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-rw-r--r--gnu/packages/python-xyz.scm285
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)))