diff options
Diffstat (limited to 'gn/packages/cwl.scm')
| -rw-r--r-- | gn/packages/cwl.scm | 150 |
1 files changed, 84 insertions, 66 deletions
diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm index be531f6..3e0576c 100644 --- a/gn/packages/cwl.scm +++ b/gn/packages/cwl.scm @@ -1,91 +1,109 @@ -;; Experimental packaging for the Common Workflow Language (started by Bruno) - (define-module (gn packages cwl) #:use-module ((guix licenses) #:prefix license:) + #:use-module (gn packages python) + #:use-module (guix download) + #:use-module (guix packages) + #:use-module (guix build-system python) #:use-module (gnu packages) #:use-module (gnu packages check) - #:use-module (gnu packages databases) - #:use-module (gnu packages python) #: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) - #:use-module (gn packages python) - #:use-module (guix download) - #:use-module (guix packages) - #:use-module (guix git-download) - #:use-module (guix utils) - ; #:use-module (guix build-system gnu) - #:use-module (guix build-system python) - ; #:use-module (guix build-system trivial) - #:use-module (srfi srfi-1)) + #:use-module (gnu packages xml)) -(define-public cwltool ; guix: needs work - (let ((commit "15539fba76993f951af9eba913bea6d677c74005")) +(define-public cwltool (package (name "cwltool") - (version "1.0.20181012180214") + (version "3.0.20200710214758") (source (origin - ; (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") ;; my repo for Python 3.7 - (commit commit))) - (file-name (git-file-name name (string-append version "-" (string-take commit 7)))) + (method url-fetch) + (uri (pypi-uri "cwltool" version)) (sha256 - (base32 - "1qwfa82car7477sy0cb5bj4964w7zq7dcw2bdcls6c2i9qdp0586")))) + (base32 + "1qbqkhinkhzg98jf24d5gnafsw23kng76rbi2hfvzl18bdsp1zz5")))) (build-system python-build-system) - (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) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'loosen-version-restrictions + (lambda _ + (substitute* "setup.py" + (("== 1.5.1") ">=1.5.1")) + #t)) + (add-after 'unpack 'modify-tests + (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") + ".")) + (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")) + (substitute* "tests/test_examples.py" + (("def test_env_filtering") + "@pytest.mark.skip(reason=\"Disabled by Guix\")\ndef test_env_filtering")) + ;; Tries to use cwl-runners. + (substitute* "tests/test_examples.py" + (("def test_v1_0_arg_empty_prefix_separate_false") + "@pytest.mark.skip(reason=\"Disabled by Guix\")\ndef test_v1_0_arg_empty_prefix_separate_false")) + #t))))) + (propagated-inputs + `(("python-bagit" ,python-bagit) + ("python-coloredlogs" ,python-coloredlogs) + ("python-mypy-extensions" ,python-mypy-extensions) ("python-prov" ,python-prov) - ("python-pytest-runner" ,python-pytest-runner) + ("python-psutil" ,python-psutil) ("python-rdflib" ,python-rdflib) - ("python-pyparsing" ,python-pyparsing) - ("python-pytest-mock" ,python-pytest-mock) - ("python-mock" ,python-mock) - ("python-subprocess32" ,python-subprocess32) + ("python-requests" ,python-requests) ("python-ruamel.yaml" ,python-ruamel.yaml) + ("python-schema-salad" ,python-schema-salad) + ("python-setuptools" ,python-setuptools) + ("python-shellescape" ,python-shellescape) + ("python-typing-extensions" ,python-typing-extensions) + ;; Not listed as needed but seems to be necessary: + ("node" ,node) ("python-cachecontrol" ,python-cachecontrol-0.11) + ("python-dateutil" ,python-dateutil) ("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-scandir" ,python-scandir) - ("python-psutil" ,python-psutil) - )) - ; (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 + ("python-networkx" ,python-networkx))) + (native-inputs + `(("python-arcp" ,python-arcp) + ("python-humanfriendly" ,python-humanfriendly) + ("python-mock" ,python-mock) + ("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-mock" ,python-pytest-mock) + ("python-pytest-runner" ,python-pytest-runner) + ("python-rdflib-jsonld" ,python-rdflib-jsonld))) + (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 cwl-runner + (package + (name "cwl-runner") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "cwl_runner" version)) + (sha256 + (base32 + "0011am2xqwchysdznayrmwhg4bfjl4wlq6m4k20z1m7gccyzjgw0")))) + (build-system python-build-system) + (propagated-inputs + `(("cwltool" ,cwltool))) (home-page - "https://github.com/common-workflow-language/common-workflow-language") - (synopsis - "Common workflow language reference implementation") + "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 reference implementation.") + (license license:asl2.0))) |