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authorEfraim Flashner2023-03-20 11:47:30 +0200
committerEfraim Flashner2023-03-20 11:47:30 +0200
commit37efc1b1366790a1df0ee45399740972140a461f (patch)
tree30466b4d2082d956cf45c27673e1c6b8351b53be /gn/packages
parentdb96964f56052bd1ac18d5696f269571fe51c1bb (diff)
downloadguix-bioinformatics-37efc1b1366790a1df0ee45399740972140a461f.tar.gz
python-pyshexc: Update to 0.9.1.
* gn/packages/python.scm (python-pyshexc): Update to 0.9.1. [arguments]: Update custom 'check phase. [propagated-inputs]: Add python-chardet, python-rdflib-shim, python-shexjsg. Remove python-rdflib, python-rdflib-jsonld, python-requests. [native-inputs]: Add python-pbr, python-requests. Remove python-shexjsg, custom test-suite git checkout. (python-shexjsg-min): Remove variable.
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/python.scm63
1 files changed, 15 insertions, 48 deletions
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index bb2c0b0..744d7b3 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -928,54 +928,34 @@ server.")
(define-public python-pyshexc
(package
(name "python-pyshexc")
- (version "0.5.4")
+ (version "0.9.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "PyShExC" version))
(sha256
- (base32
- "0hyhmc971gh25ja34j9hbkr7dg9n3jfin8668cqzjmcpjvb1jnil"))))
+ (base32 "1lq4lf0nal1v1d3vbyrr1hfkhmhphy06dyqhyw7b5zls9dfrga9m"))))
(build-system python-build-system)
(arguments
- '(#:tests? #f ; Tests aren't included in release tarball.
+ '(#:tests? #f ; It isn't clear how the tests expect to succeed.
#:phases
(modify-phases %standard-phases
(replace 'check
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
- (if tests?
- (begin (add-installed-pythonpath inputs outputs)
- (substitute* "tests/test_basic_parser.py"
- (("BasicParserTestCase.repo_url.*")
- (string-append "BasicParserTestCase.repo_url = \""
- (assoc-ref inputs "test-suite")
- "/schemas\"\n")))
- (with-directory-excursion "tests"
- (invoke "python" "build_test_harness.py")
- (invoke "python" "test_basic_parser.py")
- (invoke "python" "test_issue_2.py")
- (invoke "python" "test_shexr.py")))
- #t))))))
+ (when tests?
+ (add-installed-pythonpath inputs outputs)
+ (invoke "python" "-m" "unittest" "discover" "-s" "tests")))))))
(propagated-inputs
- `(("python-antlr4-python3-runtime" ,python-antlr4-python3-runtime)
- ("python-jsonasobj" ,python-jsonasobj)
- ("python-pyjsg" ,python-pyjsg)
- ("python-rdflib" ,python-rdflib)
- ("python-rdflib-jsonld" ,python-rdflib-jsonld)
- ("python-requests" ,python-requests)))
+ (list python-antlr4-python3-runtime
+ python-chardet
+ python-jsonasobj
+ python-pyjsg
+ python-rdflib-shim
+ python-shexjsg))
(native-inputs
- `(("python-yadict-compare" ,python-yadict-compare)
- ("python-shexjsg" ,python-shexjsg-min)
- ("test-suite"
- ,(origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/shexSpec/shexTest")
- (commit "v2.0.2")))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "1x788nyrwycfr55wbg0ay6mc8mi6wwsg81h614rx9pw6rvrsppps"))))))
+ (list python-pbr
+ python-requests
+ python-yadict-compare))
(home-page "https://github.com/shexSpec/grammar/tree/master/parsers/python")
(synopsis "Python ShExC Parser")
(description "This package converts the @dfn{Shape Expression Compact}
@@ -1096,19 +1076,6 @@ treats name/value pairs as first class attributes whenever possible.")
ShEx 2.0 language.")
(license license:cc0)))
-;; Lets use this one for tests.
-(define python-shexjsg-min
- (package
- (inherit python-shexjsg)
- (name "python-shexjsg")
- (arguments
- (substitute-keyword-arguments (package-arguments python-shexjsg)
- ((#:tests? _ #t) #f)))
- (native-inputs
- `(,@(alist-delete "python-pyshexc"
- (package-native-inputs python-shexjsg))))
- (properties `((hidden? . #t)))))
-
(define-public python-yadict-compare
(package
(name "python-yadict-compare")