;;; Copyright © 2015, 2016 Chris Marusich <cmmarusich@gmail.com>
;;; Copyright © 2016 Danny Milosavljevic <dannym+a@scratchpost.org>
;;; Copyright © 2016 Lukas Gradl <lgradl@openmailbox.org>
-;;; Copyright © 2016, 2018 Hartmut Goebel <h.goebel@crazy-compilers.com>
+;;; Copyright © 2016, 2018-2019 Hartmut Goebel <h.goebel@crazy-compilers.com>
;;; Copyright © 2016 Daniel Pimentel <d4n1@d4n1.org>
;;; Copyright © 2016 Sou Bunnbu <iyzsong@gmail.com>
;;; Copyright © 2016, 2017 Troy Sankey <sankeytms@gmail.com>
;;; Copyright © 2017 Frederick M. Muriithi <fredmanglis@gmail.com>
;;; Copyright © 2017, 2018 Adriano Peluso <catonano@gmail.com>
;;; Copyright © 2017 Ben Sturmfels <ben@sturm.com.au>
-;;; Copyright © 2017, 2018 Mathieu Othacehe <m.othacehe@gmail.com>
+;;; 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, 2018 Kei Kebreau <kkebreau@posteo.net>
;;; Copyright © 2019 Pierre Langlois <pierre.langlois@gmx.com>
;;; Copyright © 2019 Jacob MacDonald <jaccarmac@gmail.com>
;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
+;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
+;;; Copyright © 2019 Tanguy Le Carrour <tanguy@bioneland.org>
;;;
;;; This file is part of GNU Guix.
;;;
(define-public python-psutil
(package
(name "python-psutil")
- (version "5.6.2")
+ (version "5.6.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "psutil" version))
(sha256
- (base32
- "1v95vb5385qscfdvphv8l2w22bmir3d7yhpi02n58v3mlqy1r3l2"))))
+ (base32 "1wv31zly44qj0rp2acg58xbnc7bf6ffyadasq093l455q30qafl6"))))
(build-system python-build-system)
(arguments
;; FIXME: some tests does not return and times out.
(arguments
`(#:phases (modify-phases %standard-phases
(replace 'check
- (lambda _ (invoke "pytest" "-vv"))))))
+ (lambda _
+ (invoke "pytest" "-vv" "-k"
+ (string-append
+ ;; XXX: These tests fail when using Pytest 4.x and
+ ;; Babel 2.6.0. Try removing this for later versions.
+ "not test_no_inherit_metazone_marker_never_in_output"
+ " and not test_smoke_dates"
+ " and not test_smoke_numbers")))))))
(home-page "http://babel.pocoo.org/")
(synopsis
"Tools for internationalizing Python applications")
and verifies that it matches the intended target hostname.")
(license license:psfl)))
+(define-public python-boolean.py
+ (package
+ (name "python-boolean.py")
+ (version "3.6")
+ (source
+ (origin
+ ;; There's no source tarball on PyPI.
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/bastikr/boolean.py")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1wc89y73va58cj7dsx6c199zpxsy9q53dsffsdj6zmc90inqz6qs"))))
+ (build-system python-build-system)
+ (home-page "https://github.com/bastikr/boolean.py")
+ (synopsis "Boolean algebra in one Python module")
+ (description
+ "This is a small Python library that implements boolean algebra.
+It defines two base elements, @code{TRUE} and @code{FALSE}, and a
+@code{Symbol} class that can take on one of these two values. Calculations
+are done only in terms of @code{AND}, @code{OR}, and @code{NOT}---other
+compositions like @code{XOR} and @code{NAND} are emulated on top of them.
+Expressions are constructed from parsed strings or directly in Python.")
+ (license license:bsd-2)))
+
(define-public python-hdf4
(package
(name "python-hdf4")
(define-public python-cftime
(package
(name "python-cftime")
- (version "1.0.3.4")
+ (version "1.0.4.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "cftime" version))
(sha256
- (base32
- "0362dhxbzk593walyjz30dll6y2y79wialik647cbwdsf3ad0x6x"))))
+ (base32 "0w0gi6jnch38hiygl62j4xkcirv4y3dcwrvxl9p7bsk6j27lzihs"))))
(build-system python-build-system)
(propagated-inputs
`(("python-numpy" ,python-numpy)))
(define-public python2-netcdf4
(package-with-python2 python-netcdf4))
+(define-public python-license-expression
+ (package
+ (name "python-license-expression")
+ (version "0.999")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "license-expression" version))
+ (sha256
+ (base32 "08ppb0bxbrsxazy88sgpl9yffvdsabw6dkk1nc332wcz2mphwwyf"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-boolean.py" ,python-boolean.py)))
+ (home-page "https://github.com/nexB/license-expression")
+ (synopsis "Apply boolean logic to license expressions")
+ (description
+ "This Python module defines a tiny language to evaluate and compare
+license expressions using boolean logic. Logical combinations of licenses can
+be tested for equality, containment, and equivalence. They can be normalised
+and simplified. It supports SPDX license expressions as well as other naming
+conventions and aliases in the same expression.")
+ (license license:gpl2+)))
+
(define-public python-lockfile
(package
(name "python-lockfile")
(define-public python2-setuptools
(package-with-python2 python-setuptools))
+;; The setuptools provided by Python 3.7.4 is too new for Tensorflow.
+(define-public python-setuptools-for-tensorflow
+ (hidden-package
+ (package
+ (inherit python-setuptools)
+ (version "39.1.0")
+ (source (origin
+ (inherit (package-source python-setuptools))
+ (uri (pypi-uri "setuptools" version ".zip"))
+ (sha256
+ (base32
+ "1mzdhvfhnv4lggxa8rjl0dzqxvfx377gg5sqs57v89wrp09lwj65")))))))
+
(define-public python-uniseg
(package
(name "python-uniseg")
(base32
"09z4d1jiasn7k1hs5af2ckmnrd0i1d1m04bhfjhv7z6svzfdwgg3"))))
(build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ ;; Do not run pylint plugin test, as astroid is an old
+ ;; unsupported version.
+ (invoke "pytest" "-v" "-k" "not test_pylint_plugin"
+ "verboselogs/tests.py"))))))
(native-inputs
`(("python-mock" ,python-mock)
- ("python-astroid" ,python-astroid)
- ("python-pylint" ,python-pylint)))
+ ("python-pytest" ,python-pytest)))
(home-page "https://verboselogs.readthedocs.io")
(synopsis "Verbose logging level for Python's logging module")
(description
(define-public python-coloredlogs
(package
(name "python-coloredlogs")
- (version "7.3")
+ (version "10.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "coloredlogs" version))
(sha256
(base32
- "1blcann6dyg5dhps9pg12rn0q0rjrlajpmmil0gy0j4cbvnl2il9"))))
+ "0dkw6xp0r1dwgz4s2f58npx5nxfq51wf4l6qkm5ib27slgfs4sdq"))))
(build-system python-build-system)
(arguments
`(;Tests require some updated modules
(define-public python2-coloredlogs
(package-with-python2 python-coloredlogs))
+(define-public python-editorconfig
+ (package
+ (name "python-editorconfig")
+ (version "0.12.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "EditorConfig" version))
+ (sha256
+ (base32
+ "0v55z351p9qkyp3bbspwywwn28sbcknhirngjbj779n3z52z63hv"))))
+ (build-system python-build-system)
+ (home-page "https://editorconfig.org/")
+ (synopsis "EditorConfig bindings for python")
+ (description "The EditorConfig project consists of a file format for
+defining coding styles and a collection of text editor plugins that enable
+editors to read the file format and adhere to defined styles. EditorConfig
+files are easily readable and they work nicely with version control systems.")
+ ;; "fnmatch.py" and "ini.py" are licensed under psfl, the rest is bsd-2.
+ (license (list license:bsd-2 license:psfl))))
+
(define-public python-et-xmlfile
(package
(name "python-et-xmlfile")
(define-public python-six
(package
(name "python-six")
- (version "1.11.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "six" version))
(sha256
(base32
- "1scqzwc51c875z23phj48gircqjgnn3af8zy2izjwmnlxrxsgs3h"))))
+ "0wxs1q74v07ssjywbbm7x6h5v9qx209ld2yfsif4060sxi0h2sni"))))
(build-system python-build-system)
(arguments
`(#:phases
(define-public python-pyicu
(package
(name "python-pyicu")
- (version "2.2")
+ (version "2.3.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "PyICU" version))
(sha256
(base32
- "0wq9y5fi1ighgf5aws9nr87vi1w44p7q1k83rx2y3qj5d2xyhspa"))))
+ "1x4w8m7ifki9z2a187pgjr33z6z0rp2fii9b73djak1vhm9v9cnx"))))
(build-system python-build-system)
(inputs
`(("icu4c" ,icu4c)))
;; Tests don't work with python2.
#:tests? #f)))))
+(define-public python-poyo
+ (package
+ (name "python-poyo")
+ (version "0.5.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "poyo" version))
+ (sha256
+ (base32
+ "1pflivs6j22frz0v3dqxnvc8yb8fb52g11lqr88z0i8cg2m5csg2"))))
+ (build-system python-build-system)
+ (home-page "https://github.com/hackebrot/poyo")
+ (synopsis "Lightweight YAML Parser for Python")
+ (description
+ "This package provides a lightweight YAML Parser for Python. It supports
+only a chosen subset of the YAML format that is required to parse cookiecutter
+user configuration files. It does not have support for serializing into YAML
+and is not compatible with JSON.")
+ (license license:expat)))
+
(define-public scons
(package
(name "scons")
(define-public python-py
(package
(name "python-py")
- (version "1.5.4")
+ (version "1.8.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "py" version))
(sha256
(base32
- "1xxvwfn82457djf55f5n2c94699rfqnk43br8fif2r2q8gvrmm9z"))))
+ "0lsy1gajva083pzc7csj1cvbmminb7b4l6a0prdzyb3fd829nqyw"))))
(build-system python-build-system)
(arguments
;; FIXME: "ImportError: 'test' module incorrectly imported from
(define-public python-pyld
(package
(name "python-pyld")
- (version "1.0.3")
+ (version "1.0.5")
(source (origin
(method url-fetch)
(uri (pypi-uri "PyLD" version))
(sha256
(base32
- "12i2g6xdj30k7xxcibg3sc5y76snwq8l6n8fy9lyi577kgy0h2pm"))))
+ "1ywbdbsrkg533qh8xn9ifjh2mvam6v5msrjyqq73jfpvcp89qvff"))))
(build-system python-build-system)
(home-page "https://github.com/digitalbazaar/pyld")
(synopsis "Python implementation of the JSON-LD specification")
(define-public python-unidecode
(package
(name "python-unidecode")
- (version "1.1.0")
+ (version "1.1.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "Unidecode" version))
(sha256
(base32
- "00pi0czzwvbf7djhkkjyvimj60wqdx0llbddzfnax650g9b8yscc"))))
+ "1s6cp2lv4m0f00hjckjz8p6m7d3n3v16jvg353llf5ia1iqsnsib"))))
(build-system python-build-system)
(home-page "https://pypi.python.org/pypi/Unidecode")
(synopsis "ASCII transliterations of Unicode text")
(define-public python-pyjwt
(package
(name "python-pyjwt")
- (version "1.5.3")
+ (version "1.7.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "PyJWT" version))
(sha256
(base32
- "1rxsg14i33vm2i6lz0my628108c81k43v10n4h3p0gx62xdyf2sh"))
+ "15hflax5qkw1v6nssk1r0wkj83jgghskcmn875m3wgvpzdvajncd"))
(modules '((guix build utils)))
(snippet
'(begin
(package
(name "python-pympler")
(home-page "https://pythonhosted.org/Pympler/")
- (version "0.5")
+ (version "0.7")
(source (origin
(method url-fetch)
(uri (pypi-uri "Pympler" version))
(sha256
(base32
- "03qwsbilqgvnbl3a1jmpgixbr2kq6m3fvdlzyr3wdp01bwlc85kx"))))
+ "0ki7bqp1h9l1xc2k1h4vjyzsgs20i8ingvcdhszyi72s28wyf4bs"))))
(build-system python-build-system)
(arguments
`(#:phases (modify-phases %standard-phases
(define-public python2-jinja2
(package-with-python2 python-jinja2))
+(define-public python-jinja2-time
+ (package
+ (name "python-jinja2-time")
+ (version "0.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "jinja2-time" version))
+ (sha256
+ (base32
+ "0h0dr7cfpjnjj8bgl2vk9063a53649pn37wnlkd8hxjy656slkni"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-arrow" ,python-arrow)
+ ("python-jinja2" ,python-jinja2)))
+ (home-page
+ "https://github.com/hackebrot/jinja2-time")
+ (synopsis "Jinja2 Extension for Dates and Times")
+ (description
+ "This package provides an extension for the template engine Jinja2. It
+adds a 'now' tag providing a convenient access to the arrow.now() API from
+templates. A format string can be provided to control the output.")
+ (license license:expat)))
+
(define-public python-pystache
(package
(name "python-pystache")
(define-public python-pygithub
(package
(name "python-pygithub")
- (version "1.43.7")
+ (version "1.43.8")
(source
;; We fetch from the Git repo because there are no tests in the PyPI
;; archive.
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32
- "0ww92zz0ja9w6rw83vphmn8rwmcn6abg16j4q7zxjc0rrg2cfj9i"))))
+ (base32 "1625v558xga5mwhl9jqmibywy5qafmg1vqrirqz6zfq1la1d22mw"))))
(build-system python-build-system)
(arguments
`(#:phases (modify-phases %standard-phases
(define-public python-rst.linker
(package
(name "python-rst.linker")
- (version "1.10")
+ (version "1.11")
(source
(origin
(method url-fetch)
(uri (pypi-uri "rst.linker" version))
(sha256
- (base32
- "0iqaacp7pj1s8avs4kc0qg0r7dscywaq37y6l9j14glqdikk0wdj"))))
+ (base32 "0pqsfqqx8h0pq21k8l3k62kznrgaj2ala93c64s4d9rpbr4mgkd2"))))
(build-system python-build-system)
(propagated-inputs
`(("python-dateutil" ,python-dateutil)
(define-public python-language-server
(package
(name "python-language-server")
- (version "0.26.1")
+ (version "0.29.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "python-language-server" version))
(sha256
(base32
- "1vs9ckfmm534n1hq3m871916wsjvi5h4gyj6wlzg13ck6506lx0s"))))
+ "1f8qlflh6j3s7qfmzhirpl8fgidl6f0qbakdmiml96wdxzvka0s3"))))
(build-system python-build-system)
(propagated-inputs
`(("python-pluggy" ,python-pluggy)
("python-mccabe" ,python-mccabe)
("python-rope" ,python-rope)
("python-autopep8" ,python-autopep8)
+ ("python-flake8" ,python-flake8)
("python-pylint" ,python-pylint)))
(home-page "https://github.com/palantir/python-language-server")
(synopsis "Python implementation of the Language Server Protocol")
(properties `((python2-variant . ,(delay python2-cython))))))
(define-public python2-cython
- (package (inherit (package-with-python2
- (strip-python2-variant python-cython)))
- (name "python2-cython")
- (inputs
- `(("python-2" ,python-2))))) ; this is not automatically changed
+ (let ((base (package-with-python2 (strip-python2-variant python-cython))))
+ (package
+ (inherit base)
+ (name "python2-cython")
+ (inputs
+ `(("python-2" ,python-2))) ;this is not automatically changed
+ (arguments
+ (substitute-keyword-arguments (package-arguments base)
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (add-before 'check 'adjust-test_embed
+ (lambda _
+ (substitute* "runtests.py"
+ ;; test_embed goes great lengths to find the static libpythonX.Y.a
+ ;; so it can give the right -L flag to GCC when embedding static
+ ;; builds of Python. It is unaware that the Python "config"
+ ;; directory (where the static library lives) was renamed in
+ ;; Python 3, and falls back to sysconfig.get_config_var('LIBDIR'),
+ ;; which works fine, because that is where the shared library is.
+ ;;
+ ;; It also appears to be unaware that the Makefile in Demos/embed
+ ;; already unconditionally pass the static library location to GCC,
+ ;; after checking sysconfig.get_config_var('LIBPL).
+ ;;
+ ;; The effect is that the linker is unable to resolve libexpat
+ ;; symbols when building for Python 2, because neither the Python 2
+ ;; shared library nor Expat is available. To fix it, we can either
+ ;; add Expat as an input and make it visible to the linker, or just
+ ;; prevent it from overriding the Python shared library location.
+ ;; The end result is identical, so we take the easy route.
+ ((" or libname not in os\\.listdir\\(libdir\\)")
+ ""))
+ #t)))))))))
;; The RPython toolchain currently does not support Python 3.
(define-public python2-rpython
(define-public python-colorspacious
(package
(name "python-colorspacious")
- (version "1.1.0")
+ (version "1.1.2")
(source
(origin
(method git-fetch)
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0g0lxqiscy5g5rq9421vv7abg0c90jzy0zmas2z3hya6k2dr5aid"))))
+ (base32 "0x7nkphr6g5ql5fvgss8l56rgiyjgh6fm8zzs73i94ci9wzlm63w"))))
(build-system python-build-system)
(propagated-inputs
`(("python-numpy" ,python-numpy)))
(define-public python-matplotlib
(package
(name "python-matplotlib")
- (version "2.2.3")
+ (version "3.1.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "matplotlib" version))
(sha256
(base32
- "1rcc7x9ig3hpchkc4cwdvym3y451w74275fxr455zkfagrsvymbk"))))
+ "14qc109dibp32xfd9lah54djc0rc76fhbsj9cwyb328lzqmd5sqz"))))
(build-system python-build-system)
(propagated-inputs ; the following packages are all needed at run time
`(("python-cycler" ,python-cycler)
;; From version 1.4.0 'matplotlib' makes use of 'cairocffi' instead of
;; 'pycairo'. However, 'pygobject' makes use of a 'pycairo' 'context'
;; object. For this reason we need to import both libraries.
- ;; https://pythonhosted.org/cairocffi/cffi_api.html#converting-pycairo
+ ;; https://cairocffi.readthedocs.io/en/stable/cffi_api.html#converting-pycairo-wrappers-to-cairocffi
("python-pycairo" ,python-pycairo)
("python-cairocffi" ,python-cairocffi)))
(inputs
("tk" ,tk)))
(native-inputs
`(("pkg-config" ,pkg-config)
- ("python-nose" ,python-nose)
- ("python-mock" ,python-mock)))
+ ("python-pytest" ,python-pytest)
+ ("python-mock" ,python-mock)
+ ("unzip" ,unzip)
+ ("jquery-ui"
+ ,(origin
+ (method url-fetch)
+ (uri "https://jqueryui.com/resources/download/jquery-ui-1.12.1.zip")
+ (sha256
+ (base32
+ "0kb21xf38diqgxcdi1z3s9ssq36pldvyqxy56hn6pcva6rs3c8zq"))))))
(arguments
`(#:phases
(modify-phases %standard-phases
+ ;; XXX We disable all image comparison tests because we're using a
+ ;; newer version of FreeType than matplotlib expects. This leads to
+ ;; minor differences throughout the tests.
+ (add-after 'unpack 'fix-and-disable-failing-tests
+ (lambda _
+ (substitute* (append (find-files "lib/matplotlib/tests/"
+ "test_.*\\.py$")
+ (find-files "lib/mpl_toolkits/tests"
+ "test_.*\\.py$"))
+ (("^from matplotlib" match)
+ (string-append "import pytest\n" match))
+ (("( *)@image_comparison" match indent)
+ (string-append indent
+ "@pytest.mark.skip(reason=\"unknown minor image differences\")\n"
+ match)))
+ (substitute* "lib/matplotlib/tests/test_animation.py"
+ (("/bin/sh") (which "sh")))
+ (for-each delete-file
+ ;; test_normal_axes, test_get_tightbbox_polar
+ '("lib/matplotlib/tests/test_axes.py"
+ ;; test_outward_ticks
+ "lib/matplotlib/tests/test_tightlayout.py"
+ ;; Fontconfig returns no fonts.
+ "lib/matplotlib/tests/test_font_manager.py"))
+ #t))
+ (add-before 'install 'install-jquery-ui
+ (lambda* (#:key outputs inputs #:allow-other-keys)
+ (let ((dir (string-append (assoc-ref outputs "out")
+ "/lib/python3.7/site-packages/matplotlib/backends/web_backend/")))
+ (mkdir-p dir)
+ (invoke "unzip"
+ (assoc-ref inputs "jquery-ui")
+ "-d" dir))
+ #t))
+ (delete 'check)
+ (add-after 'install 'check
+ (lambda* (#:key outputs inputs #:allow-other-keys)
+ (add-installed-pythonpath inputs outputs)
+ (invoke "python" "tests.py" "-v"
+ "-m" "not network")))
(add-before 'build 'configure-environment
(lambda* (#:key outputs inputs #:allow-other-keys)
(let ((cairo (assoc-ref inputs "cairo")))
(lambda (port)
(format port "[directories]~%
basedirlist = ~a,~a~%
- [rc_options]~%
-backend = TkAgg~%"
+[packages]~%
+tests = True~%"
(assoc-ref inputs "tcl")
(assoc-ref inputs "tk")))))
#t)))))
- (home-page "http://matplotlib.org")
+ (home-page "https://matplotlib.org/")
(synopsis "2D plotting library for Python")
(description
"Matplotlib is a Python 2D plotting library which produces publication
(let ((matplotlib (package-with-python2
(strip-python2-variant python-matplotlib))))
(package (inherit matplotlib)
+ (version "2.2.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "matplotlib" version))
+ (sha256
+ (base32
+ "09i1gnrra1590brc1f8d5rh2zvnknmfgzp613ab0462qkrwj15h2"))))
+ (arguments
+ (substitute-keyword-arguments (package-arguments matplotlib)
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (replace 'install-jquery-ui
+ (lambda* (#:key outputs inputs #:allow-other-keys)
+ (let ((dir (string-append (assoc-ref outputs "out")
+ "/lib/python2.7/site-packages/"
+ "matplotlib/backends/web_backend/")))
+ (mkdir-p dir)
+ (invoke "unzip"
+ (assoc-ref inputs "jquery-ui")
+ "-d" dir))
+ #t))
+ (delete 'check))))) ; These tests weren't run the the past.
;; Make sure to use special packages for Python 2 instead
;; of those automatically rewritten by package-with-python2.
(propagated-inputs
`(("python-matplotlib" ,python-matplotlib)
("python-colorspacious" ,python-colorspacious)
("python-sphinx" ,python-sphinx)
+ ("python-sphinx-copybutton" ,python-sphinx-copybutton)
("python-sphinx-gallery" ,python-sphinx-gallery)
("python-numpydoc" ,python-numpydoc)
("python-ipython" ,python-ipython)
`(#:tests? #f ; we're only generating documentation
#:phases
(modify-phases %standard-phases
+ ;; The tests in python-matplotlib are run after the install phase, so
+ ;; we need to delete the extra phase here.
+ (delete 'check)
(replace 'build
(lambda _
(chdir "doc")
(license (package-license python-matplotlib))))
(define-public python2-matplotlib-documentation
- (package-with-python2 python-matplotlib-documentation))
+ (let ((parent (package-with-python2 python-matplotlib-documentation)))
+ (package
+ (inherit parent)
+ (native-inputs
+ (alist-delete "python-sphinx-copybutton"
+ (package-native-inputs parent))))))
(define-public python-matplotlib-venn
(package
(define-public python-pycodestyle
(package
(name "python-pycodestyle")
- (version "2.4.0")
+ (version "2.5.0")
(source
- (origin
- (method url-fetch)
- (uri (pypi-uri "pycodestyle" version))
- (sha256
- (base32
- "0fhy4vnlgpjq4qd1wdnl6pvdw7rah0ypmn8c9mkhz8clsndskz6b"))))
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "pycodestyle" version))
+ (sha256
+ (base32
+ "0v4prb05n21bm8650v0a01k1nyqjdmkrsm3zycfxh2j5k9n962p4"))))
(build-system python-build-system)
(home-page "https://pycodestyle.readthedocs.io/")
(synopsis "Python style guide checker")
(define-public python-setuptools-scm
(package
(name "python-setuptools-scm")
- (version "3.1.0")
+ (version "3.2.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "setuptools_scm" version))
(sha256
(base32
- "0h4bglwfz8b9prqljv8z3w9rgydfyxzaj05bm1y6zs5m6shz548i"))))
+ "0n3knn3p1sqlx31k2lahn7z9bacvlv8nhlfidj77vz50bxqlgasj"))))
(build-system python-build-system)
(home-page "https://github.com/pypa/setuptools_scm/")
(synopsis "Manage Python package versions in SCM metadata")
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))
(define-public python-importlib-metadata
(package
(name "python-importlib-metadata")
- (version "0.18")
+ (version "0.23")
(source
(origin
(method url-fetch)
(uri (pypi-uri "importlib_metadata" version))
(sha256
- (base32
- "1nqj6vj2z4byi8flzf2lbldhqgicsz9mkpv4k69kjd8p8qxy4vnb"))))
+ (base32 "09mdqdfv5rdrwz80jh9m379gxmvk2vhjfz0fg53hid00icvxf65a"))))
(build-system python-build-system)
(propagated-inputs
`(("python-configparser" ,python-configparser)
(define-public python-pathpy
(package
(name "python-pathpy")
- (version "11.5.0")
+ (version "11.5.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "path.py" version))
(sha256
- (base32 "1jxkf91syzxlpiwgm83fjfz1m5xh3jrvv4iyl5wjsnkk599pls5n"))))
+ (base32 "0ir9j1haq2jbi7aip6k2fa9l7q1l03k4hp1awxhjhcwzsnwp3ll8"))))
(outputs '("out" "doc"))
(build-system python-build-system)
(propagated-inputs
- `(("python-appdirs" ,python-appdirs)))
+ `(("python-appdirs" ,python-appdirs)
+ ("python-importlib-metadata" ,python-importlib-metadata)))
(native-inputs
`(("python-setuptools-scm" ,python-setuptools-scm)
("python-sphinx" ,python-sphinx)
(define-public python-traitlets
(package
(name "python-traitlets")
- (version "4.3.2")
+ (version "4.3.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "traitlets" version))
(sha256
(base32
- "0dbq7sx26xqz5ixs711k5nc88p8a0nqyz6162pwks5dpcz9d4jww"))))
+ "1xsrwgivpkxlbr4dfndfsi098s29yqgswgjc1qqn69yxklvfw8yh"))))
(build-system python-build-system)
(arguments
`(#:phases
(replace 'check (lambda _ (invoke "pytest" "-vv" "traitlets"))))))
(propagated-inputs
`(("python-ipython-genutils" ,python-ipython-genutils)
- ("python-decorator" ,python-decorator))) ;not needed for >4.3.2
+ ("python-decorator" ,python-decorator)))
(native-inputs
`(("python-pytest" ,python-pytest)))
(properties `((python2-variant . ,(delay python2-traitlets))))
(define-public python-ipykernel
(package
(name "python-ipykernel")
- (version "5.1.1")
+ (version "5.1.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "ipykernel" version))
(sha256
- (base32 "173nm29g85w8cac3fg40b27qaq26g41wgg6qn79ql1hq4w2n5sgh"))))
+ (base32 "1a08y677lpn80qzvv7z0smgggmr5m5ayf0bs6vds47xpxl9sss5k"))))
(build-system python-build-system)
(arguments
`(#:phases
;; imported at runtime during connect
("python-jupyter-client" ,python-jupyter-client)))
(native-inputs
- `(("python-pytest" ,python-pytest)
- ("python-nose" ,python-nose)))
+ `(("python-flaky" ,python-flaky)
+ ("python-nose" ,python-nose)
+ ("python-pytest" ,python-pytest)))
(home-page "https://ipython.org")
(synopsis "IPython Kernel for Jupyter")
(description
(define-public python-ipython
(package
(name "python-ipython")
- (version "7.5.0")
+ (version "7.9.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "ipython" version ".tar.gz"))
(sha256
- (base32 "09mbxq37mfn88xjnib7qfzaq9krr7gf1jxwy1p6mcjr254082h78"))))
+ (base32 "103jkw18z7fnwdal1mdbijjxi1fndzn31g887lmj7ddpf2r07lyz"))))
(build-system python-build-system)
(propagated-inputs
`(("python-backcall" ,python-backcall)
(arguments
`(#:phases
(modify-phases %standard-phases
+ (add-after 'unpack 'make-docs-reproducible
+ (lambda _
+ (substitute* "IPython/sphinxext/ipython_directive.py"
+ ((".*import datetime") "")
+ ((".*datetime.datetime.now\\(\\)") "")
+ (("%timeit") "# %timeit"))
+ #t))
;; Tests can only be run after the library has been installed and not
;; within the source directory.
(delete 'check)
(define-public python-lxml
(package
(name "python-lxml")
- (version "4.2.5")
+ (version "4.4.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "lxml" version))
(sha256
(base32
- "0zw0y9hs0nflxhl9cs6ipwwh53szi3w2x06wl0k9cylyqac0cwin"))))
+ "14jnpfcpgqr9sx8ppd286jzcbk0b36hbqsvd8jkvffipzw5v8768"))))
(build-system python-build-system)
+ (arguments
+ `(#:phases (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (invoke "make" "test"))))))
(inputs
`(("libxml2" ,libxml2)
("libxslt" ,libxslt)))
(define-public python-datrie
(package
(name "python-datrie")
- (version "0.7.1")
+ (version "0.8")
(source
(origin
(method url-fetch)
(uri (pypi-uri "datrie" version))
(sha256
(base32
- "08r0if7dry2q7p34gf7ffyrlnf4bdvnprxgydlfxgfnvq8f3f4bs"))))
+ "0338r8xgmpy78556jhms0h6qkvyjr10p8bpgdvcpqzm9lrmxmmdx"))))
(build-system python-build-system)
- (arguments
- `(#:phases (modify-phases %standard-phases
- (add-before 'build 'cythonize
- (lambda _
- ;; Regenerate Cython classes to solve ABI issues with Python
- ;; 3.7.0. See <https://github.com/pytries/datrie/issues/52>.
- (invoke "cython" "src/datrie.pyx" "src/cdatrie.pxd"
- "src/stdio_ext.pxd" "-a"))))))
(native-inputs
`(("python-cython" ,python-cython)
("python-hypothesis" ,python-hypothesis)
(define-public snakemake
(package
(name "snakemake")
- (version "5.2.4")
+ (version "5.7.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "snakemake" version))
(sha256
- (base32 "0gj0xxgiq3mp9qyyrbfzldiaq1giliqw0in64nqiz7vx49myqj7z"))))
+ (base32 "1pnpvvn8n2a78cg360wz3ldmpqrsm2wzi0c0dmvki9fnsw6fxdas"))))
(build-system python-build-system)
(arguments
;; TODO: Package missing test dependencies.
"/bin/snakemake")))
#t)))))
(propagated-inputs
- `(("python-gitpython" ,python-gitpython)
- ("python-wrapt" ,python-wrapt)
- ("python-requests" ,python-requests)
- ("python-appdirs" ,python-appdirs)
+ `(("python-appdirs" ,python-appdirs)
("python-configargparse" ,python-configargparse)
("python-datrie" ,python-datrie)
("python-docutils" ,python-docutils)
+ ("python-gitpython" ,python-gitpython)
("python-jinja2" ,python-jinja2)
("python-jsonschema" ,python-jsonschema)
("python-networkx" ,python-networkx)
+ ("python-psutil" ,python-psutil)
("python-pyyaml" ,python-pyyaml)
- ("python-ratelimiter" ,python-ratelimiter)))
+ ("python-ratelimiter" ,python-ratelimiter)
+ ("python-requests" ,python-requests)
+ ("python-wrapt" ,python-wrapt)))
(home-page "https://snakemake.readthedocs.io")
(synopsis "Python-based execution environment for make-like workflows")
(description
Python style, together with a fast and comfortable execution environment.")
(license license:expat)))
-;; This is currently needed for the pigx-* packages.
-(define-public snakemake-4
- (package (inherit snakemake)
- (version "4.4.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "snakemake" version))
- (sha256
- (base32 "0g0paia4z7w3srnqdmavq3hrb2x7qnpf81jx50njl0p7y4y0j8jv"))))
- (propagated-inputs
- `(("python-wrapt" ,python-wrapt)
- ("python-requests" ,python-requests)
- ("python-appdirs" ,python-appdirs)
- ("python-configargparse" ,python-configargparse)
- ("python-pyyaml" ,python-pyyaml)
- ("python-ratelimiter" ,python-ratelimiter)))))
-
(define-public python-pyqrcode
(package
(name "python-pyqrcode")
(uri (pypi-uri "pep8" version))
(sha256
(base32
- "002rkl4lsn6x2mxmf8ar00l0m8i3mzrc6pnzz77blyksmpsxa4x1"))))
+ "002rkl4lsn6x2mxmf8ar00l0m8i3mzrc6pnzz77blyksmpsxa4x1"))
+ (patches (search-patches "python-pep8-stdlib-tokenize-compat.patch"))))
(build-system python-build-system)
(home-page "https://pep8.readthedocs.org/")
(synopsis "Python style guide checker")
(define-public python-pyflakes
(package
(name "python-pyflakes")
- (version "2.0.0")
+ (version "2.1.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pyflakes" version))
(sha256
(base32
- "0jba28czyvimdc72llms3f17swp3i8jdcabf5w0j00adfbn64xls"))))
+ "18pq95a1xj2dgdd0m85gyfsn40jajj4xc3lp8wfv7igqhrc86xnr"))))
(build-system python-build-system)
(home-page
"https://github.com/pyflakes/pyflakes")
(define-public python2-pyflakes-0.8.1
(package-with-python2 python-pyflakes-0.8.1))
-;; This package is used by hypothesis which has thousands of dependent packages.
-;; FIXME: Consolidate this with "python-flake8" below in the next rebuild cycle.
-(define-public python-flake8-3.5
+(define-public python-flake8
(package
(name "python-flake8")
- (version "3.5.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "flake8" version))
- (sha256
- (base32
- "184b33grvvjmiwlv9kyd7yng9qv5ld24154j70z332xxg9gjclvj"))))
+ (version "3.7.7")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "flake8" version))
+ (sha256
+ (base32
+ "0qg6zggqigrd4k3gv88shd1a27d0cwgfql8vfiq2c7rl7w3rd6c5"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
- ;; Two errors don't seem to have assigned codes.
- (add-after 'unpack 'delete-broken-test
- (lambda _ (delete-file "tests/unit/test_pyflakes_codes.py") #t))
- (add-after 'unpack 'fix-problem-with-pycodestyle
- (lambda _
- ;; See https://gitlab.com/pycqa/flake8/merge_requests/230
- ;; This should no longer be needed with the next release.
- (substitute* "setup.py"
- (("PEP8_PLUGIN\\('break_around_binary_operator'\\),")
- "PEP8_PLUGIN('break_after_binary_operator'),\
-PEP8_PLUGIN('break_before_binary_operator'),"))
- #t))
(delete 'check)
(add-after 'install 'check
(lambda* (#:key inputs outputs #:allow-other-keys)
#t)))))
(propagated-inputs
`(("python-pycodestyle" ,python-pycodestyle)
+ ("python-entrypoints" ,python-entrypoints)
("python-pyflakes" ,python-pyflakes)
("python-mccabe" ,python-mccabe)))
(native-inputs
"The modular source code checker: pep8, pyflakes and co")
(description
"Flake8 is a wrapper around PyFlakes, pep8 and python-mccabe.")
- (properties `((python2-variant . ,(delay python2-flake8-3.5))))
+ (properties `((python2-variant . ,(delay python2-flake8))))
(license license:expat)))
-(define-public python2-flake8-3.5
- (let ((base (package-with-python2 (strip-python2-variant python-flake8-3.5))))
+(define-public python2-flake8
+ (let ((base (package-with-python2 (strip-python2-variant python-flake8))))
(package (inherit base)
(propagated-inputs
`(("python2-configparser" ,python2-configparser)
("python2-enum34" ,python2-enum34)
+ ("python2-typing" ,python2-typing)
,@(package-propagated-inputs base))))))
-;; Version 3.5.0 has compatibility issues with Pyflakes 2.0, so we need
-;; this newer version. Keep it as a separate variable for now to avoid
-;; rebuilding "python-hypothesis"; this should be removed in the next
-;; rebuild cycle.
-(define-public python-flake8
- (package
- (inherit python-flake8-3.5)
- (version "3.6.0")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "flake8" version))
- (sha256
- (base32
- "0w0nprx22rbvrrkbfx9v5jc5gskbm08g219l7r8wai8zfswgadba"))))
- (arguments
- (substitute-keyword-arguments (package-arguments python-flake8-3.5)
- ((#:phases phases)
- `(modify-phases ,phases
- (delete 'delete-broken-test)
- (delete 'fix-problem-with-pycodestyle)))))
- (properties `((python2-variant . ,(delay python2-flake8))))))
-
-(define-public python2-flake8
- (let ((base (package-with-python2 (strip-python2-variant python-flake8))))
- (package (inherit base)
- (propagated-inputs
- (package-propagated-inputs python2-flake8-3.5)))))
-
;; python-hacking requires flake8 <2.6.0.
(define-public python-flake8-2.5
(package
(modify-phases %standard-phases
(replace 'check
(lambda _
+ ;; Be compatible with Pytest 4:
+ ;; https://gitlab.com/pycqa/flake8-polyfill/merge_requests/7
+ (substitute* "setup.cfg"
+ (("\\[pytest\\]")
+ "[tool:pytest]"))
+
(setenv "PYTHONPATH"
(string-append (getcwd) "/build/lib:"
(getenv "PYTHONPATH")))
;; lines, but the test expects a single line...
(("env\\['COLUMNS'\\] = '80'")
"env['COLUMNS'] = '160'"))
+
+ (substitute* "Makefile"
+ ;; Recent versions of python-coverage have caused the test
+ ;; coverage to decrease (as of version 0.7). Allow that.
+ (("--fail-under=100")
+ "--fail-under=90"))
+
#t))
- (delete 'check)
- (add-after 'install 'check
+ (replace 'check
;; The test phase uses the built library and executable.
- ;; It's easier to run it after install since the build
- ;; directory contains version-specific PATH.
(lambda* (#:key inputs outputs #:allow-other-keys)
(add-installed-pythonpath inputs outputs)
(setenv "PATH" (string-append (getenv "PATH") ":"
(define-public python-fonttools
(package
(name "python-fonttools")
- (version "3.28.0")
+ (version "3.38.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "fonttools" version ".zip"))
(sha256
(base32
- "0vsvjhidpb5kywpjgz1j3fywzkddxkb0afqai18qa3h6lqjyxwpb"))))
+ "12ripk3s7skgxr1bs9r8n13r94ym3s8iir7ivfixls9fa4dabmlh"))))
(build-system python-build-system)
(native-inputs
`(("unzip" ,unzip)
(package
(name "python-debian")
(home-page "https://salsa.debian.org/python-debian-team/python-debian")
- (version "0.1.28")
+ (version "0.1.36")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri name version))
+ ;; Use git-fetch, as pypi doesn't include test suite.
+ (method git-fetch)
+ (uri (git-reference
+ (url home-page)
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "0i15f0xzx679sd0ldq2sls9pnnps9fv6vhqvnv9dzf4qhma42i0y"))))
+ "0qy6x28bj6yfikhjww932v5xq4mf5bm1iczl7acy4c7zm6mwhqfa"))))
(build-system python-build-system)
+ (arguments
+ `(#:phases (modify-phases %standard-phases
+ (add-after 'unpack 'remove-debian-specific-tests
+ ;; python-apt, apt and dpkg are not yet available in guix,
+ ;; and these tests heavily depend on them.
+ (lambda _
+ (delete-file "lib/debian/tests/test_deb822.py")
+ (delete-file "lib/debian/tests/test_debfile.py")
+ #t)))))
(propagated-inputs
- `(("python-six" ,python-six)))
+ `(("python-six" ,python-six)
+ ("python-chardet" ,python-chardet)))
(synopsis "Debian package related modules")
(description
;; XXX: Use @enumerate instead of @itemize to work around
(define-public python-bleach
(package
(name "python-bleach")
- (version "1.4.3")
+ (version "3.1.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "bleach" version))
(sha256
(base32
- "0jvg3jxrvnx7xmm9gj262v60ib452xlnwlb0navyp7jsvcd0d4qj"))))
+ "1yhrgrhkln8bd6gn3imj69g1h4xqah9gaz9q26crqr6gmmvpzprz"))))
(build-system python-build-system)
(propagated-inputs
- `(("python-html5lib" ,python-html5lib-0.9)
+ `(("python-webencodings" ,python-webencodings)
("python-six" ,python-six)))
(native-inputs
- `(("python-nose" ,python-nose)))
+ `(("python-pytest" ,python-pytest)
+ ("python-pytest-runner" ,python-pytest-runner-2)))
(home-page "https://github.com/jsocol/bleach")
(synopsis "Whitelist-based HTML-sanitizing tool")
(description "Bleach is an easy whitelist-based HTML-sanitizing tool.")
support for rich media output.")
(license license:bsd-3)))
+(define-public python-jsbeautifier
+ (package
+ (name "python-jsbeautifier")
+ (version "1.10.2")
+ (home-page "https://github.com/beautify-web/js-beautify")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url home-page)
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0wawb070ki1axb3jc9xvsrgpji52vcfif3zmjzc3z4g98m5xw4kg"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases (modify-phases %standard-phases
+ (add-after 'unpack 'chdir
+ (lambda _
+ ;; The upstream Git repository contains all the code,
+ ;; but this package only builds the python code.
+ (chdir "python")
+ #t))
+ (add-after 'unpack 'patch-python-six-requirements
+ (lambda _
+ (substitute* "python/setup.py"
+ (("six>=1.12.0")
+ "six>=1.11.0"))
+ #t)))))
+ (propagated-inputs
+ `(("python-editorconfig" ,python-editorconfig)
+ ("python-six" ,python-six)))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
+ (synopsis "JavaScript unobfuscator and beautifier")
+ (description "Beautify, unpack or deobfuscate JavaScript, leveraging
+popular online obfuscators.")
+ (license license:expat)))
+
(define-public jupyter
(package
(name "jupyter")
("python-pytest" ,python-pytest)
("python-pytest-runner" ,python-pytest-runner)))
(build-system python-build-system)
+ ;; XXX: Incompatible with Pytest 4: <https://github.com/chardet/chardet/issues/173>.
+ (arguments `(#:tests? #f))
(home-page "https://github.com/chardet/chardet")
(synopsis "Universal encoding detector for Python 2 and 3")
(description
(define-public python-atomicwrites
(package
(name "python-atomicwrites")
- (version "1.1.5")
+ (version "1.3.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "atomicwrites" version))
(sha256
(base32
- "11bm90fwm2avvf4f3ib8g925w7jr4m11vcsinn1bi6ns4bm32214"))))
+ "19ngcscdf3jsqmpcxn6zl5b6anmsajb6izp1smcd1n02midl9abm"))))
(build-system python-build-system)
(synopsis "Atomic file writes in Python")
(description "Library for atomic file writes using platform dependent tools
(base32
"0rdjmmsab550kxsssdq49jcniz77zlkpw4pvi9hvib3lsskjmh4y"))))
(build-system python-build-system)
- (arguments `(#:python ,python-2
- ;; FIXME: Python 2.7.14 moved the test.support library,
- ;; but our package has not yet been adjusted. Enable
- ;; tests when the python2 package has been fixed.
- #:tests? #f))
+ (arguments
+ `(#:python ,python-2
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (invoke "python" "test_futures.py")
+ #t)))))
(home-page "https://github.com/agronholm/pythonfutures")
(synopsis
"Backport of the concurrent.futures package from Python 3.2")
(define-public python-pluggy
(package
(name "python-pluggy")
- (version "0.7.1")
+ (version "0.11.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pluggy" version))
(sha256
(base32
- "1qbn70mksmr03hac6jgp6fiqc4l7859z8dchx2x950vhlij87swm"))))
+ "10511a54dvafw1jrk75mrhml53c7b7w4yaw7241696lc2hfvr895"))))
(build-system python-build-system)
(native-inputs
`(("python-setuptools-scm" ,python-setuptools-scm)))
(define-public python2-waitress
(package-with-python2 python-waitress))
+(define-public python-whichcraft
+ (package
+ (name "python-whichcraft")
+ (version "0.6.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "whichcraft" version))
+ (sha256
+ (base32
+ "11yfkzyplizdgndy34vyd5qlmr1n5mxis3a3svxmx8fnccdvknxc"))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
+ (home-page "https://github.com/pydanny/whichcraft")
+ (synopsis "Cross-platform cross-python shutil.which functionality")
+ (description
+ "This package provides a shim of the shutil.which function that's
+designed to work across multiple versions of Python.")
+ (license license:bsd-3)))
+
+(define-public python-cookiecutter
+ (package
+ (name "python-cookiecutter")
+ (version "1.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "cookiecutter" version))
+ (sha256
+ (base32
+ "0glsvaz8igi2wy1hsnhm9fkn6560vdvdixzvkq6dn20z3hpaa5hk"))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-freezegun" ,python-freezegun)
+ ("python-pytest" ,python-pytest)
+ ("python-pytest-catchlog" ,python-pytest-catchlog)
+ ("python-pytest-cov" ,python-pytest-cov)
+ ("python-pytest-mock" ,python-pytest-mock)))
+ (propagated-inputs
+ `(("python-binaryornot" ,python-binaryornot)
+ ("python-click" ,python-click)
+ ("python-future" ,python-future)
+ ("python-jinja2" ,python-jinja2)
+ ("python-jinja2-time" ,python-jinja2-time)
+ ("python-poyo" ,python-poyo)
+ ("python-requests" ,python-requests)
+ ("python-whichcraft" ,python-whichcraft)))
+ (home-page "https://github.com/audreyr/cookiecutter")
+ (synopsis
+ "Command-line utility that creates projects from project templates")
+ (description
+ "This package provides a command-line utility that creates projects from
+project templates, e.g. creating a Python package project from a Python package
+project template.")
+ (license license:bsd-3)))
+
(define-public python-pyquery
(package
(name "python-pyquery")
(define-public python2-pathlib2
(package
(name "python2-pathlib2")
- (version "2.3.2")
+ (version "2.3.3")
(source (origin
(method url-fetch)
(uri (pypi-uri "pathlib2" version))
(sha256
(base32
- "10yb0iv5x2hs631rcppkhbddx799d3h8pcwmkbh2a66ns3w71ccf"))))
+ "0hpp92vqqgcd8h92msm9slv161b1q160igjwnkf2ag6cx0c96695"))))
(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
(define-public python-py3status
(package
(name "python-py3status")
- (version "3.16")
+ (version "3.21")
(source
(origin
(method url-fetch)
(uri (pypi-uri "py3status" version))
(sha256
- (base32
- "1xrfph277bgjln3jbpzpgkhxad04fjvj7s3xfil42q1sxi4s3q3g"))))
+ (base32 "16z8zq83hxy48g6hh4xczbdz50qvxv9k1aahr4fqq7jis60cc262"))))
(build-system python-build-system)
(inputs
`(("file" ,file)))
(guix build utils)
(guix build python-build-system))
#:phases (modify-phases %standard-phases
- (add-after 'unpack 'unpack-libev
- (lambda* (#:key inputs #:allow-other-keys)
- (mkdir-p "deps/libev")
- ;; FIXME: gevent requires building libev, even though
- ;; it only links against the proper one.
- (invoke "tar" "-xf" (assoc-ref inputs "libev-source")
- "--strip-components=1" "-C" "deps/libev")))
(add-before 'patch-source-shebangs 'patch-hard-coded-paths
(lambda _
(substitute* "src/gevent/subprocess.py"
(setenv "CARES_EMBED" "false")
(setenv "EMBED" "false")
+ ;; Prevent building bundled libev.
+ (substitute* "setup.py"
+ (("run_make=_BUILDING")
+ "run_make=False"))
+
(let ((greenlet (string-append
(assoc-ref inputs "python-greenlet")
"/include")))
(lambda (item)
(string-prefix? "python" item)))
((python)
- (setenv "CPATH"
+ (setenv "C_INCLUDE_PATH"
(string-append greenlet "/" python)))))
#t))
(add-before 'check 'skip-timer-test
`(("python-greenlet" ,python-greenlet)
("python-objgraph" ,python-objgraph)))
(native-inputs
- `(("libev-source" ,(package-source libev))
- ("python-six" ,python-six)))
+ `(("python-six" ,python-six)))
(inputs
`(("c-ares" ,c-ares)
("libev" ,libev)))
(define-public python-lazy-object-proxy
(package
(name "python-lazy-object-proxy")
- (version "1.3.1")
+ (version "1.4.2")
(source (origin
(method url-fetch)
(uri (pypi-uri "lazy-object-proxy" version))
(sha256
(base32
- "0yha7q9bhw857fwaby785d63mffhngl9npwzlk9i0pwlkwvbx4gb"))))
+ "1wgl0fmddi0ind78a74yyk2qrr9pb5llvj1892cdpp6z6n6mn4zx"))))
+ (native-inputs
+ `(("python-setuptools-scm" ,python-setuptools-scm-3.3)))
(build-system python-build-system)
(home-page "https://github.com/ionelmc/python-lazy-object-proxy")
(synopsis "Lazy object proxy for python")
(define-public python-jedi
(package
(name "python-jedi")
- (version "0.13.3")
+ (version "0.15.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "jedi" version))
(sha256
(base32
- "0nsrjlb57njqppxmi8wjsb1dkad7qa7svx67jbkhixq66lz61c1b"))))
+ "0bp4pxhsynaarbvzblsn5x32lzp29svy3sxfy8i6m5iwz9s9r1ds"))))
(build-system python-build-system)
(arguments
- `( ;; Many tests are failing with Python 3.7.x as of version 0.13.3 (see:
- ;; https://github.com/davidhalter/jedi/issues/1263)
- #:tests? #f
- #:phases
+ `(#:phases
(modify-phases %standard-phases
+ (add-after 'unpack 'disable-file-completion-test
+ ;; A single parameterized test currently fail (see:
+ ;; https://github.com/davidhalter/jedi/issues/1395). Remove it.
+ (lambda _
+ (substitute* "test/test_api/test_completion.py"
+ ((".*'example.py', 'rb\"' \\+ join\\('\\.\\.'.*") ""))
+ #t))
(replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "py.test" "-vv")))))))
+ (lambda _
+ (setenv "HOME" "/tmp")
+ (invoke "python" "-m" "pytest"))))))
(native-inputs
`(("python-pytest" ,python-pytest)
("python-docopt" ,python-docopt)))
(license license:expat)))
(define-public python2-jedi
- (let ((base (package-with-python2 (strip-python2-variant python-jedi))))
- (package
- (inherit base)
- (arguments (substitute-keyword-arguments (package-arguments base)
- ((#:tests? _) #t))))))
+ (package-with-python2 python-jedi))
(define-public ptpython
(package
(base32
"0qc006986rb6bcbmiymwgcl1mns2jphr1j7sr7nk41nlr7gh359m"))))
(build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-tests
+ (lambda _
+ ;; TypeError: binary() got an unexpected keyword argument
+ ;; 'average_size'.
+ (substitute* "tests/test_check.py"
+ (("average_size=512") ""))
+ #t)))))
(propagated-inputs
`(("python-chardet" ,python-chardet)
("python-hypothesis" ,python-hypothesis)))
`(("python2-enum34" ,python2-enum34)
,@(package-propagated-inputs base))))))
+(define-public python-binwalk
+ (let ((commit "64201acfb5b0a9cdd9faa58c40a36dcff8612e29")
+ (revision "0"))
+ (package
+ (name "python-binwalk")
+ (version (git-version "2.1.1" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ReFirmLabs/binwalk")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1z7ca6rfp887hw5jc3sb45mm4fa0xid4lsp2z8g4r590dr7k7w15"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-before 'check 'set-pythonpath
+ (lambda _
+ (setenv "PYTHONPATH"
+ (string-append
+ (getcwd) "/src/"
+ ":" (getenv "PYTHONPATH")))
+ (setenv "HOME" "")
+ #t)))))
+ (native-inputs
+ `(("python-coverage" ,python-coverage)
+ ("python-nose" ,python-nose)))
+ (home-page "https://github.com/ReFirmLabs/binwalk")
+ (synopsis "Firmware analysis tool")
+ (description "Binwalk is a tool for analyzing, reverse engineering, and extracting firmware images")
+ (license license:expat))))
+
(define-public python-nltk
(package
(name "python-nltk")
(package
(inherit python-attrs)
(name "python-attrs-bootstrap")
- ;; Keep this on a fixed version so python-attrs can be updated without
- ;; triggering a mass-rebuild. FIXME: Update this in the next rebuild cycle.
- (version "17.4.0")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "attrs" version))
- (sha256
- (base32
- "1jafnn1kzd6qhxgprhx6y6ik1r5m2rilx25syzcmq03azp660y8w"))))
(native-inputs `())
(arguments `(#:tests? #f))))
(define-public python-astroid
(package
(name "python-astroid")
- (version "2.1.0")
+ (version "2.3.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "astroid" version))
(sha256
(base32
- "08hz675knh4294bancdapql392fmbjyimhbyrmfkz1ka7l035c1m"))))
+ "0crfhpblcy5a6nh694hc2073gw389f01yilamzqi34si2skgp8q9"))))
(build-system python-build-system)
(propagated-inputs
`(("python-lazy-object-proxy" ,python-lazy-object-proxy)
("python-six" ,python-six)
+ ("python-typed-ast" ,python-typed-ast)
("python-wrapt" ,python-wrapt)))
(native-inputs
`(("python-dateutil" ,python-dateutil)
,python2-backports-functools-lru-cache)
("python2-enum34" ,python2-enum34)
("python2-singledispatch" ,python2-singledispatch)
- ,@(package-propagated-inputs base))))))
+ ,@(alist-delete "python-typed-ast"
+ (package-propagated-inputs base)))))))
(define-public python-isort
(package
(define-public python-configparser
(package
(name "python-configparser")
- (version "3.5.0")
+ (version "3.7.1")
(source
(origin
(method url-fetch)
- (uri (string-append
- "https://bitbucket.org/ambv/configparser/get/"
- version ".tar.bz2"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (uri (pypi-uri "configparser" version))
(sha256
(base32
- "0waq40as14abwzbb321hfz4vr1fi363nscy32ga14qvfygrg96wa"))))
+ "0cnz213il9lhgda6x70fw7mfqr8da43s3wm343lwzhqx94mgmmav"))))
(build-system python-build-system)
(home-page "https://github.com/jaraco/configparser/")
(synopsis "Backport of configparser from python 3.5")
"Make loops show a progress bar on the console by just wrapping any
iterable with @code{|tqdm(iterable)|}. Offers many options to define
design and layout.")
- (license (list license:mpl2.0 license:expat))))
+ (license (list license:mpl2.0 license:expat))
+ (properties `((python2-variant . ,(delay python2-tqdm))))))
(define-public python2-tqdm
- (package-with-python2 python-tqdm))
+ (let ((tqdm (package-with-python2
+ (strip-python2-variant python-tqdm))))
+ (package (inherit tqdm)
+ (native-inputs `(("python2-functools32" ,python2-functools32)
+ ,@(package-native-inputs tqdm))))))
(define-public python-pkginfo
(package
(define-public python-pyro4
(package
(name "python-pyro4")
- (version "4.75")
+ (version "4.77")
(source
(origin
(method url-fetch)
(uri (pypi-uri "Pyro4" version))
(sha256
- (base32 "1dfpp36imddx19yv0kd28gk1l71ckhpqy6jd590wpm2680jw15rq"))))
+ (base32 "0gsjg869y4gpy265s1gj1f2qy6jn5iz8r2bwwnq78r1r5yi15zib"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ;FIXME: Some tests require network access.
+ (native-inputs
+ `(("python-cloudpickle" ,python-cloudpickle)
+ ("python-dill" ,python-dill)
+ ("python-msgpack" ,python-msgpack)))
(propagated-inputs
`(("python-serpent" ,python-serpent)))
(home-page "https://pyro4.readthedocs.io")
(define-public python-typed-ast
(package
(name "python-typed-ast")
- (version "1.3.5")
+ (version "1.4.0")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "typed-ast" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/python/typed_ast.git")
+ (commit version)))
(sha256
- (base32
- "1m7pr6qpana3cvqwiw7mlvrgvmw27ch5mx1592572xhlki8g85ak"))))
+ (base32 "0l0hz809f7i356kmqkvfsaswiidb98j9hs9rrjnfawzqcbffzgyb"))
+ (file-name (git-file-name name version))))
(build-system python-build-system)
(arguments
`(#:modules ((guix build utils)
(define-public bpython
(package
(name "bpython")
- (version "0.17.1")
+ (version "0.18")
(source
(origin
(method url-fetch)
(uri (pypi-uri "bpython" version))
(sha256
- (base32
- "0bxhxi5zxdkrf8b4gwn0d363kdz3qnypjwhm1aydki53ph8ca1w9"))))
+ (base32 "1hl6frgvr2lqaxqczl8amg9xih32b3gzv429vs0qrjb8wpdj1k2n"))))
(build-system python-build-system)
(arguments
`(#:phases
(propagated-inputs
`(("python-pygments" ,python-pygments)
("python-requests" ,python-requests)
- ("python-babel" ,python-babel) ; optional, for internationalization
+ ("python-babel" ,python-babel) ; optional, for internationalization
("python-curtsies" ,python-curtsies) ; >= 0.1.18
("python-greenlet" ,python-greenlet)
- ("python-urwid" ,python-urwid) ; for bpython-urwid only
+ ("python-urwid" ,python-urwid) ; for bpython-urwid only
("python-six" ,python-six)))
(native-inputs
`(("python-sphinx" ,python-sphinx)
(define-public python-more-itertools
(package
(name "python-more-itertools")
- (version "4.3.0")
+ (version "7.1.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "more-itertools" version))
(sha256
(base32
- "17h3na0rdh8xq30w4b9pizgkdxmm51896bxw600x84jflg9vaxn4"))))
+ "16phg2f2dvm6ci5wr49ncha5lmc0m2in3bsl33c61vzca4gkvd4b"))))
(build-system python-build-system)
- (arguments
- `(,@(if (any (cute string-prefix? <> (or (%current-system)
- (%current-target-system)))
- '("armhf" "i686"))
- '(#:phases
- (modify-phases %standard-phases
- ;; This is required for 32-bit hardware.
- ;; TODO: Try to remove this when upgrading.
- (add-after 'unpack 'patch-test
- (lambda _
- (substitute* "more_itertools/tests/test_more.py"
- (("10 \\*\\* 10") "9 ** 9"))
- #t))))
- '())))
- (propagated-inputs
- `(("python-six" ,python-six-bootstrap)))
(home-page "https://github.com/erikrose/more-itertools")
(synopsis "More routines for operating on iterables, beyond itertools")
(description "Python's built-in @code{itertools} module implements a
number of iterator building blocks inspired by constructs from APL, Haskell,
and SML. @code{more-itertools} includes additional building blocks for
working with iterables.")
+ (properties `((python2-variant . ,(delay python2-more-itertools))))
(license license:expat)))
+;; The 5.x series are the last versions supporting Python 2.7.
(define-public python2-more-itertools
- (package-with-python2 python-more-itertools))
+ (package
+ (inherit python-more-itertools)
+ (name "python2-more-itertools")
+ (version "5.0.0")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "more-itertools" version))
+ (sha256
+ (base32
+ "1r12cm6mcdwdzz7d47a6g4l437xsvapdlgyhqay3i2nrlv03da9q"))))
+ (arguments
+ `(#:python ,python2-minimal))
+ (propagated-inputs
+ `(("python2-six" ,python2-six-bootstrap)))))
(define-public python-latexcodec
(package
(define-public python-parso
(package
(name "python-parso")
- (version "0.3.1")
+ (version "0.5.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "parso" version))
(sha256
(base32
- "18p89iwcm8mnf380f92g9w0bhx5km8wxp392vvjcq4y1ld1llw1m"))))
+ "171a9ivhxwsd52h1cgsz40zgzpgzscn7yqb7sdjhy8m1lzj0wsv6"))))
(native-inputs
`(("python-pytest" ,python-pytest)))
(build-system python-build-system)
+ (arguments
+ `(#:phases (modify-phases %standard-phases
+ (replace 'check
+ (lambda _ (invoke "pytest" "-vv"))))))
(home-page "https://github.com/davidhalter/parso")
(synopsis "Python Parser")
(description "Parso is a Python parser that supports error recovery and
(define-public python-glob2
(package
(name "python-glob2")
- (version "0.6")
+ (version "0.7")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/miracle2k/python-glob2.git")
- (commit version)))
+ (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "1lm1xz3k3l0k1c5bcp9hlzmi3gp5j8dl1k3xhpiq5mnm0xq6n163"))))
+ (base32 "160nh2ay9lw2hi0rixpzb2k87r6ql56k0j2cm87lqz8xc8zbw919"))))
(build-system python-build-system)
(home-page "https://github.com/miracle2k/python-glob2/")
(synopsis "Extended Version of the python buildin glob module")
(define-public pybind11
(package
(name "pybind11")
- (version "2.2.4")
+ (version "2.3.0")
(source (origin
(method git-fetch)
(uri (git-reference
(commit (string-append "v" version))))
(sha256
(base32
- "0pa79ymcasv8br5ifbx7878id5py2jpjac3i20cqxr6gs9l6ivlv"))
+ "11b6dniri8m05spfd2a19irz82shf4sdca73566bniggrf3zclnf"))
(file-name (git-file-name name version))))
(build-system cmake-build-system)
(native-inputs
For lxml.etree this package can be useful for providing XPath 2.0 selectors,
because lxml.etree already has it's own implementation of XPath 1.0.")
(license license:expat)))
+
+(define-public python-bibtexparser
+ (package
+ (name "python-bibtexparser")
+ (version "1.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "bibtexparser" version))
+ (sha256
+ (base32
+ "0zwhfkrzf3n5847dbnfng92k7ak199l9v6x6ax3dgdidfpm6d2fz"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-pyparsing" ,python-pyparsing)))
+ (native-inputs
+ `(("python-future" ,python-future)))
+ (home-page "https://github.com/sciunto-org/python-bibtexparser")
+ (synopsis "Python library to parse BibTeX files")
+ (description "BibtexParser is a Python library to parse BibTeX files.")
+ (license (list license:bsd-3 license:lgpl3))))
+
+(define-public python-distro
+ (package
+ (name "python-distro")
+ (version "1.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "distro" version))
+ (sha256
+ (base32
+ "0mrg75w4ap7mdzyga75yaid9n8bgb345ih5mwjp3plj6v1jxwb9n"))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
+ (home-page "https://github.com/nir0s/distro")
+ (synopsis
+ "OS platform information API")
+ (description
+ "@code{distro} provides information about the OS distribution it runs on,
+such as a reliable machine-readable ID, or version information.
+
+It is the recommended replacement for Python's original
+`platform.linux_distribution` function (which will be removed in Python 3.8).
+@code{distro} also provides a command-line interface to output the platform
+information in various formats.")
+ (license license:asl2.0)))
+
+(define-public python-cairosvg
+ (package
+ (name "python-cairosvg")
+ (version "2.4.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "CairoSVG" version))
+ (sha256
+ (base32 "1bb7irxbaxxb9ahm3z5wsx1q96mm5gzskc7b6q07h9ikcnb8yrjf"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _ (invoke "pytest"))))))
+ (propagated-inputs
+ `(("python-cairocffi" ,python-cairocffi)
+ ("python-cssselect2" ,python-cssselect2)
+ ("python-defusedxml" ,python-defusedxml)
+ ("python-pillow" ,python-pillow)
+ ("python-tinycss2" ,python-tinycss2)))
+ (native-inputs
+ `(("python-pytest-flake8" ,python-pytest-flake8)
+ ("python-pytest-isort" ,python-pytest-isort)
+ ("python-pytest-runner" ,python-pytest-runner)))
+ (home-page "https://cairosvg.org/")
+ (synopsis "SVG to PDF/PS/PNG converter based on Cairo")
+ (description "CairoSVG is a SVG converter based on Cairo. It can export
+SVG files to PDF, PostScript and PNG files. The main part of CairoSVG is a
+SVG parser, trying to follow the SVG 1.1 recommendation from the W3C. Once
+parsed, the result is drawn to a Cairo surface that can be exported to
+qvarious formats: PDF, PostScript, PNG and even SVG.")
+ (license license:lgpl3+)))
+
+(define-public python-pyphen
+ (package
+ (name "python-pyphen")
+ (version "0.9.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "Pyphen" version))
+ (sha256
+ (base32 "08c9y69ry9d6m4zalhnalg86lsp9v2j5n1ziw5vxfmiihx83lqrv"))))
+ (build-system python-build-system)
+ ;; TODO: Use the Guix system hyphenation packages hyphen-* rather than the
+ ;; embedded set provided by upstream - like Debian does.
+ (home-page "https://github.com/Kozea/Pyphen")
+ (synopsis "Pure Python module to hyphenate text")
+ (description "Pyphen is a pure Python module to hyphenate text using
+existing Hunspell hyphenation dictionaries.")
+ (license (list license:gpl2 license:lgpl2.1 license:mpl1.1))))
HCoop / jackhill / guix / guix.git / blobdiff