diff options
| -rw-r--r-- | gn/packages/cwl.scm | 26 | ||||
| -rw-r--r-- | gn/packages/python.scm | 197 |
2 files changed, 155 insertions, 68 deletions
diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm index 4f04f41..6980bb8 100644 --- a/gn/packages/cwl.scm +++ b/gn/packages/cwl.scm @@ -3,6 +3,7 @@ (define-module (gn packages cwl) #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) + #:use-module (gnu packages check) #:use-module (gnu packages python) #:use-module (gnu packages python-web) #:use-module (gnu packages rdf) @@ -19,7 +20,7 @@ (define-public python-cwltool ; guix: needs work (package (name "python-cwltool") - (version "1.0.20150916041152") + (version "1.0.20181012180214") (source (origin (method url-fetch) @@ -29,17 +30,23 @@ ".tar.gz")) (sha256 (base32 - "1kqxc6nvq4nr8qdv39ycdi6fhzaipgjpmbghsz94ij6jhf5r3dq2")))) + "0pk0jlac2vl6vfihdq07agzz9dasw84yjz5ladcbwnmzzl022cg7")))) (build-system python-build-system) (inputs - `(("python-setuptools" ,python-setuptools) + `(("python-bagit" ,python-bagit) + ("python-setuptools" ,python-setuptools) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-runner" ,python-pytest-runner) + ("python-typing-extensions" ,python-typing-extensions) + ("python-prov" ,python-prov) ("python-pyparsing" ,python-pyparsing) + ("python-subprocess32" ,python-subprocess32) )) (propagated-inputs `(("python-schema-salad" ,python-schema-salad) ("python-html5lib" ,python-html5lib) )) - (arguments `(#:tests? #f)) ;; CWL includes no tests. + ; (arguments `(#:tests? #f)) ;; CWL includes no tests. (home-page "https://github.com/common-workflow-language/common-workflow-language") (synopsis @@ -54,17 +61,14 @@ (define-public python-schema-salad (package (name "python-schema-salad") - (version "1.0.2") + (version "3.0.20181129082112") (source (origin (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/source/s/schema-salad/schema-salad-" - version - ".tar.gz")) + (uri (pypi-uri "schema-salad" version)) (sha256 (base32 - "09axiiirq73s1cs21n8mkdslaca2gxc2mlayyl6yiaq98cfgfh37")))) + "1xg70v82q053vz1sg8sc99alnkrm2kk05w6698vgmngl1767sk97")))) (build-system python-build-system) (arguments `(#:tests? #f)) ;; CWL includes no tests. (inputs @@ -73,7 +77,7 @@ ("python-rdflib-jsonld" ,python-rdflib-jsonld) ("python-mistune" ,python-mistune))) (propagated-inputs - `(("python-rdflib-4.2" ,python-rdflib-4.2) + `(("python-rdflib" ,python-rdflib) ("python-avro" ,python-avro) ("python-pyyaml" ,python-pyyaml) ("python-requests" ,python-requests) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 5ce44d6..fa9696f 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -26,6 +26,7 @@ #:use-module (gnu packages python) #:use-module (gnu packages python-web) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages rdf) #:use-module (gnu packages readline) #:use-module (gnu packages statistics) #:use-module (gnu packages tex) @@ -131,6 +132,92 @@ functions.") (license license:expat)) ) +(define-public python-bagit; guix candidate +(package + (name "python-bagit") + (version "1.7.0") + (source + (origin + (method url-fetch) + (uri "https://files.pythonhosted.org/packages/ee/11/7a7fa81c0d43fb4d449d418eba57fc6c77959754c5c2259a215152810555/bagit-1.7.0.tar.gz") + (sha256 + (base32 + "1m6y04qmig0b5hzb35lnaw3d2yfydb7alyr1579yblvgs3da6j7j")))) + (build-system python-build-system) + (inputs + `(("python-setuptools-scm" ,python-setuptools-scm) + ("python-coverage" ,python-coverage) + ("python-mock" ,python-mock) + )) + (arguments `(#:tests? #f)) ;; No tests. + (home-page "https://pypi.python.org/pypi/bagit") + (synopsis + "Python bagit.") + (description + "Python bagit.") + (license license:gpl2)) +) + +(define-public python-prov ; guix candidate +(package + (name "python-prov") + (version "1.5.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "prov" version)) + (sha256 + (base32 + "1a9h406laclxalmdny37m0yyw7y17n359akclbahimdggq853jd0")))) + (build-system python-build-system) + (home-page "https://github.com/trungdong/prov") + (synopsis + "A library for W3C Provenance Data Model supporting PROV-JSON, PROV-XML and PROV-O (RDF)") + (description + "A library for W3C Provenance Data Model supporting PROV-JSON, PROV-XML and PROV-O (RDF)") + (license license:expat))) + +(define-public python-typing-extensions; guix candidate +(package + (name "python-typing-extensions") + (version "3.6.6") + (source + (origin + (method url-fetch) + (uri "https://files.pythonhosted.org/packages/fc/e6/3d2f306b12f01bde2861d67458d32c673e206d6fcc255537bf452db8f80c/typing_extensions-3.6.6.tar.gz") + (sha256 + (base32 + "07vhddjnd3mhdijyc3s0mwi9jgfjp3rr056nxqiavydbvkrvgrsi")))) + (build-system python-build-system) + (home-page "https://pypi.python.org/pypi/typing_extensions") + (synopsis + "Python typing_extensions.") + (description + "Python typing_extensions.") + (license license:gpl2)) +) + +(define-public python-subprocess32 ; guix candidate +(package + (name "python-subprocess32") + (version "0.2.9") + (source + (origin + (method url-fetch) + (uri "https://files.pythonhosted.org/packages/be/2b/beeba583e9877e64db10b52a96915afc0feabf7144dcbf2a0d0ea68bf73d/subprocess32-3.5.3.tar.gz") + (sha256 + (base32 + "1hr5fan8i719hmlmz73hf8rhq74014w07d8ryg7krvvf6692kj3b")))) + (build-system python-build-system) + (arguments `(#:tests? #f)) ;; No tests. + (home-page "https://pypi.python.org/pypi/subprocess32") + (synopsis + "Python subprocess32.") + (description + "Python subprocess32.") + (license license:gpl2)) +) + (define-public python-inotify ; guix candidate (package (name "python-inotify") @@ -218,22 +305,20 @@ functions.") (define-public python-rdflib-jsonld ; guix ready (package (name "python-rdflib-jsonld") - (version "0.3") + (version "0.4.0") (source (origin (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/source/r/rdflib-jsonld/rdflib-jsonld-" - version - ".tar.gz")) + (uri (pypi-uri "rdflib-jsonld" version)) (sha256 (base32 - "121a876k49xl85jvikyh4hzvm34456ikw66cra5dfyr15br1qjll")))) + "0bdw2pbjmpy1l4p6slsjn54bqy6crk5hk4san84xxirgd9w78iql")))) (build-system python-build-system) (inputs `(("python-setuptools" ,python-setuptools))) (propagated-inputs - `(("python-rdflib-4.2" ,python-rdflib-4.2) + `(("python-rdflib" ,python-rdflib) + ("python-isodate" ,python-isodate) ("python-pyparsing" ,python-pyparsing) ("python-html5lib" ,python-html5lib) ("python-nose" ,python-nose) @@ -250,50 +335,6 @@ functions.") (package-with-python2 python-rdflib-jsonld)) -(define-public python-rdflib-4.2 - (package - (name "python-rdflib-4.2") - (version "4.2.0") - (source - (origin - (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/source/r/rdflib/rdflib-" - version - ".tar.gz")) - (patches - ;; The patch has no effect under Python 3. - (list (search-patch "python2-rdflib-drop-sparqlwrapper.patch"))) - (sha256 - (base32 - "1h3f8yl9frjz8rsykjdjk83qsrcvld3qa7pkzh69s91h97ydl83l")))) - (build-system python-build-system) - (inputs - `(("python-html5lib" ,python-html5lib) - ("python-isodate" ,python-isodate) - ("python-pyparsing" ,python-pyparsing) - ("python-setuptools" ,python-setuptools))) - (arguments `(#:tests? #f)) ;; No tests. - (home-page "https://github.com/RDFLib/rdflib") - (synopsis - "Python RDF library") - (description - "RDFLib is a Python library for working with RDF, a simple yet -powerful language for representing information.") - (license (license:non-copyleft "file://LICENSE" - "See LICENSE in the distribution.")))) - -(define-public python2-rdflib-4.2 - (let ((base (package-with-python2 python-rdflib-4.2))) - (package - (inherit base) - (inputs - (append (package-inputs base) - `(("python-nose" ,python-nose)))) - (arguments - `(#:python ,python-2 - #:tests? #f))))) ; 3 tests fail, also outside Guix - (define-public python-rserve (package (name "python-rserve") @@ -326,20 +367,62 @@ powerful language for representing information.") (define-public python2-rserve (package-with-python2 python-rserve)) +(define-public python-setuptools + (package + (name "python-setuptools") + (version "40.6.2") + (source + (origin + (method url-fetch) + (uri "https://files.pythonhosted.org/packages/37/1b/b25507861991beeade31473868463dad0e58b1978c209de27384ae541b0b/setuptools-40.6.3.zip" + ) + (sha256 + (base32 + "1y085dnk574sxw9aymdng9gijvrsbw86hsv9hqnhv7y4d6nlsirv")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Remove included binaries which are used to build self-extracting + ;; installers for Windows. + ;; TODO: Find some way to build them ourself so we can include them. + (for-each delete-file (find-files "setuptools" "^(cli|gui).*\\.exe$")) + #t)))) + (build-system python-build-system) + ;; FIXME: Tests require pytest, which itself relies on setuptools. + ;; One could bootstrap with an internal untested setuptools. + (arguments + `(#:tests? #f)) + (home-page "https://pypi.python.org/pypi/setuptools") + (synopsis + "Library designed to facilitate packaging Python projects") + (description + "Setuptools is a fully-featured, stable library designed to facilitate +packaging Python projects, where packaging includes: +Python package and module definitions, +distribution package metadata, +test hooks, +project installation, +platform-specific details, +Python 3 support.") + ;; TODO: setuptools now bundles the following libraries: + ;; packaging, pyparsing, six and appdirs. How to unbundle? + (license (list license:psfl ; setuptools itself + license:expat ; six, appdirs, pyparsing + license:asl2.0 ; packaging is dual ASL2/BSD-2 + license:bsd-2)))) + + (define-public python-avro ; guix ready - used by CWL (package (name "python-avro") - (version "1.7.7") + (version "1.8.2") (source (origin (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/source/a/avro/avro-" - version - ".tar.gz")) + (uri (pypi-uri "avro" version)) (sha256 (base32 - "0n21lfclah7bmqnnqfqmpsrimz0s86qkxyn972jynq234n1lyynf")))) + "0nabn1hzj1880qsp7fkg7923c0xdqk4i35s15asmy2xp604f97lg")))) (build-system python-build-system) (inputs `(("python-setuptools" ,python-setuptools))) |