diff options
Diffstat (limited to 'gnu/packages/python-xyz.scm')
| -rw-r--r-- | gnu/packages/python-xyz.scm | 285 |
1 files changed, 236 insertions, 49 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 25b8cd6529..642bf1ec9d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -39,7 +39,7 @@ ;;; Copyright © 2017 Ben Sturmfels <ben@sturm.com.au> ;;; Copyright © 2017, 2018, 2019 Mathieu Othacehe <m.othacehe@gmail.com> ;;; Copyright © 2017 José Miguel Sánchez García <jmi2k@openmailbox.org> -;;; Copyright © 2017 Roel Janssen <roel@gnu.org> +;;; Copyright © 2017, 2020 Roel Janssen <roel@gnu.org> ;;; Copyright © 2017, 2018, 2019 Kei Kebreau <kkebreau@posteo.net> ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com> ;;; Copyright © 2017 Muriithi Frederick Muriuki <fredmanglis@gmail.com> @@ -413,16 +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") @@ -641,6 +642,30 @@ certificate returned by the server to which a connection has been established, and verifies that it matches the intended target hostname.") (license license:psfl))) +(define-public python-bitarray + (package + (name "python-bitarray") + (version "1.2.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "bitarray" version)) + (sha256 + (base32 + "1kxrlxfj9nrx512sfwifwl9z4v6ky3qschl0zmk3s3dvc3s7bmif")))) + (build-system python-build-system) + (home-page "https://github.com/ilanschnell/bitarray") + (synopsis "Efficient arrays of booleans") + (description "This package provides an object type which efficiently +represents an array of booleans. Bitarrays are sequence types and behave very +much like usual lists. Eight bits are represented by one byte in a contiguous +block of memory. The user can select between two representations: +little-endian and big-endian. All of the functionality is implemented in C. +Methods for accessing the machine representation are provided. This can be +useful when bit level access to binary files is required, such as portable +bitmap image files. Also, when dealing with compressed data which uses +variable bit length encoding, you may find this module useful.") + (license license:psfl))) + (define-public python-boolean.py (package (name "python-boolean.py") @@ -3208,6 +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") @@ -4794,27 +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 @@ -4824,6 +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") @@ -7328,6 +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") @@ -7386,25 +7517,6 @@ 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") @@ -7451,31 +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 @@ -19695,3 +19815,70 @@ 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))) |