@@ 297,6 297,36 @@ specification and test suite in Python.")
supersedes the RTED algorithm for computing the tree edit distance.")
(license license:expat))))
+(define-public python-ase
+ (package
+ (name "python-ase")
+ (version "3.25.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "ase" version))
+ (sha256
+ (base32 "1hk2r5042cs9shqv49w0jvf65wkyq74s6vc5drfz1275kz5ghk1p"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:test-flags
+ #~(list ;; DeprecationWarning.
+ "--deselect"
+ "ase/test/fio/test_espresso.py::test_pw_input_write_nested_flat"
+ ;; UserWarning.
+ "--deselect"
+ "ase/test/fio/test_espresso.py::TestConstraints::test_fix_scaled")))
+ (propagated-inputs (list python-matplotlib python-numpy python-scipy))
+ (native-inputs (list python-pytest python-pytest-xdist python-setuptools
+ python-wheel))
+ (inputs (list spglib))
+ (home-page "https://wiki.fysik.dtu.dk/ase/")
+ (synopsis "Atomic Simulation Environment")
+ (description "This package provides a set of tools and Python modules for
+setting up, manipulating, running, visualizing and analyzing atomistic
+simulations.")
+ (license license:lgpl2.1+)))
+
(define-public python-boost-histogram
(package
(name "python-boost-histogram")
@@ 560,6 590,29 @@ that is 20-25x faster than @code{numpy.histogram2d}.")
formulas for Python.")
(license license:expat)))
+(define-public python-geosketch
+ (package
+ (name "python-geosketch")
+ (version "1.2")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "geosketch" version))
+ (sha256
+ (base32
+ "0knch5h0p8xpm8bi3b5mxyaf1ywwimrsdmbnc1xr5icidcv9gzmv"))))
+ (build-system python-build-system)
+ (arguments '(#:tests? #false)) ;there are none
+ (propagated-inputs (list python-fbpca python-numpy python-scikit-learn))
+ (home-page "https://github.com/brianhie/geosketch")
+ (synopsis "Geometry-preserving random sampling")
+ (description "geosketch is a Python package that implements the geometric
+sketching algorithm described by Brian Hie, Hyunghoon Cho, Benjamin DeMeo,
+Bryan Bryson, and Bonnie Berger in \"Geometric sketching compactly summarizes
+the single-cell transcriptomic landscape\", Cell Systems (2019). This package
+provides an example implementation of the algorithm as well as scripts
+necessary for reproducing the experiments in the paper.")
+ (license license:expat)))
+
(define-public python-hepunits
(package
(name "python-hepunits")
@@ 579,6 632,30 @@ constants in the HEP System of Units, as derived from the basic units
originally defined by the CLHEP project.")
(license license:bsd-3)))
+(define-public python-histoprint
+ (package
+ (name "python-histoprint")
+ (version "2.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "histoprint" version))
+ (sha256
+ (base32 "07d2lk64gwhjvw4wccvwks3j4ig7g99q627jjxz4ans5a29p5pz1"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs (list python-click python-numpy python-uhi))
+ (native-inputs (list python-awkward
+ python-boost-histogram
+ python-hatch-vcs
+ python-hatchling
+ python-pytest
+ python-rich))
+ (home-page "https://github.com/scikit-hep/histoprint")
+ (synopsis "Pretty print histograms to the console")
+ (description "Histoprint uses a mix of terminal color codes and Unicode
+trickery (i.e. combining characters) to plot overlaying histograms.")
+ (license license:expat)))
+
(define-public python-imagehash
(package
(name "python-imagehash")
@@ 625,6 702,31 @@ Features:
@end itemize")
(license license:bsd-2)))
+(define-public python-meshzoo
+ (package
+ (name "python-meshzoo")
+ (version "0.9.4")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/diego-hayashi/meshzoo")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "107byfppbq16fqyp2hw7ydcvvahspzq0hzvlvzqg2zxi1aigbr68"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs
+ (list python-numpy))
+ (native-inputs (list python-flit-core python-matplotlib python-pytest))
+ (home-page "https://github.com/diego-hayashi/meshzoo")
+ (synopsis "Mesh generator for simple geometries")
+ (description
+ "@code{meshzoo} is a mesh generator for finite element or finite
+volume computations for simple domains like regular polygons, disks,
+spheres, cubes, etc.")
+ (license license:gpl3+)))
+
(define-public python-mpl-scatter-density
(package
(name "python-mpl-scatter-density")
@@ 658,6 760,30 @@ Features:
density maps, both for interactive and non-interactive use.")
(license license:bsd-2)))
+(define-public python-ndindex
+ (package
+ (name "python-ndindex")
+ (version "1.7") ;newer versions require a newer numpy
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "ndindex" version))
+ (sha256
+ (base32 "1lpgsagmgxzsas7g8yiv6wmyss8q57w92h70fn11rnpadsvx16xz"))))
+ (build-system pyproject-build-system)
+ (arguments (list #:test-flags #~(list "-c" "/dev/null"))) ;avoid coverage
+ (native-inputs
+ (list python-cython
+ python-numpy
+ python-pytest
+ python-setuptools
+ python-wheel))
+ (home-page "https://quansight-labs.github.io/ndindex/")
+ (synopsis "Python library for manipulating indices of ndarrays")
+ (description "This package provides a Python library for manipulating
+indices of @code{ndarrays}.")
+ (license license:expat)))
+
(define-public python-numdifftools
(package
(name "python-numdifftools")
@@ 913,102 1039,6 @@ or as a TikZ file for use in LaTeX documents;
factorization routine for quasi-definite linear system.")
(license license:asl2.0)))
-(define-public python-scipy
- (package
- (name "python-scipy")
- (version "1.12.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "scipy" version))
- (sha256
- (base32 "18rn15wg3lp58z204fbjjhy0h79c53yg3c4qqs9h3liniamspxab"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- #:phases
- #~(modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- ;; Step out of the source directory to avoid interference.
- (with-directory-excursion "/tmp"
- (invoke "python" "-c"
- (string-append
- "import scipy; scipy.test('fast', parallel="
- (number->string (parallel-job-count))
- ", verbose=2)"))))))
- (add-after 'check 'install-doc
- (lambda* (#:key outputs #:allow-other-keys)
- ;; FIXME: Documentation cannot be built because it requires
- ;; a newer version of pydata-sphinx-theme, which currently
- ;; cannot build without internet access:
- ;; <https://github.com/pydata/pydata-sphinx-theme/issues/628>.
- ;; Keep the phase for easy testing.
- (let ((sphinx-build (false-if-exception
- (search-input-file input "bin/sphinx-build"))))
- (if sphinx-build
- (let* ((doc (assoc-ref outputs "doc"))
- (data (string-append doc "/share"))
- (docdir (string-append
- data "/doc/"
- #$(package-name this-package) "-"
- #$(package-version this-package)))
- (html (string-append docdir "/html")))
- (with-directory-excursion "doc"
- ;; Build doc.
- (invoke "make" "html"
- ;; Building the documentation takes a very long time.
- ;; Parallelize it.
- (string-append "SPHINXOPTS=-j"
- (number->string (parallel-job-count))))
- ;; Install doc.
- (mkdir-p html)
- (copy-recursively "build/html" html)))
- (format #t "sphinx-build not found, skipping~%"))))))))
- (propagated-inputs
- (append
- (if (supported-package? python-jupytext) ; Depends on pandoc.
- (list python-jupytext)
- '())
- (list python-matplotlib
- python-mpmath
- python-mypy
- python-numpy
- python-numpydoc
- python-pydata-sphinx-theme
- python-pydevtool
- python-pythran
- python-rich-click
- python-sphinx
- python-threadpoolctl
- python-typing-extensions)))
- (inputs (list openblas pybind11-2.10))
- (native-inputs
- (list gfortran
- ;; XXX: Adding gfortran shadows GCC headers, causing a compilation
- ;; failure. Somehow also providing GCC works around it ...
- gcc
- meson-python
- pkg-config
- python-click
- python-cython-0.29.35
- python-doit
- python-hypothesis
- python-pooch
- python-pycodestyle
- python-pydevtool
- python-pytest
- python-pytest-cov
- python-pytest-timeout
- python-pytest-xdist))
- (home-page "https://scipy.org/")
- (synopsis "The Scipy library provides efficient numerical routines")
- (description "The SciPy library is one of the core packages that make up
-the SciPy stack. It provides many user-friendly and efficient numerical
-routines such as routines for numerical integration and optimization.")
- (license license:bsd-3)))
-
(define-public python-scikit-allel
(package
(name "python-scikit-allel")
@@ 1440,6 1470,102 @@ utilizing the power of scikit-learn, e.g., for pre-processing or doing
cross-validation.")
(license license:gpl3+))))
+(define-public python-scipy
+ (package
+ (name "python-scipy")
+ (version "1.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "scipy" version))
+ (sha256
+ (base32 "18rn15wg3lp58z204fbjjhy0h79c53yg3c4qqs9h3liniamspxab"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ ;; Step out of the source directory to avoid interference.
+ (with-directory-excursion "/tmp"
+ (invoke "python" "-c"
+ (string-append
+ "import scipy; scipy.test('fast', parallel="
+ (number->string (parallel-job-count))
+ ", verbose=2)"))))))
+ (add-after 'check 'install-doc
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; FIXME: Documentation cannot be built because it requires
+ ;; a newer version of pydata-sphinx-theme, which currently
+ ;; cannot build without internet access:
+ ;; <https://github.com/pydata/pydata-sphinx-theme/issues/628>.
+ ;; Keep the phase for easy testing.
+ (let ((sphinx-build (false-if-exception
+ (search-input-file input "bin/sphinx-build"))))
+ (if sphinx-build
+ (let* ((doc (assoc-ref outputs "doc"))
+ (data (string-append doc "/share"))
+ (docdir (string-append
+ data "/doc/"
+ #$(package-name this-package) "-"
+ #$(package-version this-package)))
+ (html (string-append docdir "/html")))
+ (with-directory-excursion "doc"
+ ;; Build doc.
+ (invoke "make" "html"
+ ;; Building the documentation takes a very long time.
+ ;; Parallelize it.
+ (string-append "SPHINXOPTS=-j"
+ (number->string (parallel-job-count))))
+ ;; Install doc.
+ (mkdir-p html)
+ (copy-recursively "build/html" html)))
+ (format #t "sphinx-build not found, skipping~%"))))))))
+ (propagated-inputs
+ (append
+ (if (supported-package? python-jupytext) ; Depends on pandoc.
+ (list python-jupytext)
+ '())
+ (list python-matplotlib
+ python-mpmath
+ python-mypy
+ python-numpy
+ python-numpydoc
+ python-pydata-sphinx-theme
+ python-pydevtool
+ python-pythran
+ python-rich-click
+ python-sphinx
+ python-threadpoolctl
+ python-typing-extensions)))
+ (inputs (list openblas pybind11-2.10))
+ (native-inputs
+ (list gfortran
+ ;; XXX: Adding gfortran shadows GCC headers, causing a compilation
+ ;; failure. Somehow also providing GCC works around it ...
+ gcc
+ meson-python
+ pkg-config
+ python-click
+ python-cython-0.29.35
+ python-doit
+ python-hypothesis
+ python-pooch
+ python-pycodestyle
+ python-pydevtool
+ python-pytest
+ python-pytest-cov
+ python-pytest-timeout
+ python-pytest-xdist))
+ (home-page "https://scipy.org/")
+ (synopsis "The Scipy library provides efficient numerical routines")
+ (description "The SciPy library is one of the core packages that make up
+the SciPy stack. It provides many user-friendly and efficient numerical
+routines such as routines for numerical integration and optimization.")
+ (license license:bsd-3)))
+
(define-public python-snakemake-interface-common
(package
(name "python-snakemake-interface-common")
@@ 1633,30 1759,6 @@ not usually a runtime dependency, but only a type checking, testing, and/or
docs dependency in support of other libraries.")
(license license:bsd-3)))
-(define-public python-histoprint
- (package
- (name "python-histoprint")
- (version "2.6.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "histoprint" version))
- (sha256
- (base32 "07d2lk64gwhjvw4wccvwks3j4ig7g99q627jjxz4ans5a29p5pz1"))))
- (build-system pyproject-build-system)
- (propagated-inputs (list python-click python-numpy python-uhi))
- (native-inputs (list python-awkward
- python-boost-histogram
- python-hatch-vcs
- python-hatchling
- python-pytest
- python-rich))
- (home-page "https://github.com/scikit-hep/histoprint")
- (synopsis "Pretty print histograms to the console")
- (description "Histoprint uses a mix of terminal color codes and Unicode
-trickery (i.e. combining characters) to plot overlaying histograms.")
- (license license:expat)))
-
(define-public python-hist
(package
(name "python-hist")
@@ 1785,6 1887,45 @@ geometric calculations on arrays of vectors, rather than one vector at a time
in a Python @code{for} loop.")
(license license:bsd-3)))
+(define-public python-traittypes
+ (package
+ (name "python-traittypes")
+ (version "0.2.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "traittypes" version))
+ (sha256
+ (base32 "1mlv93irdrgxrhnhq3ksi9585d55bpi4mv9dha4p8gkkjiia4vxy"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ ;; This one test fails because it doesn't raise an expected exception.
+ #:test-flags '(list "-k" "not test_bad_values")
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'numpy-compatibility
+ (lambda _
+ (substitute* "traittypes/tests/test_traittypes.py"
+ (("np\\.int") "int")))))))
+ (propagated-inputs (list python-traitlets))
+ (native-inputs
+ (list python-numpy
+ python-pandas
+ python-nose
+ python-pytest
+ python-setuptools
+ python-xarray
+ python-wheel))
+ (home-page "https://github.com/jupyter-widgets/traittypes")
+ (synopsis "Trait types for NumPy, SciPy and friends")
+ (description "The goal of this package is to provide a reference
+implementation of trait types for common data structures used in the scipy
+stack such as numpy arrays or pandas and xarray data structures. These are
+out of the scope of the main traitlets project but are a common requirement to
+build applications with traitlets in combination with the scipy stack.")
+ (license license:bsd-3)))
+
(define-public python-trimesh
(package
(name "python-trimesh")
@@ 1872,31 2013,6 @@ manipulation and analysis, in the style of the Polygon object in the Shapely
library.")
(license license:expat)))
-(define-public python-meshzoo
- (package
- (name "python-meshzoo")
- (version "0.9.4")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/diego-hayashi/meshzoo")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "107byfppbq16fqyp2hw7ydcvvahspzq0hzvlvzqg2zxi1aigbr68"))))
- (build-system pyproject-build-system)
- (propagated-inputs
- (list python-numpy))
- (native-inputs (list python-flit-core python-matplotlib python-pytest))
- (home-page "https://github.com/diego-hayashi/meshzoo")
- (synopsis "Mesh generator for simple geometries")
- (description
- "@code{meshzoo} is a mesh generator for finite element or finite
-volume computations for simple domains like regular polygons, disks,
-spheres, cubes, etc.")
- (license license:gpl3+)))
-
(define-public python-mpsplines
;; No release on PyPI no git tag, use the latest commit.
(let ((commit "4967655fca8f4d0fc0685486c8ec2f1fe2f199d2")
@@ 2078,30 2194,6 @@ support for DICOM.")
tissue-specificity metrics for gene expression.")
(license license:gpl3+)))
-(define-public python-ndindex
- (package
- (name "python-ndindex")
- (version "1.7") ;newer versions require a newer numpy
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "ndindex" version))
- (sha256
- (base32 "1lpgsagmgxzsas7g8yiv6wmyss8q57w92h70fn11rnpadsvx16xz"))))
- (build-system pyproject-build-system)
- (arguments (list #:test-flags #~(list "-c" "/dev/null"))) ;avoid coverage
- (native-inputs
- (list python-cython
- python-numpy
- python-pytest
- python-setuptools
- python-wheel))
- (home-page "https://quansight-labs.github.io/ndindex/")
- (synopsis "Python library for manipulating indices of ndarrays")
- (description "This package provides a Python library for manipulating
-indices of @code{ndarrays}.")
- (license license:expat)))
-
(define-public python-pandas-1
(package
(name "python-pandas")
@@ 2889,29 2981,6 @@ standard software: R and Python.")
analysis} (PCA), SVD, and eigendecompositions via randomized methods")
(license license:bsd-3)))
-(define-public python-geosketch
- (package
- (name "python-geosketch")
- (version "1.2")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "geosketch" version))
- (sha256
- (base32
- "0knch5h0p8xpm8bi3b5mxyaf1ywwimrsdmbnc1xr5icidcv9gzmv"))))
- (build-system python-build-system)
- (arguments '(#:tests? #false)) ;there are none
- (propagated-inputs (list python-fbpca python-numpy python-scikit-learn))
- (home-page "https://github.com/brianhie/geosketch")
- (synopsis "Geometry-preserving random sampling")
- (description "geosketch is a Python package that implements the geometric
-sketching algorithm described by Brian Hie, Hyunghoon Cho, Benjamin DeMeo,
-Bryan Bryson, and Bonnie Berger in \"Geometric sketching compactly summarizes
-the single-cell transcriptomic landscape\", Cell Systems (2019). This package
-provides an example implementation of the algorithm as well as scripts
-necessary for reproducing the experiments in the paper.")
- (license license:expat)))
-
(define-public python-einops
(package
(name "python-einops")
@@ 2953,6 3022,31 @@ necessary for reproducing the experiments in the paper.")
learning frameworks.")
(license license:expat)))
+(define-public python-upsetplot
+ (package
+ (name "python-upsetplot")
+ (version "0.9.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "UpSetPlot" version))
+ (sha256
+ (base32
+ "14l5gcj88cclkj1mf74bcy1pxq1hgsiy27fa3vxrsk32ik1nmdwm"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs
+ (list python-matplotlib python-pandas))
+ (native-inputs
+ (list python-pytest-runner python-pytest-cov
+ python-setuptools python-wheel))
+ (home-page "https://upsetplot.readthedocs.io")
+ (synopsis "Draw UpSet plots with Pandas and Matplotlib")
+ (description
+ "This is a Python implementation of UpSet plots by Lex et al.
+UpSet plots are used to visualize set overlaps; like Venn diagrams but more
+readable.")
+ (license license:bsd-3)))
+
(define-public python-xarray
(package
(name "python-xarray")
@@ 3333,31 3427,6 @@ units. It defines the @code{unyt.array.unyt_array} and
for handling arrays and scalars with units,respectively")
(license license:bsd-3)))
-(define-public python-upsetplot
- (package
- (name "python-upsetplot")
- (version "0.9.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "UpSetPlot" version))
- (sha256
- (base32
- "14l5gcj88cclkj1mf74bcy1pxq1hgsiy27fa3vxrsk32ik1nmdwm"))))
- (build-system pyproject-build-system)
- (propagated-inputs
- (list python-matplotlib python-pandas))
- (native-inputs
- (list python-pytest-runner python-pytest-cov
- python-setuptools python-wheel))
- (home-page "https://upsetplot.readthedocs.io")
- (synopsis "Draw UpSet plots with Pandas and Matplotlib")
- (description
- "This is a Python implementation of UpSet plots by Lex et al.
-UpSet plots are used to visualize set overlaps; like Venn diagrams but more
-readable.")
- (license license:bsd-3)))
-
(define-public python-vedo
(package
(name "python-vedo")
@@ 4177,45 4246,6 @@ visual integration of spatially referenced datasets.")
to do spectral analysis in Python.")
(license license:expat)))
-(define-public python-traittypes
- (package
- (name "python-traittypes")
- (version "0.2.1")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "traittypes" version))
- (sha256
- (base32 "1mlv93irdrgxrhnhq3ksi9585d55bpi4mv9dha4p8gkkjiia4vxy"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- ;; This one test fails because it doesn't raise an expected exception.
- #:test-flags '(list "-k" "not test_bad_values")
- #:phases
- '(modify-phases %standard-phases
- (add-after 'unpack 'numpy-compatibility
- (lambda _
- (substitute* "traittypes/tests/test_traittypes.py"
- (("np\\.int") "int")))))))
- (propagated-inputs (list python-traitlets))
- (native-inputs
- (list python-numpy
- python-pandas
- python-nose
- python-pytest
- python-setuptools
- python-xarray
- python-wheel))
- (home-page "https://github.com/jupyter-widgets/traittypes")
- (synopsis "Trait types for NumPy, SciPy and friends")
- (description "The goal of this package is to provide a reference
-implementation of trait types for common data structures used in the scipy
-stack such as numpy arrays or pandas and xarray data structures. These are
-out of the scope of the main traitlets project but are a common requirement to
-build applications with traitlets in combination with the scipy stack.")
- (license license:bsd-3)))
-
(define-public python-clarabel
(package
(name "python-clarabel")
@@ 4894,36 4924,6 @@ applications.")
neuronal models")
(license license:bsd-3)))
-(define-public python-ase
- (package
- (name "python-ase")
- (version "3.25.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "ase" version))
- (sha256
- (base32 "1hk2r5042cs9shqv49w0jvf65wkyq74s6vc5drfz1275kz5ghk1p"))))
- (build-system pyproject-build-system)
- (arguments
- (list #:test-flags
- #~(list ;; DeprecationWarning.
- "--deselect"
- "ase/test/fio/test_espresso.py::test_pw_input_write_nested_flat"
- ;; UserWarning.
- "--deselect"
- "ase/test/fio/test_espresso.py::TestConstraints::test_fix_scaled")))
- (propagated-inputs (list python-matplotlib python-numpy python-scipy))
- (native-inputs (list python-pytest python-pytest-xdist python-setuptools
- python-wheel))
- (inputs (list spglib))
- (home-page "https://wiki.fysik.dtu.dk/ase/")
- (synopsis "Atomic Simulation Environment")
- (description "This package provides a set of tools and Python modules for
-setting up, manipulating, running, visualizing and analyzing atomistic
-simulations.")
- (license license:lgpl2.1+)))
-
(define-public python-asap3
(package
(name "python-asap3")