diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 89 |
1 files changed, 43 insertions, 46 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b38b2835fb..3f12b28058 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5228,7 +5228,7 @@ documents.") (define-public cwltool (package (name "cwltool") - (version "3.1.20220119140128") + (version "3.1.20240112164112") (source (origin (method git-fetch) (uri (git-reference @@ -5237,56 +5237,51 @@ documents.") (file-name (git-file-name name version)) (sha256 (base32 - "1jmrm0qrqgka79avc1kq63fgh20gx6g07fc8p3iih4k85vhdyl3f")))) + "1fpc5kqgpbn48g5vlvy64p297x2wm3gfz8casgpk15ap593wwh33")))) (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'loosen-version-restrictions - (lambda _ - (substitute* "setup.py" - (("== 1.5.1") ">=1.5.1")))) ; prov - (add-after 'unpack 'dont-use-git - (lambda _ - (substitute* "gittaggers.py" - (("self.git_timestamp_tag\\(\\)") - (string-append "time.strftime('.%Y%m%d%H%M%S', time.gmtime(int(" - (string-drop ,version 4) ")))"))))) - (add-after 'unpack 'modify-tests - (lambda _ - ;; Tries to connect to the internet. - (delete-file "tests/test_content_type.py") - (delete-file "tests/test_udocker.py") - (delete-file "tests/test_http_input.py") - (substitute* "tests/test_load_tool.py" - (("def test_load_graph_fragment_from_packed") - (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" - "def test_load_graph_fragment_from_packed"))) - (substitute* "tests/test_examples.py" - (("def test_env_filtering") - (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" - "def test_env_filtering"))) - ;; Tries to use cwl-runners. - (substitute* "tests/test_examples.py" - (("def test_v1_0_arg_empty_prefix_separate_false") - (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" - "def test_v1_0_arg_empty_prefix_separate_false"))) - - (substitute* '("cwltool/schemas/v1.1/tests/env-tool1.cwl" - "cwltool/schemas/v1.1/tests/env-tool2.cwl" - "cwltool/schemas/v1.1/tests/imported-hint.cwl" - "tests/subgraph/env-tool2.cwl" - "tests/subgraph/env-tool2_req.cwl" - "tests/subgraph/env-wf2_subwf-packed.cwl" - "tests/subgraph/env-tool2_no_env.cwl") - (("\"/bin/sh\"") (string-append "\"" (which "sh") "\""))) - ;; Pytest doesn't know what to do with "-n auto" - (substitute* "tox.ini" - (("-n auto") ""))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'loosen-version-restrictions + (lambda _ + (substitute* "setup.py" + (("== 1.5.1") "> 1.5.1")))) ; prov + (add-after 'unpack 'set-version + (lambda _ + ;; Set exact version. + (substitute* "setup.py" + (("use_scm_version=True") + (string-append "version=\"" #$version "\""))))) + (add-after 'unpack 'modify-tests + (lambda _ + ;; Tries to connect to the internet. + (delete-file "tests/test_content_type.py") + (delete-file "tests/test_udocker.py") + (delete-file "tests/test_http_input.py") + (substitute* "tests/test_load_tool.py" + (("def test_load_graph_fragment_from_packed") + (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" + "def test_load_graph_fragment_from_packed"))) + (substitute* "tests/test_examples.py" + (("def test_env_filtering") + (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" + "def test_env_filtering"))) + ;; Tries to use cwl-runners. + (substitute* "tests/test_examples.py" + (("def test_v1_0_arg_empty_prefix_separate_false") + (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" + "def test_v1_0_arg_empty_prefix_separate_false"))) + (substitute* '("tests/subgraph/env-tool2.cwl" + "tests/subgraph/env-tool2_req.cwl" + "tests/subgraph/env-wf2_subwf-packed.cwl" + "tests/subgraph/env-tool2_no_env.cwl") + (("\"/bin/sh\"") (string-append "\"" (which "sh") "\"")))))))) (inputs (list python-argcomplete python-bagit python-coloredlogs + python-cwl-utils python-mypy-extensions python-prov python-pydot @@ -5296,6 +5291,7 @@ documents.") python-ruamel.yaml python-schema-salad python-shellescape + python-spython python-typing-extensions ;; Not listed as needed but still necessary: node)) @@ -5306,7 +5302,8 @@ documents.") python-pytest python-pytest-cov python-pytest-mock - python-pytest-runner)) + python-pytest-runner + python-pytest-xdist)) (home-page "https://github.com/common-workflow-language/common-workflow-language") (synopsis "Common Workflow Language reference implementation") |