diff options
Diffstat (limited to 'gnu/packages/python-xyz.scm')
| -rw-r--r-- | gnu/packages/python-xyz.scm | 359 |
1 files changed, 323 insertions, 36 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index de48d36748..50d1f4296f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -476,14 +476,14 @@ NetCDF files can also be read and modified. Python-HDF4 is a fork of (define-public python-h5py (package (name "python-h5py") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (pypi-uri "h5py" version)) (sha256 (base32 - "0mdr6wrq02ac93m1aqx9kad0ppfzmm4imlxqgyy1x4l7hmdcc9p6")))) + "0baipzv8n93m0dq0riyi8rfhzrjrfrfh8zqhszzp1j2xjac2fhc4")))) (build-system python-build-system) (arguments `(#:tests? #f ; no test target @@ -505,10 +505,11 @@ NetCDF files can also be read and modified. Python-HDF4 is a fork of `(("python-six" ,python-six) ("python-numpy" ,python-numpy))) (inputs - `(("hdf5" ,hdf5))) + `(("hdf5" ,hdf5-1.10))) (native-inputs `(("python-cython" ,python-cython) - ("python-pkgconfig" ,python-pkgconfig))) + ("python-pkgconfig" ,python-pkgconfig) + ("pkg-config" ,pkg-config))) (home-page "https://www.h5py.org/") (synopsis "Read and write HDF5 files from Python") (description @@ -671,6 +672,26 @@ API for locking files.") (define-public python2-lockfile (package-with-python2 python-lockfile)) +(define-public python-filelock + (package + (name "python-filelock") + (version "3.0.12") + (source + (origin + (method url-fetch) + (uri (pypi-uri "filelock" version)) + (sha256 + (base32 + "0ngzlvb5j8gqs2nxlp2b0jhzii792h66wsn694qm8kqixr225n0q")))) + (build-system python-build-system) + (home-page + "https://github.com/benediktschmitt/py-filelock") + (synopsis "Platform independent file lock") + (description "@code{filelock} contains a single module implementing +a platform independent file lock in Python, which provides a simple way of +inter-process communication.") + (license license:unlicense))) + (define-public python-semantic-version (package (name "python-semantic-version") @@ -2377,28 +2398,30 @@ e.g. filters, callbacks and errbacks can all be promises.") (define-public python-virtualenv (package (name "python-virtualenv") - (version "16.1.0") + (version "20.0.8") (source (origin (method url-fetch) (uri (pypi-uri "virtualenv" version)) (sha256 (base32 - "0242cg3hdq3qdvx5flyrki8lpwlgwf5k45c21ks5049fv7ygm6gq")))) + "096r7g5cv85vxymg9iqbn5z749613snlvd6p3rf1nxnrd386j0qz")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-before 'check 'disable-failing-test - (lambda _ - ;; Disable failing test. See upstream bug report - ;; https://github.com/pypa/virtualenv/issues/957 - (substitute* "tests/test_virtualenv.py" - (("skipif.*") "skipif(True, reason=\"Guix\")\n")) - #t))))) (native-inputs `(("python-mock" ,python-mock) - ("python-pytest" ,python-pytest))) + ("python-pytest" ,python-pytest) + ;; NOTE: guix lint remarks that "python-setuptools should probably not + ;; be an input at all". However, removing the input makes the build error: + ;; File "setup.py", line 4, in <module> + ;; raise RuntimeError("setuptools >= 41 required to build") + ("python-setuptools" ,python-setuptools) + ("python-setuptools-scm" ,python-setuptools-scm))) + (propagated-inputs + `(("python-appdirs" ,python-appdirs) + ("python-distlib" ,python-distlib) + ("python-filelock" ,python-filelock) + ("python-six" ,python-six) + ("python-importlib-metadata" ,python-importlib-metadata))) (home-page "https://virtualenv.pypa.io/") (synopsis "Virtual Python environment builder") (description @@ -3154,17 +3177,36 @@ used in text editing environments to provide a complete and integrated feature-set for programming Python effectively.") (license license:expat))) +(define-public python-pathspec + (package + (name "python-pathspec") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pathspec" version)) + (sha256 + (base32 + "15lvs4awlg8xzl0l4gk9y53xx4yqmqvsv44pglv39m70y85afajn")))) + (build-system python-build-system) + (home-page "https://github.com/cpburnz/python-path-specification") + (synopsis "Utility library for gitignore style pattern matching of file paths") + (description + "This package provides a utility library for gitignore style pattern +matching of file paths.") + (license license:mpl2.0))) + (define-public python-black (package (name "python-black") - (version "18.6b4") + (version "19.10b0") (source (origin (method url-fetch) (uri (pypi-uri "black" version)) (sha256 (base32 - "0i4sfqgz6w15vd50kbhi7g7rifgqlf8yfr8y78rypd56q64qn592")))) + "0f8mr0yzj78q1dx7v6ggbgfir2wv0n5z2shfbbvfdq7910xbgvf2")))) (build-system python-build-system) (arguments `(#:phases @@ -3174,16 +3216,39 @@ feature-set for programming Python effectively.") (let ((python3 (which "python3"))) (substitute* '("tests/data/fmtonoff.py" "tests/data/string_prefixes.py" - "tests/data/function.py") + "tests/data/function.py" + "tests/data/python37.py") (("#!/usr/bin/env python3(\\.[0-9]+)?" _ minor-version) (string-append "#!" python3 (if (string? minor-version) minor-version - "")))))))))) + ""))))) + #t)) + (add-after 'unpack 'disable-broken-tests + (lambda _ + ;; These tests are supposed to be skipped when the blackd + ;; dependencies are missing, but this doesn't quite work. + (substitute* "tests/test_black.py" + (("( *)class BlackDTestCase.*" match indent) + (string-append indent "@unittest.skip(\"no blackd deps\")\n" + indent "class BlackDTestCase(unittest.TestCase):\n")) + (("web.Application") "False") + (("@unittest_run_loop") "")) + + ;; Patching the above file breaks the self test + (substitute* "tests/test_black.py" + (("( *)def test_self" match indent) + (string-append indent "@unittest.skip(\"guix\")\n" match))) + #t))))) (propagated-inputs `(("python-click" ,python-click) ("python-attrs" ,python-attrs) ("python-appdirs" ,python-appdirs) - ("python-toml" ,python-toml))) + ("python-pathspec" ,python-pathspec) + ("python-regex" ,python-regex) + ("python-toml" ,python-toml) + ("python-typed-ast" ,python-typed-ast))) + (native-inputs + `(("python-setuptools-scm" ,python-setuptools-scm))) (home-page "https://github.com/ambv/black") (synopsis "The uncompromising code formatter") (description "Black is the uncompromising Python code formatter.") @@ -3740,21 +3805,20 @@ color scales, and color space conversion easy. It has support for: (define-public python-pygit2 (package (name "python-pygit2") - (version "0.28.2") + (version "1.1.0") (source (origin (method url-fetch) (uri (pypi-uri "pygit2" version)) (sha256 - (base32 "11kzj5mjkspvplnpdb6bj8dcj6rgmkk986k8hjcklyg5yaxkz32d")))) + (base32 "1hs0pqqzn1yjxqk86nq7p0lvsklwnlyi5xwyzr7d5nrs19dmsjbg")))) (build-system python-build-system) (arguments '(#:tests? #f)) ; tests don't run correctly in our environment (propagated-inputs - `(("python-six" ,python-six) + `(("python-cached-property" ,python-cached-property) ("python-cffi" ,python-cffi) - ("libgit2" ,libgit2) - ("python-tox" ,python-tox))) + ("libgit2" ,libgit2))) (native-inputs `(("python-pytest" ,python-pytest))) (home-page "https://github.com/libgit2/pygit2") @@ -3764,9 +3828,6 @@ library, libgit2 implements Git plumbing.") ;; GPL2.0 only, with linking exception. (license license:gpl2))) -(define-public python2-pygit2 - (package-with-python2 python-pygit2)) - (define-public python-pyparsing (package (name "python-pyparsing") @@ -4410,6 +4471,40 @@ by pycodestyle.") (define-public python2-autopep8 (package-with-python2 python-autopep8)) +(define-public python-distlib + (package + (name "python-distlib") + (version "0.3.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "distlib" version ".zip")) + (sha256 + (base32 + "08fyi2r246733vharl2yckw20rilci28r91mzrnnvcr638inw5if")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'build 'no-/bin/sh + (lambda _ + (substitute* '("distlib/scripts.py" "tests/test_scripts.py") + (("/bin/sh") (which "sh"))) + #t)) + (add-before 'check 'prepare-test-env + (lambda _ + (setenv "HOME" "/tmp") + ;; NOTE: Any value works, the variable just has to be present. + (setenv "SKIP_ONLINE" "1") + #t))))) + (native-inputs `(("unzip" ,unzip))) + (home-page "https://bitbucket.org/pypa/distlib") + (synopsis "Distribution utilities") + (description "Distlib is a library which implements low-level functions that +relate to packaging and distribution of Python software. It is intended to be +used as the basis for third-party packaging tools.") + (license license:psfl))) + (define-public python-distutils-extra (package (name "python-distutils-extra") @@ -7271,6 +7366,12 @@ printing of sub-tables by specifying a row range.") "linker_exe='gcc'," "linker_so='gcc -shared')"))) #t)) + (add-after 'unpack 'disable-tuning + (lambda _ + (substitute* "setup.py" + (("cpu_flags = .*") + "cpu_flags = ['sse2']\n")) + #t)) (replace 'build (lambda* (#:key inputs #:allow-other-keys) (invoke "python" "setup.py" "build" @@ -7288,7 +7389,7 @@ printing of sub-tables by specifying a row range.") `(("python-cython" ,python-cython) ("pkg-config" ,pkg-config))) (inputs - `(("hdf5" ,hdf5) + `(("hdf5" ,hdf5-1.10) ("bzip2" ,bzip2) ("zlib" ,zlib))) (home-page "http://www.pytables.org/") @@ -7300,6 +7401,84 @@ designed to efficiently cope with extremely large amounts of data.") (define-public python2-tables (package-with-python2 python-tables)) +(define-public python-pytest-black + (package + (name "python-pytest-black") + (version "0.3.8") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pytest-black" version)) + (sha256 + (base32 + "04lppqydxm0f3f3x0l8hj7v0j6d8syj34jc37yzqwqcyqsnaga81")))) + (build-system python-build-system) + (propagated-inputs + `(("python-pytest" ,python-pytest) + ("python-black" ,python-black) + ("python-toml" ,python-toml))) + (native-inputs + `(("python-setuptools-scm" ,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-get-version + (package + (name "python-get-version") + (version "2.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "get_version" version)) + (sha256 + (base32 + "1g15jyx33vkxavv9hwv275cs4g9bp2i1y942raw3fxamq8kbaml1")))) + (build-system python-build-system) + (propagated-inputs + `(("python-pygments" ,python-pygments) + ("python-pytest" ,python-pytest) + ("python-pytest-black" ,python-pytest-black) + ("python-pytest-cov" ,python-pytest-cov) + ("python-setuptools" ,python-setuptools) + ("python-testpath" ,python-testpath))) + (home-page "https://github.com/flying-sheep/get_version") + (synopsis "Version helper in the spirit of versioneer") + (description + "This package provides a version helper that lets you automatically use +the latest @code{vX.X.X} Git tag as the version in your Python package. It +also supports getting the version from Python source distributions or, once +your package is installed, via @code{pkg_resources} (part of +@code{setuptools}).") + (license license:gpl3+))) + +(define-public python-legacy-api-wrap + (package + (name "python-legacy-api-wrap") + (version "1.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "legacy-api-wrap" version)) + (sha256 + (base32 + "06qhp0g543dy98vpa41hwdalvdbsjfc3ldk474yr9sd75mhl8jh3")))) + (build-system python-build-system) + (propagated-inputs + `(("python-get-version" ,python-get-version) + ("python-pytest" ,python-pytest) + ("python-pytest-black" ,python-pytest-black) + ("python-pytest-cov" ,python-pytest-cov) + ("python-setuptools" ,python-setuptools))) + (home-page "https://github.com/flying-sheep/legacy-api-wrap") + (synopsis "Legacy API wrapper") + (description "This module defines a decorator to wrap legacy APIs. The +primary use case is APIs defined before keyword-only parameters existed.") + (license license:gpl3+))) + (define-public python-pyasn1 (package (name "python-pyasn1") @@ -8526,7 +8705,7 @@ minimal and fast API targeting the following uses: @item write and deploy hybrid multi-process applications @item write scripts to administer multiple environments @end enumerate") - (home-page "http://codespeak.net/execnet/") + (home-page "https://codespeak.net/execnet/") (license license:expat))) (define-public python2-execnet @@ -14520,7 +14699,12 @@ such as figshare or Zenodo.") "183kg1rhzz3hqizvphkd8hlbf1zxfx8737zhfkmqzxi71jmdw7pd")))) (build-system python-build-system) (native-inputs - `(("python-tox" ,python-tox) + `(("python-appdirs" ,python-appdirs) + ("python-distlib" ,python-distlib) + ("python-importlib-metadata" ,python-importlib-metadata) + ("python-filelock" ,python-filelock) + ("python-six" ,python-six) + ("python-tox" ,python-tox) ("python-virtualenv" ,python-virtualenv))) (home-page "https://github.com/k-bx/python-semver") (synopsis "Python helper for Semantic Versioning") @@ -15835,23 +16019,126 @@ infrastructure at import time, runtime, or statically (using the included pycc tool).") (license license:bsd-3))) +(define-public python-numcodecs + (package + (name "python-numcodecs") + (version "0.6.4") + (source + (origin + (method url-fetch) + (uri (pypi-uri "numcodecs" version)) + (sha256 + (base32 + "0kbfr8pl3x9glsypbq8hzim003f16ml1b1cvgrh4w1sdvgal6j7g")))) + (build-system python-build-system) + (propagated-inputs + `(("python-numpy" ,python-numpy) + ("python-msgpack" ,python-msgpack))) + (native-inputs + `(("python-pytest" ,python-pytest) + ("python-setuptools-scm" ,python-setuptools-scm))) + (home-page "https://github.com/zarr-developers/numcodecs") + (synopsis "Buffer compression and transformation codecs") + (description + "This Python package provides buffer compression and transformation +codecs for use in data storage and communication applications.") + (license license:expat))) + +(define-public python-asciitree + (package + (name "python-asciitree") + (version "0.3.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "asciitree" version)) + (sha256 + (base32 + "0vhgri2m2xlnibhz4xwn4hpbc7xacisxjqrk6k5kyppq96vbk92a")))) + (build-system python-build-system) + (home-page "https://github.com/mbr/asciitree") + (synopsis "Draws ASCII trees") + (description "This package draws tree structures using characters.") + (license license:expat))) + +(define-public python-zarr + (package + (name "python-zarr") + (version "2.4.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "zarr" version)) + (sha256 + (base32 + "026n3sjzjv2gmwx6y72b8ij0hk42bc8zdbvfj5gdqzd4i6wj3ajk")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'disable-service-tests + (lambda _ + (setenv "ZARR_TEST_ABS" "0") + (setenv "ZARR_TEST_MONGO" "0") + (setenv "ZARR_TEST_REDIS" "0") + #t)) + (replace 'check + (lambda _ + (invoke "pytest" "-vv" "-k" "not lmdb") + #t))))) + (propagated-inputs + `(("python-asciitree" ,python-asciitree) + ("python-fasteners" ,python-fasteners) + ("python-numcodecs" ,python-numcodecs) + ("python-numpy" ,python-numpy))) + (native-inputs + `(("python-pytest" ,python-pytest) + ("python-setuptools-scm" ,python-setuptools-scm))) + (home-page "https://github.com/zarr-developers/zarr-python") + (synopsis "Chunked, compressed, N-dimensional arrays for Python") + (description + "This package provides an implementation of chunked, compressed, +N-dimensional arrays for Python.") + (license license:expat))) + (define-public python-anndata (package (name "python-anndata") - (version "0.6.18") + (version "0.7.1") (source (origin (method url-fetch) (uri (pypi-uri "anndata" version)) (sha256 (base32 - "03x83yjaccbqszj7x4fwwmpil0ai59yx64d1zmf2691za3j03w73")))) + "0rnfbpr55j1a1bi2kd4mz444741hrn74kz90h5rnjr59jmpfnh09")))) (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'delete-inconvenient-tests + (lambda _ + ;; This test depends on python-scikit-learn. + (delete-file "anndata/tests/test_inplace_subset.py") + #t)) + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (invoke "pytest" "-vv")))))) (propagated-inputs `(("python-h5py" ,python-h5py) + ("python-importlib-metadata" ,python-importlib-metadata) ("python-natsort" ,python-natsort) + ("python-numcodecs" ,python-numcodecs) + ("python-packaging" ,python-packaging) ("python-pandas" ,python-pandas) - ("python-scipy" ,python-scipy))) + ("python-scipy" ,python-scipy) + ("python-zarr" ,python-zarr))) + (native-inputs + `(("python-joblib" ,python-joblib) + ("python-pytest" ,python-pytest) + ("python-setuptools-scm" ,python-setuptools-scm))) (home-page "https://github.com/theislab/anndata") (synopsis "Annotated data for data analysis pipelines") (description "Anndata is a package for simple (functional) high-level APIs |