diff options
Diffstat (limited to 'gn/packages/cwl.scm')
| -rw-r--r-- | gn/packages/cwl.scm | 90 |
1 files changed, 62 insertions, 28 deletions
diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm index 4f04f41..5a01dbf 100644 --- a/gn/packages/cwl.scm +++ b/gn/packages/cwl.scm @@ -3,9 +3,14 @@ (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 node) #:use-module (gnu packages rdf) + #:use-module (gnu packages serialization) + #:use-module (gnu packages time) + #:use-module (gnu packages version-control) #:use-module (gn packages python) #:use-module (guix download) #:use-module (guix packages) @@ -16,55 +21,84 @@ ; #:use-module (guix build-system trivial) #:use-module (srfi srfi-1)) -(define-public python-cwltool ; guix: needs work +(define-public cwltool ; guix: needs work + (let ((commit "e12d36b6efbc5d4a6ff7b4fbfd7387bff8f72727")) (package - (name "python-cwltool") - (version "1.0.20150916041152") + (name "cwltool") + (version "1.0.20181012180214") (source (origin - (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/source/c/cwltool/cwltool-" - version - ".tar.gz")) + ; (method url-fetch) + ; (uri (string-append + ; "https://pypi.python.org/packages/source/c/cwltool/cwltool-" + ; version + ; ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/genenetwork/cwltool.git") + (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 - "1kqxc6nvq4nr8qdv39ycdi6fhzaipgjpmbghsz94ij6jhf5r3dq2")))) + "1zhba1hfizrw3bxfmhpjds92pj79hyyv5k7sglw24z52kg1in67p")))) (build-system python-build-system) - (inputs - `(("python-setuptools" ,python-setuptools) + (propagated-inputs ; a lot of these are used for testing + `(("git" ,git) + ("node" ,node) + ("python-bagit" ,python-bagit) + ("python-arcp" ,python-arcp) + ("python-setuptools" ,python-setuptools) + ("python-dateutil" ,python-dateutil) + ("python-pytest-cov" ,python-pytest-cov) + ("python-prov" ,python-prov) + ("python-pytest-runner" ,python-pytest-runner) + ("python-rdflib" ,python-rdflib) ("python-pyparsing" ,python-pyparsing) - )) - (propagated-inputs - `(("python-schema-salad" ,python-schema-salad) + ("python-pytest-mock" ,python-pytest-mock) + ("python-mock" ,python-mock) + ("python-subprocess32" ,python-subprocess32) + ("python-ruamel.yaml" ,python-ruamel.yaml) + ("python-cachecontrol" ,python-cachecontrol) + ("python-lxml" ,python-lxml) + ("python-mypy-extensions" ,python-mypy-extensions) + ("python-mistune" ,python-mistune) + ("python-networkx" ,python-networkx) + ("python-schema-salad" ,python-schema-salad) ("python-html5lib" ,python-html5lib) + ("python-rdflib-jsonld" ,python-rdflib-jsonld) + ("python-typing-extensions" ,python-typing-extensions) + ("python-scandir" ,python-scandir) + ("python-psutil" ,python-psutil) )) - (arguments `(#:tests? #f)) ;; CWL includes no tests. + ; (arguments `(#:tests? #f)) ;; CWL includes no tests. + (arguments + `(;#:phases + ; (modify-phases %standard-phases + ; (replace 'check + ; (lambda* (#:key inputs outputs #:allow-other-keys) + ; (invoke "python" "-m" "pytest") + ; ))) + #:tests? #f)) ; Disable for now + (home-page "https://github.com/common-workflow-language/common-workflow-language") (synopsis "Common workflow language reference implementation") (description "Common workflow language reference implementation") - (license license:asl2.0))) - -(define-public python2-cwltool - (package-with-python2 python-cwltool)) + (license license:asl2.0)))) (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 +107,7 @@ ("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) @@ -87,5 +121,5 @@ "Schema Annotations for Linked Avro Data (SALAD)") (license license:asl2.0))) -(define-public python2-schema-salad - (package-with-python2 python-schema-salad)) +; (define-public python2-schema-salad +; (package-with-python2 python-schema-salad)) |