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author | Efraim Flashner | 2020-05-07 04:33:47 -0500 |
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committer | Efraim Flashner | 2020-05-07 04:35:57 -0500 |
commit | a6a4e2c24eb10c903e079e76b1b1fde2cd0f2d21 (patch) | |
tree | a82f6a46c875fed7d6a93da6c4388903bc608c22 /gn/packages | |
parent | 163385ed0f3d954dc9d0f834a676f0bb182ce72d (diff) | |
download | guix-bioinformatics-a6a4e2c24eb10c903e079e76b1b1fde2cd0f2d21.tar.gz |
gn: Add python-pyshexc and dependants.
Diffstat (limited to 'gn/packages')
-rw-r--r-- | gn/packages/python.scm | 225 |
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))) |