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authorEfraim Flashner2023-03-20 11:50:36 +0200
committerEfraim Flashner2023-03-20 11:50:36 +0200
commitb179e31d8081683d4bb55cbc926684bbed9cb53c (patch)
tree143027d1f10b92e72fb8b0f9b139fd6d28e27cb9
parent37efc1b1366790a1df0ee45399740972140a461f (diff)
downloadguix-bioinformatics-b179e31d8081683d4bb55cbc926684bbed9cb53c.tar.gz
python-pyshex: Update to 0.8.1.
* gn/packages/python.scm (python-pyshex): Update to 0.8.1. [arguments]: Remove custom 'patch-source phase. Update custom 'check phase. [propagated-inputs]: Add python-chardet, python-rdflib-shim, python-sparqlslurper. Remove python-rdflib, python-rdflib-jsonld, python-pbr, python-sparql-slurper. [native-inputs]: Add python-pbr, python-unitttest2.
-rw-r--r--gn/packages/python.scm52
1 files changed, 18 insertions, 34 deletions
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 744d7b3..a2f8157 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -874,52 +874,36 @@ server.")
(define-public python-pyshex
(package
(name "python-pyshex")
- (version "0.7.14")
+ (version "0.8.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "PyShEx" version))
(sha256
- (base32
- "1fy664bh6hpmr4cf49fwwxng36kv7s6b2986hbv0cqcypc4ri2cs"))))
+ (base32 "1l3hprspx5l4zl28p1m79mwfxy5c86601jq3x3damyi7zr2lsp1w"))))
(arguments
'(#:phases
(modify-phases %standard-phases
- (add-after 'unpack 'patch-source
- (lambda _
- (substitute* "requirements.txt"
- ((">=.*") "\n"))
- #t))
(replace 'check
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
- (if tests?
- (begin
- (delete-file "tests/test_cli/test_evaluate.py")
- (delete-file "tests/test_cli/test_sparql_options.py")
- (delete-file "tests/test_issues/test_fhir.py")
- (delete-file "tests/test_issues/test_issue_30.py")
- (delete-file "tests/test_pyshex_utils/test_schema_loader.py")
- (delete-file "tests/test_shex_manifest/test_basics.py")
- (delete-file "tests/test_shextest_validation/test_manifest_shex_json.py")
- (delete-file "tests/test_shextest_validation/test_manifest_shex_shexc.py")
- (delete-file "tests/test_support_libraries/test_prefixlib.py")
- (delete-file "tests/test_utils/test_manifest.py")
- (delete-file "tests/test_utils/test_sparql_query.py")
- (delete-file "tests/test_utils/test_n3_mapper.py")
- (invoke "python" "-m" "unittest"))
- #t))))))
+ (when tests?
+ (add-installed-pythonpath inputs outputs)
+ (setenv "SKIP_EXTERNAL_URLS" "true")
+ (invoke "python" "-m" "unittest" "-k"
+ "test_sparql_options")))))))
(build-system python-build-system)
(propagated-inputs
- `(("python-cfgraph" ,python-cfgraph)
- ("python-pyshexc" ,python-pyshexc)
- ("python-rdflib" ,python-rdflib)
- ("python-pbr" ,python-pbr)
- ("python-rdflib-jsonld" ,python-rdflib-jsonld)
- ("python-requests" ,python-requests)
- ("python-shexjsg" ,python-shexjsg)
- ("python-sparql-slurper" ,python-sparql-slurper)
- ("python-sparqlwrapper" ,python-sparqlwrapper)
- ("python-urllib3" ,python-urllib3)))
+ (list python-cfgraph
+ python-chardet
+ python-pyshexc
+ python-rdflib-shim
+ python-requests
+ python-shexjsg
+ python-sparqlslurper
+ python-sparqlwrapper
+ python-urllib3))
+ (native-inputs
+ (list python-pbr python-unittest2))
(home-page "https://github.com/hsolbrig/PyShEx")
(synopsis "Python ShEx Implementation")
(description "This package provides a python ShEx Implementation.")