diff options
Diffstat (limited to 'gnu/packages/python-xyz.scm')
| -rw-r--r-- | gnu/packages/python-xyz.scm | 614 |
1 files changed, 444 insertions, 170 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 31cafd47d1..657ebabe93 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -23,7 +23,7 @@ ;;; Copyright © 2016 Daniel Pimentel <d4n1@d4n1.org> ;;; Copyright © 2016 Sou Bunnbu <iyzsong@gmail.com> ;;; Copyright © 2016, 2017 Troy Sankey <sankeytms@gmail.com> -;;; Copyright © 2016, 2017 ng0 <ng0@n0.is> +;;; Copyright © 2016, 2017 Nikita <nikita@n0.is> ;;; Copyright © 2016 Dylan Jeffers <sapientech@sapientech@openmailbox.org> ;;; Copyright © 2016 David Craven <david@craven.ch> ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Marius Bakke <mbakke@fastmail.com> @@ -67,6 +67,7 @@ ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz> ;;; Copyright © 2019, 2020 Tanguy Le Carrour <tanguy@bioneland.org> ;;; Copyright © 2019 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> +;;; Copyright © 2020 Riku Viitanen <riku.viitanen@protonmail.com> ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> ;;; Copyright © 2020 sirgazil <sirgazil@zoho.com> ;;; Copyright © 2020 Sebastian Schott <sschott@mailbox.org> @@ -412,16 +413,17 @@ data for video and audio files.") (define-public python-psutil (package (name "python-psutil") - (version "5.6.5") + (version "5.7.0") (source (origin (method url-fetch) (uri (pypi-uri "psutil" version)) (sha256 - (base32 "0isil5jxwwd8awz54qk28rpgjg43i5l6yl70g40vxwa4r4m56lfh")))) + (base32 "03jykdi3dgf1cdal9bv4fq9zjvzj9l9bs99gi5ar81sdl5nc2pk8")))) (build-system python-build-system) (arguments - ;; FIXME: some tests does not return and times out. + ;; FIXME: some tests do not return and time out. Some tests fail because + ;; some processes survive kill(). '(#:tests? #f)) (home-page "https://www.github.com/giampaolo/psutil") (synopsis "Library for retrieving information on running processes") @@ -706,7 +708,7 @@ Expressions are constructed from parsed strings or directly in Python.") (propagated-inputs `(("numpy" ,python-numpy))) (inputs `(("hdf4" ,hdf4) - ("libjpeg" ,libjpeg) + ("libjpeg" ,libjpeg-turbo) ("zlib" ,zlib))) (arguments `(#:phases @@ -1587,14 +1589,14 @@ from the Python interpreter, or as a small part of a larger application.") (define-public python-six (package (name "python-six") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (pypi-uri "six" version)) (sha256 (base32 - "0wxs1q74v07ssjywbbm7x6h5v9qx209ld2yfsif4060sxi0h2sni")))) + "02lw67hprv57hyg3cfy02y3ixjk3nzwc0dx3c4ynlvkfwkfdnsr3")))) (build-system python-build-system) (arguments `(#:phases @@ -1603,8 +1605,7 @@ from the Python interpreter, or as a small part of a larger application.") (lambda _ (invoke "py.test" "-v")))))) (native-inputs - `(("python-py" ,python-py) - ("python-pytest" ,python-pytest-bootstrap))) + `(("python-pytest" ,python-pytest-bootstrap))) (home-page "https://pypi.org/project/six/") (synopsis "Python 2 and 3 compatibility utilities") (description @@ -2186,14 +2187,14 @@ server.") (define-public python-py (package (name "python-py") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (pypi-uri "py" version)) (sha256 (base32 - "0lsy1gajva083pzc7csj1cvbmminb7b4l6a0prdzyb3fd829nqyw")))) + "1ajjazg3913n0sp3vjyva9c2qh5anx8ziryng935f89604a0h9sy")))) (build-system python-build-system) (arguments ;; FIXME: "ImportError: 'test' module incorrectly imported from @@ -2288,6 +2289,16 @@ from git information. (base32 "1lrsjgblnapfimd0alsi1as5nz2lfqv97131l7d6anbjzq2rjri8")))) (build-system python-build-system) + (arguments + '(#:phases (modify-phases %standard-phases + ;; The package works fine with newer Pytest and Hypothesis, but + ;; has pinned older versions to stay compatible with Python 2. + (add-before 'check 'loosen-pytest-requirement + (lambda _ + (substitute* "setup.py" + (("pytest<5") "pytest") + (("hypothesis<5") "hypothesis")) + #t))))) (native-inputs `(("python-hypothesis" ,python-hypothesis) ("python-pytest" ,python-pytest) @@ -2679,10 +2690,20 @@ memory usage and transliteration quality.") (find-files "." "\\.pyc$")) #t)))) (build-system python-build-system) + (arguments + '(#:phases (modify-phases %standard-phases + (replace 'check + (lambda _ + ;; Mimic upstream commit 3a20892442b34c7 to get + ;; rid of dependency on pytest-runner < 5.0. + ;; Remove substitution for PyJWT > 1.7.1. + (substitute* "setup.py" + ((".*pytest-runner.*") + "")) + (invoke "pytest" "-vv")))))) (native-inputs `(("python-pytest" ,python-pytest) - ("python-pytest-cov" ,python-pytest-cov) - ("python-pytest-runner" ,python-pytest-runner))) + ("python-pytest-cov" ,python-pytest-cov))) (home-page "https://github.com/progrium/pyjwt") (synopsis "JSON Web Token implementation in Python") (description @@ -3212,6 +3233,77 @@ reStructuredText.") (base32 "0x22fs3pdmr42kvz6c654756wja305qv6cx1zbhwlagvxgr4xrji")))))) +(define-public python-restructuredtext-lint + (package + (name "python-restructuredtext-lint") + (version "1.3.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "restructuredtext-lint" version)) + (sha256 + (base32 + "026rdy5h82ng4vqxk8fnprii9d6qxf7hkygiv0a8afjvdlsxmcwp")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + (invoke "nosetests" "-v")) + #t))))) + (propagated-inputs + `(("python-docutils" ,python-docutils))) + (native-inputs + `(("python-nose" ,python-nose))) + (home-page "https://github.com/twolfson/restructuredtext-lint") + (synopsis "reStructuredText linter") + (description "This package provides a linter for the reStructuredText +format.") + (license license:unlicense))) + +(define-public python-doc8 + (package + (name "python-doc8") + (version "0.8.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "doc8" version)) + (sha256 + (base32 + "0hw5w8mpgsp51qg8nnq28p7y1jiksvz7a0axnn5bkgss3af9zy1d")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + (invoke "pytest" "-v")) + #t))))) + (propagated-inputs + `(("python-chardet" ,python-chardet) + ("python-docutils" ,python-docutils) + ("python-restructuredtext-lint" ,python-restructuredtext-lint) + ("python-six" ,python-six) + ("python-stevedore" ,python-stevedore))) + (native-inputs + `(("python-testtools" ,python-testtools) + ("python-pytest" ,python-pytest))) + (home-page "https://launchpad.net/doc8") + (synopsis + "Style checker for Sphinx (or other) RST documentation") + (description + "Doc8 is an opinionated style checker for reStructured Text and plain +text styles of documentation.") + (license license:asl2.0))) + (define-public python-pygments (package (name "python-pygments") @@ -3675,21 +3767,21 @@ Server (PLS).") (define-public python-language-server (package (name "python-language-server") - (version "0.31.7") + (version "0.32.0") (source (origin (method url-fetch) (uri (pypi-uri "python-language-server" version)) (sha256 (base32 - "0f8rljff4h2ay9m2n9ang7axai37nzd39zd7m6c90rci5wh8cmxh")))) + "0j5swacmjps9sas1gfwg0xi84rmjhfhz20cwg3k4058d20rs20ip")))) (build-system python-build-system) (propagated-inputs `(("python-pluggy" ,python-pluggy) ("python-jsonrpc-server" ,python-jsonrpc-server) ;; Note: Remove the special versions of Jedi and Parso when updating ;; this package. - ("python-jedi" ,python-jedi-0.15) + ("python-jedi" ,python-jedi) ("python-yapf" ,python-yapf) ("python-pyflakes" ,python-pyflakes) ("python-pydocstyle" ,python-pydocstyle) @@ -3903,7 +3995,13 @@ provides additional functionality on the produced Mallard documents.") (setenv "CFLAGS" "-O0") (invoke "python" "runtests.py" "-vv" - "-j" (number->string (parallel-job-count)))))))) + "-j" (number->string (parallel-job-count)) + ;; XXX: On 32-bit architectures, running the parallel tests + ;; fails on many-core systems, see + ;; <https://github.com/cython/cython/issues/2807>. + ,@(if (not (target-64bit?)) + '("-x" "run.parallel") + '()))))))) (home-page "https://cython.org/") (synopsis "C extensions for Python") (description "Cython is an optimising static compiler for both the Python @@ -3923,18 +4021,6 @@ writing C extensions for Python as easy as Python itself.") (substitute-keyword-arguments (package-arguments base) ((#:phases phases) `(modify-phases ,phases - ;; XXX: On i686-linux, running the parallel tests fails on many-core - ;; systems, see <https://github.com/cython/cython/issues/2807>. - ;; TODO: Move this logic to the regular check phase in a future - ;; rebuild cycle. - ,@(if (string-prefix? "i686" (%current-system)) - '((replace 'check - (lambda _ - (setenv "CFLAGS" "-O0") - (invoke "python" "runtests.py" "-vv" - "-j" (number->string (parallel-job-count)) - "-x" "run.parallel")))) - '()) (add-before 'check 'adjust-test_embed (lambda _ (substitute* "runtests.py" @@ -4356,13 +4442,13 @@ library, libgit2 implements Git plumbing.") (define-public python-pyparsing (package (name "python-pyparsing") - (version "2.3.1") + (version "2.4.6") (source (origin (method url-fetch) (uri (pypi-uri "pyparsing" version)) (sha256 - (base32 "0yk6xl885b91dmlhlsap7x78hk2rdr879fln9anbq6k4ca42djb6")))) + (base32 "17wn5zlijc9m9zj26gy3f541y7smpj8rfhl51d025c2gm210b0sc")))) (build-system python-build-system) (outputs '("out" "doc")) (arguments @@ -4804,27 +4890,38 @@ toolkits.") three-way Venn diagrams in @code{matplotlib}.") (license license:expat))) -(define-public python2-pysnptools +(define-public python-pysnptools (package - (name "python2-pysnptools") - (version "0.3.13") + (name "python-pysnptools") + (version "0.4.11") (source (origin (method url-fetch) (uri (pypi-uri "pysnptools" version)) (sha256 (base32 - "0lnis5xsl7bi0hz4f7gbicahzi5zlxkc21nk3g374xv8fb5hb3qm")))) + "0gxr0bjix307wvk0qh7vkafbxbzfpdmq0wlswpxyyaymy0fwcypv")))) (build-system python-build-system) (arguments - `(#:python ,python-2 ; only Python 2.7 is supported - #:tests? #f)) ; test files (e.g. examples/toydata.bim) not included + `(#:tests? #f ; no test data are included + #:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (if tests? + (begin + (add-installed-pythonpath inputs outputs) + (invoke "python3" "pysnptools/test.py")) + #t)))))) (propagated-inputs - `(("python2-numpy" ,python2-numpy) - ("python2-scipy" ,python2-scipy) - ("python2-pandas" ,python2-pandas))) + `(("python-dill" ,python-dill) + ("python-h5py" ,python-h5py) + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-psutil" ,python-psutil) + ("python-scipy" ,python-scipy))) (native-inputs - `(("python2-cython" ,python2-cython))) + `(("python-cython" ,python-cython))) (home-page "http://microsoftgenomics.github.io/PySnpTools/") (synopsis "Library for reading and manipulating genetic data") (description @@ -4834,6 +4931,9 @@ those files. It can also efficiently manipulate ranges of integers using set operators such as union, intersection, and difference.") (license license:asl2.0))) +(define-public python2-pysnptools + (package-with-python2 python-pysnptools)) + (define-public python-socksipy-branch (package (name "python-socksipy-branch") @@ -5147,7 +5247,7 @@ the OleFileIO module from PIL, the Python Image Library.") (inputs `(("freetype" ,freetype) ("lcms" ,lcms) - ("libjpeg" ,libjpeg) + ("libjpeg" ,libjpeg-turbo) ("libtiff" ,libtiff) ("libwebp" ,libwebp) ("openjpeg" ,openjpeg) @@ -5649,13 +5749,13 @@ child application and control it as if a human were typing commands.") (define-public python-setuptools-scm (package (name "python-setuptools-scm") - (version "3.2.0") + (version "3.4.3") (source (origin (method url-fetch) (uri (pypi-uri "setuptools_scm" version)) (sha256 (base32 - "0n3knn3p1sqlx31k2lahn7z9bacvlv8nhlfidj77vz50bxqlgasj")))) + "083k93wi7mrmp1cn28hcbnr6sivbgls0y7zz2m5qzn1wg04a3f16")))) (build-system python-build-system) (home-page "https://github.com/pypa/setuptools_scm/") (synopsis "Manage Python package versions in SCM metadata") @@ -5665,18 +5765,6 @@ child application and control it as if a human were typing commands.") them as the version argument or in a SCM managed file.") (license license:expat))) -;; Needed by python-lazy-object-proxy, remove on next update cycle. -(define-public python-setuptools-scm-3.3 - (package - (inherit python-setuptools-scm) - (version "3.3.3") - (source (origin - (method url-fetch) - (uri (pypi-uri "setuptools_scm" version)) - (sha256 - (base32 - "19cyndx23xmpbhz4qrwmfwsmnnaczd0dw7qg977ksq2dbvxy29dx")))))) - (define-public python2-setuptools-scm (package-with-python2 python-setuptools-scm)) @@ -5715,9 +5803,17 @@ older Python versions.") "0y3hg12iby1qyaspnbisz4s4vxax7syikk3skznwqizqyv89y9yk")))) (build-system python-build-system) (arguments - `(#:python ,python-2)) - (native-inputs - `(("python-wheel" ,python2-wheel))) + `(#:python ,python-2 + #:phases (modify-phases %standard-phases + ;; The build system tests for python-wheel, but it is + ;; not required for Guix nor the test suite. Just drop + ;; it to make bootstrapping pytest easier. + (add-after 'unpack 'drop-wheel-dependency + (lambda _ + (substitute* "setup.cfg" + (("^[[:blank:]]+wheel") + "")) + #t))))) (propagated-inputs `(("python-pathlib2" ,python2-pathlib2) ("python-typing" ,python2-typing))) @@ -5728,21 +5824,33 @@ older Python versions.") for older versions of Python.") (license license:asl2.0))) +;; For importlib-metadata-bootstrap below. +(define-public python2-importlib-resources-bootstrap + (hidden-package + (package/inherit + python2-importlib-resources + (name "python2-importlib-resources-bootstrap") + (propagated-inputs + `(("python-pathlib2-bootstrap" ,python2-pathlib2-bootstrap) + ("python-typing" ,python2-typing)))))) + (define-public python-importlib-metadata (package (name "python-importlib-metadata") - (version "1.4.0") + (version "1.5.0") (source (origin (method url-fetch) (uri (pypi-uri "importlib_metadata" version)) (sha256 - (base32 "1n76444v7zn910xrhh8954jdn4byxbn9f1jck6b85a716mbh2z7i")))) + (base32 + "00ikdj4gjhankdljnz7g5ggak4k9lql2926x0x117ir9j2lv7x86")))) (build-system python-build-system) (propagated-inputs `(("python-zipp" ,python-zipp))) (native-inputs `(("python-setuptools-scm" ,python-setuptools-scm) + ("python-pyfakefs" ,python-pyfakefs) ("python-packaging" ,python-packaging))) (home-page "https://importlib-metadata.readthedocs.io/") (synopsis "Read metadata from Python packages") @@ -5762,6 +5870,10 @@ need to use the older and less efficient @code{pkg_resources} package.") (package/inherit base (name "python2-importlib-metadata") + (native-inputs + `(("python-setuptools-scm" ,python2-setuptools-scm) + ("python-pyfakefs" ,python2-pyfakefs-bootstrap) + ("python-packaging" ,python2-packaging-bootstrap))) (propagated-inputs `(("python-configparser" ,python2-configparser) ("python-contextlib2" ,python2-contextlib2) @@ -5769,6 +5881,22 @@ need to use the older and less efficient @code{pkg_resources} package.") ("python-pathlib2" ,python2-pathlib2) ,@(package-propagated-inputs base)))))) +;; This package is used by python2-pytest, and thus must not depend on it. +(define-public python2-importlib-metadata-bootstrap + (hidden-package + (package/inherit + python2-importlib-metadata + (name "python2-importlib-metadata-bootstrap") + (arguments + `(#:tests? #f + ,@(package-arguments python2-importlib-metadata))) + (propagated-inputs + `(("python-zipp" ,python2-zipp-bootstrap) + ("python-pathlib2" ,python2-pathlib2-bootstrap) + ("python-configparser" ,python2-configparser) + ("python-contextlib2" ,python2-contextlib2-bootstrap) + ("python-importlib-resources" ,python2-importlib-resources-bootstrap)))))) + (define-public python-jaraco-packaging (package (name "python-jaraco-packaging") @@ -7174,6 +7302,8 @@ Python 2 and Python 3.") (modify-phases %standard-phases (replace 'check (lambda _ + (setenv "PYTHONPATH" (string-append "./build/lib:" + (getenv "PYTHONPATH"))) (invoke "py.test" "-v")))))) (native-inputs `(("python2-pytest" ,python2-pytest))) @@ -7308,6 +7438,27 @@ PEP 8.") (define-public python2-pyflakes (package-with-python2 python-pyflakes)) +;; Flake8 2.6 requires an older version of pyflakes. +;; This should be removed ASAP. +(define-public python-pyflakes-1.2 + (package (inherit python-pyflakes) + (version "1.2.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pyflakes" version)) + (sha256 + (base32 + "17hkw8yd44cr8fz13phy4aih3r5j2p7ild4zlvqdh2c8dmiinjif")))) + (arguments + '(#:phases + (modify-phases %standard-phases + ;; This one test fails. + (replace 'check + (lambda _ (invoke "pytest" "-vv" "-k" "not test_f_string")))))) + (native-inputs + `(("python-pytest" ,python-pytest))))) + (define-public python-mccabe (package (name "python-mccabe") @@ -7366,35 +7517,16 @@ complexity of Python source code.") (define-public python2-pep8-1.5.7 (package-with-python2 python-pep8-1.5.7)) -;; Flake8 2.4.1 requires an older version of pyflakes. -;; This should be removed ASAP. -(define-public python-pyflakes-0.8.1 - (package (inherit python-pyflakes) - (version "0.8.1") - (source - (origin - (method url-fetch) - (uri (pypi-uri "pyflakes" version)) - (sha256 - (base32 - "0sbpq6pqm1i9wqi41mlfrsc5rk92jv4mskvlyxmnhlbdnc80ma1z")))) - (arguments - ;; XXX Tests not compatible with Python 3.5. - '(#:tests? #f)))) - -(define-public python2-pyflakes-0.8.1 - (package-with-python2 python-pyflakes-0.8.1)) - (define-public python-flake8 (package (name "python-flake8") - (version "3.7.7") + (version "3.7.9") (source (origin (method url-fetch) (uri (pypi-uri "flake8" version)) (sha256 (base32 - "0qg6zggqigrd4k3gv88shd1a27d0cwgfql8vfiq2c7rl7w3rd6c5")))) + "1yscj6avirm6m12bjh4fn2lfgxaamqsjh9pirdqfi0fcgq8ils25")))) (build-system python-build-system) (arguments `(#:phases @@ -7412,8 +7544,7 @@ complexity of Python source code.") ("python-mccabe" ,python-mccabe))) (native-inputs `(("python-mock" ,python-mock) - ("python-pytest" ,python-pytest-bootstrap) - ("python-pytest-runner" ,python-pytest-runner))) + ("python-pytest" ,python-pytest-bootstrap))) (home-page "https://gitlab.com/pycqa/flake8") (synopsis "The modular source code checker: pep8, pyflakes and co") @@ -7432,31 +7563,39 @@ complexity of Python source code.") ("python2-typing" ,python2-typing) ,@(package-propagated-inputs base)))))) -;; python-hacking requires flake8 <2.6.0. -(define-public python-flake8-2.5 +;; python-hacking requires flake8 <2.7.0. +(define-public python-flake8-2.6 (package (inherit python-flake8) - (version "2.5.5") + (version "2.6.2") (source (origin (method url-fetch) (uri (pypi-uri "flake8" version)) (sha256 (base32 - "1snylqwbmrylbx3r1wpz8ggk98f6bcag4441ag8mm2l7wyn58sij")))) + "0y57hzal0j84dh9i1g1g6dc4aywvrnhy2fjmmbglpv5ajihxh713")))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-later-pycodestyles + (lambda __ + (substitute* '("flake8.egg-info/requires.txt" + "setup.py") + (("pycodestyle >= 2.0, < 2.1") + "pycodestyle >= 2.0")) + #t)) + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (invoke "pytest" "-v") + #t))))) (propagated-inputs `(("python-pep8" ,python-pep8) - ,@(package-propagated-inputs python-flake8))) - (properties `((python2-variant . ,(delay python2-flake8-2.5)))))) - -(define-public python2-flake8-2.5 - (package - (inherit python2-flake8) - (version (package-version python-flake8-2.5)) - (source (origin - (inherit (package-source python-flake8-2.5)))) - (propagated-inputs - `(("python2-pep8" ,python2-pep8) - ,@(package-propagated-inputs python2-flake8))))) + ("python-pycodestyle" ,python-pycodestyle) + ("python-entrypoints" ,python-entrypoints) + ("python-pyflakes" ,python-pyflakes-1.2) + ("python-mccabe" ,python-mccabe))))) (define-public python-flake8-polyfill (package @@ -7680,13 +7819,13 @@ add functionality and customization to your projects with their own plugins.") (define-public python-fonttools (package (name "python-fonttools") - (version "3.38.0") + (version "4.6.0") (source (origin (method url-fetch) (uri (pypi-uri "fonttools" version ".zip")) (sha256 (base32 - "12ripk3s7skgxr1bs9r8n13r94ym3s8iir7ivfixls9fa4dabmlh")))) + "1mq9kdzhcsp96bhv7smnrpdg1s4z5wh70bsl99c0jmcrahqdisqq")))) (build-system python-build-system) (native-inputs `(("unzip" ,unzip) @@ -7702,8 +7841,18 @@ also contains a tool called “TTX” which converts TrueType/OpenType fonts to from an XML-based format.") (license license:expat))) +;; Fonttools 4.x dropped support for Python 2, so stick with 3.x here. (define-public python2-fonttools - (package-with-python2 python-fonttools)) + (let ((base (package-with-python2 (strip-python2-variant python-fonttools)))) + (package/inherit + base + (version "3.44.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "fonttools" version ".zip")) + (sha256 + (base32 + "0v6399g755f2hn1ry62i5b6gdinf2fpx2966v3bxh6bjw1accb5p"))))))) (define-public python-ly (package @@ -9229,6 +9378,18 @@ the standard library.") (native-inputs `(("python2-unittest2" ,python2-unittest2)))))) +;; This package is used by python2-pytest via python2-importlib-metadata, +;; and thus can not depend on python-unittest2 (which depends on pytest). +(define-public python2-contextlib2-bootstrap + (hidden-package + (package/inherit + python2-contextlib2 + (name "python2-contextlib2-bootstrap") + (arguments + `(#:tests? #f + ,@(package-arguments python2-contextlib2))) + (native-inputs '())))) + (define-public python-texttable (package (name "python-texttable") @@ -9702,14 +9863,14 @@ library as well as on the command line.") (define-public python-pluggy (package (name "python-pluggy") - (version "0.11.0") + (version "0.13.1") (source (origin (method url-fetch) (uri (pypi-uri "pluggy" version)) (sha256 (base32 - "10511a54dvafw1jrk75mrhml53c7b7w4yaw7241696lc2hfvr895")))) + "1c35qyhvy27q9ih9n899f3h4sdnpgq027dbiilly2qb5cvgarchm")))) (build-system python-build-system) (native-inputs `(("python-setuptools-scm" ,python-setuptools-scm))) @@ -9717,10 +9878,30 @@ library as well as on the command line.") (description "Pluggy is an extraction of the plugin manager as used by Pytest but stripped of Pytest specific details.") (home-page "https://pypi.org/project/pluggy/") + (properties `((python2-variant . ,(delay python2-pluggy)))) (license license:expat))) (define-public python2-pluggy - (package-with-python2 python-pluggy)) + (let ((base (package-with-python2 (strip-python2-variant + python-pluggy)))) + (package/inherit + base + (propagated-inputs + `(("python-importlib-metadata" ,python2-importlib-metadata)))))) + +;; This package requires python2-importlib-metadata, but that package +;; ends up needing python2-pluggy via python2-pytest, so we need this +;; variant to solve the circular dependency. +(define-public python2-pluggy-bootstrap + (hidden-package + (package/inherit + python2-pluggy + (name "python2-pluggy-bootstrap") + (arguments + `(#:tests? #f + ,@(package-arguments python2-pluggy))) + (propagated-inputs + `(("python-importlib-metadata" ,python2-importlib-metadata-bootstrap)))))) (define-public python-tox (package @@ -9874,13 +10055,16 @@ python-xdo for newer bindings.)") (arguments `(#:phases (modify-phases %standard-phases (replace 'check - (lambda _ - (invoke "pytest" "-vv")))))) + (lambda* (#:key tests? #:allow-other-keys) + (if tests? + (invoke "nosetests" "-v") + (format #t "test suite not run~%")) + #t))))) (propagated-inputs `(("python-markupsafe" ,python-markupsafe))) (native-inputs `(("python-mock" ,python-mock) - ("python-pytest" ,python-pytest))) + ("python-nose" ,python-nose))) (home-page "https://www.makotemplates.org/") (synopsis "Templating language for Python") (description "Mako is a templating language for Python that compiles @@ -10405,13 +10589,13 @@ anymore.") (define-public python2-pathlib2 (package (name "python2-pathlib2") - (version "2.3.3") + (version "2.3.5") (source (origin (method url-fetch) (uri (pypi-uri "pathlib2" version)) (sha256 (base32 - "0hpp92vqqgcd8h92msm9slv161b1q160igjwnkf2ag6cx0c96695")))) + "0s4qa8c082fdkb17izh4mfgwrjd1n5pya18wvrbwqdvvb5xs9nbc")))) (build-system python-build-system) ;; We only need the the Python 2 variant, since for Python 3 our minimum ;; version is 3.4 which already includes this package as part of the @@ -10978,13 +11162,13 @@ graphviz.") (define-public python-gevent (package (name "python-gevent") - (version "1.4.0") + (version "20.5.0") (source (origin (method url-fetch) (uri (pypi-uri "gevent" version)) (sha256 (base32 - "1lchr4akw2jkm5v4kz7bdm4wv3knkfhbfn9vkkz4s5yrkcxzmdqy")) + "1yppsrs0ccld9j9zfbsd0bxb987b2zkh2ar7whjxcrqzpkvg3iqx")) (modules '((guix build utils))) (snippet '(begin @@ -11010,14 +11194,16 @@ graphviz.") (find-files "src/greentest" "\\.py$")) #t)) (add-before 'build 'do-not-use-bundled-sources - (lambda* (#:key inputs #:allow-other-keys) + (lambda _ (setenv "GEVENTSETUP_EMBED" "0") ;; Prevent building bundled libev. (substitute* "setup.py" (("run_make=_BUILDING") "run_make=False")) - + #t)) + (add-before 'build 'add-greenlet-on-C_INCLUDE_PATH + (lambda* (#:key inputs #:allow-other-keys) (let ((greenlet (string-append (assoc-ref inputs "python-greenlet") "/include"))) @@ -11068,9 +11254,6 @@ graphviz.") "test_thread.py" "test_threading.py" "test__threading_2.py" - ;; FIXME: test_patch_twice_warning_events fails for - ;; no apparent reason. Needs more investigation! - "test__monkey.py" ;; These tests rely on KeyboardInterrupts which do not ;; work inside the build container for some reason ;; (lack of controlling terminal?). @@ -11078,12 +11261,15 @@ graphviz.") "test__issues461_471.py" ;; TODO: Patch out the tests that use getprotobyname, etc ;; instead of disabling all the tests from these files. + "test__resolver_dnspython.py" + "test__doctests.py" "test__all__.py" "test___config.py" "test__execmodules.py"))) (call-with-output-file "skipped_tests.txt" (lambda (port) - (display (string-join disabled-tests "\n") port))) + (format port "~a~%" + (string-join disabled-tests "\n")))) #t))) (replace 'check (lambda _ @@ -11666,7 +11852,7 @@ it will manage (install/update) them for you.") (base32 "1w1aaay424ciz8fz3fkzxb0pxzfxn184f2whpyn4fx72bn50x47k")))) (native-inputs - `(("python-setuptools-scm" ,python-setuptools-scm-3.3))) + `(("python-setuptools-scm" ,python-setuptools-scm))) (build-system python-build-system) (home-page "https://github.com/ionelmc/python-lazy-object-proxy") (synopsis "Lazy object proxy for python") @@ -11932,6 +12118,14 @@ characters, mouse support, and auto suggestions.") (arguments `(#:phases (modify-phases %standard-phases + (add-before 'check 'adjust-test-for-python-3.8 + (lambda _ + ;; Mimic upstream commit e7feeef64 to allow for extra output lines + ;; in TestSetupReadline on Python 3.8. Remove for jedi > 0.17.0. + (substitute* "test/test_utils.py" + (("assert len\\(difference\\) < 20") + "assert len(difference) < 22")) + #t)) (replace 'check (lambda _ (setenv "HOME" "/tmp") @@ -11955,20 +12149,6 @@ well.") (define-public python2-jedi (package-with-python2 python-jedi)) -;; python-language-server requires 0.15 specifically. Remove once unused. -(define-public python-jedi-0.15 - (package - (inherit python-jedi) - (version "0.15.2") - (source (origin - (method url-fetch) - (uri (pypi-uri "jedi" version)) - (sha256 - (base32 - "01zqasl690x1i6dq4mvh13pz0cw8i276xsivsrnn00x90iqm42g9")))) - (propagated-inputs - `(("python-parso" ,python-parso-0.5))))) - (define-public ptpython (package (name "ptpython") @@ -12915,14 +13095,14 @@ possible on all supported Python versions.") (define-public python-cheetah (package (name "python-cheetah") - (version "3.1.0") + (version "3.2.4") (source (origin (method url-fetch) (uri (pypi-uri "Cheetah3" version)) (sha256 (base32 - "1ihag9cxll6b86fc8v5lkhmr3brdbi4yiz16zpgw79yylmv8fgr9")))) + "0ar5dqjnqaw0c17mymd6xgd81jn9br9fblawr0x438v1571bkaya")))) (build-system python-build-system) (arguments `(#:modules ((guix build utils) @@ -12937,6 +13117,12 @@ possible on all supported Python versions.") (("#!/usr/bin/env python") (string-append "#!" (which "python")))) #t)) + (add-after 'unpack 'fix-tests + (lambda _ + (substitute* "Cheetah/Tests/ImportHooks.py" + (("os.path.dirname\\(__file__\\)") + (string-append "'" (getcwd) "/Cheetah/Tests'"))) + #t)) (replace 'check (lambda _ (let ((cwd (getcwd))) @@ -12992,7 +13178,7 @@ Features: (define-public python-dulwich (package (name "python-dulwich") - (version "0.18.6") + (version "0.19.16") (source (origin (method url-fetch) @@ -13001,7 +13187,7 @@ Features: (pypi-uri "dulwich" version))) (sha256 (base32 - "1aa1xfrxkc3j9s4xi0llhf5gndyi9ryprcxsqfa5fcb8ph34981q")))) + "0l589jl0lxx59yq0p6vmgw0q0hmfh48iqwyy0x6g1dmz93262igp")))) (build-system python-build-system) (arguments `(#:phases @@ -13021,7 +13207,8 @@ Features: (setenv "PYTHONHASHSEED" "random") #t))))) (propagated-inputs - `(("python-fastimport" ,python-fastimport))) + `(("python-fastimport" ,python-fastimport) + ("python-urllib3" ,python-urllib3))) (native-inputs `(("python-mock" ,python-mock) ("python-geventhttpclient" ,python-geventhttpclient) @@ -13346,13 +13533,13 @@ instead of servers and network commands.") (define-public python-automat (package (name "python-automat") - (version "0.7.0") + (version "20.2.0") (source (origin (method url-fetch) (uri (pypi-uri "Automat" version)) (sha256 (base32 - "03ivg70n3b1cbcd2zvjhk8y4kmqxcvhmili39lmgx09dza1qpmyb")))) + "0cyzrcqiibwdsp4y0djkllnzab8m5faa4s0d1kpi23k1fhy80ybr")))) (build-system python-build-system) ;; We disable the tests because they require python-twisted, while ;; python-twisted depends on python-automat. Twisted is optional, but the @@ -13426,13 +13613,13 @@ and bit flag values.") (define-public python-attrs (package (name "python-attrs") - (version "19.1.0") + (version "19.3.0") (source (origin (method url-fetch) (uri (pypi-uri "attrs" version)) (sha256 (base32 - "16g33zr5f449lqc5wgvzpknxryfzrfsxcr6kpgxwn7l5fkv71f7h")))) + "0wky4h28n7xnr6xv69p9z6kv8bzn50d10c3drmd9ds8gawbcxdzp")))) (build-system python-build-system) (arguments `(#:modules ((guix build utils) @@ -13774,14 +13961,16 @@ of @code{functools.lru_cache} from python 3.3.") (define-public python-configparser (package (name "python-configparser") - (version "3.7.1") + (version "4.0.2") (source (origin (method url-fetch) (uri (pypi-uri "configparser" version)) (sha256 (base32 - "0cnz213il9lhgda6x70fw7mfqr8da43s3wm343lwzhqx94mgmmav")))) + "1priacxym85yjcf68hh38w55nqswaxp71ryjyfdk222kg9l85ln7")))) + (native-inputs + `(("python-setuptools_scm" ,python-setuptools-scm))) (build-system python-build-system) (home-page "https://github.com/jaraco/configparser/") (synopsis "Backport of configparser from python 3.5") @@ -14006,13 +14195,13 @@ It supports both normal and Unicode strings.") (define-public python-scandir (package (name "python-scandir") - (version "1.9.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (pypi-uri "scandir" version)) (sha256 - (base32 "0r3hvf1a9jm1rkqgx40gxkmccknkaiqjavs8lccgq9s8khh5x5s4")))) + (base32 "1bkqwmf056pkchf05ywbnf659wqlp6lljcdb0y88wr9f0vv32ijd")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases @@ -14147,7 +14336,11 @@ several utilities, as well as an API for building localization tools.") (arguments `(#:phases (modify-phases %standard-phases (replace 'check - (lambda _ (invoke "py.test" "-vv")))))) + (lambda* (#:key tests? #:allow-other-keys) + (if tests? + (invoke "py.test" "-vv") + (format #t "test suite not run~%")) + #t))))) (native-inputs `(("python-pretend" ,python-pretend) ("python-pytest" ,python-pytest))) @@ -14168,6 +14361,29 @@ information.") (define-public python2-packaging (package-with-python2 python-packaging)) +;; Variants with minimal dependencies, for bootstrapping Pytest. +(define-public python-packaging-bootstrap + (hidden-package + (package/inherit + python-packaging + (name "python-packaging-bootstrap") + (native-inputs '()) + (propagated-inputs + `(("python-pyparsing" ,python-pyparsing))) + (arguments '(#:tests? #f))))) + +(define-public python2-packaging-bootstrap + (hidden-package + (package/inherit + python2-packaging + (name "python2-packaging-bootstrap") + (native-inputs '()) + (propagated-inputs + `(("python-pyparsing" ,python2-pyparsing))) + (arguments + `(#:tests? #f + ,@(package-arguments python2-packaging)))))) + (define-public python-relatorio (package (name "python-relatorio") @@ -15930,14 +16146,14 @@ based on the CPython 2.7 and 3.7 parsers.") (define-public python-typing (package (name "python-typing") - (version "3.6.6") + (version "3.7.4.1") (source (origin (method url-fetch) (uri (pypi-uri "typing" version)) (sha256 (base32 - "0ba9acs4awx15bf9v3nrs781msbd2nx826906nj6fqks2bvca9s0")))) + "08xs7s5pyq99hbrzw23inczmidz90krvpv9q5p1qrvh6yzrydpwi")))) (build-system python-build-system) (home-page "https://docs.python.org/3/library/typing.html") (synopsis "Type hints for Python") @@ -16158,14 +16374,14 @@ file system events on Linux.") (define-public python-more-itertools (package (name "python-more-itertools") - (version "7.1.0") + (version "8.2.0") (source (origin (method url-fetch) (uri (pypi-uri "more-itertools" version)) (sha256 (base32 - "16phg2f2dvm6ci5wr49ncha5lmc0m2in3bsl33c61vzca4gkvd4b")))) + "01x5nwm1zxmnd06cllbdd095xxc2nd25ing1a726m2kd30rbkpdi")))) (build-system python-build-system) (home-page "https://github.com/erikrose/more-itertools") (synopsis "More routines for operating on iterables, beyond itertools") @@ -16189,7 +16405,7 @@ working with iterables.") (base32 "1r12cm6mcdwdzz7d47a6g4l437xsvapdlgyhqay3i2nrlv03da9q")))) (arguments - `(#:python ,python2-minimal)) + `(#:python ,python-2)) (propagated-inputs `(("python2-six" ,python2-six-bootstrap))))) @@ -16282,19 +16498,6 @@ Parso is also able to list multiple syntax errors in your Python file.") (define-public python2-parso (package-with-python2 python-parso)) -;; This version is required for Jedi@0.15, which in turn is needed for -;; python-language-server. -(define-public python-parso-0.5 - (package - (inherit python-parso) - (version "0.5.2") - (source (origin - (method url-fetch) - (uri (pypi-uri "parso" version)) - (sha256 - (base32 - "1qgvrkpma7vylrk047mxxvqd66nwqk978n3ig2w8iz9m3bgjbksm")))))) - (define-public python-async-generator (package (name "python-async-generator") @@ -17111,14 +17314,15 @@ that is accessible to other projects developed in Cython.") (base32 "0fm0w5id2yhqld95hg2m636vjgkz377rvgdfqaxc25vbylr9lklp")))) (build-system python-build-system) - (native-inputs - `(("python-tox" ,python-tox))) + (arguments + ;; FIXME: Tests require many extra dependencies, and would introduce + ;; a circular dependency on hypothesis, which uses this package. + '(#:tests? #f)) (propagated-inputs `(("python-appdirs" ,python-appdirs) ("python-distlib" ,python-distlib) ("python-filelock" ,python-filelock) - ("python-importlib-metadata" ,python-importlib-metadata) ;; python < 3.8 - ("python-six" ,python-six))) + ("python-six" ,python-six-bootstrap))) (home-page "http://www.grantjenks.com/docs/sortedcontainers/") (synopsis "Sorted List, Sorted Dict, Sorted Set") (description @@ -17126,6 +17330,9 @@ that is accessible to other projects developed in Cython.") pure-Python.") (license license:asl2.0))) +(define-public python2-sortedcontainers + (package-with-python2 python-sortedcontainers)) + (define-public python-cloudpickle (package (name "python-cloudpickle") @@ -19588,3 +19795,70 @@ workspace...") dependencies. It implements the @uref{http://opensoundcontrol.org/spec-1_0, Open Sound Control 1.0} specification.") (license license:unlicense))) + +(define-public python-voluptuous + (package + (name "python-voluptuous") + (version "0.11.7") + (source + (origin + (method url-fetch) + (uri (pypi-uri "voluptuous" version)) + (sha256 + (base32 + "0mplkcpb5d8wjf8vk195fys4y6a3wbibiyf708imw33lphfk9g1a")))) + (build-system python-build-system) + (native-inputs + `(("python-nose" ,python-nose))) + (home-page "https://github.com/alecthomas/voluptuous") + (synopsis "Python data validation library") + (description + "Voluptuous is a Python data validation library. It is primarily +intended for validating data coming into Python as JSON, YAML, etc.") + (license license:bsd-3))) + +(define-public python-cmd2 + (package + (name "python-cmd2") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "cmd2" version)) + (sha256 + (base32 + "1f18plbc9yyvhn0js3d2bii9yld8zfl775gxsaw9jza5pmlg9ss2")))) + (build-system python-build-system) + (propagated-inputs + `(("python-attrs" ,python-attrs) + ("python-colorama" ,python-colorama) + ("python-pyperclip" ,python-pyperclip) + ("python-wcwidth" ,python-wcwidth))) + (native-inputs + `(("python-codecov" ,python-codecov) + ("python-coverage" ,python-coverage) + ("python-doc8" ,python-doc8) + ("python-flake8" ,python-flake8) + ("python-invoke" ,python-invoke) + ("python-mock" ,python-mock) + ("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-mock" ,python-pytest-mock) + ("python-setuptools-scm" ,python-setuptools-scm) + ("python-sphinx" ,python-sphinx) + ("python-sphinx-autobuild" ,python-sphinx-autobuild) + ("python-sphinx-rtd-theme" ,python-sphinx-rtd-theme) + ("python-tox" ,python-tox) + ("python-twine" ,python-twine) + ("which" ,which))) + (home-page "https://github.com/python-cmd2/cmd2") + (synopsis "Tool for building interactive command line applications") + (description + "Cmd2 is a tool for building interactive command line applications in +Python. Its goal is to make it quick and easy for developers to build +feature-rich and user-friendly interactive command line applications. It +provides a simple API which is an extension of Python's built-in @code{cmd} +module. @code{cmd2} provides a wealth of features on top of @code{cmd} to +make your life easier and eliminates much of the boilerplate code which would +be necessary when using @code{cmd}.") + (license license:expat))) |