diff options
Diffstat (limited to 'gnu/packages/python-xyz.scm')
| -rw-r--r-- | gnu/packages/python-xyz.scm | 151 |
1 files changed, 94 insertions, 57 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e54fcf0695..3b06b55817 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -99,7 +99,7 @@ ;;; Copyright © 2021 LibreMiami <packaging-guix@libremiami.org> ;;; Copyright © 2021 Xinglu Chen <public@yoctocell.xyz> ;;; Copyright © 2021 Raghav Gururajan <rg@raghavgururajan.name> -;;; Copyright © 2021 jgart <jgart@dismail.de> +;;; Copyright © 2021, 2023 jgart <jgart@dismail.de> ;;; Copyright © 2021 Danial Behzadi <dani.behzi@ubuntu.com> ;;; Copyright © 2021 Maxime Devos <maximedevos@telenet.be> ;;; Copyright © 2021 Hugo Lecomte <hugo.lecomte@inria.fr> @@ -5764,6 +5764,28 @@ which only supports flat sequences, and allows you to apply a function to each leaf preserving the overall structure.") (license license:asl2.0))) +(define-public python-pyment + (package + (name "python-pyment") + (version "0.3.4") + (source + (origin + (method git-fetch) + (uri + (git-reference + (url "https://github.com/dadadel/pyment") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0gbx9wmqsxdx85v5sg79lv2zxmy16j5dwi8bip07i1nyvzc5gvn0")))) + (build-system python-build-system) + (native-inputs (list python-pytest)) + (home-page "https://github.com/dadadel/pyment/") + (synopsis "Convert Python docstrings automatically") + (description "Pyment is a command line tool and library that can be +used to convert between several docstring styles.") + (license license:gpl3+))) + (define-public python-docstring-parser (package (name "python-docstring-parser") @@ -11443,30 +11465,38 @@ Python style, together with a fast and comfortable execution environment.") (file-name (git-file-name name version)) (sha256 (base32 "09yrpi9f86r9yvcm2dfjs5zy87c4j31bxama77kfd6y8yfrrjlai")))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments - '(#:phases - (modify-phases %standard-phases - ;; For cluster execution Snakemake will call Python. Since there is - ;; no suitable GUIX_PYTHONPATH set, cluster execution will fail. We - ;; fix this by calling the snakemake wrapper instead. + (list + #:phases + #~(modify-phases %standard-phases + ;; For cluster execution Snakemake will call Python. Since there is + ;; no suitable GUIX_PYTHONPATH set, cluster execution will fail. We + ;; fix this by calling the snakemake wrapper instead. - ;; XXX: There is another instance of sys.executable on line 692, but - ;; it is not clear how to patch it. - (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"))))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (setenv "HOME" "/tmp") - ;; This test attempts to change S3 buckets on AWS and fails - ;; because there are no AWS credentials. - (delete-file "tests/test_tibanna.py") - (invoke "pytest"))))))) + ;; XXX: There is another instance of sys.executable on line 692, but + ;; it is not clear how to patch it. + (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 #$output "/bin/snakemake"))))) + (add-after 'unpack 'patch-version + (lambda _ + (substitute* "setup.py" + (("version=versioneer.get_version\\(\\)") + (format #f "version=~s" #$version))) + (substitute* '("snakemake/_version.py" + "versioneer.py") + (("0\\+unknown") #$version)))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" "/tmp") + ;; This test attempts to change S3 buckets on AWS and fails + ;; because there are no AWS credentials. + (delete-file "tests/test_tibanna.py") + (invoke "pytest"))))))) (propagated-inputs (list python-appdirs python-configargparse @@ -11511,32 +11541,41 @@ Python style, together with a fast and comfortable execution environment.") (file-name (git-file-name name version)) (sha256 (base32 "1qrqbmx4cbis0wxr6dl2rdjv9v627sbirsz6v5c31vlbqwkvs04q")))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments - '(#:phases - (modify-phases %standard-phases - ;; For cluster execution Snakemake will call Python. Since there is - ;; no suitable GUIX_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" - (("self\\.get_python_executable\\(\\),") - "") - (("\"-m snakemake\"") - (string-append "\"" (assoc-ref outputs "out") - "/bin/snakemake" "\""))))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (setenv "HOME" "/tmp") - ;; This test attempts to change S3 buckets on AWS and fails - ;; because there are no AWS credentials. - (delete-file "tests/test_tibanna.py") - ;; It's a similar story with this test, which requires access - ;; to the Google Storage service. - (delete-file "tests/test_google_lifesciences.py") - (invoke "pytest"))))))) + (list + #:phases + #~(modify-phases %standard-phases + ;; For cluster execution Snakemake will call Python. Since there is + ;; no suitable GUIX_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" + (("self\\.get_python_executable\\(\\),") + "") + (("\"-m snakemake\"") + (string-append "\"" #$output + "/bin/snakemake" "\""))))) + (add-after 'unpack 'patch-version + (lambda _ + (substitute* "setup.py" + (("version=versioneer.get_version\\(\\)") + (format #f "version=~s" #$version))) + (substitute* '("snakemake/_version.py" + "versioneer.py") + (("0\\+unknown") #$version)))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" "/tmp") + ;; This test attempts to change S3 buckets on AWS and fails + ;; because there are no AWS credentials. + (delete-file "tests/test_tibanna.py") + ;; It's a similar story with this test, which requires access + ;; to the Google Storage service. + (delete-file "tests/test_google_lifesciences.py") + (invoke "pytest"))))))) (propagated-inputs (list python-appdirs python-configargparse @@ -14158,13 +14197,13 @@ implementations of ASN.1-based codecs and protocols.") (define-public python-asn1tools (package (name "python-asn1tools") - (version "0.158.0") + (version "0.166.0") (source (origin (method url-fetch) (uri (pypi-uri "asn1tools" version)) (sha256 - (base32 "1k88a1azmyvp2ab6qcf2i40dig5abhyn7cmlyhmwwh8kr3syvma0")))) + (base32 "1hragm8dsm10rlyz67xslj01bycprlnimdmq1i2acns6kl6difpn")))) (build-system python-build-system) (propagated-inputs (list python-bitstruct python-diskcache python-prompt-toolkit @@ -23212,17 +23251,15 @@ Git.") (define-public python-setuptools-rust (package (name "python-setuptools-rust") - (version "1.1.2") + (version "1.6.0") (source (origin (method url-fetch) (uri (pypi-uri "setuptools-rust" version)) (sha256 - (base32 "1lb57qx1azklgzmalflq960agvwci4bwddw0zvlc9zy00fsvkbd0")))) - (build-system python-build-system) + (base32 "0qi274r0fcnvxa8vs8vyhcknnzhq8pd0ig5zk1wmjc63x96p6vn8")))) + (build-system pyproject-build-system) (arguments '(#:tests? #f)) ;no tests - (native-inputs - (list python-setuptools-scm)) (propagated-inputs (list python-semantic-version python-typing-extensions)) (home-page "https://github.com/PyO3/setuptools-rust") @@ -32287,13 +32324,13 @@ than trying to just split strings.") (define-public python-srsly (package (name "python-srsly") - (version "2.4.6") + (version "2.4.7") (source (origin (method url-fetch) (uri (pypi-uri "srsly" version)) (sha256 (base32 - "0vsafkvk4g0p5m0dqrczqvlyza837i20xxmb24rrqk5s78r1zd27")))) + "022x0djlkl6pgh9yrd4avlai1n6y4hxm9l1xnb6630kpi12wrhlk")))) (build-system pyproject-build-system) (arguments (list |