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authorEfraim Flashner2020-05-07 04:33:47 -0500
committerEfraim Flashner2020-05-07 04:35:57 -0500
commita6a4e2c24eb10c903e079e76b1b1fde2cd0f2d21 (patch)
treea82f6a46c875fed7d6a93da6c4388903bc608c22 /gn/packages
parent163385ed0f3d954dc9d0f834a676f0bb182ce72d (diff)
downloadguix-bioinformatics-a6a4e2c24eb10c903e079e76b1b1fde2cd0f2d21.tar.gz
gn: Add python-pyshexc and dependants.
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/python.scm225
1 files changed, 225 insertions, 0 deletions
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 66d8d60..0574043 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -27,6 +27,7 @@
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages rdf)
@@ -1254,3 +1255,227 @@ and record oriented data modeling and the Semantic Web.")
(synopsis "Python ShEx Implementation")
(description "Python ShEx Implementation")
(license license:asl2.0)))
+
+(define-public python-pyshexc
+ (package
+ (name "python-pyshexc")
+ (version "0.3.4")
+ (source
+ (origin
+ ;; Release doesn't include the test suite.
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/shexSpec/grammar")
+ ;; Releases aren't tagged.
+ (commit "033f1a60954d39c88ac516179dbaa780d6db585d")))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "07zjizq5lcgx581cznl9mzfmbyxr9h93r9sy23f1xifsafr3s2xh"))))
+ (build-system python-build-system)
+ (arguments
+ '(#:tests? #f ; Test suite isn't well supported :/
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-source
+ (lambda* (#:key inputs #:allow-other-keys)
+ (chdir "parsers/python")
+ (substitute* "tests/test_basic_parser.py"
+ (("BasicParserTestCase.repo_url.*")
+ (string-append "BasicParserTestCase.repo_url = \""
+ (assoc-ref inputs "test-suite")
+ "/shemas\"\n")))
+ #t))
+ (replace 'check
+ (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+ (if tests?
+ (begin (add-installed-pythonpath inputs outputs)
+ (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))))))
+ (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)
+ ("python-shexjsg" ,python-shexjsg)))
+ (native-inputs
+ `(("python-yadict-compare" ,python-yadict-compare)
+ ("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"))))))
+ (home-page "https://github.com/shexSpec/grammar/tree/master/parsers/python")
+ (synopsis "Python ShExC Parser")
+ (description "This package converts the @dfn{Shape Expression Compact}
+(ShExC) into @dfn{Python JSON Schema Binding} (pyjsg) objects.")
+ (license license:asl2.0)))
+
+(define-public python-antlr4-python3-runtime
+ (package
+ (name "python-antlr4-python3-runtime")
+ (version "4.8")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "antlr4-python3-runtime" version))
+ (sha256
+ (base32
+ "0cyv8l216i921gxhbc96f797vkijmmc40a6jwys758qj0mfkyy8m"))))
+ (build-system python-build-system)
+ (home-page "https://www.antlr.org/")
+ (synopsis "ANTLR runtime for Python")
+ (description "This package provides the ANTLR runtime for Python.")
+ (license license:bsd-3)))
+
+(define-public python-jsonasobj
+ (package
+ (name "python-jsonasobj")
+ (version "1.2.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "jsonasobj" version))
+ (sha256
+ (base32
+ "1yj8y3k3fb7lk043f1zhmhb2lzjlfpnxajb92rpxmjzja93yxx0y"))))
+ (build-system python-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-source
+ (lambda _
+ (substitute* "setup.py"
+ (("yadict_compare") "['dict_compare"))
+ #t)))))
+ (native-inputs
+ `(("python-yadict-compare" ,python-yadict-compare)))
+ (home-page "https://github.com/hsolbrig/jsonasobj")
+ (synopsis "JSON as python objects")
+ (description
+ "This package provides an extension to the core python json library that
+treats name/value pairs as first class attributes whenever possible.")
+ (license license:asl2.0)))
+
+(define-public python-shexjsg
+ (package
+ (name "python-shexjsg")
+ (version "0.6.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "ShExJSG" version))
+ (sha256
+ (base32
+ "04pb32g1y024rdyp5h7kq3pkgyp7jadwa737y6zfpdvqf25d3jvi"))))
+ (build-system python-build-system)
+ (arguments
+ '(#:tests? #f ; Skip tests, they fail due to pyshexc missing.
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-source
+ (lambda _
+ (substitute* '("requirements.txt"
+ "requirements-dev.txt")
+ (("pyshexc.*") "") ; no loops
+ (("==.*") "\n"))
+ #t)))))
+ (propagated-inputs
+ `(("python-antlr4-python3-runtime" ,python-antlr4-python3-runtime)
+ ("python-certifi" ,python-certifi)
+ ("python-chardet" ,python-chardet)
+ ("python-idna" ,python-idna)
+ ("python-isodate" ,python-isodate)
+ ("python-requests" ,python-requests)
+ ("python-urllib3" ,python-urllib3)))
+ (native-inputs
+ `(("python-jsonasobj" ,python-jsonasobj)
+ ("python-pbr" ,python-pbr)
+ ("python-pyjsg" ,python-pyjsg)
+ ("python-pyparsing" ,python-pyparsing)
+ ;("python-pyshexc" ,python-pyshexc) ; yay loops!
+ ("python-rdflib" ,python-rdflib)
+ ("python-rdflib-jsonld" ,python-rdflib-jsonld)
+ ("python-six" ,python-six)
+ ("python-yadict-compare" ,python-yadict-compare)))
+ (home-page "https://github.com/hsolbrig/ShExJSG")
+ (synopsis "Astract Syntax Tree for the ShEx 2.0 language")
+ (description "This package provides an astract syntax tree for the
+ShEx 2.0 language.")
+ (license license:cc0)))
+
+(define-public python-yadict-compare
+ (package
+ (name "python-yadict-compare")
+ (version "1.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "yadict_compare" version))
+ (sha256
+ (base32
+ "1kkcw82cp6mf3jailckd9gya4r7wjyz4gc5azsj2njj4wqn081rw"))))
+ (build-system python-build-system)
+ (arguments '(#:tests? #f))
+ (home-page "https://github.com/hsolbrig/dict_compare")
+ (synopsis "Dictionary comparison tool with filtering and reporting")
+ (description
+ "A dictionary comparison tool that allows the injection of filters and
+handles recursion and lists.")
+ (license license:bsd-3)))
+
+(define-public python-pyjsg
+ (package
+ (name "python-pyjsg")
+ (version "0.9.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "PyJSG" version))
+ (sha256
+ (base32
+ "1zpd34svis4pc2hdry02mavz699i2dmaxir9q59ldxdy40jfrhq0"))))
+ (build-system python-build-system)
+ (arguments
+ '(#:tests? #f ; tests not included
+ #:phases
+ (modify-phases %standard-phases
+ ;; From tox.ini
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (for-each
+ (lambda (dir)
+ (invoke "python" "-m" "unittest" "discover" "-s" dir))
+ '("tests/test_issues"
+ "tests/test_basics"
+ "tests/test_jsglib"
+ "tests/test_parser_impl"
+ "tests/test_python_generator"
+ "tests_standalone"
+ "tests_standalone_2"))
+ #t))))))
+ (propagated-inputs
+ `(("python-antlr4-python3-runtime" ,python-antlr4-python3-runtime)
+ ("python-jsonasobj" ,python-jsonasobj)
+ ("python-requests" ,python-requests)))
+ (native-inputs
+ `(("python-unittest2" ,python-unittest2)
+ ("python-yadict-compare" ,python-yadict-compare)))
+ (home-page "https://github.com/hsolbrig/pyjsg")
+ (synopsis
+ "Python JSON Schema Grammar bindings")
+ (description
+ "A tool to create Python classes that represent JSON objects defined in JSG.")
+ (license license:asl2.0)))