mirror of
https://codeberg.org/guix/guix.git
synced 2025-10-02 02:15:12 +00:00
gnu: packages/python-science: Sort packages.
*gnu/packages/python-science.scm (python-ase, python-geosketch, python-histoprint, python-meshzoo, python-ndindex, python-scipy, python-traittypes, python-upsetplot): Sort variables alphabetically. Change-Id: I1fc194b17e3babf084c961bf09596d27e834fd6a
This commit is contained in:
Sharlatan Hellseher
parent
f1c56803ea
commit
4f2c0a5638
1 changed files with 286 additions and 286 deletions
|
|
@ -297,6 +297,36 @@ specification and test suite in Python.")
|
||||||
supersedes the RTED algorithm for computing the tree edit distance.")
|
supersedes the RTED algorithm for computing the tree edit distance.")
|
||||||
(license license:expat))))
|
(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
|
(define-public python-boost-histogram
|
||||||
(package
|
(package
|
||||||
(name "python-boost-histogram")
|
(name "python-boost-histogram")
|
||||||
|
|
@ -560,6 +590,29 @@ that is 20-25x faster than @code{numpy.histogram2d}.")
|
||||||
formulas for Python.")
|
formulas for Python.")
|
||||||
(license license:expat)))
|
(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
|
(define-public python-hepunits
|
||||||
(package
|
(package
|
||||||
(name "python-hepunits")
|
(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.")
|
originally defined by the CLHEP project.")
|
||||||
(license license:bsd-3)))
|
(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
|
(define-public python-imagehash
|
||||||
(package
|
(package
|
||||||
(name "python-imagehash")
|
(name "python-imagehash")
|
||||||
|
|
@ -625,6 +702,31 @@ Features:
|
||||||
@end itemize")
|
@end itemize")
|
||||||
(license license:bsd-2)))
|
(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
|
(define-public python-mpl-scatter-density
|
||||||
(package
|
(package
|
||||||
(name "python-mpl-scatter-density")
|
(name "python-mpl-scatter-density")
|
||||||
|
|
@ -658,6 +760,30 @@ Features:
|
||||||
density maps, both for interactive and non-interactive use.")
|
density maps, both for interactive and non-interactive use.")
|
||||||
(license license:bsd-2)))
|
(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
|
(define-public python-numdifftools
|
||||||
(package
|
(package
|
||||||
(name "python-numdifftools")
|
(name "python-numdifftools")
|
||||||
|
|
@ -913,102 +1039,6 @@ or as a TikZ file for use in LaTeX documents;
|
||||||
factorization routine for quasi-definite linear system.")
|
factorization routine for quasi-definite linear system.")
|
||||||
(license license:asl2.0)))
|
(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
|
(define-public python-scikit-allel
|
||||||
(package
|
(package
|
||||||
(name "python-scikit-allel")
|
(name "python-scikit-allel")
|
||||||
|
|
@ -1440,6 +1470,102 @@ utilizing the power of scikit-learn, e.g., for pre-processing or doing
|
||||||
cross-validation.")
|
cross-validation.")
|
||||||
(license license:gpl3+))))
|
(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
|
(define-public python-snakemake-interface-common
|
||||||
(package
|
(package
|
||||||
(name "python-snakemake-interface-common")
|
(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.")
|
docs dependency in support of other libraries.")
|
||||||
(license license:bsd-3)))
|
(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
|
(define-public python-hist
|
||||||
(package
|
(package
|
||||||
(name "python-hist")
|
(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.")
|
in a Python @code{for} loop.")
|
||||||
(license license:bsd-3)))
|
(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
|
(define-public python-trimesh
|
||||||
(package
|
(package
|
||||||
(name "python-trimesh")
|
(name "python-trimesh")
|
||||||
|
|
@ -1872,31 +2013,6 @@ manipulation and analysis, in the style of the Polygon object in the Shapely
|
||||||
library.")
|
library.")
|
||||||
(license license:expat)))
|
(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
|
(define-public python-mpsplines
|
||||||
;; No release on PyPI no git tag, use the latest commit.
|
;; No release on PyPI no git tag, use the latest commit.
|
||||||
(let ((commit "4967655fca8f4d0fc0685486c8ec2f1fe2f199d2")
|
(let ((commit "4967655fca8f4d0fc0685486c8ec2f1fe2f199d2")
|
||||||
|
|
@ -2078,30 +2194,6 @@ support for DICOM.")
|
||||||
tissue-specificity metrics for gene expression.")
|
tissue-specificity metrics for gene expression.")
|
||||||
(license license:gpl3+)))
|
(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
|
(define-public python-pandas-1
|
||||||
(package
|
(package
|
||||||
(name "python-pandas")
|
(name "python-pandas")
|
||||||
|
|
@ -2889,29 +2981,6 @@ standard software: R and Python.")
|
||||||
analysis} (PCA), SVD, and eigendecompositions via randomized methods")
|
analysis} (PCA), SVD, and eigendecompositions via randomized methods")
|
||||||
(license license:bsd-3)))
|
(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
|
(define-public python-einops
|
||||||
(package
|
(package
|
||||||
(name "python-einops")
|
(name "python-einops")
|
||||||
|
|
@ -2953,6 +3022,31 @@ necessary for reproducing the experiments in the paper.")
|
||||||
learning frameworks.")
|
learning frameworks.")
|
||||||
(license license:expat)))
|
(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
|
(define-public python-xarray
|
||||||
(package
|
(package
|
||||||
(name "python-xarray")
|
(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")
|
for handling arrays and scalars with units,respectively")
|
||||||
(license license:bsd-3)))
|
(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
|
(define-public python-vedo
|
||||||
(package
|
(package
|
||||||
(name "python-vedo")
|
(name "python-vedo")
|
||||||
|
|
@ -4177,45 +4246,6 @@ visual integration of spatially referenced datasets.")
|
||||||
to do spectral analysis in Python.")
|
to do spectral analysis in Python.")
|
||||||
(license license:expat)))
|
(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
|
(define-public python-clarabel
|
||||||
(package
|
(package
|
||||||
(name "python-clarabel")
|
(name "python-clarabel")
|
||||||
|
|
@ -4894,36 +4924,6 @@ applications.")
|
||||||
neuronal models")
|
neuronal models")
|
||||||
(license license:bsd-3)))
|
(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
|
(define-public python-asap3
|
||||||
(package
|
(package
|
||||||
(name "python-asap3")
|
(name "python-asap3")
|
||||||
|
|
|
||||||
Loading…
Add table
Add a link
Reference in a new issue