diff options
Diffstat (limited to 'gn/packages/python.scm')
| -rw-r--r-- | gn/packages/python.scm | 532 |
1 files changed, 313 insertions, 219 deletions
diff --git a/gn/packages/python.scm b/gn/packages/python.scm index d9c4511..510546d 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -9,8 +9,11 @@ #:use-module (gnu packages image) #:use-module (gnu packages libffi) #:use-module (gnu packages linux) + #:use-module (gnu packages maths) #:use-module (gnu packages monitoring) #:use-module (gnu packages pcre) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages protobuf) #:use-module (gnu packages python) #:use-module (gnu packages python-build) #:use-module (gnu packages python-check) @@ -29,6 +32,7 @@ #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) + #:use-module (guix gexp) #:use-module (guix utils) #:use-module (guix build-system python) #:use-module (srfi srfi-1)) @@ -251,12 +255,6 @@ Python 3 support.") (package-with-python2 python-avro)) -; env IPFS_PATH=/export/ipfs/ ipfs add -r htmlgen/ -; added QmUD9LMJTE8q5wYkUyAwLdz2QCGXWt457iFnyYQAGfsN3j htmlgen/htmlgen-2.2.2-gn.tar.gz -; added QmZLWsPHLFTU3hWAfdTwj3RXFrS8Ma7KEixne1suWuYqeG htmlgen -; penguin2:~/tmp$ env IPFS_PATH=/export/ipfs/ ipfs pin add -r QmZLWsPHLFTU3hWAfdTwj3RXFrS8Ma7KEixne1suWuYqeG -; pinned QmZLWsPHLFTU3hWAfdTwj3RXFrS8Ma7KEixne1suWuYqeG recursively - (define-public python2-htmlgen-gn ; guix obsolete (package (name "python2-htmlgen-gn") @@ -265,7 +263,7 @@ Python 3 support.") (method url-fetch) ;; http://files.genenetwork.org/software/contrib/htmlgen-2.2.2-gn.tar.gz (uri (string-append - "http://ipfs.genenetwork.org/ipfs/QmZLWsPHLFTU3hWAfdTwj3RXFrS8Ma7KEixne1suWuYqeG/htmlgen-" version "-gn.tar.gz")) + "https://files.genenetwork.org/software/htmlgen-2.2.2-gn.tar.gz")) (sha256 (base32 "1lwsk56rymhrma46cbyh3g64ksmq1vsih3qkrc2vh0lpba825y7r")) @@ -360,13 +358,6 @@ Python 3 support.") (description #f) (license #f))) -; penguin2:~/tmp$ env IPFS_PATH=/export/ipfs/ ipfs add -r Imaging/ -; added QmV8Rew1re8gBTLsaqMU4bd7euFUPEpjiD572mtoz6KhPn Imaging/Imaging-1.1.6-gn.tar.gz -; added QmdkzQpVMLZVtywpYesynt9c7H8w7hHZRYKq8woN7stfpD Imaging -; env IPFS_PATH=/export/ipfs/ ipfs pin add -r QmdkzQpVMLZVtywpYesynt9c7H8w7hHZRYKq8woN7stfpD -; pinned QmdkzQpVMLZVtywpYesynt9c7H8w7hHZRYKq8woN7stfpD recursively - - (define-public python2-pil1-gn ; guix obsolete (package (name "python2-pil1") ; works with GN2 @@ -427,11 +418,6 @@ capabilities to the Python interpreter.") "file://README" "See 'README' in the distribution.")))) -; agrigento:~/izip/git/opensource/genenetwork$ scp ./contrib/piddle-1.0.15-gn.tgz penguin2.genenetwork.org -; penguin2:~$ env IPFS_PATH=/export/ipfs/ ipfs add piddle-1.0.15-gn.tgz -; added QmSMptV2VALL2s7igqRqKJ8ALNvhqFRUYVG54kEF7ac6ve piddle-1.0.15-gn.tgz -; penguin2:~$ env IPFS_PATH=/export/ipfs/ ipfs pin add -r QmSMptV2VALL2s7igqRqKJ8ALNvhqFRUYVG54kEF7ac6ve -; pinned QmSMptV2VALL2s7igqRqKJ8ALNvhqFRUYVG54kEF7ac6ve recursively (define-public python2-piddle-gn ; guix obsolete (package @@ -440,7 +426,7 @@ capabilities to the Python interpreter.") (source (origin (method url-fetch) (uri (string-append - "http://ipfs.genenetwork.org/ipfs/QmeKcMb8AdwZNUcAaTASVpZ39ipwJn8eBoqqDfoCzQYmNk/piddle-" version ".tgz")) + "https://files.genenetwork.org/software/piddle-1.0.15-gn.tgz")) (sha256 (base32 "05gjnn31v7p0kh58qixrpcizcxqf3b7zv4a5kk8nsmqwgxh0c6gq")))) @@ -707,8 +693,7 @@ clusters (computers connected via network).") (define GN1-thirdparty-sources (origin (method url-fetch/tarbomb) - ;; ipfs get QmTPwYT2pehdxdG1TiHEzVzLgbeuhJ4utXShuz3twA84AB - (uri "file:///gnu/store/p33a2sh3x2nhiiphdw9nly80njg6p8fi-thirdparty.tgz") + (uri "https://files.genenetwork.org/software/thirdparty.tgz") (file-name "GN1-thirdparty") (sha256 (base32 @@ -851,37 +836,68 @@ spreadsheets without the need for COM objects.") (base32 "1lg1klrczvzfan89y3bl9ykrknl3nb01vvai37fkww24apzyibjf")))))) +(define-public python-py-dateutil + (package + (name "python-py-dateutil") + (version "2.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "py-dateutil" version)) + (sha256 + (base32 + "0j5hyhn2yqwyapbhvdvw14a0ydhdl6ddw95nii091iarf6hjryky")))) + (build-system python-build-system) + (arguments + (list + #:tests? #f ; Package is unmaintained since ~2014 + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "test.py"))))))) + (propagated-inputs (list python-six)) + (home-page "https://bitbucket.org/cld/dateutil") + (synopsis "Extensions to the standard Python datetime module") + (description "Extensions to the standard Python datetime module") + (license license:bsd-3))) + (define-public python-arvados-python-client (package (name "python-arvados-python-client") - (version "2.0.2") + (version "2.5.0") (source (origin (method url-fetch) (uri (pypi-uri "arvados-python-client" version)) (sha256 - (base32 - "19l4w6m5426x5k2kick630dh2jx26j16ycs2nhbfgr4cd43d29y4")))) + (base32 "1j08aykj0v2z2bqwr5nfnbjgc1yzdnfdafcnxbf2jbwqh8kx7zc9")) + (modules '((guix build utils))) + (snippet + '(begin + (substitute* "setup.py" + ;; Don't set a maximum version of pycurl. + (("(pycurl >=([[:digit:]]+\\.?)+),.*" _ pycurl) + (string-append pycurl "',\n"))))))) (build-system python-build-system) (arguments `(#:tests? #f)) ; tests not included? (propagated-inputs - `(("python-ciso8601" ,python-ciso8601) - ("python-future" ,python-future) - ;("python-google-api-python-client" ,python-google-api-python-client) - ("python-google-api-client" ,python-google-api-client) - ("python-httplib2" ,python-httplib2) - ("python-pycurl" ,python-pycurl) - ("python-ruaml.yaml" ,python38-ruaml.yaml-0.15.76) - ("python-setuptools" ,python-setuptools) - ("python-oauth2client" ,python-oauth2client) - ("python-uritemplate" ,python-uritemplate) - ("python-ws4py" ,python-ws4py))) + (list python-ciso8601 + python-future + python-google-api-client + python-google-api-core-1 + python-google-auth-1 + python-httplib2 + python-protobuf + python-pycurl + python-pyparsing-2.4.7 ; < 3 + python-ruamel.yaml + python-ws4py)) (native-inputs - `(("python-mock" ,python-mock) - ("python-pbr" ,python-pbr-1.6.0) - ("python-pyyaml" ,python-pyyaml) - )) + (list python-mock + python-pbr-1.6.0 + python-pyyaml)) (home-page "https://arvados.org") (synopsis "Arvados client library") (description "This package provides the arvados module, an API client for @@ -899,46 +915,35 @@ server.") (method url-fetch) (uri (pypi-uri "PyShEx" version)) (sha256 - (base32 - "1fy664bh6hpmr4cf49fwwxng36kv7s6b2986hbv0cqcypc4ri2cs")))) + (base32 "1fy664bh6hpmr4cf49fwwxng36kv7s6b2986hbv0cqcypc4ri2cs")))) (arguments - '(#:phases + '(#:tests? #f ; Tests try to use the internet. + #:phases (modify-phases %standard-phases - (add-after 'unpack 'patch-source + (add-after 'unpack 'drop-rdflib-namespace-rdfnamespace (lambda _ - (substitute* "requirements.txt" - ((">=.*") "\n")) - #t)) + ;; _RDFNamespace is in rdflib-5 + ;; https://github.com/hsolbrig/PyShEx/commit/d138a5b4f2249212f2141b7b9bbaff6696ee9415 + (substitute* "pyshex/prefixlib.py" + (("XMLNS, _RDFNamespace") "XMLNS")))) (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"))))))) (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-pyshexc-0.7 + python-rdflib + python-requests + python-shexjsg + python-sparql-slurper + 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.") @@ -947,44 +952,97 @@ 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 + (list python-pbr + python-requests + python-yadict-compare)) + (home-page "https://github.com/shexSpec/grammar-python-antlr") + (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-pyshexc-0.7 + (package + (inherit python-pyshexc) + (name "python-pyshexc") + (version "0.7.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/shexSpec/grammar") + (commit (string-append "v" version)))) + (file-name (git-file-name "shexspec-grammar" version)) + (sha256 + (base32 "08wsknjq8zyi3hk01w6yl6z8jld63l6l64n43gjhj0jphbm4s9iz")) + (modules '((guix build utils))) + (snippet + '(begin + (substitute* "parsers/python/setup.cfg" + (("python-requires = 3") "python_requires = >=3.6")))))) + (arguments + `(#:tests? #f ; Tests try to access the internet. + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "parsers/python") + (setenv "PBR_VERSION" ,version))) + (replace 'check + (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + (substitute* "tests/__init__.py" + (("schemas_base =.*") + (string-append "schemas_base = \"" + (assoc-ref inputs "test-suite") + "/schemas\"\n"))) + (substitute* "tests/test_shexr.py" + (("https://raw.githubusercontent.com/shexSpec/shexTest/master/validation/manifest") + (string-append (assoc-ref inputs "test-suite") + "/validation/manifest"))) + (substitute* "tests/test_issue_9.py" + (("https://raw.githubusercontent.com/shexSpec/shexTest/master/schemas/1dotNS2.shex") + (search-input-file inputs "/schemas/1dotNS2.shex"))) + (symlink (assoc-ref inputs "test-suite") + "../../../shexTest") + (invoke "python" "-m" "unittest" "discover" "-s" "tests"))))))) + (propagated-inputs + (list python-antlr4-python3-runtime + python-certifi + python-jsonasobj + python-rdflib-shim + python-requests + python-shexjsg)) (native-inputs - `(("python-yadict-compare" ,python-yadict-compare) - ("python-shexjsg" ,python-shexjsg-min) + `(("python-pbr" ,python-pbr) + ("python-unittest2" ,python-unittest2) + ("python-yadict-compare" ,python-yadict-compare) ("test-suite" ,(origin (method git-fetch) @@ -995,23 +1053,18 @@ server.") (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))) + (home-page "https://github.com/shexSpec/grammar/tree/master/parsers/python"))) (define-public python-antlr4-python3-runtime (package (name "python-antlr4-python3-runtime") - (version "4.7.1") + (version "4.9.3") (source (origin (method url-fetch) (uri (pypi-uri "antlr4-python3-runtime" version)) (sha256 - (base32 - "1lrzmagawmavyw1n1z0qarvs2jmbnbv0p89dah8g7klj8hnbf9hv")))) + (base32 "06w8fz73rk8vzjz9rydfk56g4mbqpyl81yhypc14jab886dlc97j")))) (build-system python-build-system) (home-page "https://www.antlr.org/") (synopsis "ANTLR runtime for Python") @@ -1051,84 +1104,39 @@ treats name/value pairs as first class attributes whenever possible.") (define-public python-shexjsg (package (name "python-shexjsg") - (version "0.6.5") + (version "0.8.2") (source (origin (method url-fetch) (uri (pypi-uri "ShExJSG" version)) (sha256 - (base32 - "1nn69sl5j949qy21nl5gr56cxfhmml1vng08hayxqfj6vn3ay3gg")))) + (base32 "1dnhpk6n6vzadkv13y7r6y2mi1pzv4y19vmxh91k9ykpqngn4ypi")))) (build-system python-build-system) (arguments '(#:phases (modify-phases %standard-phases - (add-after 'unpack 'patch-source - (lambda _ - (substitute* '("requirements.txt" - "requirements-dev.txt") - (("pyshexc.*") "") ; no loops - (("==.*") "\n")) - #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)))))) + ;; Tries to download files from the internet. + (substitute* "tests/test_shexj.py" + (("skipIf\\(False") "skipIf(True")) + (invoke "python" "-m" "unittest")))))))) (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))) + (list python-pyjsg)) (native-inputs - `(("python-jsonasobj" ,python-jsonasobj) - ("python-pbr" ,python-pbr) - ("python-pyparsing" ,python-pyparsing) - ("python-pyshexc" ,python-pyshexc) - ("python-rdflib" ,python-rdflib) - ("python-rdflib-jsonld" ,python-rdflib-jsonld) - ("python-six" ,python-six) - ("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")))))) + (list python-jsonasobj + python-pbr + python-rdflib-shim + python-requests + 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))) -;; 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") @@ -1160,31 +1168,17 @@ handles recursion and lists.") (define-public python-pyjsg (package (name "python-pyjsg") - (version "0.9.2") + (version "0.11.10") (source (origin - (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)) + (method url-fetch) + (uri (pypi-uri "PyJSG" version)) (sha256 - (base32 - "0fhpvb6i6xhyd6hnwknw0y2k33cb7iwj07g009lw96r580vprxs4")))) + (base32 "1ylbx2pc06qsvb8cqnr8nysvmw55f8nkm05ybcwjpyik53zy7mjb")))) (build-system python-build-system) (arguments '(#: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) @@ -1193,30 +1187,20 @@ handles recursion and lists.") (lambda (dir) (invoke "python" "-m" "unittest" "discover" "-s" dir)) '("tests/test_issues" - "tests/test_basics" + ;"tests/test_basics" "tests/test_jsglib" "tests/test_parser_impl" "tests/test_python_generator" "tests_standalone" - "tests_standalone_2")) - #t)))))) + "tests_standalone_2")))))))) (propagated-inputs - `(("python-antlr4-python3-runtime" ,python-antlr4-python3-runtime) - ("python-jsonasobj" ,python-jsonasobj) - ("python-requests" ,python-requests))) + (list python-antlr4-python3-runtime + python-jsonasobj)) (native-inputs - `(("python-unittest2" ,python-unittest2) - ("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")))))) + (list python-pbr + python-requests + python-unittest2 + python-yadict-compare)) (home-page "https://github.com/hsolbrig/pyjsg") (synopsis "Python JSON Schema Grammar bindings") (description @@ -1245,30 +1229,37 @@ handles recursion and lists.") (description "This package provides a SPARQL Slurper for rdflib.") (license license:asl2.0))) -(define-public python38-ruaml.yaml-0.15.76 ;; no longer in use +(define-public python-sparqlslurper (package - (inherit python-ruamel.yaml) - (name "python-ruamel.yaml") - (version "0.15.76") - (source - (origin - (method url-fetch) - (uri (pypi-uri "ruamel.yaml" "0.15.78")) - (sha256 - (base32 - "0pwxgrma6k47kvsphqz5yrhwnfrhwsrhn6sjp8p21s91wdgkqyc5")))) + (name "python-sparqlslurper") + (version "0.5.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "sparqlslurper" version)) + (sha256 + (base32 "0ipma74dr5jvsxwaa9al147mn9vv3v5r9lb9hajm4qgwcjqfp0lj")))) + (build-system python-build-system) (arguments - `(#:tests? #f ; suprise test failures + '(#:tests? #f ; Tests try to use the internet. #:phases (modify-phases %standard-phases - ;; For some unknown reason we need: ruamel.yaml<=0.15.77,>=0.15.54 - ;; But 0.15.78 is the first which builds with python-3.8. - (add-after 'unpack 'patch-source - (lambda _ - (substitute* "__init__.py" - (("0\\.15\\.78") "0.15.76") - (("15, 78") "15, 76")) - #t))))))) + (replace 'check + (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + (invoke "python" "-m" "unittest"))))))) + (propagated-inputs + (list python-rdflib-shim + python-sparqlwrapper)) + (native-inputs + (list python-pbr python-unittest2)) + (home-page "http://github.com/hsolbrig/sparqlslurper") + (synopsis "SPARQL Slurper for rdflib") + (description "This package provides an implementation of a +@code{rdflibGraph} that acts as a cache for a SPARQL endpoint. SPARQL Slurper +translates the @code{Graph.triples()} function into the corresponding SPARQL +query and resolves it against an endpoint.") + (license license:cc0))) (define-public python2-ruamel.ordereddict (package @@ -1299,6 +1290,22 @@ handles recursion and lists.") sorted order.") (license license:expat))) +(define-public python-pytest-5 + (package + (inherit python-pytest) + (name "python-pytest") + (version "5.4.3") + (source (origin + (method url-fetch) + (uri (pypi-uri "pytest" version)) + (sha256 + (base32 + "1n67lk8iwlsmfdm8663k8l7isllg1xd3n9p1yla7885szhdk6ybr")))) + (build-system python-build-system) + (native-inputs + (modify-inputs (package-native-inputs python-pytest) + (prepend python-argcomplete python-requests))))) + (define-public python-pytest-4 (package (inherit python-pytest) @@ -1315,9 +1322,33 @@ sorted order.") ((#:tests? _ #f) #f))) (native-inputs `(("python-argcomplete" ,python-argcomplete) + ("python-atomicwrites" ,python-atomicwrites) ("python-requests" ,python-requests) ,@(package-native-inputs python-pytest))))) +(define-public python-pytest-runner-4 + (package + (inherit python-pytest-runner) + (name "python-pytest-runner") + (version "4.5.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "pytest-runner" version)) + (sha256 + (base32 + "1vzilbayx5mznsdm1r258m3616374p6kvhsbj4j6238j9djkvjyi")))))) + +(define-public python-pytest-runner-2 + (package + (inherit python-pytest-runner) + (version "2.12.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "pytest-runner" version)) + (sha256 + (base32 + "11ivjj9hfphkv4yfb2g74av4yy86y8gcbf7gbif0p1hcdfnxg3w6")))))) + (define-public python-pandas-plink (package (name "python-pandas-plink") @@ -1784,3 +1815,66 @@ file format spec.") (license:fsf-free (string-append "https://web.archive.org/web/20190211105114/" "http://www.repoze.org/LICENSE.txt"))))) +(define-public python-rdflib-shim + (package + (name "python-rdflib-shim") + (version "1.0.3") + (source (origin + (method url-fetch) + (uri (pypi-uri "rdflib_shim" version)) + (sha256 + (base32 + "03gwsjcinbyyqrhs2jfhs6mr7j69dfn5djihd0mv9al654gd2mfr")) + (modules '((guix build utils))) + (snippet + '(begin + (substitute* "requirements.txt" + (("rdflib-jsonld==0.6.1") "rdflib-jsonld")))))) + (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + (invoke "python" "-m" "unittest" "discover" "-s" "tests"))))))) + (propagated-inputs + (list python-rdflib python-rdflib-jsonld)) + (native-inputs + (list python-pbr)) + (home-page "http://hsolbrig.github.io/rdflib-shim") + (synopsis "Shim for rdflib 5 and 6 incompatibilities") + (description "Shim for rdflib 5 and 6 incompatibilities") + (license license:cc0))) + +(define-public python-h5py-2 + (package + (name "python-h5py") + (version "2.10.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "h5py" version)) + (sha256 + (base32 + "0baipzv8n93m0dq0riyi8rfhzrjrfrfh8zqhszzp1j2xjac2fhc4")))) + (build-system python-build-system) + (arguments + `(#:tests? #f ;no test target + #:phases (modify-phases %standard-phases + (add-after 'unpack 'fix-hdf5-paths + (lambda* (#:key inputs #:allow-other-keys) + (setenv "HDF5_DIR" + (assoc-ref inputs "hdf5"))))))) + (propagated-inputs (list python-six python-numpy)) + (inputs (list hdf5-1.10)) + (native-inputs (list python-cython python-pkgconfig pkg-config)) + (home-page "https://www.h5py.org/") + (synopsis "Read and write HDF5 files from Python") + (description + "The h5py package provides both a high- and low-level interface to the +HDF5 library from Python. The low-level interface is intended to be a +complete wrapping of the HDF5 API, while the high-level component supports +access to HDF5 files, datasets and groups using established Python and NumPy +concepts.") + (license license:bsd-3))) |