@@ 1757,6 1757,51 @@ implementation of the ASDF Standard.")
Astropy objects.")
(license license:bsd-3)))
+(define-public python-asdf-compression
+ ;; TODO: No release, change to tag when it's ready.
+ (let ((commit "7cfd07c6f789d4919e5730e0cda150fb20da4139")
+ (revision "1"))
+ (package
+ (name "python-asdf-compression")
+ (version (git-version "0.0.1" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/asdf-format/asdf-compression")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "198y3mnl9kvhva479k6g9zbynjg8apsrwy7lq26g5q6v55s16hgc"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'build 'set-version
+ (lambda _
+ (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" "0.0.1"))))))
+ (native-inputs
+ (list python-numpy
+ python-pytest
+ python-setuptools
+ python-setuptools-scm
+ python-wheel))
+ (propagated-inputs
+ (list python-asdf
+ python-blosc
+ python-lz4
+ python-zstandard))
+ (home-page "https://github.com/asdf-format/asdf-compression")
+ (synopsis "ASDF extension to support various compression algorithms")
+ (description
+ "This package includes a plugin for the Python library ASDF to add
+support for reading and writing various compression algorithms including:
+@url{https://www.blosc.org/python-blosc/reference.html,Blosc},
+@url{https://python-lz4.readthedocs.io/en/stable/lz4.frame.html,LZ4 Frame},
+@url{http://facebook.github.io/zstd/,Zstandard}.")
+ (license license:bsd-3))))
+
(define-public python-asdf-zarr
(package
(name "python-asdf-zarr")
@@ 2042,6 2087,140 @@ simulated Astronomical data in Python.")
mining in astronomy.")
(license license:bsd-2)))
+;; XXX: Upgrading to the latest version requires Python3.11+ and fresh
+;; versions of numpy, PyYAML, packaging, Pandas and matplotlib, see
+;; <https://github.com/astropy/astropy/blob/v7.0.0/CHANGES.rst
+;; #other-changes-and-additions>.
+(define-public python-astropy
+ (package
+ (name "python-astropy")
+ (version "6.1.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "astropy" version))
+ (sha256
+ (base32 "1vspagb4vbmkl6fm3mr78577dgdq992ggwkd5qawpdh6cccaq1d4"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Remove Python bundles.
+ (with-directory-excursion "astropy/extern"
+ (for-each delete-file-recursively '("ply" "configobj")))
+ ;; Remove cextern bundles. Check bundled versions against available
+ ;; in Guix in the future update of astropy.
+ ;; Linking against an external cfitsio version has been removed,
+ ;; see https://github.com/astropy/astropy/pull/14311
+ (with-directory-excursion "cextern"
+ (for-each delete-file-recursively '("expat" "wcslib")))))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ #~(list "--pyargs" "astropy"
+ "--numprocesses" (number->string (parallel-job-count))
+ "-k" (string-join
+ ;; Skip tests that need remote data.
+ (list "not remote_data"
+ ;; ValueError: The truth value of an array with more than
+ ;; one element is ambiguous. Use a.any() or a.all()
+ "test_table_comp[t16-t26]"
+ ;; UnboundLocalError: local variable 'ihd'
+ ;; referenced before assignment
+ "test_delay_doc_updates")
+ " and not "))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'preparations
+ (lambda _
+ ;; Use our own libraries in place of bundles.
+ (setenv "ASTROPY_USE_SYSTEM_ALL" "1")
+ ;; Relax xfail tests.
+ (substitute* "pyproject.toml"
+ (("xfail_strict = true") "xfail_strict = false"))
+ ;; Replace reference to external ply.
+ (substitute* "astropy/utils/parsing.py"
+ (("astropy.extern.ply") "ply"))
+ ;; Replace reference to external configobj.
+ (substitute* "astropy/config/configuration.py"
+ (("from astropy.extern.configobj ") ""))))
+ ;; This file is opened in both install and check phases.
+ (add-before 'install 'writable-compiler
+ (lambda _
+ (make-file-writable "astropy/_compiler.c")))
+ (replace 'check
+ (lambda* (#:key tests? test-flags #:allow-other-keys)
+ (when tests?
+ (setenv "HOME" "/tmp")
+ ;; Step out of the source directory to avoid interference; we
+ ;; want to run the installed code with extensions etc.
+ (with-directory-excursion #$output
+ (apply invoke "pytest" "-vv" test-flags))))))))
+ (native-inputs
+ (list nss-certs-for-test
+ pkg-config
+ python-cython-3
+ python-extension-helpers
+ python-ipython
+ python-objgraph
+ python-pandas
+ python-pytest
+ python-pytest-astropy
+ python-pytest-astropy-header
+ python-pytest-mpl
+ python-pytest-xdist
+ python-scikit-image
+ python-setuptools
+ python-setuptools-scm
+ python-sgp4
+ python-skyfield
+ python-threadpoolctl
+ python-timezonefinder
+ python-wheel))
+ (inputs
+ (list expat wcslib))
+ (propagated-inputs
+ (list python-astropy-iers-data
+ python-configobj
+ python-h5py
+ python-jplephem
+ python-matplotlib
+ python-numpy
+ python-packaging
+ python-ply
+ python-pyarrow
+ python-pyerfa
+ python-pyyaml
+ python-scipy))
+ (home-page "https://www.astropy.org/")
+ (synopsis "Core package for Astronomy in Python")
+ (description
+ "Astropy is a single core package for Astronomy in Python. It contains
+much of the core functionality and some common tools needed for performing
+astronomy and astrophysics.")
+ (license license:bsd-3)))
+
+;; A bare minimal package, mainly to use in tests and reduce closure
+;; size. Tests are left out in the main package to slim down native-inputs.
+(define-public python-astropy-minimal
+ (package/inherit python-astropy
+ (name "python-astropy-minimal")
+ (arguments
+ (substitute-keyword-arguments (package-arguments python-astropy)
+ ((#:tests? _ #t) #f)))
+ (native-inputs
+ (list nss-certs-for-test
+ pkg-config
+ python-cython-3
+ python-extension-helpers
+ python-setuptools
+ python-setuptools-scm
+ python-wheel))
+ (propagated-inputs
+ (modify-inputs (package-propagated-inputs python-astropy)
+ (delete python-matplotlib
+ python-scipy)))))
+
(define-public python-bayesicfitting
(package
(name "python-bayesicfitting")
@@ 2232,6 2411,83 @@ attempting to maintain ISTP compliance
@end itemize")
(license license:expat)))
+(define-public python-ci-watson
+ (package
+ (name "python-ci-watson")
+ (version "0.8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "ci_watson" version))
+ (sha256
+ (base32 "1rlhs8y0splmzr76z1s35zl68qm748nlayha8m81b0zhkhicxvhg"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'patch-pypojrect-toml
+ (lambda _
+ (substitute* "setup.cfg"
+ ;; ImportError: Error importing plugin " no:legacypath": No
+ ;; module named ' no:legacypath'
+ (("-p no:legacypath") "")))))))
+ (native-inputs
+ (list python-pytest-astropy-header
+ python-setuptools
+ python-wheel))
+ (propagated-inputs
+ (list python-crds
+ python-pytest
+ python-readchar
+ python-requests))
+ (home-page "https://github.com/spacetelescope/ci_watson")
+ (synopsis "Helper functions for STScI software")
+ (description
+ "This package contains a helper functionality to test ROMAN and JWST.")
+ (license license:bsd-3)))
+
+(define-public python-cmyt
+ (package
+ (name "python-cmyt")
+ (version "2.0.2")
+ (source
+ (origin
+ (method git-fetch) ; no tests in the PyPI tarball
+ (uri (git-reference
+ (url "https://github.com/yt-project/cmyt")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1d257xlgxc06x47k07xn5ml2kjqzc7dgjal4bl9x2w6b90xn0pm1"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'relax-requirements
+ (lambda _
+ (substitute* "pyproject.toml"
+ ;; numpy>=1.26
+ ((">=1.26") ">=1.23")))))))
+ (native-inputs
+ (list python-colorspacious
+ python-pytest
+ python-pytest-mpl
+ python-hatchling))
+ (propagated-inputs
+ (list python-matplotlib
+ python-numpy))
+ (home-page "https://yt-project.org/")
+ (synopsis "Matplotlib colormaps from the yt project")
+ (description
+ "This package provides a range of colormaps designed for scientific use
+with Matplotlib. It includes perceptually uniform sequential colormaps such
+as @code{abre}, @code{dusk}, @code{kepl}, and @code{octarine}, as well as
+monochromatic sequential colormaps like @code{blue}, @code{green}, and
+@code{red}, and others (@code{algae}, @code{pastel}, and @code{xray}).")
+ (license license:bsd-3)))
+
(define-public python-coolest
(package
(name "python-coolest")
@@ 3883,140 4139,6 @@ instruments.")
"This package provides an image processing toolbox for Solar Physics.")
(license license:bsd-2)))
-;; XXX: Upgrading to the latest version requires Python3.11+ and fresh
-;; versions of numpy, PyYAML, packaging, Pandas and matplotlib, see
-;; <https://github.com/astropy/astropy/blob/v7.0.0/CHANGES.rst
-;; #other-changes-and-additions>.
-(define-public python-astropy
- (package
- (name "python-astropy")
- (version "6.1.7")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "astropy" version))
- (sha256
- (base32 "1vspagb4vbmkl6fm3mr78577dgdq992ggwkd5qawpdh6cccaq1d4"))
- (modules '((guix build utils)))
- (snippet
- '(begin
- ;; Remove Python bundles.
- (with-directory-excursion "astropy/extern"
- (for-each delete-file-recursively '("ply" "configobj")))
- ;; Remove cextern bundles. Check bundled versions against available
- ;; in Guix in the future update of astropy.
- ;; Linking against an external cfitsio version has been removed,
- ;; see https://github.com/astropy/astropy/pull/14311
- (with-directory-excursion "cextern"
- (for-each delete-file-recursively '("expat" "wcslib")))))))
- (build-system pyproject-build-system)
- (arguments
- (list
- #:test-flags
- #~(list "--pyargs" "astropy"
- "--numprocesses" (number->string (parallel-job-count))
- "-k" (string-join
- ;; Skip tests that need remote data.
- (list "not remote_data"
- ;; ValueError: The truth value of an array with more than
- ;; one element is ambiguous. Use a.any() or a.all()
- "test_table_comp[t16-t26]"
- ;; UnboundLocalError: local variable 'ihd'
- ;; referenced before assignment
- "test_delay_doc_updates")
- " and not "))
- #:phases
- #~(modify-phases %standard-phases
- (add-after 'unpack 'preparations
- (lambda _
- ;; Use our own libraries in place of bundles.
- (setenv "ASTROPY_USE_SYSTEM_ALL" "1")
- ;; Relax xfail tests.
- (substitute* "pyproject.toml"
- (("xfail_strict = true") "xfail_strict = false"))
- ;; Replace reference to external ply.
- (substitute* "astropy/utils/parsing.py"
- (("astropy.extern.ply") "ply"))
- ;; Replace reference to external configobj.
- (substitute* "astropy/config/configuration.py"
- (("from astropy.extern.configobj ") ""))))
- ;; This file is opened in both install and check phases.
- (add-before 'install 'writable-compiler
- (lambda _
- (make-file-writable "astropy/_compiler.c")))
- (replace 'check
- (lambda* (#:key tests? test-flags #:allow-other-keys)
- (when tests?
- (setenv "HOME" "/tmp")
- ;; Step out of the source directory to avoid interference; we
- ;; want to run the installed code with extensions etc.
- (with-directory-excursion #$output
- (apply invoke "pytest" "-vv" test-flags))))))))
- (native-inputs
- (list nss-certs-for-test
- pkg-config
- python-cython-3
- python-extension-helpers
- python-ipython
- python-objgraph
- python-pandas
- python-pytest
- python-pytest-astropy
- python-pytest-astropy-header
- python-pytest-mpl
- python-pytest-xdist
- python-scikit-image
- python-setuptools
- python-setuptools-scm
- python-sgp4
- python-skyfield
- python-threadpoolctl
- python-timezonefinder
- python-wheel))
- (inputs
- (list expat wcslib))
- (propagated-inputs
- (list python-astropy-iers-data
- python-configobj
- python-h5py
- python-jplephem
- python-matplotlib
- python-numpy
- python-packaging
- python-ply
- python-pyarrow
- python-pyerfa
- python-pyyaml
- python-scipy))
- (home-page "https://www.astropy.org/")
- (synopsis "Core package for Astronomy in Python")
- (description
- "Astropy is a single core package for Astronomy in Python. It contains
-much of the core functionality and some common tools needed for performing
-astronomy and astrophysics.")
- (license license:bsd-3)))
-
-;; A bare minimal package, mainly to use in tests and reduce closure
-;; size. Tests are left out in the main package to slim down native-inputs.
-(define-public python-astropy-minimal
- (package/inherit python-astropy
- (name "python-astropy-minimal")
- (arguments
- (substitute-keyword-arguments (package-arguments python-astropy)
- ((#:tests? _ #t) #f)))
- (native-inputs
- (list nss-certs-for-test
- pkg-config
- python-cython-3
- python-extension-helpers
- python-setuptools
- python-setuptools-scm
- python-wheel))
- (propagated-inputs
- (modify-inputs (package-propagated-inputs python-astropy)
- (delete python-matplotlib
- python-scipy)))))
-
(define-public python-astropy-healpix
(package
(name "python-astropy-healpix")
@@ 4271,83 4393,6 @@ be as fast as possible so some of the readability has been sacrificed,
specifically in the C code.")
(license license:bsd-3)))
-(define-public python-ci-watson
- (package
- (name "python-ci-watson")
- (version "0.8.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "ci_watson" version))
- (sha256
- (base32 "1rlhs8y0splmzr76z1s35zl68qm748nlayha8m81b0zhkhicxvhg"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- #:phases
- #~(modify-phases %standard-phases
- (add-after 'unpack 'patch-pypojrect-toml
- (lambda _
- (substitute* "setup.cfg"
- ;; ImportError: Error importing plugin " no:legacypath": No
- ;; module named ' no:legacypath'
- (("-p no:legacypath") "")))))))
- (native-inputs
- (list python-pytest-astropy-header
- python-setuptools
- python-wheel))
- (propagated-inputs
- (list python-crds
- python-pytest
- python-readchar
- python-requests))
- (home-page "https://github.com/spacetelescope/ci_watson")
- (synopsis "Helper functions for STScI software")
- (description
- "This package contains a helper functionality to test ROMAN and JWST.")
- (license license:bsd-3)))
-
-(define-public python-cmyt
- (package
- (name "python-cmyt")
- (version "2.0.2")
- (source
- (origin
- (method git-fetch) ; no tests in the PyPI tarball
- (uri (git-reference
- (url "https://github.com/yt-project/cmyt")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "1d257xlgxc06x47k07xn5ml2kjqzc7dgjal4bl9x2w6b90xn0pm1"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- #:phases
- #~(modify-phases %standard-phases
- (add-after 'unpack 'relax-requirements
- (lambda _
- (substitute* "pyproject.toml"
- ;; numpy>=1.26
- ((">=1.26") ">=1.23")))))))
- (native-inputs
- (list python-colorspacious
- python-pytest
- python-pytest-mpl
- python-hatchling))
- (propagated-inputs
- (list python-matplotlib
- python-numpy))
- (home-page "https://yt-project.org/")
- (synopsis "Matplotlib colormaps from the yt project")
- (description
- "This package provides a range of colormaps designed for scientific use
-with Matplotlib. It includes perceptually uniform sequential colormaps such
-as @code{abre}, @code{dusk}, @code{kepl}, and @code{octarine}, as well as
-monochromatic sequential colormaps like @code{blue}, @code{green}, and
-@code{red}, and others (@code{algae}, @code{pastel}, and @code{xray}).")
- (license license:bsd-3)))
-
(define-public python-hvpy
(package
(name "python-hvpy")
@@ 6461,51 6506,6 @@ PYSYNPHOT, utilizing Astropy and covering the non-instrument specific portions
of the old packages.")
(license license:bsd-3)))
-(define-public python-asdf-compression
- ;; TODO: No release, change to tag when it's ready.
- (let ((commit "7cfd07c6f789d4919e5730e0cda150fb20da4139")
- (revision "1"))
- (package
- (name "python-asdf-compression")
- (version (git-version "0.0.1" revision commit))
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/asdf-format/asdf-compression")
- (commit commit)))
- (file-name (git-file-name name version))
- (sha256
- (base32 "198y3mnl9kvhva479k6g9zbynjg8apsrwy7lq26g5q6v55s16hgc"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- #:phases
- #~(modify-phases %standard-phases
- (add-before 'build 'set-version
- (lambda _
- (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" "0.0.1"))))))
- (native-inputs
- (list python-numpy
- python-pytest
- python-setuptools
- python-setuptools-scm
- python-wheel))
- (propagated-inputs
- (list python-asdf
- python-blosc
- python-lz4
- python-zstandard))
- (home-page "https://github.com/asdf-format/asdf-compression")
- (synopsis "ASDF extension to support various compression algorithms")
- (description
- "This package includes a plugin for the Python library ASDF to add
-support for reading and writing various compression algorithms including:
-@url{https://www.blosc.org/python-blosc/reference.html,Blosc},
-@url{https://python-lz4.readthedocs.io/en/stable/lz4.frame.html,LZ4 Frame},
-@url{http://facebook.github.io/zstd/,Zstandard}.")
- (license license:bsd-3))))
-
(define-public python-asdf-standard
(package
(name "python-asdf-standard")