ ;; optimizations by gcc leading to around 15% speedup.
+ ;; This is the default starting from python 3.10.
+ "CFLAGS=-fno-semantic-interposition"
+ (string-append "LDFLAGS=-Wl,-rpath=" #$output "/lib"
+ " -fno-semantic-interposition"))
+ ;; With no -j argument tests use all available cpus, so provide one.
+ #:make-flags
+ `(list (string-append (format #f "TESTOPTS=-j~d"
+ (parallel-job-count))
+ ;; those tests fail on low-memory systems
+ " --exclude"
+ " test_mmap"
+ " test_socket"
+ " test_threading"
+ " test_asyncio"
+ " test_shutdown"
+ ,@(if (system-hurd?)
+ '(" test_posix" ;multiple errors
+ " test_time"
+ " test_pty"
+ " test_shutil"
+ " test_tempfile" ;chflags: invalid argument:
+ ;; tbv14c9t/dir0/dir0/dir0/test0.txt
+ " test_os" ;stty: 'standard input':
+ ;; Inappropriate ioctl for device
+ " test_openpty" ;No such file or directory
+ " test_selectors" ;assertEqual(NUM_FDS // 2, len(fds))
+ ;; 32752 != 4
+ " test_compileall" ;multiple errors
+ " test_poll" ;list index out of range
+ " test_subprocess" ;runs over 10min
+ " test_asyncore" ;multiple errors
+ " test_threadsignals"
+ " test_eintr" ;Process return code is -14
+ " test_io" ;multiple errors
+ " test_logging"
+ " test_signal"
+ " test_flags" ;ERROR
+ " test_bidirectional_pty"
+ " test_create_unix_connection"
+ " test_unix_sock_client_ops"
+ " test_open_unix_connection"
+ " test_open_unix_connection_error"
+ " test_read_pty_output"
+ " test_write_pty"
+ " test_concurrent_futures" ;freeze
+ " test_venv" ;freeze
+ " test_multiprocessing_forkserver" ;runs over 10min
+ " test_multiprocessing_spawn" ;runs over 10min
+ " test_builtin"
+ " test_capi"
+ " test_dbm_ndbm"
+ " test_exceptions"
+ " test_faulthandler"
+ " test_getopt"
+ " test_importlib"
+ " test_json"
+ " test_multiprocessing_fork"
+ " test_multiprocessing_main_handling"
+ " test_pdb "
+ " test_regrtest"
+ " test_sqlite")
+ '())))
+
+ #:modules
+ '((ice-9 ftw)
+ (ice-9 match)
+ (guix build utils)
+ (guix build gnu-build-system))
+
+ #:phases
+ #~(modify-phases %standard-phases
+ #$@(if (system-hurd?)
+ `((add-after 'unpack
+ 'disable-multi-processing
+ (lambda _
+ (substitute* "Makefile.pre.in"
+ (("-j0")
+ "-j1")))))
+ '())
+ (add-before 'configure 'patch-lib-shells
+ (lambda _
+ ;; This variable is used in setup.py to enable cross compilation
+ ;; specific switches. As it is not set properly by configure
+ ;; script, set it manually.
+ #$@(if (%current-target-system)
+ '((setenv "_PYTHON_HOST_PLATFORM" ""))
+ '())
+ ;; Filter for existing files, since some may not exist in all
+ ;; versions of python that are built with this recipe.
+ (substitute* (filter file-exists?
+ '("Lib/subprocess.py"
+ "Lib/popen2.py"
+ "Lib/distutils/tests/test_spawn.py"
+ "Lib/test/support/__init__.py"
+ "Lib/test/test_subprocess.py"))
+ (("/bin/sh")
+ (which "sh")))))
+ (add-before 'configure 'do-not-record-configure-flags
+ (lambda* (#:key configure-flags #:allow-other-keys)
+ ;; Remove configure flags from the installed '_sysconfigdata.py'
+ ;; and 'Makefile' so we don't end up keeping references to the
+ ;; build tools.
+ ;;
+ ;; Preserve at least '--with-system-ffi' since otherwise the
+ ;; thing tries to build libffi, fails, and we end up with a
+ ;; Python that lacks ctypes.
+ (substitute* "configure"
+ (("^CONFIG_ARGS=.*$")
+ (format #f "CONFIG_ARGS='~a'\n"
+ (if (member "--with-system-ffi"
+ configure-flags)
+ "--with-system-ffi" ""))))))
+ (add-before 'check 'pre-check
+ (lambda _
+ ;; 'Lib/test/test_site.py' needs a valid $HOME
+ (setenv "HOME"
+ (getcwd))))
+ (add-after 'unpack 'set-source-file-times-to-1980
+ ;; XXX One of the tests uses a ZIP library to pack up some of the
+ ;; source tree, and fails with "ZIP does not support timestamps
+ ;; before 1980". Work around this by setting the file times in the
+ ;; source tree to sometime in early 1980.
+ (lambda _
+ (let ((circa-1980 (* 10 366 24 60 60)))
+ (ftw "."
+ (lambda (file stat flag)
+ (utime file circa-1980 circa-1980) #t)))))
+ (add-after 'unpack 'remove-windows-binaries
+ (lambda _
+ ;; Delete .exe from embedded .whl (zip) files
+ (for-each (lambda (whl)
+ (let ((dir "whl-content")
+ (circa-1980 (* 10 366 24 60 60)))
+ (mkdir-p dir)
+ (with-directory-excursion dir
+ (let ((whl (string-append "../" whl)))
+ (invoke "unzip" whl)
+ (for-each delete-file
+ (find-files "." "\\.exe$"))
+ (delete-file whl)
+ ;; Reset timestamps to prevent them from ending
+ ;; up in the Zip archive.
+ (ftw "."
+ (lambda (file stat flag)
+ (utime file circa-1980
+ circa-1980) #t))
+ (apply invoke "zip" "-X" whl
+ (find-files "."
+ #:directories? #t))))
+ (delete-file-recursively dir)))
+ (find-files "Lib/ensurepip" "\\.whl$"))))
+ (add-after 'install 'remove-tests
+ ;; Remove 25 MiB of unneeded unit tests. Keep test_support.*
+ ;; because these files are used by some libraries out there.
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (match (scandir (string-append out "/lib")
+ (lambda (name)
+ (string-prefix? "python" name)))
+ ((pythonX.Y)
+ (let ((testdir (string-append out "/lib/" pythonX.Y
+ "/test")))
+ (with-directory-excursion testdir
+ (for-each delete-file-recursively
+ (scandir testdir
+ (match-lambda
+ ((or "." "..")
+ #f)
+ ("support" #f)
+ (file (not (string-prefix?
+ "test_support."
+ file))))))
+ (call-with-output-file "__init__.py"
+ (const #t))))
+ (let ((libdir (string-append out "/lib/" pythonX.Y)))
+ (for-each (lambda (directory)
+ (let ((dir (string-append libdir "/"
+ directory)))
+ (when (file-exists? dir)
+ (delete-file-recursively dir))))
+ '("email/test" "ctypes/test"
+ "unittest/test"
+ "tkinter/test"
+ "sqlite3/test"
+ "bsddb/test"
+ "lib-tk/test"
+ "json/tests"
+ "distutils/tests"))))))))
+ (add-after 'remove-tests 'move-tk-inter
+ (lambda* (#:key outputs inputs #:allow-other-keys)
+ ;; When Tkinter support is built move it to a separate output so
+ ;; that the main output doesn't contain a reference to Tcl/Tk.
+ (let ((out (assoc-ref outputs "out"))
+ (tk (assoc-ref outputs "tk")))
+ (when tk
+ (match (find-files out "tkinter.*\\.so")
+ ((tkinter.so)
+ ;; The .so is in OUT/lib/pythonX.Y/lib-dynload, but we
+ ;; want it under TK/lib/pythonX.Y/site-packages.
+ (let* ((len (string-length out))
+ (target (string-append tk "/"
+ (string-drop (dirname
+ (dirname
+ tkinter.so))
+ len)
+ "/site-packages")))
+ (install-file tkinter.so target)
+ (delete-file tkinter.so))))
+ ;; Remove explicit store path references.
+ (let ((tcl (assoc-ref inputs "tcl"))
+ (tk (assoc-ref inputs "tk")))
+ (substitute* (find-files (string-append out "/lib")
+ "^(_sysconfigdata_.*\\.py|Makefile)$")
+ (((string-append "-L" tk "/lib"))
+ "")
+ (((string-append "-L" tcl "/lib"))
+ "")))))))
+ (add-after 'move-tk-inter 'move-idle
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; when idle is built, move it to a separate output to save some
+ ;; space (5MB)
+ (let ((out (assoc-ref outputs "out"))
+ (idle (assoc-ref outputs "idle")))
+ (when idle
+ (for-each (lambda (file)
+ (let ((target (string-append idle
+ "/bin/"
+ (basename
+ file))))
+ (install-file file
+ (dirname target))
+ (delete-file file)))
+ (find-files (string-append out "/bin")
+ "^idle"))
+ (match (find-files out "^idlelib$"
+ #:directories? #t)
+ ((idlelib)
+ (let* ((len (string-length out))
+ (target (string-append idle "/"
+ (string-drop
+ idlelib len)
+ "/site-packages")))
+ (mkdir-p (dirname target))
+ (rename-file idlelib target))))))))
+ (add-after 'move-idle 'rebuild-bytecode
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; Disable hash randomization to ensure the generated .pycs
+ ;; are reproducible.
+ (setenv "PYTHONHASHSEED" "0")
+
+ (for-each (lambda (output)
+ ;; XXX: Delete existing pycs generated by the build
+ ;; system beforehand because the -f argument does
+ ;; not necessarily overwrite all files, leading to
+ ;; indeterministic results.
+ (for-each (lambda (pyc)
+ (delete-file pyc))
+ (find-files output "\\.pyc$"))
+
+ (apply invoke
+ #$(if (%current-target-system)
+ "python3"
+ #~(string-append #$output "/bin/python3"))
+ `("-m" "compileall"
+ "-o" "0"
+ "-o" "1"
+ "-o" "2"
+ "-f" ;force rebuild
+ "--invalidation-mode=unchecked-hash"
+ ;; Don't build lib2to3, because it's Python
+ ;; 2 code.
+ "-x" "lib2to3/.*"
+ ,output)))
+ (map cdr outputs))))
+ (add-before 'check 'set-TZDIR
+ (lambda* (#:key inputs native-inputs #:allow-other-keys)
+ ;; test_email requires the Olson time zone database.
+ (setenv "TZDIR"
+ (string-append (assoc-ref (or native-inputs
+ inputs) "tzdata")
+ "/share/zoneinfo"))))
+ (add-after 'install 'add-libxcrypt-reference-pkgconfig
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((libxcrypt
+ (false-if-exception
+ (dirname
+ (search-input-file inputs "lib/libcrypt.so.1")))))
+ (when libxcrypt
+ (substitute*
+ (find-files (string-append #$output "/lib/pkgconfig")
+ ".*\\.pc")
+ (("Libs:")
+ (string-append "Libs: " "-L" libxcrypt " -lcrypt")))))))
+ (add-after 'install 'install-sitecustomize.py
+ #$(customize-site version)))))
+ (inputs (list bzip2
+ expat
+ gdbm
+ libffi ;for ctypes
+ libxcrypt ;crypto module slated for removal in 3.13
+ sqlite ;for sqlite extension
+ openssl
+ readline
+ zlib
+ tcl
+ tk)) ;for tkinter
+ (native-inputs `(("tzdata" ,tzdata-for-tests)
+ ("unzip" ,unzip)
+ ("zip" ,(@ (gnu packages compression) zip))
+ ("pkg-config" ,pkg-config)
+ ("sitecustomize.py" ,(local-file (search-auxiliary-file
+ "python/sitecustomize.py")))
+ ;; When cross-compiling, a native version of Python itself is needed.
+ ,@(if (%current-target-system)
+ `(("python" ,this-package)
+ ("which" ,which))
+ '())))
+ (native-search-paths
+ (list (guix-pythonpath-search-path version)
+ ;; Used to locate tzdata by the zoneinfo module introduced in
+ ;; Python 3.9.
+ (search-path-specification
+ (variable "PYTHONTZPATH")
+ (files (list "share/zoneinfo")))))))
+
(define-public python-3.12
(package
(name "python-next")
@@ 1051,7 1450,7 @@ data types.")
(define-public python-next python-3.12)
;; Current 3.x version.
-(define-public python-3 python-3.10)
+(define-public python-3 python-3.11)
;; Current major version.
(define-public python python-3)
@@ 1088,10 1487,10 @@ data types.")
(build-system gnu-build-system)
(arguments
(substitute-keyword-arguments (package-arguments python)
- ((#:configure-flags flags '())
- `(cons "--with-pydebug" ,flags))))
- (synopsis
- "Python with the debug hooks enabled")
+ ((#:configure-flags configure-flags)
+ #~(append #$configure-flags
+ (list "--with-pydebug")))))
+ (synopsis "Python with the debug hooks enabled")
(description
"This variant of Python provides an interpreter built with
@code{--with-pydebug} to help develop and debug extensions. See
M gnu/packages/qt.scm => gnu/packages/qt.scm +11 -9
@@ 4033,7 4033,7 @@ Python.")
(define-public python-sip
(package
(name "python-sip")
- (version "6.8.6")
+ (version "6.10.0")
(source
(origin
(method url-fetch)
@@ 4043,18 4043,20 @@ Python.")
"/sip-" version ".tar.gz")))
(sha256
(base32
- "0ykxq0607f2sdwbl5cxbp0y8pl14bsgzc9nhifpxbibfivj5kjbz"))
+ "176jylhzs2ci2r9f3l75k9dpwhp1dn0qv2cy9phdp62cgmlia1gs"))
+ (modules '((guix build utils)))
+ (snippet
+ ;; Relax setuptools dependency
+ #~(substitute* "pyproject.toml"
+ (("\"setuptools>=.*\",") "\"setuptools\",")))
(patches (search-patches "python-sip-include-dirs.patch"))))
(build-system pyproject-build-system)
(arguments
(list #:tests? #f)) ; No test system found.
(native-inputs
- (list python-wrapper python-setuptools python-setuptools-scm-next))
+ (list python-setuptools python-setuptools-scm-next python-wheel))
(propagated-inputs
- (list python-tomli
- python-packaging
- python-setuptools
- python-wheel))
+ (list python-packaging python-setuptools))
(home-page "https://www.riverbankcomputing.com/software/sip/intro")
(synopsis "Python binding creator for C and C++ libraries")
(description
@@ 5137,7 5139,7 @@ color-related widgets.")
(define-public python-shiboken-2
(package
(name "python-shiboken-2")
- (version "5.15.10")
+ (version "5.15.16")
(source (origin
(method url-fetch)
(uri (string-append "mirror://qt/QtForPython/pyside2/PySide2-"
@@ 5145,7 5147,7 @@ color-related widgets.")
version ".tar.xz"))
(sha256
(base32
- "0fnkx8ax2lkin3bpqbz4zbdrdin2ixb4d6s3c0xghh9sc79r3xia"))))
+ "0q3ky0fai3wr8kr1q82vdg5byhbn5sfdymmb554afpi72zyxcgkd"))))
(build-system cmake-build-system)
(inputs
(list clang-toolchain
M gnu/packages/radio.scm => gnu/packages/radio.scm +0 -1
@@ 3272,7 3272,6 @@ satellites.")
(native-inputs
(list python-mock
python-mox3
- python-pep8
python-pytest
python-pytest-mock
python-pyyaml
M gnu/packages/sphinx.scm => gnu/packages/sphinx.scm +22 -32
@@ 81,10 81,15 @@
(arguments
(list
#:test-flags
- ;; These require Internet access.
- #~(list "-k" (string-append "not test_latex_images"
- " and not test_build_latex_doc[lualatex-manual]"
- " and not est_build_latex_doc[lualatex-howto]"))
+ #~(list "-k" (string-join
+ (list
+ ;; These require Internet access.
+ "not test_latex_images"
+ "test_build_latex_doc[lualatex-manual]"
+ "est_build_latex_doc[lualatex-howto]"
+ ;; AssertionError: assert...list of weak references to the object...
+ "test_autodoc_default_options")
+ " and not "))
#:phases
#~(modify-phases %standard-phases
(add-before 'check 'pre-check
@@ 192,7 197,10 @@ sources.")
" and not test_viewcode"
;; These fail with pygments 2.10+. They are harmless.
" and not test_additional_targets_should_not_be_translated"
- " and not test_additional_targets_should_be_translated"))
+ " and not test_additional_targets_should_be_translated"
+ ;; As in Sphinx@6:
+ ;; AssertionError: assert...list of weak references to the object...
+ " and not test_autodoc_default_options"))
#:phases
'(modify-phases %standard-phases
(add-before 'check 'pre-check
@@ 262,25 270,6 @@ sources.")
(texlive-updmap.cfg
(list texlive-cm-super texlive-tex-gyre))))))
-;; Some packages do not support Sphinx 5 yet. Remove when unused.
-(define-public python-sphinx-4
- (package
- (inherit python-sphinx-5)
- (version "4.5.0")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "Sphinx" version))
- (sha256
- (base32
- "1rp28jryxwy24y8vpacclqihbizyi6b1s6id86pibvm46ybcmy3v"))))
- (propagated-inputs
- (modify-inputs (package-propagated-inputs python-sphinx)
- (replace "python-docutils" python-docutils-0.15)))
- (native-inputs
- (modify-inputs (package-native-inputs python-sphinx)
- (delete python-flit-core)
- (append python-setuptools python-wheel)))))
-
(define-public python-sphinxcontrib-apidoc
(package
(name "python-sphinxcontrib-apidoc")
@@ 603,7 592,15 @@ supported with @code{sphinx-issues}.")
(sha256
(base32 "1ivqz6yv96a2jp59kylg1gbkrmzq6zwilppz3ij0zrkjn25zb97k"))))
(build-system pyproject-build-system)
- (propagated-inputs (list python-docutils-0.15 python-sphinx-4))
+ (arguments
+ (list #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'loosen-requirements
+ (lambda _
+ (substitute* "setup.py"
+ (("sphinx>=2,<5")
+ "sphinx>=2,<6")))))))
+ (propagated-inputs (list python-docutils-0.16 python-sphinx-5))
(native-inputs
(list python-pytest
python-pytest-regressions
@@ 1229,13 1226,6 @@ enabled web server.")
documenting acceptable argument types and return value types of functions.")
(license license:expat)))
-(define-public python-sphinx-autodoc-typehints-5
- (package/inherit python-sphinx-autodoc-typehints
- (propagated-inputs
- (modify-inputs
- (package-propagated-inputs python-sphinx-autodoc-typehints)
- (replace "python-sphinx" python-sphinx-5)))))
-
(define-public python-sphinx-pytest
(package
(name "python-sphinx-pytest")
M gnu/packages/statistics.scm => gnu/packages/statistics.scm +24 -31
@@ 916,7 916,7 @@ comparison and diagnostics.")
(define-public python-pymc
(package
(name "python-pymc")
- (version "5.11.0")
+ (version "5.21.0")
(source (origin
(method git-fetch) ; no tests in PyPI
(uri (git-reference
@@ 925,28 925,17 @@ comparison and diagnostics.")
(file-name (git-file-name name version))
(sha256
(base32
- "0x94qzq3z02fxlliz1xfdpb2pbn7nhp4skzcxz6qdavbj9xqcxys"))))
+ "0azkbl0mpanza35ibdqdm21bf45n3xi26wy01lnxzxqblcjcny9l"))))
(build-system pyproject-build-system)
(arguments
(list #:tests? #f ; tests are too computationally intensive
#:phases #~(modify-phases %standard-phases
(add-after 'unpack 'versioneer
(lambda _
- (with-output-to-file "setup.cfg"
- (lambda ()
- (display "\
-[versioneer]
-VCS = git
-style = pep440
-versionfile_source = pymc/_version.py
-versionfile_build = pymc/_version.py
-tag_prefix =
-parentdir_prefix = pymc-
-")))
- (invoke "versioneer" "install")
- (substitute* "setup.py"
- (("versioneer.get_version\\(\\)")
- (string-append "\"" #$version "\"")))))
+ (invoke "versioneer" "install")
+ (substitute* "setup.py"
+ (("version=versioneer.get_version\\(),")
+ (format #f "version=~s," #$version)))))
;; To create the compiledir for tests.
(add-before 'check 'write-permissions
(lambda* (#:key tests? #:allow-other-keys)
@@ 1009,24 998,18 @@ and a lot more.")
(define-public python-patsy
(package
(name "python-patsy")
- (version "0.5.2")
+ (version "1.0.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "patsy" version))
(sha256
(base32
- "17dn72519gvwifw3i8mzwlslxmxkl8ihzfrxg1iblsk70iwdwlsh"))))
- (build-system python-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests? (invoke "pytest" "-vv")))))))
+ "1i60b6s8zj0w2ks63ip4mr8z14p6pixp76rm9q2qr0gc3qwsk1p7"))))
+ (build-system pyproject-build-system)
(propagated-inputs
- (list python-numpy python-scipy python-six))
+ (list python-numpy python-scipy))
(native-inputs
- (list python-pytest))
+ (list python-pytest python-pytest-cov python-setuptools python-wheel))
(home-page "https://github.com/pydata/patsy")
(synopsis "Describe statistical models and build design matrices")
(description
@@ 3333,7 3316,7 @@ statistical summary in arrays and enumerables.")
(define-public python-pgmpy
(package
(name "python-pgmpy")
- (version "0.1.24")
+ (version "1.0.0")
(source
(origin
(method git-fetch) ;pypi package does not include test data
@@ 3343,8 3326,14 @@ statistical summary in arrays and enumerables.")
(file-name (git-file-name name version))
(sha256
(base32
- "0fvzh6v0yhgdryczamvzhfy2ymywkh0ssx4rl47xnfvi43hnij90"))))
+ "1hg6wrg3jcac71zn4gknni1wrn38wa86ka3sgp2bndz59mx6sr2s"))))
(build-system pyproject-build-system)
+ (arguments
+ (list #:test-flags
+ #~(list "-k" (string-append
+ "not test_pillai"
+ " and not test_estimate_with_cache_no_llm_calls"
+ " and not test_estimate_with_orientations"))))
(propagated-inputs (list python-daft
python-joblib
python-networkx
@@ 3358,7 3347,11 @@ statistical summary in arrays and enumerables.")
python-statsmodels
python-tqdm))
(native-inputs (list python-mock
- python-pytest))
+ python-pyro-ppl
+ python-pytest
+ python-setuptools
+ python-wheel
+ python-xgboost))
(home-page "https://github.com/pgmpy/pgmpy")
(synopsis "Probabilistic Graphical Models library")
(description "This package provides a library for Probabilistic
M gnu/packages/tor.scm => gnu/packages/tor.scm +38 -17
@@ 44,6 44,7 @@
#:use-module (gnu packages)
#:use-module (gnu packages base)
#:use-module (gnu packages libevent)
+ #:use-module (gnu packages libffi)
#:use-module (gnu packages linux)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
@@ 261,7 262,7 @@ networks.")
(define-public onionshare-cli
(package
(name "onionshare-cli")
- (version "2.6")
+ (version "2.6.3")
(source
(origin
(method git-fetch)
@@ 270,32 271,53 @@ networks.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "1bhrp019a0923h7dnfxhgvgvdp81blvnsbnvzy34hp827abxf3ic"))
- (patches (search-patches "onionshare-cli-async-mode.patch"))))
- (build-system python-build-system)
+ (base32 "16yr25llnbgl2iwk458ca0rhrxsmpfx72q4gdg4a52i6g546p3hd"))))
+ (build-system pyproject-build-system)
(native-inputs
- (list python-pytest))
+ (list python-cython-3
+ python-poetry-core
+ python-pytest
+ python-wheel))
(inputs
- ;; TODO: obfs4proxy
(list python-click
+ python-cffi
python-colorama
python-eventlet
python-flask
- python-flask-httpauth
+ python-flask-compress
python-flask-socketio
- python-pynacl
+ python-gevent
+ python-gevent-websocket
+ python-packaging
python-psutil
- python-pycryptodome
+ python-pynacl
python-pysocks
+ python-qrcode
python-requests
+ python-setuptools
python-stem
python-unidecode
- python-urllib3
+ python-urllib3-next
+ python-waitress
+ python-werkzeug
tor))
(arguments
(list
#:phases
#~(modify-phases %standard-phases
+ (add-after 'unpack 'relax-requirements
+ (lambda _
+ ;; All tests passed, and the CLI is working in runtime, relax
+ ;; Poetry way too strict requirements.
+ (substitute* "cli/pyproject.toml"
+ (("2.3.2") "^3.0.0") ; flask = "2.3.2"
+ (("5.3.4") "5.5.1") ; flask-socketio = "5.3.4"
+ (("23.9.1") "24.11.1") ; gevent = "^23.9.1"
+ (("7.4.2") "8.0.0") ; qrcode = "^7.4.2"
+ (("70.0.0") "67.6.1") ; setuptools = ">=70.0.0"
+ (("1.8.1") "^1.8.1") ; stem = "1.8.1"
+ (("3.0.6") "^3.0.6") ; werkzeug = "3.0.6"
+ (("0.41.2") "0.40.0")))) ; wheel = "^0.41.2"
(add-after 'unpack 'bake-tor
(lambda* (#:key inputs #:allow-other-keys)
(substitute* (list "cli/onionshare_cli/common.py"
@@ 307,16 329,15 @@ networks.")
(search-input-directory inputs "share/tor")))))
(add-before 'build 'change-directory
(lambda _ (chdir "cli")))
- (replace 'check
+ (add-before 'check 'pre-check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(setenv "HOME" "/tmp")
- ;; Greendns is not needed for testing, and if eventlet tries to
- ;; load it, an OSError is thrown when getprotobyname is called.
- ;; Thankfully there is an environment variable to disable the
- ;; greendns import, so use it:
- (setenv "EVENTLET_NO_GREENDNS" "yes")
- (invoke "pytest" "-v" "./tests")))))))
+ ;; Greendns is not needed for testing, and if eventlet tries
+ ;; to load it, an OSError is thrown when getprotobyname is
+ ;; called. Thankfully there is an environment variable to
+ ;; disable the greendns import, so use it:
+ (setenv "EVENTLET_NO_GREENDNS" "yes")))))))
(home-page "https://onionshare.org/")
(synopsis "Securely and anonymously share files")
(description "OnionShare lets you securely and anonymously share files,
M gnu/packages/tryton.scm => gnu/packages/tryton.scm +56 -38
@@ 4,6 4,7 @@
;;; Copyright © 2021 Maxime Devos <maximedevos@telenet.be>
;;; Copyright © 2021 Hartmut Goebel <h.goebel@crazy-compilers.com>
;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2025 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ 23,24 24,29 @@
(define-module (gnu packages tryton)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (gnu packages)
+ #:use-module (gnu packages base)
#:use-module (gnu packages bash)
#:use-module (gnu packages check)
#:use-module (gnu packages databases)
#:use-module (gnu packages finance)
#:use-module (gnu packages glib)
#:use-module (gnu packages gnome)
+ #:use-module (gnu packages graphviz)
#:use-module (gnu packages gtk)
#:use-module (gnu packages pdf)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-build)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages time)
#:use-module (gnu packages xml)
+ #:use-module (guix gexp)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix utils)
- #:use-module (guix build-system python))
+ #:use-module (guix build-system python)
+ #:use-module (guix build-system pyproject))
(define (guix-trytonpath-search-path version)
"Generate a GUIX_TRYTOND_MODULES_PATH search path specification, using
@@ 58,41 64,49 @@ installed in the same environments. Collecting only paths actually containing
(define-public trytond
(package
(name "trytond")
- (version "6.2.10")
+ (version "7.4.4")
(source
(origin
(method url-fetch)
(uri (pypi-uri "trytond" version))
(sha256
- (base32 "0s53ig8snbs9936h99pwa0lwhcrd3j3cbpwlmf90mf1chrif7zca"))
- (patches (search-patches "trytond-add-egg-modules-to-path.patch"
- "trytond-add-guix_trytond_path.patch"))))
- (build-system python-build-system)
+ (base32 "1bwa631qz07k6s5fbki3ph6sx0ch9yss2q4sa1jb67z6angiwv5f"))
+ (patches (search-patches "trytond-add-guix_trytond_path.patch"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ '(list "-k"
+ (string-append
+ ;; "modules" is [None], but should be a list of modules.
+ "not ModuleTestCase"
+ ;; fixture 'self' not found
+ " and not test_method"))
+ #:phases
+ '(modify-phases %standard-phases
+ (add-before 'check 'preparations
+ (lambda _
+ (setenv "DB_NAME" ":memory:")
+ (setenv "HOME" "/tmp"))))))
(propagated-inputs
(list python-dateutil
python-defusedxml
python-genshi
python-lxml
- python-magic
python-passlib
python-polib
- python-psycopg2
python-relatorio
python-sql
- python-werkzeug-1.0 ;setup.py requires werkzeug<2
- python-wrapt))
+ python-werkzeug))
(native-inputs
- (list python-mock python-pillow))
+ (list python-pillow
+ python-pydot
+ python-pytest
+ python-setuptools
+ python-wheel
+ tzdata-for-tests))
(native-search-paths
(list (guix-trytonpath-search-path (package-version python))))
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-before 'check 'preparations
- (lambda _
- (setenv "DB_NAME" ":memory:")
- (setenv "HOME" "/tmp")
- #t)))))
(home-page "https://www.tryton.org/")
(synopsis "Tryton Server")
(description "Tryton is a three-tier high-level general purpose
@@ 104,30 118,33 @@ and security.")
(define-public tryton
(package
(name "tryton")
- (version "6.2.7")
+ (version "7.4.4")
(source
(origin
(method url-fetch)
(uri (pypi-uri "tryton" version))
(sha256
- (base32 "1bvwkrj2mmnddaif60g2np2jpx8lq5ka32xlhd4rlnshnbryrm5q"))))
- (build-system python-build-system)
+ (base32 "0q0qa4pjbpc0h8r9hlnm5dh315w5i7mzqpdrlw1c8qvigpl1rf7g"))))
+ (build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-before 'check 'change-home
- (lambda _
- ;; Change from /homeless-shelter to /tmp for write permission.
- (setenv "HOME" "/tmp")))
- (add-after 'install 'wrap-gi-python
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out"))
- (gi-typelib-path (getenv "GI_TYPELIB_PATH")))
- (wrap-program (string-append out "/bin/tryton")
- `("GI_TYPELIB_PATH" ":" prefix (,gi-typelib-path)))))))))
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'check 'change-home
+ (lambda _
+ ;; Change from /homeless-shelter to /tmp for write permission.
+ (setenv "HOME" "/tmp")))
+ (add-after 'install 'wrap-gi-python
+ (lambda _
+ (let ((gi-typelib-path (getenv "GI_TYPELIB_PATH")))
+ (wrap-program (string-append #$output "/bin/tryton")
+ `("GI_TYPELIB_PATH" ":" prefix (,gi-typelib-path)))))))))
(native-inputs
(list `(,glib "bin")
- gobject-introspection))
+ gobject-introspection
+ python-pytest
+ python-setuptools
+ python-wheel))
(inputs (list bash-minimal)) ;for wrap-program
(propagated-inputs
(list (librsvg-for-system)
@@ 145,19 162,20 @@ and security.")
(define-public python-proteus
(package
(name "python-proteus")
- (version "6.2.3")
+ (version "7.4.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "proteus" version))
(sha256
- (base32 "0xx8kqzgs66rgz6bk5favnjs0akz6znz81vmjwpwp2wpq7094fsr"))))
- (build-system python-build-system)
+ (base32 "1q3d0hkvmfsmxbx2qqp8zpslyy11mzwh0q2dkrh958yfyrzi1550"))))
+ (build-system pyproject-build-system)
;; Tests require python-trytond-party which requires python-proteus.
(arguments
`(#:tests? #f))
(propagated-inputs
(list python-dateutil python-defusedxml))
+ (native-inputs (list python-setuptools python-wheel))
(home-page "http://www.tryton.org/")
(synopsis "Library to access a Tryton server as a client")
(description
M gnu/packages/version-control.scm => gnu/packages/version-control.scm +46 -49
@@ 2702,7 2702,7 @@ execution of any hook written in any language before every commit.")
(native-search-paths
(list (search-path-specification
(variable "HGEXTENSIONPATH")
- (files '("lib/python3.10/site-packages/hgext3rd")))))
+ (files '("lib/python3.11/site-packages/hgext3rd")))))
(home-page "https://www.mercurial-scm.org/")
(synopsis "Decentralized version control system")
(description
@@ 4312,53 4312,50 @@ defects faster.")
(license license:expat)))
(define-public gita
- (let ((commit "e41b504dca90a25e9be27f296da7ce22e5782893")
- (revision "1"))
- (package
- (name "gita")
- (version (git-version "0.12.9" revision commit))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/nosarthur/gita")
- (commit commit)))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "1k03zgcbhl91cgyh4k7ywyjp00y63q4bqbimncqh5b3lni8l8j5l"))))
- (build-system python-build-system)
- (native-inputs
- (list git ;for tests
- python-pytest))
- (propagated-inputs
- (list python-pyyaml))
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (substitute* "tests/test_main.py"
- (("'gita\\\\n'") "'source\\n'")
- (("'gita'") "'source'"))
- (invoke (search-input-file inputs "/bin/git")
- "init")
- (add-installed-pythonpath inputs outputs)
- (invoke (search-input-file inputs "/bin/pytest")
- "-vv" "tests")))
- (add-after 'install 'install-shell-completions
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (bash-completion (string-append out "/etc/bash_completion.d"))
- (zsh-completion (string-append out "/etc/zsh/site-functions")))
- (mkdir-p bash-completion)
- (copy-file ".gita-completion.bash"
- (string-append bash-completion "/gita"))
- (mkdir-p zsh-completion)
- (copy-file ".gita-completion.zsh"
- (string-append zsh-completion "/_gita"))))))))
- (home-page "https://github.com/nosarthur/gita")
- (synopsis "Command-line tool to manage multiple Git repos")
- (description "This package provides a command-line tool to manage
+ (package
+ (name "gita")
+ (version "0.16.7.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/nosarthur/gita")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "118dzmjgml0c32yllr2178ash2hvgn201i463bv4y0qbywajm9ax"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags #~(list "--ignore" "tests/test_main.py")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'check 'pre-check
+ (lambda _
+ (invoke (string-append
+ #$(this-package-native-input "git-minimal") "/bin/git")
+ "init")))
+ (add-after 'install 'install-shell-completions
+ (lambda _
+ (let* ((out #$output)
+ (bash-completion (string-append out "/etc/bash_completion.d"))
+ (zsh-completion (string-append out "/etc/zsh/site-functions")))
+ (mkdir-p bash-completion)
+ (copy-file "auto-completion/bash/.gita-completion.bash"
+ (string-append bash-completion "/gita"))
+ (mkdir-p zsh-completion)
+ (copy-file "auto-completion/zsh/.gita-completion.zsh"
+ (string-append zsh-completion "/_gita"))))))))
+ (native-inputs
+ (list git-minimal/pinned ;for tests
+ python-pytest
+ python-setuptools
+ python-wheel))
+ (propagated-inputs
+ (list python-argcomplete))
+ (home-page "https://github.com/nosarthur/gita")
+ (synopsis "Command-line tool to manage multiple Git repos")
+ (description "This package provides a command-line tool to manage
multiple Git repos.
This tool does two things:
@@ 4369,7 4366,7 @@ commit message side by side
@end itemize
If several repos are related, it helps to see their status together.")
- (license license:expat))))
+ (license license:expat)))
(define-public ghq
(package
M gnu/packages/video.scm => gnu/packages/video.scm +11 -18
@@ 3221,7 3221,7 @@ YouTube.com and many more sites.")
python-mutagen
python-pycryptodomex
python-requests-next ; TODO Remove this special package
- python-urllib3-next ; TODO Remove this one too
+ python-urllib3-1.26 ; TODO Remove this one too
python-websockets))
(native-inputs
(append
@@ 3799,34 3799,28 @@ and custom quantization matrices.")
(define-public streamlink
(package
(name "streamlink")
- (version "6.3.1")
+ (version "7.1.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "streamlink" version))
(sha256
(base32
- "0i2qym2plm4gpcq50vl67j69m8a4zz9mb8gi2xryx28pbnpdzh4k"))
- (snippet
- #~(begin (use-modules (guix build utils))
- (substitute* "pyproject.toml"
- (("trio >=0\\.22") "trio >=0.21"))))))
- (build-system python-build-system)
+ "1mvg8lw3rkng6ciryziqh9r4ffj0ls7k0sv3byk3439s5d2qxh31"))))
+ (build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "python" "-m" "pytest")))))))
+ (list
+ #:test-flags #~(list "-k" "not test_no_cache")))
(native-inputs
(list python-freezegun
- python-requests-mock
python-pytest
- python-pytest-asyncio
- python-pytest-trio))
+ python-pytest-trio
+ python-requests-mock
+ python-setuptools
+ python-wheel))
(propagated-inputs
(list python-certifi
+ python-exceptiongroup
python-isodate
python-lxml
python-pycountry
@@ 3835,7 3829,6 @@ and custom quantization matrices.")
python-requests
python-trio
python-trio-websocket
- python-typing-extensions
python-urllib3
python-websocket-client))
(home-page "https://github.com/streamlink/streamlink")
M gnu/packages/web.scm => gnu/packages/web.scm +6 -1
@@ 7217,6 7217,12 @@ efficient where possible.")
(list
#:phases
'(modify-phases %standard-phases
+ (add-after 'unpack 'remove-rednose-dependency
+ (lambda _
+ (substitute* "setup.py"
+ (("'rednose'") ""))
+ (substitute* '("requirements.txt" "setup.cfg")
+ (("rednose.*") ""))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
@@ 7230,7 7236,6 @@ efficient where possible.")
python-httplib2
python-nose
python-pyparsing
- python-rednose
python-requests
python-sure
python-tornado))
M gnu/packages/wxwidgets.scm => gnu/packages/wxwidgets.scm +40 -11
@@ 13,6 13,7 @@
;;; Copyright © 2023 Malte Frank Gerdes <malte.f.gerdes@gmail.com>
;;; Copyright © 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2025 Ekaitz Zarraga <ekaitz@elenq.tech>
+;;; Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
;;;
;;; This file is part of GNU Guix.
;;;
@@ 37,6 38,7 @@
#:use-module ((guix licenses) #:prefix l:)
#:use-module (guix build-system glib-or-gtk)
#:use-module (guix build-system perl)
+ #:use-module (guix build-system pyproject)
#:use-module (guix build-system python)
#:use-module (guix utils)
#:use-module (gnu packages)
@@ 57,7 59,9 @@
#:use-module (gnu packages photo)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-build)
#:use-module (gnu packages python-xyz)
+ #:use-module (gnu packages qt)
#:use-module (gnu packages sdl)
#:use-module (gnu packages video)
#:use-module (gnu packages web)
@@ 318,26 322,38 @@ and many other languages.")
(define-public python-wxpython
(package
(name "python-wxpython")
- (version "4.2.0")
+ (version "4.2.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "wxPython" version))
(sha256
- (base32
- "1iw6xp76b3fmdqwbqmsx9i1razzpfki5z1hq6l8mszlxa32fng36"))
+ (base32 "1fp2717a96hd5pdai6hlzc4pngdazxas55apjv2w5zb71xjv1g2x"))
(modules '((guix build utils)))
- (snippet
- '(begin
- ;; Remove bundled wxwidgets
- (delete-file-recursively "ext/wxWidgets")))
- (patches (search-patches "python-wxwidgets-type-errors.patch"))))
- (build-system python-build-system)
+ (snippet #~(begin
+ ;; Remove bundled wxWidgets
+ (delete-file-recursively "ext/wxWidgets")))))
+ (build-system pyproject-build-system)
(outputs '("out" "debug"))
(arguments
(list
+ #:modules '((guix build pyproject-build-system)
+ (guix build utils)
+ (ice-9 ftw)
+ (ice-9 match)
+ (srfi srfi-26))
#:phases
#~(modify-phases %standard-phases
+ (add-after 'unpack 'patch-avoid-circular-import
+ (lambda _
+ (substitute* "wx/__init__.py"
+ (("^import wx\\.__version__.*$") "\
+try:
+ import wx.__version__
+except ImportError:
+ pass\n")
+ (("^__version__ = .*")
+ (format #f "__version__ = ~s~%" #$version)))))
(add-before 'build 'configure
(lambda* (#:key inputs #:allow-other-keys)
;; Configure the build options provided to the 'build.py' build
@@ 357,11 373,24 @@ and many other languages.")
(string-append "#" all)))
;; The build script tries to write to demo/version.py. So, we set
;; correct write permissions.
- (chmod "demo/version.py" #o644))))))
+ (chmod "demo/version.py" #o644)))
+ (add-before 'check 'add-missing-.so
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((site (site-packages inputs outputs)))
+ (with-directory-excursion (string-append site "/wx")
+ (for-each
+ (match-lambda
+ ("siplib"
+ (rename-file "siplib" "siplib.so"))
+ ((? (cut string-prefix? "_" <>) file)
+ (unless (string-prefix? "__" file)
+ (rename-file file (string-append file ".so"))))
+ (_ #t))
+ (scandir ".")))))))))
(inputs
(list gtk+ wxwidgets))
(native-inputs
- (list pkg-config python-waf))
+ (list pkg-config python-setuptools python-waf python-wheel))
(propagated-inputs
(list python-attrdict3 python-numpy python-pillow python-six))
(home-page "https://wxpython.org/")