Merge branch 'master' into core-updates

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Marius Bakke 2020-03-10 20:50:02 +01:00
commit 50b99c90c8
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137 changed files with 3801 additions and 1464 deletions

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@ -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