diff options
Diffstat (limited to 'gnu/packages/python-xyz.scm')
| -rw-r--r-- | gnu/packages/python-xyz.scm | 166 |
1 files changed, 93 insertions, 73 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 56c2732018..bbc51590b6 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -29,7 +29,7 @@ ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Marius Bakke <marius@gnu.org> ;;; 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, 2021 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Julien Lepiller <julien@lepiller.eu> ;;; Copyright © 2016–2021 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be> @@ -1103,9 +1103,6 @@ NetCDF files can also be read and modified. Python-HDF4 is a fork of @url{http://hdfeos.org/software/pyhdf.php,pyhdf}.") (license license:expat))) -(define-public python2-hdf4 - (package-with-python2 python-hdf4)) - (define-public python-h5py (package (name "python-h5py") @@ -2284,28 +2281,6 @@ 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") @@ -2825,14 +2800,14 @@ matching them against a list of media-ranges.") (define-public python-miniboa (package (name "python-miniboa") - (version "1.0.7") + (version "1.0.8") (source (origin (method url-fetch) (uri (pypi-uri "miniboa" version)) (sha256 (base32 - "09jh3pn4rh7kh7jayanf8jzy6gp03791b5a193w6148cf3i6k9m3")))) + "002c1aki9hsrwj5plrwdrf3sk8rn95fqylqyjx2arrjfpsih4dgs")))) (build-system python-build-system) (home-page "https://github.com/shmup/miniboa") (synopsis "Simple, single-threaded Telnet server") @@ -5310,23 +5285,16 @@ color scales, and color space conversion easy. It has support for: (description (package-description python-numpy)) (license (package-license python-numpy)))) -(define-public python2-numpy-documentation - (let ((numpy-documentation (package-with-python2 python-numpy-documentation))) - (package - (inherit numpy-documentation) - (native-inputs `(("python2-functools32" ,python2-functools32) - ,@(package-native-inputs numpy-documentation)))))) - (define-public python-pygit2 (package (name "python-pygit2") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (pypi-uri "pygit2" version)) (sha256 - (base32 "1j71iskvirkm8jzfmwdm79v69878m9iix8a8cn4xidgr3nmkisyb")))) + (base32 "0qjd5aqpmla64da4pb47vdnrmnqdbn7248a4fzs7f5q1ax7fmb3s")))) (build-system python-build-system) (arguments '(#:tests? #f)) ; tests don't run correctly in our environment @@ -6236,13 +6204,13 @@ the OleFileIO module from PIL, the Python Image Library.") (define-public python-pikepdf (package (name "python-pikepdf") - (version "2.12.1") + (version "2.12.2") (source (origin (method url-fetch) (uri (pypi-uri "pikepdf" version)) (sha256 - (base32 "1si1x4dc4i4ghyirjfws1zkgiwk8kypnpp4gf68haascrdy7znqw")))) + (base32 "1r68zh8whp8wg4brjf5vha8h1ly8pjqyb37pfw91hyxfn6cm9wsz")))) (build-system python-build-system) (arguments `(#:tests? #false)) ;require python-xmp-toolkit @@ -7054,9 +7022,6 @@ cluster directly from Python. You can directly map Python functions onto the cluster without needing to write any wrapper code yourself.") (license license:gpl3+))) -(define-public python2-gridmap - (package-with-python2 python-gridmap)) - (define-public python-honcho (package (name "python-honcho") @@ -8844,9 +8809,6 @@ more advanced mathematics.") multiprecision arithmetic.") (license license:lgpl3+))) -(define-public python2-bigfloat - (package-with-python2 python-bigfloat)) - (define-public python-sympy (package (name "python-sympy") @@ -9100,25 +9062,29 @@ applications.") (define-public python-pyzmq (package (name "python-pyzmq") - (version "22.0.3") + (version "22.1.0") (source (origin (method url-fetch) (uri (pypi-uri "pyzmq" version)) (sha256 - (base32 "0bgrn65cxfz1c1sjrgyq5dy1mkhppxxbizd5wvrl03cq4zhkrxpp")))) + (base32 "0pa1y97z75xqyca9xfp9zrzksydbgzsxf8yh0hwp0rgahpfxch3h")))) (build-system python-build-system) (arguments `(#:configure-flags (list (string-append "--zmq=" (assoc-ref %build-inputs "zeromq"))) - ;; FIXME: You must build pyzmq with 'python setup.py build_ext - ;; --inplace' for 'python setup.py test' to work. - #:tests? #f)) + #:phases + (modify-phases %standard-phases + (add-before 'check 'build-extensions + (lambda _ + ;; Cython extensions have to be built before running the tests. + (invoke "python" "setup.py" "build_ext" "--inplace")))))) (inputs `(("zeromq" ,zeromq))) (native-inputs `(("pkg-config" ,pkg-config) - ("python-nose" ,python-nose))) + ("python-cython" ,python-cython) + ("python-pytest" ,python-pytest))) (home-page "https://github.com/zeromq/pyzmq") (synopsis "Python bindings for 0MQ") (description @@ -13292,7 +13258,7 @@ ISO 8859, etc.).") ("python-pytest-cov" ,python-pytest-cov) ("python-pytest-xdist" ,python-pytest-xdist))) (inputs - `(("qtbase" ,qtbase))) + `(("qtbase" ,qtbase-5))) (propagated-inputs `(("python-h5py" ,python-h5py) ("python-numpy" ,python-numpy) @@ -13687,6 +13653,56 @@ is made as zipfile like as possible.") (define-public python2-rarfile (package-with-python2 python-rarfile)) +(define-public python-rich + (package + (name "python-rich") + (version "10.2.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "rich" version)) + (sha256 + (base32 + "1z5m5brcdf3vndpavcqj5nl35xby4x5rfj48klhwqycfqf3g9cqp")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key inputs tests? #:allow-other-keys) + (when tests? + (copy-recursively (string-append + (assoc-ref inputs "tests") "/tests") + "tests") + (invoke "python" "-m" "pytest" "-vv"))))))) + (propagated-inputs + `(("python-attrs" ,python-attrs) + ("python-colorama" ,python-colorama) + ("python-commonmark" ,python-commonmark) + ("python-ipywidgets" ,python-ipywidgets) + ("python-pygments" ,python-pygments) + ("python-typing-extensions" ,python-typing-extensions))) + (native-inputs + `(("python-pytest" ,python-pytest) + ("tests" + ;; The release on pypi comes without tests. We can't build from this + ;; checkout, though, because installation requires an invocation of + ;; poetry. + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/willmcgugan/rich") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "19f4svb363sn5708qkpa6lakmiwzyb25h8kmh7bqrsbbrvi9hr70")))))) + (home-page "https://github.com/willmcgugan/rich") + (synopsis "Render rich text and more to the terminal") + (description + "This is a Python package for rendering rich text, tables, progress bars, +syntax highlighting, markdown and more to the terminal.") + (license license:expat))) + (define-public python-magic (package (name "python-magic") @@ -14266,9 +14282,6 @@ graphviz.") format.") (license license:gpl2+))) -(define-public python2-fastimport - (package-with-python2 python-fastimport)) - (define-public python-twisted (package (name "python-twisted") @@ -15147,13 +15160,13 @@ collections of data.") (define-public python-prompt-toolkit (package (name "python-prompt-toolkit") - (version "3.0.9") + (version "3.0.18") (source (origin (method url-fetch) (uri (pypi-uri "prompt_toolkit" version)) (sha256 - (base32 "0bvjp62cs6aj9lrh7njzxdjgg8pjfw3qgmr551243d9ivmcapvn5")))) + (base32 "1g1kq1aimhm23k2dmlmnznfzc83l6ly65g0h32hqz8injcdz3d71")))) (build-system python-build-system) (arguments `(#:phases @@ -15257,18 +15270,19 @@ well.") (define-public ptpython (package (name "ptpython") - (version "3.0.5") + (version "3.0.17") (source (origin (method url-fetch) (uri (pypi-uri "ptpython" version)) (sha256 (base32 - "0c2ry5gwi2v99slna62j8r2bwq0hpzmvgdryqg9m6x57vbjfg52h")))) + "1phk1grcvn456igjg8gwjjg8bf4kszddq5nd5sdlz3hslg62a7ci")))) (build-system python-build-system) (arguments - '(#:tests? #f)) ; FIXME: No tests in pypi tarball. + `(#:tests? #f)) ;there are no tests (propagated-inputs `(("python-appdirs" ,python-appdirs) + ("python-black" ,python-black) ("python-jedi" ,python-jedi) ("python-prompt-toolkit" ,python-prompt-toolkit) ("python-pygments" ,python-pygments))) @@ -16867,8 +16881,9 @@ and bit flag values.") (arguments `(#:phases (modify-phases %standard-phases (replace 'check - (lambda _ - (invoke "pytest")))))) + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest"))))))) (native-inputs `(("python-coverage" ,python-coverage) ("python-hypothesis" ,python-hypothesis) @@ -21160,18 +21175,26 @@ library's @code{threading} module.") (define-public python-toolz (package (name "python-toolz") - (version "0.9.0") + (version "0.11.1") (source (origin (method url-fetch) (uri (pypi-uri "toolz" version)) (sha256 (base32 - "1j9i7fdjnx9dz35fdj5gvgxx6585ja9sxgaiv65if77nlxz0m7wj")))) + "1grz3zvw5ixwqqlbv0n7j11mlcxb66cirh5i9x9zw8kqy0hpk967")))) (build-system python-build-system) - ;; FIXME: tests cannot be computed: "Can't perform this operation for - ;; unregistered loader type" - (arguments '(#:tests? #f)) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + (invoke "python" "-m" "pytest" "--doctest-modules" + "--pyargs" "toolz"))))))) + (native-inputs + `(("python-pytest" ,python-pytest))) (home-page "https://github.com/pytoolz/toolz/") (synopsis "List processing tools and functional utilities") (description @@ -21386,9 +21409,6 @@ This Python package wraps the Blosc library.") append on old values. Partd excels at shuffling operations.") (license license:bsd-3))) -(define-public python2-partd - (package-with-python2 python-partd)) - (define-public python-fsspec (package (name "python-fsspec") @@ -25204,14 +25224,14 @@ disk files in asyncio applications.") (define-public python-dataclasses (package (name "python-dataclasses") - (version "0.7") + (version "0.8") (source (origin (method url-fetch) (uri (pypi-uri "dataclasses" version)) (sha256 (base32 - "1rh8111fbws2vxyf2qy2zw3x6p6cq1jfz8pf904gig5qwg56sjj9")))) + "15sc12nrc7gxwb30vfa6frzdnpmbap9ibi1fr1yrbkra6izhcyc4")))) (build-system python-build-system) (home-page "https://github.com/ericvsmith/dataclasses") @@ -25499,7 +25519,7 @@ implementations.") ("swig" ,swig))) (inputs `(("python-wrapper" ,python-wrapper) - ("qtbase" ,qtbase) + ("qtbase" ,qtbase-5) ("libxi" ,libxi) ("libice" ,libice) ("soqt" ,soqt) |