;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2013, 2014, 2015, 2016, 2019 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2014, 2017 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2014, 2017, 2021 Eric Bavier <bavier@posteo.net>
;;; Copyright © 2014, 2015 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2015 Omar Radwan <toxemicsquire4@gmail.com>
;;; Copyright © 2015 Pierre-Antoine Rault <par@rigelk.eu>
;;; Copyright © 2016 Dylan Jeffers <sapientech@sapientech@openmailbox.org>
;;; Copyright © 2016 David Craven <david@craven.ch>
;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Marius Bakke <marius@gnu.org>
-;;; Copyright © 2016, 2017 Stefan Reichör <stefan@xsteve.at>
+;;; Copyright © 2016, 2017, 2021 Stefan Reichör <stefan@xsteve.at>
;;; Copyright © 2016, 2017, 2019 Alex Vong <alexvong1995@gmail.com>
;;; Copyright © 2016, 2017, 2018 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2016, 2017, 2018, 2020, 2021 Julien Lepiller <julien@lepiller.eu>
;;; 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, 2020 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2017, 2020, 2021 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>
-;;; Copyright © 2017, 2019 Brendan Tildesley <mail@brendan.scot>
+;;; Copyright © 2017, 2019, 2021 Brendan Tildesley <mail@brendan.scot>
;;; Copyright © 2018 Ethan R. Jones <ethanrjones97@gmail.com
;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
;;; Copyright © 2019, 2020 Brett Gilio <brettg@gnu.org>
;;; Copyright © 2019 Sam <smbaines8@gmail.com>
;;; Copyright © 2019 Jack Hill <jackhill@jackhill.us>
-;;; Copyright © 2019, 2020 Guillaume Le Vaillant <glv@posteo.net>
+;;; Copyright © 2019, 2020, 2021 Guillaume Le Vaillant <glv@posteo.net>
;;; Copyright © 2019, 2020 Alex Griffin <a@ajgrf.com>
;;; Copyright © 2019, 2020 Pierre Langlois <pierre.langlois@gmx.com>
;;; Copyright © 2019 Jacob MacDonald <jaccarmac@gmail.com>
;;; Copyright © 2020 EuAndreh <eu@euandre.org>
;;; Copyright © 2021 Sharlatan Hellseher <sharlatanus@gmail.com>
;;; Copyright © 2021 Ellis Kenyő <me@elken.dev>
+;;; Copyright © 2021 LibreMiami <packaging-guix@libremiami.org>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (gnu packages icu4c)
#:use-module (gnu packages image)
#:use-module (gnu packages imagemagick)
+ #:use-module (gnu packages jupyter)
#:use-module (gnu packages kerberos)
#:use-module (gnu packages libevent)
#:use-module (gnu packages libffi)
(define-public python2-psutil
(let ((base (package-with-python2 (strip-python2-variant python-psutil))))
- (package
- (inherit base)
+ (package/inherit base
(propagated-inputs
`(("python2-enum34" ,python2-enum34) ;optional
,@(package-propagated-inputs base))))))
and verifies that it matches the intended target hostname.")
(license license:psfl)))
+(define-public python-bidict
+ (package
+ (name "python-bidict")
+ (version "0.21.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "bidict" version))
+ (sha256
+ (base32
+ "02dy0b1k7qlhn7ajyzkrvxhyhjj0hzcq6ws3zjml9hkdz5znz92g"))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-coverage" ,python-coverage)
+ ("python-hypothesis" ,python-hypothesis-5.23) ; use_true_random=... from >=5.19.0
+ ("python-pre-commit" ,python-pre-commit)
+ ("python-py" ,python-py)
+ ("python-pytest" ,python-pytest)
+ ("python-pytest-benchmark" ,python-pytest-benchmark)
+ ("python-pytest-cov" ,python-pytest-cov)
+ ("python-setuptools-scm" ,python-setuptools-scm)
+ ("python-sortedcollections" ,python-sortedcollections)
+ ("python-sortedcontainers" ,python-sortedcontainers)
+ ("python-sphinx" ,python-sphinx)
+ ("python-sphinx-autodoc-typehints" ,python-sphinx-autodoc-typehints)
+ ("python-tox" ,python-tox)))
+ (arguments
+ `(#:phases (modify-phases %standard-phases
+ (add-after 'unpack 'relax-reqs
+ (lambda _
+ (substitute* "setup.py"
+ (("sortedcollections < 2") "sortedcollections"))
+ #t))
+ (replace 'check
+ (lambda _ (invoke "./run_tests.py"))))))
+ (home-page "https://bidict.readthedocs.io")
+ (synopsis "Bidirectional mapping library")
+ (description "The @code{bidict} library provides several data structures
+for working with bidirectional mappings in Python.")
+ (license license:mpl2.0)))
+
(define-public python-bitarray
(package
(name "python-bitarray")
@code{subprocess} feature.")
(license license:expat)))
-(define-public python2-sh
- (package-with-python2 python-sh))
-
(define-public python-cftime
(package
(name "python-cftime")
(define-public python2-serpent
(let ((base (package-with-python2 (strip-python2-variant python-serpent))))
- (package
- (inherit base)
+ (package/inherit base
(propagated-inputs
`(("python-enum34" ,python2-enum34)
,@(package-propagated-inputs base))))))
license:asl2.0 ; packaging is dual ASL2/BSD-2
license:bsd-2))))
+(define-public python-setuptools-declarative-requirements
+ (package
+ (name "python-setuptools-declarative-requirements")
+ (version "1.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri
+ "setuptools-declarative-requirements"
+ version))
+ (sha256
+ (base32
+ "1l8zmcnp9h8sp8hsw7b81djaa1a9yig0y7i4phh5pihqz1gdn7yi"))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-pytest" ,python-pytest)
+ ("python-setuptools-scm" ,python-setuptools-scm)))
+ (propagated-inputs
+ `(("python-toml" ,python-toml)
+ ("python-wheel" ,python-wheel)))
+ (home-page
+ "https://github.com/s0undt3ch/setuptools-declarative-requirements")
+ (synopsis "File support for setuptools declarative setup.cfg")
+ (description
+ "This package provides file support for setuptools declarative
+@code{setup.cfg}.")
+ (license license:asl2.0)))
+
;; The setuptools provided by Python 3.7.4 is too new for Tensorflow.
(define-public python-setuptools-for-tensorflow
(hidden-package
(define-public python2-humanfriendly
(let ((base (package-with-python2
(strip-python2-variant python-humanfriendly))))
- (package (inherit base)
+ (package/inherit base
(propagated-inputs
`(("python2-monotonic" ,python2-monotonic)
,@(package-propagated-inputs base))))))
"1hgz8jq19wlz8vwqj900ry8cjv578nz4scc91mlc8944yid6573c"))))
(build-system python-build-system)
(propagated-inputs
- `(("python-greenlet" ,python-greenlet)))
+ `(("python-dnspython" ,python-dnspython)
+ ("python-greenlet" ,python-greenlet)
+ ("python-monotonic" ,python-monotonic)))
(arguments
;; TODO: Requires unpackaged 'enum-compat'.
'(#:tests? #f))
(build-system python-build-system)
(home-page "https://github.com/scour-project/scour")
(synopsis "Scour is an SVG optimizer/cleaner written in Python")
- (description "The goal of Scour is to output a file that renderes
+ (description "The goal of Scour is to output a file that renders
identically at a fraction of the size by removing a lot of redundant
information created by most SVG editors. Optimization options are typically
lossless but can be tweaked for more aggressive cleaning.")
(license license:asl2.0)))
+(define-public python-mappy
+ (package
+ (name "python-mappy")
+ (version "2.18")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "mappy" version))
+ (sha256
+ (base32
+ "1a05p7rkmxa6qhm108na8flzj2v45jab06drk59kzk1ip2sgvzqq"))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-cython" ,python-cython)))
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "https://github.com/lh3/minimap2")
+ (synopsis "Python binding for minimap2")
+ (description "This package provides a convenient interface to minimap2,
+a fast and accurate C program to align genomic and transcribe nucleotide
+sequences.")
+ (license license:expat)))
+
(define-public python-mechanize
(package
(name "python-mechanize")
(define-public python2-empy
(let ((base (package-with-python2 (strip-python2-variant python-empy))))
- (package
- (inherit base)
+ (package/inherit base
(arguments `(,@(package-arguments base)
#:tests? #t)))))
(define-public python2-parse-type
(let ((base (package-with-python2
(strip-python2-variant python-parse-type))))
- (package (inherit base)
+ (package/inherit base
(propagated-inputs
`(("python2-enum34" ,python2-enum34)
,@(package-propagated-inputs base))))))
(define-public python2-polib
(let ((base (package-with-python2 (strip-python2-variant python-polib))))
- (package
- (inherit base)
+ (package/inherit base
(arguments `(,@(package-arguments base)
;; Tests don't work with python2.
#:tests? #f)))))
(define-public python2-jsonschema
(let ((jsonschema (package-with-python2
(strip-python2-variant python-jsonschema))))
- (package (inherit jsonschema)
+ (package/inherit jsonschema
(propagated-inputs
`(("python2-functools32" ,python2-functools32)
,@(package-propagated-inputs jsonschema))))))
(define-public python2-kitchen
(package-with-python2 python-kitchen))
+(define-public python-roman
+ (package
+ (name "python-roman")
+ (version "3.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "roman" version))
+ (sha256
+ (base32
+ "0gyp2bmw47jgpm8j64gydzqq838bgxz5gh6cm57lxlr7p26sqiic"))))
+ (build-system python-build-system)
+ (home-page "https://github.com/zopefoundation/roman")
+ (synopsis "Integer to Roman numerals converter")
+ (description
+ "This package provides a small helper library to convert Arabic Numbers
+to Roman Numerals.")
+ (license license:psfl)))
+
(define-public python-unidecode
(package
(name "python-unidecode")
(properties `((python2-variant . ,(delay python2-pystache))))))
(define-public python2-pystache
- (package (inherit (package-with-python2
- (strip-python2-variant python-pystache)))
- (arguments
- `(#:python ,python-2
- #:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda _
- (invoke "python" "test_pystache.py"))))))))
+ (let ((base (package-with-python2
+ (strip-python2-variant python-pystache))))
+ (package/inherit base
+ (arguments
+ `(#:python ,python-2
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (invoke "python" "test_pystache.py")))))))))
(define-public python-joblib
(package
(sha256
(base32
"05mps9r966r3dpqw6zrs1nlwjdf5y4960hl9m7abwb3qyfnarwyc"))))
+ (replacement python-pygments/fixed)
(build-system python-build-system)
(arguments
;; FIXME: Tests require sphinx, which depends on this.
(license license:bsd-2)
(properties `((python2-variant . ,(delay python2-pygments))))))
+(define python-pygments/fixed
+ (package/inherit python-pygments
+ (version "2.7.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "Pygments" version))
+ (sha256
+ (base32
+ "0dy35ry5qa8dpklk4fkj9kfpw2qb4mh5ha9866kw30wf96dx0jfz"))))))
+
;; Pygments 2.6 and later does not support Python 2.
(define-public python2-pygments
(let ((base (package-with-python2 (strip-python2-variant python-pygments))))
(base32
"1zmhnswy0wxfn0xprs9aqsvx2c3kmzfn2wx14q8cv3vpkxdamj4q")))))))
+(define-public python-pygments-github-lexers
+ (package
+ (name "python-pygments-github-lexers")
+ (version "0.0.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "pygments-github-lexers" version))
+ (sha256
+ (base32
+ "0cz14clcc9z4pn79ll8hp3xzgsrfjscak5zfsvlgrz6ngkkmgjma"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-pygments" ,python-pygments)))
+ (home-page "https://github.com/liluo/pygments-github-lexers")
+ (synopsis "Pygments Github custom lexers")
+ (description "This package installs Github custom lexers to Pygments.")
+ (license license:bsd-3)))
+
(define-public python-bump2version
(package
(name "python-bump2version")
(define-public python-pygithub
(package
(name "python-pygithub")
- (version "1.43.8")
+ (version "1.54.1")
(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 "1625v558xga5mwhl9jqmibywy5qafmg1vqrirqz6zfq1la1d22mw"))))
+ (base32 "1nl74bp5ikdnrc8xq0qr25ryl1mvarf0xi43k8w5jzlrllhq0nkq"))))
(build-system python-build-system)
(arguments
- `(#:phases (modify-phases %standard-phases
- ;; Some tests rely on the network.
- (add-after 'unpack 'disable-failing-tests
- (lambda _
- (substitute* "tests/Issue142.py"
- (("testDecodeJson") "disabled_testDecodeJson"))
- #t))
- (add-before 'check 'prepare-for-tests
- (lambda _
- (for-each (lambda (f)
- (chmod f #o666))
- (find-files "./tests"))
- (system* "python" "-m" "lib2to3" "-w" "-n" "tests")
- (setenv "PYTHONPATH"
- (string-append "./tests:" (getenv "PYTHONPATH")))
- #t)))))
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "pytest"))
+ #t)))))
(propagated-inputs
- `(("python-deprecated" ,python-deprecated)
+ `(("python-cryptography" ,python-cryptography)
+ ("python-deprecated" ,python-deprecated)
("python-pyjwt" ,python-pyjwt)
("python-requests" ,python-requests)))
- (native-inputs `(("python-httpretty" ,python-httpretty)))
+ (native-inputs
+ `(("python-httpretty" ,python-httpretty)
+ ("python-pytest" ,python-pytest)))
(home-page "https://pygithub.readthedocs.io/en/latest/")
(synopsis "Python library for the GitHub API")
(description "This library allows managing GitHub resources such as
(define-public python-cython
(package
(name "python-cython")
- (version "0.29.21")
+ (version "0.29.22")
(source
(origin
(method url-fetch)
(uri (pypi-uri "Cython" version))
(sha256
- (base32
- "1bcwpra7c6k30yvic3sw2v3rq2dr40ypc4zqif6kr52mpn4wnyp5"))))
+ (base32 "01jl3544qwsi8lp6anbl55566xqkjd53x452i7m6gnfilv3q6syz"))))
(build-system python-build-system)
;; we need the full python package and not just the python-wrapper
;; because we need libpython3.3m.so
(define-public python2-cython
(let ((base (package-with-python2 (strip-python2-variant python-cython))))
- (package
- (inherit base)
+ (package/inherit base
(name "python2-cython")
(inputs
`(("python-2" ,python-2))) ;this is not automatically changed
(define-public python2-numpydoc
(let ((base (package-with-python2
(strip-python2-variant python-numpydoc))))
- (package
- (inherit base)
+ (package/inherit base
(propagated-inputs
`(("python2-jinja2" ,python2-jinja2)
,@(package-propagated-inputs base))))))
(description (package-description python-matplotlib))
(license (package-license python-matplotlib))))
-(define-public python2-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
(name "python-matplotlib-venn")
(define-public python-pycodestyle
(package
(name "python-pycodestyle")
- (version "2.6.0")
+ (version "2.7.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pycodestyle" version))
(sha256
(base32
- "0bhr6ia0hmgx3nhgibc9pmkzhlh1zcqk707i5fbxgs702ll7v2n5"))))
+ "1vqwmzmjdv331kmfq3q9j3as2x7r2r49lf83r9w4147pdg8c32f3"))))
(build-system python-build-system)
(arguments
`(#:phases
(define-public python-pikepdf
(package
(name "python-pikepdf")
- (version "2.8.0.post1")
+ (version "2.10.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pikepdf" version))
(sha256
- (base32 "08miajml3mzlaqxr8phzymshmkkm93f8vv1dvq5gzkj15kysqhpp"))))
+ (base32 "09wfj1hjvj3r9gv7ywrqd7h3d0bz64bvils8sm3ghj90jhalb03s"))))
(build-system python-build-system)
(arguments
`(#:tests? #false)) ;require python-xmp-toolkit
(description "This package is a fork of Pillow which adds support for SIMD
parallelism.")))
+(define-public python-imagecodecs
+ (package
+ (name "python-imagecodecs")
+ (version "2021.3.31")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "imagecodecs" version))
+ (sha256
+ (base32
+ "0q7pslb6wd56vbcq2mdxwsiha32mxjr7mgqqfbq5w42q601p9pi0"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Unbundle 3rd party modules.
+ (delete-file-recursively "3rdparty")
+ ;; Delete pre-generated Cython files.
+ (for-each delete-file (find-files "imagecodecs" "_.*\\.c$"))
+ #t))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #f ; Tests are disabled, because dependencies are missing.
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'create-configuration
+ (lambda* (#:key inputs #:allow-other-keys)
+ ;; By default everything is enabled. We can selectively disable
+ ;; extensions (and thus dependencies) by deleting them from the
+ ;; EXTENSIONS dictionary. This is upstream’s preferred way.
+ (call-with-output-file "imagecodecs_distributor_setup.py"
+ (lambda (port)
+ (format port "\
+def customize_build(EXTENSIONS, OPTIONS):
+ del EXTENSIONS['aec']
+ del EXTENSIONS['avif']
+ del EXTENSIONS['bitshuffle']
+ del EXTENSIONS['deflate']
+ del EXTENSIONS['jpeg2k']
+ del EXTENSIONS['jpeg12']
+ del EXTENSIONS['jpegls']
+ del EXTENSIONS['jpegxl']
+ del EXTENSIONS['jpegxr']
+ del EXTENSIONS['lerc']
+ del EXTENSIONS['ljpeg']
+ del EXTENSIONS['lzf']
+ del EXTENSIONS['zfp']
+ del EXTENSIONS['zopfli']
+ OPTIONS['cythonize']
+")))
+ #t)))))
+ (inputs
+ `(("c-blosc" ,c-blosc)
+ ("giflib" ,giflib)
+ ("google-brotli" ,google-brotli)
+ ("libjpeg-turbo" ,libjpeg-turbo)
+ ("libpng" ,libpng)
+ ("libtiff" ,libtiff)
+ ("libwebp" ,libwebp)
+ ("lz4" ,lz4)
+ ("snappy" ,snappy)
+ ("xz" ,xz)
+ ("zlib" ,zlib)
+ ("zstd" ,zstd "lib")))
+ (propagated-inputs
+ `(("python-numpy" ,python-numpy)))
+ (native-inputs
+ ;; For building.
+ `(("python-cython" ,python-cython)
+ ;; For testing. Incomplete.
+ ;("python-numcodecs" ,python-numcodecs)
+ ;("python-zarr" ,python-zarr)
+ ;("python-pytest" ,python-pytest)
+ ))
+ (home-page "https://www.lfd.uci.edu/~gohlke/")
+ (synopsis
+ "Image transformation, compression, and decompression codecs")
+ (description
+ "Imagecodecs is a Python library that provides block-oriented, in-memory
+buffer transformation, compression, and decompression functions for use in the
+tifffile, czifile, and other scientific image input/output modules.")
+ (license license:bsd-3)))
+
(define-public python-roifile
(package
(name "python-roifile")
- (version "2020.5.28")
+ (version "2020.11.28")
(source
(origin
(method url-fetch)
(uri (pypi-uri "roifile" version))
(sha256
(base32
- "1vwbwfsw745gyqymff6dllc5zqjsgqmxaw245sw4an6yw9rcbzc0"))))
+ "04argnc7qccybkrj9ww18bf81ghsghhh93hnqy3p111rcdlyn66p"))))
(build-system python-build-system)
(arguments `(#:tests? #f)) ; there are none
(propagated-inputs
(define-public python-tifffile
(package
(name "python-tifffile")
- (version "2020.6.3")
+ (version "2021.4.8")
(source
(origin
(method url-fetch)
(uri (pypi-uri "tifffile" version))
(sha256
(base32
- "0xv3ynkbrsibqvx7250075idb7wm3canjd6lx2nzf3cbp6l07577"))))
+ "16r0hw7shka1bqf28bv198lj2jhf2r9gy3s5zv4nf5cfsfm8pajm"))))
(build-system python-build-system)
;; Tests require lfdfiles, which depends on tifffile
(arguments `(#:tests? #f))
(propagated-inputs
`(("python-numpy" ,python-numpy)
- ;;("python-lfdfiles" ,python-lfdfiles)
- ("python-roifile" ,python-roifile)))
+ ("python-imagecodecs" ,python-imagecodecs)))
(home-page "https://www.lfd.uci.edu/~gohlke/")
(synopsis "Read and write TIFF(r) files")
(description "This package lets you read image and metadata from many
(define-public python-lfdfiles
(package
(name "python-lfdfiles")
- (version "2020.1.1")
+ (version "2021.2.22")
(source
(origin
(method url-fetch)
(uri (pypi-uri "lfdfiles" version))
(sha256
(base32
- "1n9bkfn4vxl0lbhzd0m35lq86ayx5fwcj3ghpfl2vbjbsnfp3h47"))))
+ "12fxm4v805dgjrih7x6jnl1wd7y7jw1rkhjs3d4am8s6qk1cbar2"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Delete pre-generated Cython files.
+ (for-each delete-file (find-files "lfdfiles" "_.*\\.c$"))
+ #t))))
(build-system python-build-system)
+ (arguments
+ `(#:tests? #f)) ; No tests exist, despite a test dependency on pytest.
(propagated-inputs
`(("python-click" ,python-click)
("python-numpy" ,python-numpy)
("python-tifffile" ,python-tifffile)))
+ (native-inputs `(("python-cython" ,python-cython)))
(home-page "https://www.lfd.uci.edu/~gohlke/")
(synopsis "Work with LFD data files")
(description
(define-public python-xlsxwriter
(package
(name "python-xlsxwriter")
- (version "1.3.7")
+ (version "1.3.9")
(source
(origin
;; There are no tests in the PyPI tarball.
(commit (string-append "RELEASE_" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "1qg40r2mwrqfmhaxnary1cfgi0dwwazp5qga7c9p2cdji2v0x5rm"))))
+ (base32 "04idf331rp0iyhlnh7268jmim8ydw4jjb81hr5rh548sqnq4bhpl"))))
(build-system python-build-system)
(home-page "https://github.com/jmcnamara/XlsxWriter")
(synopsis "Python module for creating Excel XLSX files")
PNG, PostScript, PDF, and SVG file output.")
(license license:bsd-3)))
-(define-public python2-cairocffi
- (package-with-python2 python-cairocffi))
-
(define-public python-decorator
(package
(name "python-decorator")
@end enumerate")
(license license:bsd-3)))
-(define-public python2-ipyparallel
- (let ((ipyparallel (package-with-python2 python-ipyparallel)))
- (package
- (inherit ipyparallel)
- (propagated-inputs
- `(("python2-futures" ,python2-futures)
- ,@(package-propagated-inputs ipyparallel))))))
-
(define-public python-ipython-cluster-helper
(package
(name "python-ipython-cluster-helper")
(define-public python2-traitlets
(let ((traitlets (package-with-python2 (strip-python2-variant python-traitlets))))
- (package
- (inherit traitlets)
+ (package/inherit traitlets
(propagated-inputs
`(("python2-enum34" ,python2-enum34)
,@(package-propagated-inputs traitlets))))))
(define-public python-jupyter-core
(package
(name "python-jupyter-core")
- (version "4.4.0")
+ (version "4.7.1")
(source
(origin
(method url-fetch)
(uri (string-append (pypi-uri "jupyter_core" version)))
(sha256
(base32
- "1dy083rarba8prn9f9srxq3c7n7vyql02ycrqq306c40lr57aw5s"))))
+ "1d12j5hkff0xiax87pnhmzbsph3jqqzhz16h8xld7z2y4armq0kr"))))
(build-system python-build-system)
;; FIXME: not sure how to run the tests
(arguments `(#:tests? #f))
"Jupyter core is the base package on which Jupyter projects rely.")
(license license:bsd-3)))
-(define-public python2-jupyter-core
- (package-with-python2 python-jupyter-core))
-
(define-public python-jupyter-client
(package
(name "python-jupyter-client")
- (version "5.2.4")
+ (version "6.1.12")
(source
(origin
(method url-fetch)
(uri (pypi-uri "jupyter_client" version))
(sha256
(base32
- "0l9mh7ccrpl3lppym3dnky8n1nk7xarzzdcxf4q2s7aw203cpydm"))))
+ "10p7fcgvv9hvz9zical9wk68ks5ssak2ykbzx65wm1k1hk8a3g64"))))
(build-system python-build-system)
;; Tests fail because of missing native python kernel which I assume is
;; provided by the ipython package, which we cannot use because it would
;; cause a dependency cycle.
(arguments
`(#:tests? #f
-
#:phases (modify-phases %standard-phases
(add-after 'unpack 'set-tool-file-names
(lambda* (#:key inputs #:allow-other-keys)
(inputs
`(("iproute" ,iproute)))
(propagated-inputs
- `(("python-pyzmq" ,python-pyzmq)
- ("python-traitlets" ,python-traitlets)
- ("python-jupyter-core" ,python-jupyter-core)))
+ `(("python-dateutil" ,python-dateutil)
+ ("python-jupyter-core" ,python-jupyter-core)
+ ("python-pyzmq" ,python-pyzmq)
+ ("python-tornado" ,python-tornado-6)
+ ("python-traitlets" ,python-traitlets)))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
(home-page "https://jupyter.org/")
(synopsis "Jupyter protocol implementation and client libraries")
(description
(define-public python-ipykernel
(package
(name "python-ipykernel")
- (version "5.1.3")
+ (version "5.5.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "ipykernel" version))
(sha256
- (base32 "1a08y677lpn80qzvv7z0smgggmr5m5ayf0bs6vds47xpxl9sss5k"))))
+ (base32 "02f55cjkp5q64x7ikjxznbxwjpkdmfy237b9kg7dk1pxmzvy90m6"))))
(build-system python-build-system)
(arguments
`(#:phases
("python-pytest" ,python-pytest)))
(home-page "https://ipython.org")
(synopsis "IPython Kernel for Jupyter")
- (description
- "This package provides the IPython kernel for Jupyter.")
- (properties `((python2-variant . ,(delay python2-ipykernel))))
- (license license:bsd-3)))
-
-;; Version 5.x and above no longer support Python 2.
-(define-public python2-ipykernel
- (package
- (name "python2-ipykernel")
- (version "4.10.1")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "ipykernel" version))
- (sha256
- (base32 "1yzmdiy1djsszqp54jzd8ym8h4hpl67zjq83j2kxbkp0rwmlpdzf"))))
- (build-system python-build-system)
- (arguments
- `(#:python ,python-2))
- (propagated-inputs
- `(("python2-ipython" ,python2-ipython)
- ;; imported at runtime during connect
- ("python2-jupyter-client" ,python2-jupyter-client)
- ("python2-tornado" ,python2-tornado)
- ("python2-traitlets" ,python2-traitlets)))
- (native-inputs
- `(("python2-mock" ,python2-mock)
- ("python2-nose" ,python2-nose)
- ("python2-pytest" ,python2-pytest)
- ("python2-pytest-cov" ,python2-pytest-cov)))
- (home-page "https://ipython.org")
- (synopsis "IPython Kernel for Jupyter")
(description
"This package provides the IPython kernel for Jupyter.")
(license license:bsd-3)))
(define-public python-backcall
(package
(name "python-backcall")
- (version "0.1.0")
+ (version "0.2.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "backcall" version))
(sha256
(base32
- "1r01dqch3f8fdj3n6fviw8hxqrs6w5v0qw4izmvqzry1w9dxiv1q"))))
+ "07jy4562lvnhkk6kfr3cphmizy88anlhmbwb8kdzlz2ypqkvzgaw"))))
(build-system python-build-system)
(home-page "https://github.com/takluyver/backcall/")
(synopsis "Specifications for callback functions passed in to an API")
(define-public python-urwid
(package
(name "python-urwid")
- (version "2.1.0")
+ (version "2.1.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "urwid" version))
(sha256
(base32
- "11ndnhxd41m13darf5s0c6bafdpkzq1l6mfb04wbzdmyc1hg75h8"))))
+ "1bky2bra6673xx8jy0826znw6cmxs89wcwwzda8d025j3jffx2sq"))))
(build-system python-build-system)
(home-page "http://urwid.org")
(synopsis "Console user interface library for Python")
(description
"Urwid is a curses-based UI/widget library for Python. It includes many
features useful for text console applications.")
+ (properties `((python2-variant . ,(delay python2-urwid))))
(license license:lgpl2.1+)))
(define-public python2-urwid
- (package-with-python2 python-urwid))
+ (let ((base (package-with-python2
+ (strip-python2-variant python-urwid))))
+ (package/inherit base
+ (version "2.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "urwid" version))
+ (sha256
+ (base32
+ "11ndnhxd41m13darf5s0c6bafdpkzq1l6mfb04wbzdmyc1hg75h8")))))))
+
+(define-public python-urwid-readline
+ (package
+ (name "python-urwid-readline")
+ (version "0.12")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/rr-/urwid_readline")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0sq5qgxj7gcfww3ww7idr87isnmp0hi36n241b3q395x1zafdv22"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "python" "-m" "pytest"))
+ #t)))))
+ (propagated-inputs
+ `(("python-urwid" ,python-urwid)))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
+ (home-page "https://github.com/rr-/urwid_readline")
+ (synopsis "Text input widget for urwid that supports readline shortcuts")
+ (description
+ "This package provides a textbox edit widget for @code{python-urwid} that
+supports @code{readline} shortcuts.")
+ (license license:expat)))
(define-public python-urwidtrees
(package
(license license:expat)))
(define-public python2-dbus
- (package (inherit python-dbus)
+ (package/inherit python-dbus
(name "python2-dbus")
(inputs `(("python" ,python-2)
,@(alist-delete "python"
(define-public python-beautifulsoup4
(package
(name "python-beautifulsoup4")
- (version "4.9.1")
+ (version "4.9.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "beautifulsoup4" version))
(sha256
(base32
- "1mvzlw3pzbhsvl3z8784s5h7iiflm2hggiy1fxyrrxwnbc8lvk3k"))))
+ "09gbd49mwz86k572r1231x2rdp82p42zlnw0bz9b9mfi58r9wwl4"))))
(build-system python-build-system)
(arguments
`(#:phases
(properties `((python2-variant . ,(delay python2-beautifulsoup4))))))
(define-public python2-beautifulsoup4
- (package
- (inherit (package-with-python2
- (strip-python2-variant python-beautifulsoup4)))
- (arguments `(#:python ,python-2))))
+ (let ((base (package-with-python2
+ (strip-python2-variant python-beautifulsoup4))))
+ (package/inherit base
+ (arguments `(#:python ,python-2)))))
(define-public python-soupsieve
(package
(name "python-soupsieve")
- (version "2.0.1")
+ (version "2.2.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "soupsieve" version))
(sha256
(base32
- "0ch2rhvsbwfpvzm4kzy81rclbzr533yv83hzg1gx55byfa0w37d5"))))
+ "1k70gpn2d3vgdyxbdy536dgm4kchcraxz6lmgsfg3324iy2789q5"))))
(build-system python-build-system)
(arguments `(#:tests? #f))
;;XXX: 2 tests fail currently despite claming they were to be
Python.")
(license license:lgpl2.1+)))
+(define-public python-amply
+ (package
+ (name "python-amply")
+ (version "0.1.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "amply" version))
+ (sha256
+ (base32
+ "0f1db9zp0rsfzxvaz55xwh8h5rfdgr9a2a715g06ic8nknsdq4nb"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-docutils" ,python-docutils)
+ ("python-pyparsing" ,python-pyparsing)))
+ (native-inputs
+ `(("python-setuptools-scm" ,python-setuptools-scm)))
+ (home-page "https://github.com/willu47/amply")
+ (synopsis "Load and manipulate AMPL/GLPK data as Python data structures")
+ (description
+ "Amply allows you to load and manipulate AMPL/GLPK data as Python data
+structures.")
+ (license license:epl1.0)))
+
+(define-public python-pulp
+ (package
+ (name "python-pulp")
+ (version "2.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "PuLP" version))
+ (sha256
+ (base32
+ "1dammrg0f1v0r028i3rpxbf2bsyxmjq0q6ihb4x2wsdki44z3bxj"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-amply" ,python-amply)))
+ (home-page "https://github.com/coin-or/pulp")
+ (synopsis "Linear Programming modeler")
+ (description
+ "PuLP is a Linear Programming modeler written in Python. PuLP can
+generate MPS or LP files and call GLPK, COIN CLP/CBC, CPLEX, and GUROBI to
+solve linear problems.")
+ (license license:expat)))
+
+(define-public python-toposort
+ (package
+ (name "python-toposort")
+ (version "1.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "toposort" version))
+ (sha256
+ (base32
+ "1b2hppzjg3p006qya3yfdnp76dwq8frl97lypdam0kw4xxb8yhm7"))))
+ (build-system python-build-system)
+ (home-page "https://gitlab.com/ericvsmith/toposort")
+ (synopsis "Topological sort algorithm")
+ (description
+ "This package provides an implementation of a topological sort
+algorithm.")
+ (license license:asl2.0)))
+
(define-public snakemake
(package
(name "snakemake")
- (version "5.7.1")
+ (version "5.32.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "snakemake" version))
(sha256
- (base32 "1pnpvvn8n2a78cg360wz3ldmpqrsm2wzi0c0dmvki9fnsw6fxdas"))))
+ (base32 "13013gdavwvyj1qr9xfi9fpwhb3km8c3z53bja5b7ic3sb2z6dgz"))))
(build-system python-build-system)
(arguments
;; TODO: Package missing test dependencies.
;; this by calling the snakemake wrapper instead.
(add-after 'unpack 'call-wrapper-not-wrapped-snakemake
(lambda* (#:key outputs #:allow-other-keys)
- (substitute* "snakemake/executors.py"
+ (substitute* "snakemake/executors/__init__.py"
(("\\{sys.executable\\} -m snakemake")
(string-append (assoc-ref outputs "out")
"/bin/snakemake")))
("python-gitpython" ,python-gitpython)
("python-jinja2" ,python-jinja2)
("python-jsonschema" ,python-jsonschema)
+ ("python-nbformat" ,python-nbformat)
("python-networkx" ,python-networkx)
("python-psutil" ,python-psutil)
+ ("python-pulp" ,python-pulp)
("python-pyyaml" ,python-pyyaml)
("python-ratelimiter" ,python-ratelimiter)
("python-requests" ,python-requests)
+ ("python-toposort" ,python-toposort)
("python-wrapt" ,python-wrapt)))
(home-page "https://snakemake.readthedocs.io")
(synopsis "Python-based execution environment for make-like workflows")
(define-public python-pyzmq
(package
(name "python-pyzmq")
- (version "17.1.2")
+ (version "22.0.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pyzmq" version))
(sha256
- (base32 "1pyxxrz60f88ffm0y6vpbx3q8jcr9ybz8fcilihwzwhh36n84ax7"))))
+ (base32 "0bgrn65cxfz1c1sjrgyq5dy1mkhppxxbizd5wvrl03cq4zhkrxpp"))))
(build-system python-build-system)
(arguments
`(#:configure-flags
(define-public python2-pep517
(let ((base (package-with-python2
(strip-python2-variant python-pep517))))
- (package
- (inherit base)
+ (package/inherit base
(name "python2-pep517")
(arguments
`(#:tests? #f
(define-public python-pyflakes
(package
(name "python-pyflakes")
- (version "2.2.0")
+ (version "2.3.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pyflakes" version))
(sha256
(base32
- "1j3zqbiwkyicvww499bblq33x0bjpzdrxajhaysr7sk7x5gdgcim"))))
+ "1ny10364ciqh4ripasj4zzv4145l21l3s85m3qlrvfq5pk58xg7m"))))
(build-system python-build-system)
(home-page
"https://github.com/pyflakes/pyflakes")
(define-public python-flake8
(package
(name "python-flake8")
- (version "3.8.4")
+ (version "3.9.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "flake8" version))
(sha256
(base32
- "0fvcrsbyzjpcli8ldbpsdbpmf238nkvwc1dy4hy82lf63rvfinma"))))
+ "1w65iyjnrwipv4dbcqxh725ri7mdx01d6pjyggd97c0j5cvkx1vq"))))
(build-system python-build-system)
(arguments
`(#:phases
(define-public python2-flake8
(let ((base (package-with-python2 (strip-python2-variant python-flake8))))
- (package (inherit base)
+ (package/inherit base
(propagated-inputs
`(("python2-configparser" ,python2-configparser)
("python2-enum34" ,python2-enum34)
in pyflakes and pycodestyle.")
(license license:expat)))
+(define-public python-flake8-continuation
+ (package
+ (name "python-flake8-continuation")
+ (version "1.0.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "flake8-continuation" version))
+ (sha256
+ (base32
+ "0dzaw8jr7yhlabxhrblnrizxx17xa9ngjnbr1kidg5lapq6b9q1y"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-flake8" ,python-flake8)
+ ("python-pycodestyle" ,python-pycodestyle)
+ ("python-six" ,python-six)))
+ (home-page "https://github.com/planetlabs/flake8-continuation")
+ (synopsis "Flake8 Line Continuation Plugin")
+ (description "A Flake8 plugin that checks for the line continuation
+style to be in the preferred method according to PEP-8, specifically:
+@quotation
+The preferred way of wrapping long lines is by using Python's implied
+line continuation inside parentheses, brackets and braces. Long lines
+can be broken over multiple lines by wrapping expressions in parentheses.
+These should be used in preference to using a backslash for line continuation.
+@end quotation")
+ (license license:asl2.0)))
+
(define-public python-flake8-implicit-str-concat
(package
(name "python-flake8-implicit-str-concat")
correct string literal concatenation.
It looks for style problems like implicitly concatenated string literals on
-the same line (which can be introduced by the code formating tool Black), or
+the same line (which can be introduced by the code formatting tool Black), or
unnecessary plus operators for explicit string literal concatenation.")
(license license:expat)))
lints.")
(license license:bsd-2)))
+(define-public python-flake8-quotes
+ (package
+ (name "python-flake8-quotes")
+ (version "3.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "flake8-quotes" version))
+ (sha256
+ (base32
+ "0ph5s6lxgpzz4an0ax6s5xjqypqmngwr5b1i0h9pqhzghplic49z"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-flake8" ,python-flake8)))
+ (home-page "https://github.com/zheller/flake8-quotes/")
+ (synopsis "Flake8 lint for quotes")
+ (description "This package provides a Flake8 lint for quotes.")
+ (license license:expat)))
+
(define-public python-autoflake
(package
(name "python-autoflake")
(define-public python-markdown
(package
(name "python-markdown")
- (version "3.2.1")
+ (version "3.3.4")
(source
(origin
(method url-fetch)
(uri (pypi-uri "Markdown" version))
(sha256
(base32
- "00k91gwhxnm8jdnm2v5xjz9irj6dbi7afywz2hpakqdbxs1ydzlh"))))
+ "0jbs73nincha8fkfxx267sfxac6pl0ckszjbqbb8gk4dhs8v9d9i"))))
(build-system python-build-system)
(native-inputs
`(("python-nose" ,python-nose)
(properties `((python2-variant . ,(delay python2-llfuse))))))
(define-public python2-llfuse
- (package (inherit (package-with-python2
- (strip-python2-variant python-llfuse)))
- (propagated-inputs `(("python2-contextlib2" ,python2-contextlib2)))))
+ (let ((base (package-with-python2
+ (strip-python2-variant python-llfuse))))
+ (package/inherit base
+ (propagated-inputs `(("python2-contextlib2" ,python2-contextlib2))))))
(define-public python-msgpack
(package
designed to efficiently cope with extremely large amounts of data.")
(license license:bsd-3)))
-(define-public python2-tables
- (package-with-python2 python-tables))
-
(define-public python-sniffio
(package
(name "python-sniffio")
(define-public python-ipaddress
(package
(name "python-ipaddress")
- (version "1.0.22")
+ (version "1.0.23")
(source (origin
(method url-fetch)
(uri (pypi-uri "ipaddress" version))
(sha256
(base32
- "0b570bm6xqpjwqis15pvdy6lyvvzfndjvkynilcddjj5x98wfimi"))))
+ "1qp743h30s04m3cg3yk3fycad930jv17q7dsslj4mfw0jlvf1y5p"))))
(build-system python-build-system)
(home-page "https://github.com/phihag/ipaddress")
(synopsis "IP address manipulation library")
(license license:asl2.0)))
(define-public python2-tlsh
- (package
- (inherit python-tlsh)
+ (package/inherit python-tlsh
(name "python2-tlsh")
(inputs `(("python" ,python-2)))))
(package-with-python2 python-libarchive-c))
(define-public python-file
- (package
- (inherit file)
+ (package/inherit file
(name "python-file")
(build-system python-build-system)
(arguments
(define-public python-nbformat
(package
(name "python-nbformat")
- (version "4.4.0")
+ (version "5.1.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "nbformat" version))
(sha256
(base32
- "00nlf08h8yc4q73nphfvfhxrcnilaqanb8z0mdy6nxk0vzq4wjgp"))))
+ "1j6idwsw59cslsssvlkg2bkfpvd6ri7kghbp14jwcw87sy57h5mm"))))
(build-system python-build-system)
- (arguments `(#:tests? #f)) ; no test target
(propagated-inputs
`(("python-ipython-genutils" ,python-ipython-genutils)
("python-jsonschema" ,python-jsonschema)
("python-jupyter-core" ,python-jupyter-core)
("python-traitlets" ,python-traitlets)))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
(home-page "https://jupyter.org")
(synopsis "Jupyter Notebook format")
(description "This package provides the reference implementation of the
Jupyter Notebook format and Python APIs for working with notebooks.")
+ (properties `((python2-variant . ,(delay python2-nbformat))))
(license license:bsd-3)))
(define-public python2-nbformat
- (package-with-python2 python-nbformat))
+ (let ((parent (package-with-python2
+ (strip-python2-variant python-nbformat))))
+ (package
+ (inherit parent)
+ (version "4.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "nbformat" version))
+ (sha256
+ (base32
+ "00nlf08h8yc4q73nphfvfhxrcnilaqanb8z0mdy6nxk0vzq4wjgp")))))))
(define-public python-bleach
(package
(define-public python-nbconvert
(package
(name "python-nbconvert")
- (version "5.0.0b1")
+ (version "6.0.7")
(source
(origin
(method url-fetch)
(uri (pypi-uri "nbconvert" version))
(sha256
(base32
- "0brclbb18l4nmd5qy3dl9wn05rjdh1fz4rmzdlfqacj12rcdvdgp"))))
+ "00lhqaxn481qvk2w5568asqlsnvrw2fm61p1vssx3m7vdnl17g6b"))))
(build-system python-build-system)
(arguments
- `(;; The "bdist_egg" target is disabled by default, causing the installation
- ;; to fail.
- #:configure-flags (list "bdist_egg")
- ;; FIXME: 5 failures, 40 errors.
- #:tests? #f))
- ;; #:phases
- ;; (modify-phases %standard-phases
- ;; (replace 'check
- ;; (lambda _
- ;; (zero? (system* "py.test" "-v")))))
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? inputs outputs #:allow-other-keys)
+ (when tests?
+ (add-installed-pythonpath inputs outputs)
+
+ ;; This seems to require Chromium.
+ (delete-file "nbconvert/exporters/tests/test_webpdf.py")
+
+ ;; This depends on the python3 kernel, which is provided by a
+ ;; package that depends on nbconvert.
+ (delete-file "nbconvert/preprocessors/tests/test_execute.py")
+
+ ;; Most of these tests fail because nbconvert fails to execute
+ ;; itself.
+ (delete-file "nbconvert/tests/test_nbconvertapp.py")
+
+ ;; One test here fails with an unclear error. It looks like
+ ;; "%%pylabprint" is supposed to be expanded to some other
+ ;; code, but isn't.
+ (delete-file "nbconvert/filters/tests/test_strings.py")
+
+ ;; Some tests need HOME
+ (setenv "HOME" "/tmp")
+ (invoke "pytest")))))))
(native-inputs
`(("python-pytest" ,python-pytest)))
(propagated-inputs
`(("python-bleach" ,python-bleach)
+ ("python-defusedxml" ,python-defusedxml)
("python-entrypoints" ,python-entrypoints)
("python-jinja2" ,python-jinja2)
("python-jupyter-core" ,python-jupyter-core)
("python-mistune" ,python-mistune)
+ ("python-nbclient" ,python-nbclient)
("python-nbformat" ,python-nbformat)
+ ("python-pandocfilters" ,python-pandocfilters)
("python-pygments" ,python-pygments)
+ ("python-jupyterlab-pygments" ,python-jupyterlab-pygments)
+ ("python-testpath" ,python-testpath)
("python-traitlets" ,python-traitlets)))
(home-page "https://jupyter.org")
(synopsis "Converting Jupyter Notebooks")
@item ReStructured Text (rst)
@item executable script
@end enumerate\n")
- (license license:bsd-3)))
+ (license license:bsd-3)
+ (properties `((python2-variant . ,(delay python2-nbconvert))))))
(define-public python2-nbconvert
- (package-with-python2 python-nbconvert))
+ (let ((parent
+ (package-with-python2
+ (strip-python2-variant python-nbconvert))))
+ (package
+ (inherit parent)
+ (version "5.0.0b1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "nbconvert" version))
+ (sha256
+ (base32
+ "0brclbb18l4nmd5qy3dl9wn05rjdh1fz4rmzdlfqacj12rcdvdgp"))))
+ (arguments
+ `(;; The "bdist_egg" target is disabled by default, causing the installation
+ ;; to fail.
+ #:configure-flags (list "bdist_egg")
+ ;; FIXME: 5 failures, 40 errors.
+ #:tests? #f))
+ (propagated-inputs
+ `(("python-bleach" ,python-bleach)
+ ("python-entrypoints" ,python-entrypoints)
+ ("python-jinja2" ,python-jinja2)
+ ("python-jupyter-core" ,python-jupyter-core)
+ ("python-mistune" ,python-mistune)
+ ("python-nbformat" ,python-nbformat)
+ ("python-pygments" ,python-pygments)
+ ("python-traitlets" ,python-traitlets))))))
(define-public python-notebook
(package
(name "python-notebook")
- (version "5.7.4")
+ (version "6.3.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "notebook" version))
(sha256
(base32
- "0jm7324mbxljmn9hgapj66q7swyz5ai92blmr0jpcy0h80x6f26r"))))
+ "0zfwr87ndjzmdp9adpc9lby1hdqdkjp2q7c9vff3wiw1dj6kkjfb"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'check
- (lambda _
+ (lambda* (#:key tests? inputs outputs #:allow-other-keys)
;; These tests require a browser
(delete-file-recursively "notebook/tests/selenium")
- ;; Some tests need HOME
- (setenv "HOME" "/tmp")
- ;; This file contains "warningfilters", which are not supported
- ;; by this version of nose.
- (delete-file "setup.cfg")
- (with-directory-excursion "/tmp"
- (invoke "nosetests" "-v"))
- #t)))))
+ (when tests?
+ (add-installed-pythonpath inputs outputs)
+ ;; Some tests need HOME
+ (setenv "HOME" "/tmp")
+ (with-directory-excursion "/tmp"
+ (invoke "pytest" "-vv"
+ ;; TODO: This tests fails because nbconvert does not
+ ;; list "python" as a format.
+ "-k" "not test_list_formats"))))))))
(propagated-inputs
- `(("python-jupyter-core" ,python-jupyter-core)
- ("python-nbformat" ,python-nbformat)
+ `(("python-argon2-cffi" ,python-argon2-cffi)
+ ("python-ipykernel" ,python-ipykernel)
+ ("python-ipython-genutils" ,python-ipython-genutils)
+ ("python-jinja2" ,python-jinja2)
+ ("python-jupyter-client" ,python-jupyter-client)
+ ("python-jupyter-core" ,python-jupyter-core)
("python-nbconvert" ,python-nbconvert)
+ ("python-nbformat" ,python-nbformat)
("python-prometheus-client" ,python-prometheus-client)
+ ("python-pyzmq" ,python-pyzmq)
("python-send2trash" ,python-send2trash)
- ("python-terminado" ,python-terminado)))
+ ("python-terminado" ,python-terminado)
+ ("python-tornado" ,python-tornado-6)
+ ("python-traitlets" ,python-traitlets)))
(native-inputs
- `(("python-nose" ,python-nose)
- ("python-sphinx" ,python-sphinx)
- ("python-requests" ,python-requests)))
+ `(("python-coverage" ,python-coverage)
+ ("python-nbval" ,python-nbval)
+ ("python-pytest" ,python-pytest)
+ ("python-pytest-cov" ,python-pytest-cov)
+ ("python-requests" ,python-requests)
+ ("python-requests-unixsocket" ,python-requests-unixsocket)))
(home-page "https://jupyter.org/")
(synopsis "Web-based notebook environment for interactive computing")
(description
(define-public python2-notebook
(let ((base (package-with-python2
(strip-python2-variant python-notebook))))
- (package (inherit base)
+ (package/inherit base
(native-inputs
`(("python2-mock" ,python2-mock)
,@(package-native-inputs base)))
"1ismyaxbv9d56yqqqb8xl58hg0iq0bbyy014a53y1g3hfbc8g7q7"))))
(build-system python-build-system)
(propagated-inputs
- `(("python-ipykernel" ,python-ipykernel)
- ("python-notebook" ,python-notebook)))
- (native-inputs
- `(("python-certifi" ,python-certifi)
- ("python-nose" ,python-nose)))
+ `(("python-notebook" ,python-notebook)))
(home-page "https://ipython.org")
(synopsis "IPython HTML widgets for Jupyter")
(description "This package provides interactive HTML widgets for Jupyter
notebooks.")
(license license:bsd-3)))
-(define-public python2-widgetsnbextension
- (package-with-python2 python-widgetsnbextension))
-
(define-public python-ipywidgets
(package
(name "python-ipywidgets")
- (version "7.5.1")
+ (version "7.6.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "ipywidgets" version))
(sha256
(base32
- "15sww2mvnkqlvx55gwa82v05062a8j1xpncnqna4k9sl53hgcig9"))))
+ "1w217j8i53x14l7b05fk300k222zs9vkcjaa1rbrw3sk43k466lz"))))
(build-system python-build-system)
(propagated-inputs
- `(("python-ipython" ,python-ipython)
+ `(("python-ipykernel" ,python-ipykernel)
+ ("python-ipython" ,python-ipython)
+ ("python-jupyterlab-widgets" ,python-jupyterlab-widgets)
+ ("python-nbformat" ,python-nbformat)
("python-traitlets" ,python-traitlets)
("python-widgetsnbextension" ,python-widgetsnbextension)))
(native-inputs
- `(("python-nose" ,python-nose)
- ("python-pytest" ,python-pytest)))
+ `(("python-mock" ,python-mock)
+ ("python-pytest" ,python-pytest)
+ ("python-pytest-cov" ,python-pytest-cov)))
(home-page "https://ipython.org")
(synopsis "IPython HTML widgets for Jupyter")
(description "Ipywidgets are interactive HTML widgets for Jupyter
in the data.")
(license license:bsd-3)))
-(define-public python2-ipywidgets
- (package-with-python2 python-ipywidgets))
-
(define-public python-jupyter-console
(package
(name "python-jupyter-console")
(synopsis "Jupyter terminal console")
(description "This package provides a terminal-based console frontend for
Jupyter kernels. It also allows for console-based interaction with non-Python
-Jupyter kernels such as IJulia and IRKernel.")
- (properties `((python2-variant . ,(delay python2-jupyter-console))))
- (license license:bsd-3)))
-
-(define-public python2-jupyter-console
- (package
- (name "python2-jupyter-console")
- (version "5.2.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "jupyter_console" version))
- (sha256
- (base32
- "1kam1qzgwr7srhm5r6aj90di5sws4bq0jmiw15452ddamb9yspal"))))
- (build-system python-build-system)
- (arguments
- `(#:python ,python-2
- #:tests? #f)) ; Tests only run in a TTY.
- (propagated-inputs
- `(("python2-ipykernel" ,python2-ipykernel)
- ("python2-jupyter-client" ,python2-jupyter-client)
- ("python2-prompt-toolkit" ,python2-prompt-toolkit-1)
- ("python2-pygments" ,python2-pygments)))
- (native-inputs
- `(("python2-nose" ,python2-nose)))
- (home-page "https://jupyter.org")
- (synopsis "Jupyter terminal console")
- (description "This package provides a terminal-based console frontend for
-Jupyter kernels. It also allows for console-based interaction with non-Python
Jupyter kernels such as IJulia and IRKernel.")
(license license:bsd-3)))
;; the functionality in both packages working, strip down the
;; python-jupyter-console package when using it as an input to python-ipython.
(define python-jupyter-console-minimal
- (package
- (inherit python-jupyter-console)
+ (package/inherit python-jupyter-console
(name "python-jupyter-console-minimal")
(arguments
(substitute-keyword-arguments
(define-public python2-contextlib2
(let ((base (package-with-python2
(strip-python2-variant python-contextlib2))))
- (package
- (inherit base)
+ (package/inherit base
(arguments
(substitute-keyword-arguments (package-arguments base)
((#:phases phases)
(home-page "https://github.com/click-contrib/click-log")
(license license:expat)))
+(define-public python-click-default-group
+ (package
+ (name "python-click-default-group")
+ (version "1.2.2")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "click-default-group" version))
+ (sha256
+ (base32
+ "015r78jk8gznfw0dphpwaqcx5mhg5822b55w5xbb6i7sin70wmnr"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #f)) ; no target
+ (propagated-inputs
+ `(("python-click" ,python-click)))
+ (synopsis "Extends click.Group")
+ (description "This package extends click.Group to invoke a command without
+explicit subcommand name.")
+ (home-page "https://github.com/click-contrib/click-default-group")
+ (license license:bsd-3)))
+
(define-public python-structlog
(package
(name "python-structlog")
(define-public python-icalendar
(package
(name "python-icalendar")
- (version "4.0.5")
+ (version "4.0.7")
(source (origin
(method url-fetch)
(uri (pypi-uri "icalendar" version))
(sha256
(base32
- "14ynjj65kfmlcvpb7k097w789wvxncd3cr3xz5m1jz9yl9v6vv5q"))))
+ "19574j3jwssm2dkqykih4568xqfgjsa3hcd79yl5s2vfys3qvh8g"))))
(build-system python-build-system)
(propagated-inputs
`(("python-dateutil" ,python-dateutil)
(define-public python2-promise
(let ((promise (package-with-python2
(strip-python2-variant python-promise))))
- (package (inherit promise)
+ (package/inherit promise
(arguments (substitute-keyword-arguments (package-arguments promise)
((#:tests? _) #t)))
(native-inputs
(propagated-inputs
`(("python-importlib-metadata" ,python2-importlib-metadata-bootstrap))))))
+(define-public python-plumbum
+ (package
+ (name "python-plumbum")
+ (version "1.7.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "plumbum" version))
+ (sha256
+ (base32 "1kidj821k79dw064rlxh84xamb9h79ychg3pgj81jlvm5hs48xri"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #f)) ;no tests
+ (native-inputs
+ ;; XXX: Not actually used since there are no tests but required for
+ ;; build.
+ `(("python-pytest" ,python-pytest)))
+ (home-page "https://plumbum.readthedocs.io")
+ (synopsis "Python shell combinators library")
+ (description
+ "Plumbum is a library of tools for replacing shell scripts with Python
+code.")
+ (license license:expat)))
+
+(define-public python-deprecation
+ (package
+ (name "python-deprecation")
+ (version "2.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "deprecation" version))
+ (sha256
+ (base32
+ "1zqqjlgmhgkpzg9ss5ki8wamxl83xn51fs6gn2a8cxsx9vkbvcvj"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-packaging" ,python-packaging)))
+ (native-inputs
+ `(("python-unittest2" ,python-unittest2)))
+ (home-page "https://deprecation.readthedocs.io/")
+ (synopsis "Python library to handle automated deprecations")
+ (description
+ "This is a library that enables automated deprecations. It offers the
+@code{deprecated()} decorator to wrap functions, providing proper warnings
+both in documentation and via Python’s warnings system, as well as the
+@code{deprecation.fail_if_not_removed()} decorator for test methods to ensure
+that deprecated code is eventually removed.")
+ (license license:asl2.0)))
+
(define-public python-tox
(package
(name "python-tox")
manipulation library.")
(license license:expat)))
+(define-public python-uncertainties
+ (package
+ (name "python-uncertainties")
+ (version "3.1.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "uncertainties" version))
+ (sha256
+ (base32
+ "00z9xl40czmqk0vmxjvmjvwb41r893l4dad7nj1nh6blw3kw28li"))))
+ (build-system python-build-system)
+ ;; While there are test files, there is no "tests" directory, so the tests
+ ;; fail.
+ (arguments '(#:tests? #false))
+ (propagated-inputs
+ `(("python-future" ,python-future)))
+ (native-inputs
+ `(("python-nose" ,python-nose)
+ ("python-numpy" ,python-numpy)))
+ (home-page "https://uncertainties-python-package.readthedocs.io/")
+ (synopsis "Calculations with uncertainties")
+ (description
+ "The uncertainties package transparently handles calculations with
+numbers with uncertainties. It can also yield the derivatives of any
+expression.")
+ (license license:bsd-3)))
+
+(define-public python-asteval
+ (package
+ (name "python-asteval")
+ (version "0.9.23")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "asteval" version))
+ (sha256
+ (base32
+ "0f54sd4w1a72ij1bcxs2x7dk9xf8bzclawijf1z18bqx9f96l2gm"))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
+ (home-page "https://github.com/newville/asteval")
+ (synopsis "Minimalistic evaluator of Python expressions")
+ (description
+ "This package provides a minimalistic evaluator of Python expression
+using the @code{ast} module")
+ (license license:expat)))
+
+(define-public python-lmfit
+ (package
+ (name "python-lmfit")
+ (version "1.0.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "lmfit" version))
+ (sha256
+ (base32
+ "0iab33jjb60f8kn0k0cqb0vjp1mdskks2n3kpn97zkw5cvjhq2b7"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-asteval" ,python-asteval)
+ ("python-numpy" ,python-numpy)
+ ("python-scipy" ,python-scipy)
+ ("python-uncertainties" ,python-uncertainties)))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
+ (home-page "https://lmfit.github.io/lmfit-py/")
+ (synopsis "Least-Squares minimization with bounds and constraints")
+ (description
+ "Lmfit provides a high-level interface to non-linear optimization and
+curve fitting problems for Python. It builds on and extends many of the
+optimization methods of @code{scipy.optimize}. Initially inspired by (and
+named for) extending the Levenberg-Marquardt method from
+@code{scipy.optimize.leastsq}, lmfit now provides a number of useful
+enhancements to optimization and data fitting problems.")
+ (license license:bsd-3)))
+
(define-public python-boto
(package
(name "python-boto")
(define-public python2-anyjson
(let ((anyjson (package-with-python2
(strip-python2-variant python-anyjson))))
- (package
- (inherit anyjson)
+ (package/inherit anyjson
(arguments `(;; Unlike the python 3 variant, we do run tests. See above!
#:tests? #t
,@(package-arguments anyjson)))
(define-public python2-amqp
(let ((amqp (package-with-python2
(strip-python2-variant python-amqp))))
- (package
- (inherit amqp)
+ (package/inherit amqp
(arguments `(;; Tries to run coverage tests with nose-cover3, which seems
;; unmaintained. Weirdly, does not do this on the python 3
;; version?
(define-public python2-kombu
(let ((kombu (package-with-python2
(strip-python2-variant python-kombu))))
- (package
- (inherit kombu)
+ (package/inherit kombu
(arguments `(;; FIXME: 'TestTransport.test_del_sync' fails on python2.
;; It works fine on the python3 variant.
#:tests? #f
(define-public python2-billiard
(let ((billiard (package-with-python2
(strip-python2-variant python-billiard))))
- (package
- (inherit billiard)
+ (package/inherit billiard
(native-inputs `(("python2-unittest2" ,python2-unittest2)
("python2-mock" ,python2-mock)
,@(package-native-inputs billiard))))))
(define-public python2-celery
(let ((celery (package-with-python2
(strip-python2-variant python-celery))))
- (package
- (inherit celery)
+ (package/inherit celery
(native-inputs `(("python2-unittest2" ,python2-unittest2)
("python2-mock" ,python2-mock)
,@(package-native-inputs celery))))))
(define-public python2-whoosh
(let ((whoosh (package-with-python2 (strip-python2-variant python-whoosh))))
- (package (inherit whoosh)
+ (package/inherit whoosh
(propagated-inputs
`(("python2-backport-ssl-match-hostname"
,python2-backport-ssl-match-hostname)
(define-public python2-jellyfish
(let ((jellyfish (package-with-python2
(strip-python2-variant python-jellyfish))))
- (package (inherit jellyfish)
+ (package/inherit jellyfish
(native-inputs `(("python2-unicodecsv" ,python2-unicodecsv)
,@(package-native-inputs jellyfish))))))
(license license:gpl2)))
(define-public python-rope
- (package
- (inherit python2-rope)
+ (package/inherit python2-rope
(name "python-rope")
(arguments `(#:python ,python-wrapper
;; XXX: Only partial python3 support, results in some failing
(define-public python-fastimport
(package
(name "python-fastimport")
- (version "0.9.8")
+ (version "0.9.9")
(source
(origin
(method url-fetch)
(uri (pypi-uri "fastimport" version))
(sha256
- (base32 "1fb3b7y3sw55f6wykxx478ybkirz0l52lgdqmbhmc0h0jzmyiwmj"))))
+ (base32 "06gk14qgm9dxx3pzjn0ckdbywc8ial2bjfzddqwlr4bn1nnqkbll"))))
(build-system python-build-system)
(home-page "https://github.com/jelmer/python-fastimport")
(synopsis "VCS fastimport parser and generator in Python")
(define-public python-tabulate
(package
(name "python-tabulate")
- (version "0.8.7")
+ (version "0.8.9")
(source (origin
(method url-fetch)
(uri (pypi-uri "tabulate" version))
(sha256
(base32
- "01shi7bmj09f0bcm5s0c9skys063lzp76p0n4a2xmg041ni269yv"))))
+ "19qkdz8xwk5jxa5xn53mnk76qnh4ysm81vzj664jw1b0azr167gb"))))
(build-system python-build-system)
(arguments
;; FIXME: The pypi release tarball is missing a 'test/common.py'
(define-public poetry
(package
(name "poetry")
- (version "1.1.4")
+ (version "1.1.5")
;; Poetry can only be built from source with Poetry.
(source
(origin
(uri (pypi-uri "poetry" version))
(sha256
(base32
- "1a2kgfiw66fvxhlqk5qc83s6l38czfh5hcsrbiy7qq5yfc8mlsll"))))
+ "1dvx08ksv5wnsj45db23921rj136akmcnxa0kmlsddf3wbh6wcka"))))
(build-system python-build-system)
(arguments
`(#:tests? #f ;; Pypi does not have tests.
(define-public ptpython-2
(let ((base (package-with-python2 (strip-python2-variant ptpython))))
- (package
- (inherit base)
+ (package/inherit base
(name "ptpython2"))))
(define-public python-stem
relays publish about themselves.")
(license license:lgpl3)))
-(define-public python2-stem
- (package-with-python2 python-stem))
-
(define-public python-pyserial
(package
(name "python-pyserial")
- (version "3.4")
+ (version "3.5")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pyserial" version))
(sha256
(base32
- "09y68bczw324a4jb9a1cfwrbjhq179vnfkkkrybbksp0vqgl0bbf"))))
+ "1nyd4m4mnrz8scbfqn4zpq8gnbl4x42w5zz62vcgpzqd2waf0xrw"))))
(build-system python-build-system)
(arguments
'(#:tests? #f)) ; FIXME: 3/49 tests are failing.
(define-public python2-binaryornot
(let ((base (package-with-python2 (strip-python2-variant python-binaryornot))))
- (package (inherit base)
+ (package/inherit base
(propagated-inputs
`(("python2-enum34" ,python2-enum34)
,@(package-propagated-inputs base))))))
(define-public glances
(package
(name "glances")
- (version "3.1.4")
+ (version "3.1.6")
(source
(origin
(method url-fetch)
(uri (pypi-uri "Glances" version))
(sha256
- (base32 "0dc47gbvp9a3wxppdqihxpglxxaxbj3hcvzgcxxq8zcsciah3plq"))
+ (base32 "11xbm8jgcxha191ly7q76nab1ilabiz14mqf6i3y6aw5xvgg017c"))
(modules '((guix build utils)))
(snippet
'(begin
to Python.")
(license license:expat)))
-(define-public python2-graphql-core
- (package-with-python2 python-graphql-core))
-
(define-public python-graphql-relay
(package
(name "python-graphql-relay")
(define-public python2-setproctitle
(let ((base (package-with-python2
(strip-python2-variant python-setproctitle))))
- (package
- (inherit base)
+ (package/inherit base
(native-inputs `(("python2-nose" ,python2-nose)
,@(package-native-inputs base))))))
(define-public python2-argcomplete
(let ((variant (package-with-python2
(strip-python2-variant python-argcomplete))))
- (package
- (inherit variant)
+ (package/inherit variant
(arguments
(substitute-keyword-arguments (package-arguments variant)
((#:phases phases '%standard-phases)
(define-public python2-xopen
(let ((base (package-with-python2
(strip-python2-variant python-xopen))))
- (package
- (inherit base)
+ (package/inherit base
(propagated-inputs `(("python2-bz2file" ,python2-bz2file)
,@(package-propagated-inputs base))))))
;; Can be used with either license.
(license (list license:asl2.0 license:gpl2+))))
-(define-public python2-dulwich
- (package-with-python2 python-dulwich))
-
(define-public python-pbkdf2
(package
(name "python-pbkdf2")
;;https://bitbucket.org/fdik/pypeg/issues/36/test-failures-on-py35
'(#:tests? #f))
(home-page "https://fdik.org/pyPEG/")
- (synopsis "Parsering Expression Grammars in Python")
+ (synopsis "Parsing Expression Grammars in Python")
(description "PyPEG is an intrinsic parser interpreter framework for
Python. It is based on Parsing Expression Grammars, PEG. With pyPEG you can
parse many formal languages.")
(define-public python2-isort
(let ((base (package-with-python2
(strip-python2-variant python-isort))))
- (package (inherit base)
+ (package/inherit base
(native-inputs
`(("python2-futures" ,python2-futures)
,@(package-native-inputs base))))))
make common patterns shorter and easier.")
(license license:bsd-2)))
-(define-public python2-utils
- (package-with-python2 python-utils))
-
(define-public python-diff-match-patch
(package
(name "python-diff-match-patch")
(define-public python2-radon
(let ((base (package-with-python2 (strip-python2-variant python-radon))))
- (package
- (inherit base)
+ (package/inherit base
(propagated-inputs
`(("python-configparser" ,python2-configparser)
("python-future" ,python2-future)
(define-public python2-rfc6555
(let ((base (package-with-python2
(strip-python2-variant python-rfc6555))))
- (package
- (inherit base)
+ (package/inherit base
(propagated-inputs
`(("python2-selectors2" ,python2-selectors2))))))
(define-public python2-activepapers
(let ((base (package-with-python2
(strip-python2-variant python-activepapers))))
- (package
- (inherit base)
+ (package/inherit base
(arguments
(substitute-keyword-arguments (package-arguments base)
((#:phases phases)
(license license:bsd-3)))
(define-public python2-send2trash
- (package
- (inherit (package-with-python2 (strip-python2-variant python-send2trash)))
- (arguments
- (substitute-keyword-arguments (package-arguments python-send2trash)
- ((#:phases phases)
- `(modify-phases ,phases
- (add-before 'check 'setenv
- (lambda _
- (setenv "PYTHONPATH"
- (string-append (getcwd) ":" (getenv "PYTHONPATH")))
- #t))))))))
+ (let ((base (package-with-python2
+ (strip-python2-variant python-send2trash))))
+ (package/inherit base
+ (arguments
+ (substitute-keyword-arguments (package-arguments python-send2trash)
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (add-before 'check 'setenv
+ (lambda _
+ (setenv "PYTHONPATH"
+ (string-append (getcwd) ":" (getenv "PYTHONPATH")))
+ #t)))))))))
(define-public python-pyfavicon
(package
(define-public python-yamllint
(package
(name "python-yamllint")
- (version "1.26.0")
+ (version "1.26.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "yamllint" version))
(sha256
- (base32 "11qhs1jk9pwvyk5k3q5blh9sq42dh1ywdf1f3i2zixf7hncwir5h"))))
+ (base32 "090krlxj7az0d9yl8i20vjrqi66dfxx7y5xakjhxzsfp7qmldnc7"))))
(build-system python-build-system)
(propagated-inputs
`(("python-pathspec" ,python-pathspec)
inferring type information using compile-time introspection.")
(license license:bsd-3)))
+(define-public python-pooch
+ (package
+ (name "python-pooch")
+ (version "1.3.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "pooch" version))
+ (sha256
+ (base32 "1618adsg9r8fsv422sv35z1i723q3a1iir5v7dv2sklh4pl4im1h"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #f)) ;requires online data
+ (propagated-inputs
+ `(("python-appdirs" ,python-appdirs)
+ ("python-packaging" ,python-packaging)
+ ("python-requests" ,python-requests)))
+ (home-page "https://github.com/fatiando/pooch")
+ (synopsis "Manage your Python library's sample data files")
+ (description
+ "Pooch manages your Python library's sample data files: it automatically
+downloads and stores them in a local directory, with support for versioning
+and corruption checks.")
+ (license license:bsd-3)))
+
(define-public python-fasteners
(package
(name "python-fasteners")
that is accessible to other projects developed in Cython.")
(license license:bsd-3)))
+(define-public python-sortedcollections
+ (package
+ (name "python-sortedcollections")
+ (version "2.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "sortedcollections" version))
+ (sha256
+ (base32
+ "1kfabpnjyjm5ml2zspry9jy3xq49aybchgaa4ahic2jqdjfn1sfq"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-sortedcontainers" ,python-sortedcontainers)))
+ (arguments '(#:tests? #f)) ; Tests not included in release tarball.
+ (home-page "http://www.grantjenks.com/docs/sortedcollections/")
+ (synopsis "Python Sorted Collections")
+ (description "Sorted Collections is a Python sorted collections library.")
+ (license license:asl2.0)))
+
(define-public python-sortedcontainers
(package
(name "python-sortedcontainers")
(define-public python2-cloudpickle
(let ((base (package-with-python2 (strip-python2-variant python-cloudpickle))))
- (package
- (inherit base)
+ (package/inherit base
(native-inputs
`(("python-mock" ,python2-mock)
,@(package-native-inputs base)))
(define-public python2-reparser
(let ((reparser (package-with-python2
(strip-python2-variant python-reparser))))
- (package (inherit reparser)
+ (package/inherit reparser
(propagated-inputs
`(("python2-enum34" ,python2-enum34)
,@(package-propagated-inputs reparser))))))
(define-public python-astor
(package
(name "python-astor")
- (version "0.7.1")
+ (version "0.8.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "astor" version))
(sha256
(base32
- "13gv6f2xz9i564byp21gcpc0l3w4cs23k1wbcam8kky2ls3hvhwm"))))
+ "0ppscdzzvxpznclkmhhj53iz314x3pfv4yc7c6gwxqgljgdgyvka"))))
(build-system python-build-system)
;; FIXME: There are two errors and two test failures.
(arguments `(#:tests? #f))
(define-public python2-pylzma
(package-with-python2 python-pylzma))
+(define-public python-ifaddr
+ (package
+ (name "python-ifaddr")
+ (version "0.1.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "ifaddr" version))
+ (sha256
+ (base32
+ "150sxdlicwrphmhnv03ykxplyd2jdrxz0mikgnivavgilrn8m7hz"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _ (invoke "nosetests"))))))
+ (native-inputs
+ `(("python-nose" ,python-nose)))
+ (home-page "https://github.com/pydron/ifaddr")
+ (synopsis "Network interface and IP address enumeration library")
+ (description "This package provides a network interface and IP address
+enumeration library in Python.")
+ (license license:expat)))
+
+(define-public python-zeroconf
+ (package
+ (name "python-zeroconf")
+ (version "0.28.8")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "zeroconf" version))
+ (sha256
+ (base32
+ "0narq8haa3b375vfblbyil77n8bw0wxqnanl91pl0wwwm884mqjb"))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-nose" ,python-nose)))
+ (propagated-inputs
+ `(("python-ifaddr" ,python-ifaddr)))
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _ ;; Networking isn't available for these tests.
+ (invoke "nosetests" "-v"
+ "--exclude" "test_integration_with_listener_ipv6"
+ "--exclude" "test_launch_and_close_v6_only"
+ "--exclude" "test_launch_and_close_v4_v6"
+ "--exclude" "test_launch_and_close"))))))
+ (home-page "https://github.com/jstasiak/python-zeroconf")
+ (synopsis "Pure Python mDNS service discovery")
+ (description
+ "Pure Python multicast DNS (mDNS) service discovery library (Bonjour/Avahi
+compatible).")
+ (license license:lgpl2.1+)))
+
(define-public python2-zeroconf
(package
(name "python2-zeroconf")
(define-public python-flit
(package
(name "python-flit")
- (version "3.0.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "flit" version))
- (sha256
- (base32
- "14q8qa48bli2mniznc8b54qkwvhbik4kw99y01fi5gzzl620zzml"))))
+ (version "3.2.0")
+ ;; We fetch the sources via git because on pypi the package is split into
+ ;; two parts: flit and flit_core; flit_core cannot be built without flit.
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/takluyver/flit")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0fpqxpz5bv2xpv1akmc0c8yfss6sj09wdzxrlf3qw1lp1jhbzpyc"))))
(build-system python-build-system)
(arguments
- `(#:tests? #f)) ; XXX: Check requires network access.
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-before 'build 'bootstrap
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((home (string-append (getcwd) "/home")))
+ (mkdir-p home)
+ (setenv "HOME" home))
+ (for-each make-file-writable (find-files "."))
+ (copy-recursively (assoc-ref inputs "python-testpath")
+ (string-append (getcwd) "/testpath"))
+ (substitute* "pyproject.toml"
+ (("\"testpath\",") ""))
+ (invoke "python" "bootstrap_dev.py")))
+ (replace 'build
+ (lambda _
+ ;; A ZIP archive should be generated, but it fails with "ZIP does
+ ;; not support timestamps before 1980". Luckily,
+ ;; SOURCE_DATE_EPOCH is respected, which we set to some time in
+ ;; 1980.
+ (setenv "SOURCE_DATE_EPOCH" "315532800")
+ (for-each (lambda (toml)
+ (invoke "python3" "-m" "flit"
+ "--debug" "--ini-file" toml
+ "build"))
+ '("testpath/pyproject.toml"
+ "pyproject.toml"))
+ (with-directory-excursion "flit_core"
+ (invoke "python" "build_dists.py"))))
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (add-installed-pythonpath inputs outputs)
+ (let ((out (assoc-ref outputs "out")))
+ (delete-file-recursively "./home")
+ (for-each (lambda (wheel)
+ (format #true wheel)
+ (invoke "python" "-m" "pip" "install"
+ wheel (string-append "--prefix=" out)))
+ (append
+ (find-files "flit_core/dist" "\\.whl$")
+ (find-files "dist" "\\.whl$")))))))
+ #:tests? #f)) ; XXX: Check requires network access.
+ (propagated-inputs
+ `(("python-pytoml" ,python-pytoml)
+ ("python-toml" ,python-toml)))
+ (native-inputs
+ `(("python-docutils" ,python-docutils)
+ ("python-responses" ,python-responses)
+ ("python-pygments-github-lexers" ,python-pygments-github-lexers)
+ ("python-pytest" ,python-pytest)
+ ("python-pytest-cov" ,python-pytest-cov)
+ ("python-sphinx" ,python-sphinx)
+ ("python-sphinxcontrib-github-alt" ,python-sphinxcontrib-github-alt)
+ ;; This package needs testpath, but testpath also needs flit...
+ ("python-testpath"
+ ,(let ((name "python-testpath")
+ (version "0.4.4"))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/jupyter/testpath")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1fwv4d3p54xx1x942s104irr35lszvv6jnr4nn1scsfvc0m1qmbk")))))))
(home-page "https://flit.readthedocs.io/")
(synopsis
"Simple packaging tool for simple packages")
;; This invokation is taken from tox.ini.
(invoke "nosetests" "-d" "-v" "tests/"))))))
(home-page "https://github.com/akesterson/dpath-python")
- (synopsis "Filesystem-like pathing and searching for dictionaries")
+ (synopsis "File-system-like pathing and searching for dictionaries")
(description
"@code{python-dpath} is a library for accessing and searching
dictionaries via /slashed/paths ala xpath.
-Basically it lets you glob over a dictionary as if it were a filesystem. It
+Basically it lets you glob over a dictionary as if it were a file system. It
allows you to specify globs (ala the bash eglob syntax, through some advanced
fnmatch.fnmatch magic) to access dictionary elements, and provides some
facility for filtering those results.")
"NestedText is a file format for holding data that is to be entered, edited, or
viewed by people. It allows data to be organized into a nested collection of
dictionaries, lists, and strings. In this way it is similar to JSON and YAML, but
-without the complexity and risk of YAML and without the syntatic clutter of JSON.
+without the complexity and risk of YAML and without the syntactic clutter of JSON.
NestedText is both simple and natural. Only a small number of concepts and rules must
be kept in mind when creating it. It is easily created, modified, or viewed with
a text editor and easily understood and used by both programmers and non-programmers.")
(license license:expat))) ; MIT license
+(define-public python-nest-asyncio
+ (package
+ (name "python-nest-asyncio")
+ (version "1.5.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "nest_asyncio" version))
+ (sha256
+ (base32
+ "1anha29fcijminn5bh2icnx8x7nk39lna9wkc72262i12p2s3idg"))))
+ (build-system python-build-system)
+ (home-page "https://github.com/erdewit/nest_asyncio")
+ (synopsis "Patch asyncio to allow nested event loops")
+ (description
+ "By design @code{asyncio} does not allow its event loop to be nested.
+This presents a practical problem: when in an environment where the event loop
+is already running it's impossible to run tasks and wait for the result. This
+module patches @code{asyncio} to allow nested use of @code{asyncio.run} and
+@code{loop.run_until_complete}.")
+ (license license:bsd-3)))
+
(define-public python-parallel
(package
(name "python-parallel")
(define-public python-djvulibre
(package
(name "python-djvulibre")
- (version "0.8.5")
+ (version "0.8.6")
(source
(origin
(method url-fetch)
(uri (pypi-uri "python-djvulibre" version))
(sha256
- (base32 "1c0lvpg7j2525cv52s3q5sg7hfnakkb8rmghg0jc02gshsxmrj4f"))))
+ (base32 "089smpq29ll0z37lnq26r2f72d31i33xm9fw9pc6hlcsm6nbjbiv"))))
(build-system python-build-system)
(native-inputs
`(("ghostscript" ,ghostscript)
"This package provides a Python library that can parse OPML, FOAF, and
iGoogle subscription lists.")
(license license:expat)))
+
+(define-public python-smartypants
+ (package
+ (name "python-smartypants")
+ (version "2.0.1")
+ (source
+ (origin
+ ;; There's no source tarball for 2.0.1 on PyPI.
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/leohemsted/smartypants.py")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "00p1gnb9pzb3svdq3c5b9b332gsp50wrqqa39gj00m133zadanjp"))))
+ (build-system python-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ ;; Its `setup.py test` doesn't report failure with exit status, so
+ ;; we use `nose` instead.
+ (lambda _
+ (invoke "nosetests" "-v" "--exclude=^load_tests$"))))))
+ (native-inputs
+ ;; For tests.
+ `(("python-docutils" ,python-docutils)
+ ("python-nose" ,python-nose)
+ ("python-pygments" ,python-pygments)))
+ (home-page "https://github.com/leohemsted/smartypants.py")
+ (synopsis "Translate punctuation characters into smart quotes")
+ (description
+ "@command{smartpants} can perform the following transformations:
+@enumerate
+@item Straight quotes ( \" and ' ) into \"curly\" quote HTML entities
+@item Backticks-style quotes (``like this'') into \"curly\" quote HTML
+entities
+@item Dashes (-- and ---) into en- and em-dash entities
+@item Three consecutive dots (... or . . .) into an ellipsis entity
+@end enumerate")
+ (license license:bsd-3)))
+
+(define-public python-typogrify
+ (package
+ (name "python-typogrify")
+ (version "2.0.7")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "typogrify" version))
+ (sha256
+ (base32
+ "0f6b2gnnxjbx1fbmkcscc6qjr4hi78kwm1wx4b766ha3va66dr4b"))))
+ (build-system python-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (invoke "nosetests" "-v"))))))
+ (propagated-inputs
+ `(("python-smartypants" ,python-smartypants)))
+ (native-inputs
+ ;; For tests.
+ `(("python-nose" ,python-nose)))
+ (home-page "https://github.com/mintchaos/typogrify")
+ (synopsis "Filters to transform text into typographically-improved HTML")
+ (description
+ "@code{typogrify} provides a set of custom filters that automatically
+apply various transformations to plain text in order to yield
+typographically-improved HTML. While often used in conjunction with Jinja and
+Django template systems, the filters can be used in any environment.")
+ (license license:bsd-3)))
+
+(define-public python-ld
+ (package
+ (name "python-ld")
+ (version "0.5.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "ld" version))
+ (sha256
+ (base32
+ "1k4ydp5rgkv4985v459kcl06i1igjm1ywvh2vkbi9ck1zyyri1z5"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-six" ,python-six)))
+ (home-page "https://github.com/nir0s/ld")
+ (synopsis "OS platform information API")
+ (description
+ "The ld package provides information about the GNU/Linux distribution it
+runs on, such as a reliable machine-readable ID, or version information.")
+ (license license:asl2.0)))
+
+(define-public python-quicktions
+ (package
+ (name "python-quicktions")
+ (version "1.11")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "quicktions" version))
+ (sha256
+ (base32
+ "1px21a6x527i1bsr2p6bbf3jziqpvd1vjkvvzh13gsy4iip0yvzn"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; This file is generated by Cython.
+ (delete-file "src/quicktions.c") #t))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-before 'build 'cythonize-sources
+ (lambda _
+ (with-directory-excursion "src"
+ (invoke "cython" "quicktions.pyx"))))
+ (replace 'check
+ (lambda* (#:key tests? inputs outputs #:allow-other-keys)
+ (when tests?
+ (add-installed-pythonpath inputs outputs)
+ (invoke "pytest"))
+ #t)))))
+ (native-inputs
+ `(("python-cython" ,python-cython)
+ ("python-pytest" ,python-pytest)))
+ (home-page "https://github.com/scoder/quicktions")
+ (synopsis "Fast fractions data type for rational numbers")
+ (description
+ "This package provides fast fractions data type for rational numbers. It
+is the cythonized version of @code{fractions.Fraction}.")
+ (license license:psfl)))
+
+(define-public python-pathvalidate
+ (package
+ (name "python-pathvalidate")
+ (version "2.4.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "pathvalidate" version))
+ (sha256
+ (base32 "0s14ycjgb44lxr2wg8lrq3b7kybmmrbf7yqz47xrqgn2gr6dk6rw"))))
+ (build-system python-build-system)
+ (arguments
+ '(#:tests? #f))
+ ;; Tests disabled because of circular dependencies.
+ ;; pathvalidate tests depend on pytest-md-report, which
+ ;; depends on pathvalidate.
+ (native-inputs
+ `(("python-allpairspy" ,python-allpairspy)
+ ("python-click" ,python-click)
+ ("python-faker" ,python-faker)
+ ("python-pytest" ,python-pytest)))
+ (home-page "https://github.com/thombashi/pathvalidate")
+ (synopsis "Sanitize strings representing paths")
+ (description
+ "@code{pathvalidate} is a Python library to sanitize/validate strings
+representing paths or filenames.")
+ (license license:expat)))
HCoop / jackhill / guix / guix.git / blobdiff