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gnu: python-schema-salad: Update to 8.5.20240102191335.

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* 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>
This commit is contained in:
Arun Isaac 2023-10-22 12:41:28 +01:00
parent e5ae409276
commit 65584b9ba8
No known key found for this signature in database
GPG key ID: 2E25EE8B61802BB3
1 changed files with 38 additions and 23 deletions
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gnu/packages/bioinformatics.scm
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@ -4994,37 +4994,52 @@ Note that this package has been deprecated in favor of @code{pyfaidx}.")
(define-public python-schema-salad (define-public python-schema-salad
(package (package
(name "python-schema-salad") (name "python-schema-salad")
(version "8.2.20211116214159") (version "8.5.20240102191335")
(source (source
(origin (origin
(method url-fetch) (method url-fetch)
(uri (pypi-uri "schema-salad" version)) (uri (pypi-uri "schema-salad" version))
(sha256 (sha256
(base32 (base32
"005dh2y45x92zl8sf2sqjmfvcqr4hrz8dfckgkckv87003v7lwqc")))) "035202p696i3jylb8b3nm9qcxsqby15hhqn1dl4nrz73a17p0ckx"))))
(build-system pyproject-build-system) (build-system pyproject-build-system)
(arguments (arguments
`(#:phases (list
(modify-phases %standard-phases #:phases
(add-before 'check 'skip-failing-tests #~(modify-phases %standard-phases
(lambda _ (add-after 'unpack 'set-version
;; Skip tests that require network access. (lambda _
(substitute* "schema_salad/tests/test_cwl11.py" ;; Set exact version.
(("^def test_(secondaryFiles|outputBinding)" all) (substitute* "setup.py"
(string-append "@pytest.mark.skip(reason=" (("use_scm_version=True")
"\"test requires network access\")\n" (string-append "version=\"" #$version "\"")))))
all)))))))) (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 (propagated-inputs
(list python-cachecontrol (list python-cachecontrol
python-lockfile python-importlib-resources
python-mistune python-mistune-next
python-mypy-extensions
python-rdflib python-rdflib
python-rdflib-jsonld
python-requests python-requests
python-ruamel.yaml python-ruamel.yaml))
python-typing-extensions))
(native-inputs (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") (home-page "https://github.com/common-workflow-language/schema_salad")
(synopsis "Schema Annotations for Linked Avro Data (SALAD)") (synopsis "Schema Annotations for Linked Avro Data (SALAD)")
(description (description