diff options
Diffstat (limited to 'gnu/packages/python-xyz.scm')
| -rw-r--r-- | gnu/packages/python-xyz.scm | 175 |
1 files changed, 144 insertions, 31 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8e8b6c6bfa..a7ea87e023 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -49,7 +49,7 @@ ;;; Copyright © 2018 Mathieu Lirzin <mthl@gnu.org> ;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com> ;;; Copyright © 2016, 2018 Tomáš Čech <sleep_walker@gnu.org> -;;; Copyright © 2018-2023 Nicolas Goaziou <mail@nicolasgoaziou.fr> +;;; Copyright © 2018-2024 Nicolas Goaziou <mail@nicolasgoaziou.fr> ;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com> ;;; Copyright © 2018, 2019, 2021, 2023 Clément Lassieur <clement@lassieur.org> ;;; Copyright © 2018, 2019, 2020, 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com> @@ -136,6 +136,7 @@ ;;; Copyright © 2023 Amade Nemes <nemesamade@gmail.com> ;;; Copyright © 2023 Bruno Victal <mirai@makinata.eu> ;;; Copyright © 2023 Kaelyn Takata <kaelyn.alexi@protonmail.com> +;;; Copyright © 2023 dan <i@dan.games> ;;; Copyright © 2023 Dominik Delgado Steuter <d@delgado.nrw> ;;; Copyright © 2023 Ivan Vilata-i-Balaguer <ivan@selidor.net> ;;; Copyright © 2023 Ontje Lünsdorf <ontje.luensdorf@dlr.de> @@ -6058,6 +6059,54 @@ 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-pypugjs + (package + (name "python-pypugjs") + (version "5.9.12") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/kakulukia/pypugjs") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0zj7a560h973cl7brfw1nmyhgm8rp8j80wnih0shvhmw4ql23lpa")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases #~(modify-phases %standard-phases + ;; Our pyramid is outdated and pyramid-mako is not packaged. + (add-after 'unpack 'disable-pyramid + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "setup.py" + (("'pyramid") + "#'pyramid")))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "-m" "pytest" "-v" + "pypugjs/testsuite/"))))))) + (native-inputs (list python-coverage + python-django + python-jinja2 + python-flake8 + python-flask + python-mako + python-nose + python-poetry-core + python-pytest + python-tornado-6 + python-wheel)) + (propagated-inputs (list python-charset-normalizer python-six)) + (home-page "https://github.com/kakulukia/pypugjs") + (synopsis "Convert Pug source files into different template languages") + (description + "PyPugJS is a high-performance port of PugJS for Python, that converts +any @file{.pug} source into different template languages: Django, Jinja2, +Mako, and Tornado.") + (license license:expat))) ;; MIT + (define-public python-pysdl2 (package (name "python-pysdl2") @@ -6173,26 +6222,20 @@ bookmarks using a declarative input in the form of a markdown file.") (define-public python-joblib (package (name "python-joblib") - (version "1.1.1") + (version "1.3.2") (source (origin (method url-fetch) (uri (pypi-uri "joblib" version)) (sha256 (base32 - "0019p280s2k941mihl67l7y6amwx86639xp3zvpsg1lmyish67rh")))) - (build-system python-build-system) + "1cbjjzsh9hzaqr2cqja95673p7j88b8bd02hjpkq8xz147k6by4j")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (setenv "JOBLIB_MULTIPROCESSING" "0") - (invoke "pytest" "-v" "joblib" - ;; We disable this test to avoid having to depend on ipython/jupyter - "-k" "not test_parallel_call_cached_function_defined_in_jupyter"))))))) - (native-inputs - (list python-pytest)) + (list + #:test-flags ; disabled to avoid having to depend on ipython/jupyter + #~(list "-k" "not test_parallel_call_cached_function_defined_in_jupyter"))) + (native-inputs (list python-pytest)) + (propagated-inputs (list python-psutil)) (home-page "https://joblib.readthedocs.io/") (synopsis "Using Python functions as pipeline jobs") (description @@ -11434,6 +11477,27 @@ removal, line continuation, indentation, comment processing, identifier processing, values parsing, case insensitive comparison, and more.") (license license:expat))) +(define-public python-pypytools + (package + (name "python-pypytools") + (version "0.6.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pypytools" version)) + (sha256 + (base32 "0ag5xyzagprji0m2pkqsfy8539s003mn41pl6plbmh6iwi9w0h51")))) + (build-system python-build-system) + (arguments (list #:tests? #f)) ; no tests + (propagated-inputs (list python-py)) + (home-page "https://github.com/antocuni/pypytools/") + (synopsis + "Tools to use PyPy-specific features, with CPython fallbacks") + (description + "This package provides a collection of useful tools to use PyPy-specific +features, with CPython fallbacks.") + (license license:x11))) + (define-public python-simplegeneric (package (name "python-simplegeneric") @@ -12801,19 +12865,18 @@ approach.") (build-system python-build-system) (arguments ;; TODO: Package missing test dependencies. - '(#:tests? #f - #:phases - (modify-phases %standard-phases - ;; For cluster execution Snakemake will call Python. Since there is - ;; no suitable PYTHONPATH set, cluster execution will fail. We fix - ;; this by calling the snakemake wrapper instead. - (add-after 'unpack 'call-wrapper-not-wrapped-snakemake - (lambda* (#:key outputs #:allow-other-keys) - (substitute* "snakemake/executors/__init__.py" - (("\\{sys.executable\\} -m snakemake") - (string-append (assoc-ref outputs "out") - "/bin/snakemake"))) - #t))))) + (list + #:tests? #f + #:phases + #~(modify-phases %standard-phases + ;; For cluster execution Snakemake will call Python. Since there is + ;; no suitable PYTHONPATH set, cluster execution will fail. We fix + ;; this by calling the snakemake wrapper instead. + (add-after 'unpack 'call-wrapper-not-wrapped-snakemake + (lambda _ + (substitute* "snakemake/executors/__init__.py" + (("\\{sys.executable\\} -m snakemake") + (string-append #$output "/bin/snakemake")))))))) (propagated-inputs (list python-appdirs python-configargparse @@ -12944,7 +13007,22 @@ Python style, together with a fast and comfortable execution environment.") "") (("\"-m snakemake\"") (string-append "\"" #$output - "/bin/snakemake" "\""))))) + "/bin/snakemake" "\"")) + ;; The snakemake command produced by format_job_exec contains + ;; references to /gnu/store. Prior to patching above that's + ;; just a reference to Python; after patching it's a reference + ;; to the snakemake executable. + ;; + ;; In Tibanna execution mode Snakemake arranges for a certain + ;; Docker image to be deployed to AWS. It then passes its own + ;; command line to Tibanna. This is misguided because it only + ;; ever works if the local Snakemake command was run inside + ;; the same Docker image. In the case of using Guix this is + ;; never correct, so we need to replace the store reference. + (("tibanna_args.command = command") + (string-append + "tibanna_args.command = command.replace('" + #$output "/bin/snakemake', 'python3 -m snakemake')"))))) (add-after 'unpack 'patch-version (lambda _ (substitute* "setup.py" @@ -14265,6 +14343,41 @@ extensions, and several HTML output formats. A command line wrapper markdown_py is also provided to convert Markdown files to HTML.") (license license:bsd-3))) +(define-public python-markdown2 + (package + (name "python-markdown2") + (version "2.4.13") + (source + (origin + (method git-fetch) ; no tests data in PyPi package + (uri (git-reference + (url "https://github.com/trentm/python-markdown2") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0m1wy8i4xmna5b97dvks8cfjmc1wid8pxmd2h82869d0ajva3r6a")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? test-flags #:allow-other-keys) + (when tests? + (with-directory-excursion "test" + (invoke "python" "testall.py")))))))) + (native-inputs + (list python-pygments)) + (home-page "https://github.com/trentm/python-markdown2") + (synopsis "Fast and complete Python implementation of Markdown") + (description + "This package provides a fast and complete Python implementation of +Markdown. It was written to closely match the behaviour of the original +Perl-implemented Markdown.pl. It also comes with a number of +extensions (called @code{extras}) for things like syntax coloring, tables, +header-ids.") + (license license:expat))) + (define-public python-mdx-include (package (name "python-mdx-include") @@ -30562,7 +30675,7 @@ accessor layer.") (define-public pyzo (package (name "pyzo") - (version "4.13.3") + (version "4.15.0") (source (origin (method git-fetch) @@ -30572,7 +30685,7 @@ accessor layer.") (file-name (git-file-name name version)) (sha256 (base32 - "1m0mrp20wjvy804214f4zzlbaqrakam0g3qr562yn2mjcgfba554")))) + "0m2sp65q21hhlfkvyby4sjc8cmwv3l0avw42xsna8za8ax9xadxr")))) (build-system python-build-system) (arguments `(#:phases |