diff options
| author | Arun Isaac <arunisaac@systemreboot.net> | 2023-10-22 12:41:28 +0100 |
|---|---|---|
| committer | Arun Isaac <arunisaac@systemreboot.net> | 2024-02-22 13:02:42 +0000 |
| commit | 65584b9ba87116c80b1bed90a136f15a0dcb8900 (patch) | |
| tree | 0b87576452c10b3208ddd67918ae133501938403 | |
| parent | e5ae409276412927a7aca905bc49f1591b80a5e4 (diff) | |
gnu: python-schema-salad: Update to 8.5.20240102191335.
* gnu/packages/bioinformatics.scm (python-schema-salad): Update to
8.5.20240102191335.
[native-inputs]: Add python-pytest-xdist.
[propagated-inputs]: Add python-importlib-resources and
python-mypy-extensions. Remove python-lockfile, python-rdflib-jsonld and
python-typing-extensions. Replace python-mistune with python-mistune-next.
[arguments]: Use G-expressions. Set exact version number. Skip more tests that
require network access.
Change-Id: I4de4704f58f40fdf9bf4c02e41c2c353beaa3eb2
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 61 |
1 files changed, 38 insertions, 23 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5ec7075665..935126d782 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4994,37 +4994,52 @@ Note that this package has been deprecated in favor of @code{pyfaidx}.") (define-public python-schema-salad (package (name "python-schema-salad") - (version "8.2.20211116214159") + (version "8.5.20240102191335") (source - (origin - (method url-fetch) - (uri (pypi-uri "schema-salad" version)) - (sha256 - (base32 - "005dh2y45x92zl8sf2sqjmfvcqr4hrz8dfckgkckv87003v7lwqc")))) + (origin + (method url-fetch) + (uri (pypi-uri "schema-salad" version)) + (sha256 + (base32 + "035202p696i3jylb8b3nm9qcxsqby15hhqn1dl4nrz73a17p0ckx")))) (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-before 'check 'skip-failing-tests - (lambda _ - ;; Skip tests that require network access. - (substitute* "schema_salad/tests/test_cwl11.py" - (("^def test_(secondaryFiles|outputBinding)" all) - (string-append "@pytest.mark.skip(reason=" - "\"test requires network access\")\n" - all)))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'set-version + (lambda _ + ;; Set exact version. + (substitute* "setup.py" + (("use_scm_version=True") + (string-append "version=\"" #$version "\""))))) + (add-before 'check 'skip-failing-tests + (lambda _ + ;; Skip tests that require network access. + (let ((skip-test + (lambda (test-pattern) + (string-append "@pytest.mark.skip(reason=" + "\"test requires network access\")\n" + test-pattern)))) + (substitute* "schema_salad/tests/test_cg.py" + (("^def test_(load(_by_yaml_metaschema|_metaschema|_cwlschema|)|include|idmap|idmap2)\\(" all) + (skip-test all))) + (substitute* "schema_salad/tests/test_cwl11.py" + (("^def test_(secondaryFiles|outputBinding|yaml_tab_error)\\(" all) + (skip-test all))) + (substitute* "schema_salad/tests/test_examples.py" + (("^def test_bad_schemas\\(" all) + (skip-test all))))))))) (propagated-inputs (list python-cachecontrol - python-lockfile - python-mistune + python-importlib-resources + python-mistune-next + python-mypy-extensions python-rdflib - python-rdflib-jsonld python-requests - python-ruamel.yaml - python-typing-extensions)) + python-ruamel.yaml)) (native-inputs - (list python-black python-pytest python-pytest-runner)) + (list python-black python-pytest python-pytest-runner python-pytest-xdist)) (home-page "https://github.com/common-workflow-language/schema_salad") (synopsis "Schema Annotations for Linked Avro Data (SALAD)") (description |