diff options
| -rw-r--r-- | README.org | 2 | ||||
| -rw-r--r-- | gn/packages/python.scm | 273 |
2 files changed, 233 insertions, 42 deletions
diff --git a/README.org b/README.org index d11f3c6..5f49a2d 100644 --- a/README.org +++ b/README.org @@ -9,6 +9,8 @@ interest can be found at 2. https://github.com/UMCUGenetics/guix-additions 3. https://github.com/ekg/guix-genomics +Also see [[http://git.genenetwork.org/pjotrp/guix-notes/src/branch/master/CHANNELS.org][Guix notes]] for a list of channels. + To easily use the packages from this repo, simply add it to your `channels` list in ~/.config/guix/channels.scm as described [[https://guix.gnu.org/manual/en/html_node/Channels.html][here]]: diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 4bfe648..7ea0211 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -1185,40 +1185,105 @@ generation, and transformation to RDF. Salad provides a bridge between document and record oriented data modeling and the Semantic Web.") (license license:asl2.0))) +(define-public python-cfgraph + (package + (name "python-cfgraph") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "CFGraph" version)) + (sha256 + (base32 + "0x7yz0lvqb6mkhl5fbml27sppmscgpf8v2ism9jzzf0h982ffzxm")))) + (build-system python-build-system) + (propagated-inputs + `(("python-rdflib" ,python-rdflib))) + (home-page "https://github.com/hsolbrig/CFGraph") + (synopsis "Rdflib collections flattening graph") + (description + "Rdflib collections flattening graph.") + (license license:asl2.0))) + +(define-public python-pyshex + (package + (name "python-pyshex") + (version "0.7.14") + (source + (origin + (method url-fetch) + (uri (pypi-uri "PyShEx" version)) + (sha256 + (base32 + "1fy664bh6hpmr4cf49fwwxng36kv7s6b2986hbv0cqcypc4ri2cs")))) + (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)))))) + (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))) + (home-page "https://github.com/hsolbrig/PyShEx") + (synopsis "Python ShEx Implementation") + (description "This package provides a python ShEx Implementation.") + (license license:asl2.0))) + (define-public python-pyshexc (package (name "python-pyshexc") - (version "0.3.4") + (version "0.5.4") (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)) + (method url-fetch) + (uri (pypi-uri "PyShExC" version)) (sha256 (base32 - "07zjizq5lcgx581cznl9mzfmbyxr9h93r9sy23f1xifsafr3s2xh")))) + "0hyhmc971gh25ja34j9hbkr7dg9n3jfin8668cqzjmcpjvb1jnil")))) (build-system python-build-system) (arguments - '(#:tests? #f ; Test suite isn't well supported :/ + '(#:tests? #f ; Tests aren't included in release tarball. #: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) + (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") @@ -1231,10 +1296,10 @@ and record oriented data modeling and the Semantic Web.") ("python-pyjsg" ,python-pyjsg) ("python-rdflib" ,python-rdflib) ("python-rdflib-jsonld" ,python-rdflib-jsonld) - ("python-requests" ,python-requests) - ("python-shexjsg" ,python-shexjsg))) + ("python-requests" ,python-requests))) (native-inputs `(("python-yadict-compare" ,python-yadict-compare) + ("python-shexjsg" ,python-shexjsg-min) ("test-suite" ,(origin (method git-fetch) @@ -1254,14 +1319,14 @@ and record oriented data modeling and the Semantic Web.") (define-public python-antlr4-python3-runtime (package (name "python-antlr4-python3-runtime") - (version "4.8") + (version "4.7.1") (source (origin (method url-fetch) (uri (pypi-uri "antlr4-python3-runtime" version)) (sha256 (base32 - "0cyv8l216i921gxhbc96f797vkijmmc40a6jwys758qj0mfkyy8m")))) + "1lrzmagawmavyw1n1z0qarvs2jmbnbv0p89dah8g7klj8hnbf9hv")))) (build-system python-build-system) (home-page "https://www.antlr.org/") (synopsis "ANTLR runtime for Python") @@ -1281,7 +1346,8 @@ and record oriented data modeling and the Semantic Web.") "1yj8y3k3fb7lk043f1zhmhb2lzjlfpnxajb92rpxmjzja93yxx0y")))) (build-system python-build-system) (arguments - '(#:phases + '(#:tests? #f ; Tests not included in release tarball. + #:phases (modify-phases %standard-phases (add-after 'unpack 'patch-source (lambda _ @@ -1300,18 +1366,17 @@ treats name/value pairs as first class attributes whenever possible.") (define-public python-shexjsg (package (name "python-shexjsg") - (version "0.6.3") + (version "0.6.5") (source (origin (method url-fetch) (uri (pypi-uri "ShExJSG" version)) (sha256 (base32 - "04pb32g1y024rdyp5h7kq3pkgyp7jadwa737y6zfpdvqf25d3jvi")))) + "1nn69sl5j949qy21nl5gr56cxfhmml1vng08hayxqfj6vn3ay3gg")))) (build-system python-build-system) (arguments - '(#:tests? #f ; Skip tests, they fail due to pyshexc missing. - #:phases + '(#:phases (modify-phases %standard-phases (add-after 'unpack 'patch-source (lambda _ @@ -1319,31 +1384,66 @@ treats name/value pairs as first class attributes whenever possible.") "requirements-dev.txt") (("pyshexc.*") "") ; no loops (("==.*") "\n")) - #t))))) + #t)) + (replace 'check + (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (if tests? + (begin (add-installed-pythonpath inputs outputs) + (substitute* '("tests/test_shexc.py" + "tests/test_shexj.py") + (("shexTestRepository =.*") + (string-append "shexTestRepository = \"" + (assoc-ref inputs "test-suite") + "/schemas\"\n"))) + (invoke "python" "-m" "unittest")) + #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-pyjsg" ,python-pyjsg) ("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-pyshexc" ,python-pyshexc) ("python-rdflib" ,python-rdflib) ("python-rdflib-jsonld" ,python-rdflib-jsonld) ("python-six" ,python-six) - ("python-yadict-compare" ,python-yadict-compare))) + ("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/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))) +;; 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") @@ -1356,7 +1456,15 @@ ShEx 2.0 language.") (base32 "1kkcw82cp6mf3jailckd9gya4r7wjyz4gc5azsj2njj4wqn081rw")))) (build-system python-build-system) - (arguments '(#:tests? #f)) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (with-directory-excursion "test" + (invoke "python" "-m" "unittest" "discover" "-s" "test"))))))) + (native-inputs + `(("python-unittest2" ,python-unittest2))) (home-page "https://github.com/hsolbrig/dict_compare") (synopsis "Dictionary comparison tool with filtering and reporting") (description @@ -1367,19 +1475,31 @@ handles recursion and lists.") (define-public python-pyjsg (package (name "python-pyjsg") - (version "0.9.0") + (version "0.9.2") (source (origin - (method url-fetch) - (uri (pypi-uri "PyJSG" version)) + (method git-fetch) + (uri (git-reference + ;; Releases aren't tagged in the repository. + (url "https://github.com/hsolbrig/pyjsg") + (commit "9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7"))) + (file-name (git-file-name name version)) (sha256 (base32 - "1zpd34svis4pc2hdry02mavz699i2dmaxir9q59ldxdy40jfrhq0")))) + "0fhpvb6i6xhyd6hnwknw0y2k33cb7iwj07g009lw96r580vprxs4")))) (build-system python-build-system) (arguments - '(#:tests? #f ; tests not included - #:phases + '(#:phases (modify-phases %standard-phases + (add-after 'unpack 'patch-source + (lambda* (#:key inputs #:allow-other-keys) + (for-each (lambda (file) + (make-file-writable file)) + (find-files "." ".")) + (substitute* "tests_standalone_2/test_xsfacet.py" + (("\\.\\.', '\\.\\.', '\\.\\.', 'shexSpec', 'shexTest") + (assoc-ref inputs "test-suite"))) + #t)) ;; From tox.ini (replace 'check (lambda* (#:key tests? #:allow-other-keys) @@ -1401,10 +1521,79 @@ handles recursion and lists.") ("python-requests" ,python-requests))) (native-inputs `(("python-unittest2" ,python-unittest2) - ("python-yadict-compare" ,python-yadict-compare))) + ("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/hsolbrig/pyjsg") - (synopsis - "Python JSON Schema Grammar bindings") + (synopsis "Python JSON Schema Grammar bindings") (description "A tool to create Python classes that represent JSON objects defined in JSG.") (license license:asl2.0))) + +(define-public python-sparqlwrapper + (package + (name "python-sparqlwrapper") + (version "1.8.5") + (source + (origin + (method url-fetch) + (uri (pypi-uri "SPARQLWrapper" version)) + (sha256 + (base32 + "0g7va1l37iq96abqqn6b4a6sjxxh5m3h1svsw1h1c56siidnp9nn")))) + (build-system python-build-system) + (arguments + '(#:tests? #f ; 2to3 doesn't quite do it for the test suite. + #:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (if tests? + (begin ;; from run_tests_py3.sh + (invoke "2to3" "-wn" "--no-diffs" "test") + (substitute* "test/wrapper_test.py" + (("urllib2._opener") "urllib.request._opener")) + (setenv "PYTHONPATH" + (string-append "SPARQLWrapper:" + (getenv "PYTHONPATH"))) + (invoke "nosetests")) + #t)))))) + (propagated-inputs + `(("python-rdflib" ,python-rdflib))) + (native-inputs + `(("python-nose" ,python-nose))) + (home-page "https://rdflib.dev/sparqlwrapper/") + (synopsis "SPARQL Endpoint interface to Python") + (description + "THis package provides a SPARQL Endpoint interface to Python.") + (license license:w3c))) + +(define-public python-sparql-slurper + (package + (name "python-sparql-slurper") + (version "0.3.4") + (source + (origin + (method url-fetch) + (uri (pypi-uri "sparql_slurper" version)) + (sha256 + (base32 + "1m9jlck7ny5dyr762l4xrsn7ll4v48fccjkm062ihhvhbsjf0iil")))) + (build-system python-build-system) + (arguments '(#:tests? #f)) ; Tests require network access. + (propagated-inputs + `(("python-pbr" ,python-pbr) + ("python-rdflib" ,python-rdflib) + ("python-sparqlwrapper" ,python-sparqlwrapper))) + (home-page "https://github.com/hsolbrig/sparql_slurper") + (synopsis "SPARQL Slurper for rdflib") + (description "This package provides a SPARQL Slurper for rdflib.") + (license license:asl2.0))) |