From 4c24186ae0798cd3263c1647d5f9aab0719b3d15 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Mon, 27 Apr 2020 13:09:02 +0200 Subject: gnu: Add python-bitarray. * gnu/packages/python-xyz.scm (python-bitarray): New variable. --- gnu/packages/python-xyz.scm | 26 +++++++++++++++++++++++++- 1 file changed, 25 insertions(+), 1 deletion(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 9460a59e31..31cafd47d1 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -39,7 +39,7 @@ ;;; Copyright © 2017 Ben Sturmfels ;;; Copyright © 2017, 2018, 2019 Mathieu Othacehe ;;; Copyright © 2017 José Miguel Sánchez García -;;; Copyright © 2017 Roel Janssen +;;; Copyright © 2017, 2020 Roel Janssen ;;; Copyright © 2017, 2018, 2019 Kei Kebreau ;;; Copyright © 2017 Rutger Helling ;;; Copyright © 2017 Muriithi Frederick Muriuki @@ -640,6 +640,30 @@ 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") -- cgit v1.2.3 From 39a96b99fe66c2cf7ff8ff023f3839647332ebd9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 29 Apr 2020 13:37:22 +0200 Subject: gnu: Add python-restructuredtext-lint. * gnu/packages/python-xyz.scm (python-restructuredtext-lint): New variable. --- gnu/packages/python-xyz.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 31cafd47d1..45789d7eb5 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3212,6 +3212,38 @@ 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-pygments (package (name "python-pygments") -- cgit v1.2.3 From ff5ca61d15e979f1a91d77f950af13c76dd9b00a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 29 Apr 2020 13:41:13 +0200 Subject: gnu: Add python-doc8. * gnu/packages/python-xyz.scm (python-doc8): New variable. --- gnu/packages/python-xyz.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 45789d7eb5..decc1ce8a6 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3244,6 +3244,45 @@ 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") -- cgit v1.2.3 From ad2736717a475fa696b4fe637d722f31ed520a8d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 28 Apr 2020 13:41:38 +0200 Subject: gnu: python-psutil: Update to 5.7.0. * gnu/packages/python-xyz.scm (python-psutil): Update to 5.7.0. --- gnu/packages/python-xyz.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index decc1ce8a6..6f881161fd 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -412,16 +412,17 @@ 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") -- cgit v1.2.3 From 88f8a7c6100302e66e9a0058ae018042cdd27b62 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 29 Apr 2020 14:12:37 +0200 Subject: gnu: Add python-voluptuous. * gnu/packages/python-xyz.scm (python-voluptuous): New variable. --- gnu/packages/python-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 6f881161fd..e6088bd6ce 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19660,3 +19660,24 @@ 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))) -- cgit v1.2.3 From 7e3ddb6904e27b18f364b7c3b161f2927017155c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 29 Apr 2020 14:12:49 +0200 Subject: gnu: Add python-cmd2. * gnu/packages/python-xyz.scm (python-cmd2): New variable. --- gnu/packages/python-xyz.scm | 46 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e6088bd6ce..c37ed2bfa0 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19681,3 +19681,49 @@ Open Sound Control 1.0} specification.") "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))) -- cgit v1.2.3 From 37130eccd23eccfdc6653c3e73321fea4000d51d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 29 Apr 2020 22:16:31 +0200 Subject: gnu: Remove python2-pyflakes-0.8.1. * gnu/packages/python-xyz.scm (python2-pyflakes-0.8.1): Remove variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c37ed2bfa0..c6c6bf2c3e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -7454,9 +7454,6 @@ complexity of Python source code.") ;; 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") -- cgit v1.2.3 From a6559240098d8b8ff7f799f57aecf96a53a88401 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 29 Apr 2020 22:19:25 +0200 Subject: gnu: Replace python-pyflakes-0.8.1 with python-pyflakes-1.2. * gnu/packages/python-xyz.scm (python-pyflakes-0.8.1): Remove variable. (python-pyflakes-1.2): New variable. * gnu/packages/openstack.scm (python-hacking)[propagated-inputs]: Replace python-pyflakes-0.8.1 with python-pyflakes-1.2. --- gnu/packages/python-xyz.scm | 37 +++++++++++++++++++++---------------- 1 file changed, 21 insertions(+), 16 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c6c6bf2c3e..80185f49e0 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -7380,6 +7380,27 @@ 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") @@ -7438,22 +7459,6 @@ 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 python-flake8 (package (name "python-flake8") -- cgit v1.2.3 From 7fea8e076fd2405c0d53d7ee5d7a36936215ffcc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 29 Apr 2020 22:23:19 +0200 Subject: gnu: Remove python2-flake8-2.5. * gnu/packages/python-xyz.scm (python2-flake8-2.5): Remove variable. (python-flake8-2.5)[properties]: Remove. --- gnu/packages/python-xyz.scm | 13 +------------ 1 file changed, 1 insertion(+), 12 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 80185f49e0..1110360afd 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -7519,18 +7519,7 @@ complexity of Python source code.") "1snylqwbmrylbx3r1wpz8ggk98f6bcag4441ag8mm2l7wyn58sij")))) (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))))) + ,@(package-propagated-inputs python-flake8))))) (define-public python-flake8-polyfill (package -- cgit v1.2.3 From 7b0e0fd5a2f963758d4c9161e9f2844e56289dad Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 29 Apr 2020 22:24:49 +0200 Subject: gnu: python-flake8-2.5: Update to 2.6.2. * gnu/packages/python-xyz.scm (python-flake8-2.5): Update to 2.6.2; rename it... (python-flake8-2.6): ...to this. [arguments]: Add phase "use-later-pycodestyles", and move "check" phase after "install". [propagated-inputs]: Explicitly list python-pycodestyle, python-entrypoints, python-pyflakes-1.2, and python-mccabe. --- gnu/packages/python-xyz.scm | 29 ++++++++++++++++++++++++----- 1 file changed, 24 insertions(+), 5 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 1110360afd..0f4351d152 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -7506,20 +7506,39 @@ 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))))) + ("python-pycodestyle" ,python-pycodestyle) + ("python-entrypoints" ,python-entrypoints) + ("python-pyflakes" ,python-pyflakes-1.2) + ("python-mccabe" ,python-mccabe))))) (define-public python-flake8-polyfill (package -- cgit v1.2.3 From cf1ae793753e9da0d774f4a5495648f15d400b49 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 30 Apr 2020 13:06:01 +0200 Subject: gnu: python2-pysnptools: Update to 0.4.11. * gnu/packages/python-xyz.scm (python2-pysnptools): Update to 0.4.11; implement in terms of... (python-pysnptools): ...this new variable. [propagated-inputs]: Add python-dill, python-h5py, and python-psutil. --- gnu/packages/python-xyz.scm | 34 ++++++++++++++++++++++++---------- 1 file changed, 24 insertions(+), 10 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 0f4351d152..74280befea 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -4876,27 +4876,38 @@ 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 @@ -4906,6 +4917,9 @@ 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") -- cgit v1.2.3