diff options
| -rw-r--r-- | gn/packages/cwl.scm | 66 | ||||
| -rw-r--r-- | gn/packages/python.scm | 10 |
2 files changed, 55 insertions, 21 deletions
diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm index 3e0576c..9871ed9 100644 --- a/gn/packages/cwl.scm +++ b/gn/packages/cwl.scm @@ -2,29 +2,61 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (gn packages python) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix packages) #:use-module (guix build-system python) #:use-module (gnu packages) #:use-module (gnu packages check) + #:use-module (gnu packages graphviz) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) #: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 (gnu packages xml)) -(define-public cwltool +(define-public python-pydot ;; can be updated in GNU Guix - this is a copy (package - (name "cwltool") - (version "3.0.20200710214758") + (name "python-pydot") + (version "1.4.1") (source - (origin - (method url-fetch) - (uri (pypi-uri "cwltool" version)) - (sha256 - (base32 - "1qbqkhinkhzg98jf24d5gnafsw23kng76rbi2hfvzl18bdsp1zz5")))) + (origin + (method url-fetch) + (uri (pypi-uri "pydot" version)) + (sha256 + (base32 + "00az4cbf8bv447lkk9xi6pjm7gcc7ia33y4pm71fwfwis56rv76l")))) + (build-system python-build-system) + (native-inputs + ;; For tests. + `(("python-chardet" ,python-chardet))) + (propagated-inputs + `(("python-pyparsing" ,python-pyparsing))) + (home-page "https://github.com/erocarrera/pydot") + (synopsis "Python interface to Graphviz's DOT language") + (description + "Pydot provides an interface to create, handle, modify and process +graphs in Graphviz's DOT language, written in pure Python.") + (license license:expat))) + + +(define-public cwltool + (let ((commit "78fe9d41ee5a44f8725dfbd7028e4a5ee42949cf") + (revision "1")) + (package + (name "cwltool") + (version "3.0.20201117141248") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/common-workflow-language/cwltool.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1awf99n7aglxc5zszrlrv6jxp355jp45ws7wpsgjlgcdv7advn0w")))) (build-system python-build-system) (arguments `(#:phases @@ -38,9 +70,7 @@ (lambda _ ;; Tries to connect to the internet. (delete-file "tests/test_udocker.py") - (substitute* "tests/test_http_input.py" - (("https://raw.githubusercontent.com/common-workflow-language/cwltool/main") - ".")) + (delete-file "tests/test_http_input.py") (substitute* "tests/test_load_tool.py" (("def test_load_graph_fragment_from_packed") "@pytest.mark.skip(reason=\"Disabled by Guix\")\ndef test_load_graph_fragment_from_packed")) @@ -53,10 +83,13 @@ "@pytest.mark.skip(reason=\"Disabled by Guix\")\ndef test_v1_0_arg_empty_prefix_separate_false")) #t))))) (propagated-inputs - `(("python-bagit" ,python-bagit) + `(("git" ,git) + ("python-argcomplete" ,python-argcomplete) + ("python-bagit" ,python-bagit) ("python-coloredlogs" ,python-coloredlogs) ("python-mypy-extensions" ,python-mypy-extensions) ("python-prov" ,python-prov) + ("python-pydot" ,python-pydot) ("python-psutil" ,python-psutil) ("python-rdflib" ,python-rdflib) ("python-requests" ,python-requests) @@ -85,7 +118,7 @@ (synopsis "Common workflow language reference implementation") (description "Common workflow language reference implementation.") - (license license:asl2.0))) + (license license:asl2.0)))) (define-public cwl-runner (package @@ -105,5 +138,6 @@ "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))) + "Common workflow language alternate entry point to allow cwl-runner +script as an implementation-agnostic script interpreter.") + (license license:asl2.0))) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 00194e1..a9c2770 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -1100,14 +1100,14 @@ server.") (define-public python-schema-salad (package (name "python-schema-salad") - (version "7.0.20200612160654") + (version "7.0.20200811075006") (source (origin (method url-fetch) (uri (pypi-uri "schema-salad" version)) (sha256 (base32 - "15ma3lb6fkfc6sj75hnmmg0jj8q3pc5yrlyx15lpdd4dcp2jc39s")))) + "0wanbwmqb189x1m0vacnhpivfsr8rwbqknngivzxxs8j46yj80bg")))) (build-system python-build-system) (propagated-inputs `(("python-cachecontrol" ,python-cachecontrol-0.11) @@ -1116,8 +1116,8 @@ server.") ("python-rdflib" ,python-rdflib) ("python-rdflib-jsonld" ,python-rdflib-jsonld) ("python-requests" ,python-requests) - ;; This needs to be fixed before upstreaming - ("python-ruamel.yaml" ,python38-ruaml.yaml-0.15.76) + ;; This needs to be fixed before upstreaming - fixed? + ("python-ruamel.yaml" ,python-ruamel.yaml) ("python-setuptools" ,python-setuptools) ("python-typing-extensions" ,python-typing-extensions))) (native-inputs @@ -1528,7 +1528,7 @@ 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 +(define-public python38-ruaml.yaml-0.15.76 ;; no longer in use (package (inherit python-ruamel.yaml) (name "python-ruamel.yaml") |