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gnu: cwltool: Update to 3.1.20240112164112.

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* gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20240112164112.
[arguments]: Use G-expressions. Set version in setup.py. Do not attempt to
substitute files cwltool/schemas/v1.1/tests/env-tool1.cwl,
cwltool/schemas/v1.1/tests/env-tool2.cwl and
cwltool/schemas/v1.1/tests/imported-hint.cwl that have been removed in this
release. Do not remove "-n auto" from pytest flags.
[inputs]: Add python-cwl-utils and python-spython.
[native-inputs]: Add python-pytest-xdist.

Change-Id: If1be7cdf39b767c5ef2a1dbddfdc95f59ea98cb6

Change-Id: I2ba81e8569abcf43cd0fad33daab1e4f8689e77f
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
This commit is contained in:
Arun Isaac 2023-10-22 20:22:43 +01:00
parent 8ded262f04
commit 58233e6c21
No known key found for this signature in database
GPG key ID: 2E25EE8B61802BB3
1 changed files with 43 additions and 46 deletions
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89
gnu/packages/bioinformatics.scm
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@ -5228,7 +5228,7 @@ (define-public python-cwl-utils
(define-public cwltool (define-public cwltool
(package (package
(name "cwltool") (name "cwltool")
(version "3.1.20220119140128") (version "3.1.20240112164112")
(source (origin (source (origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
@ -5237,56 +5237,51 @@ (define-public cwltool
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"1jmrm0qrqgka79avc1kq63fgh20gx6g07fc8p3iih4k85vhdyl3f")))) "1fpc5kqgpbn48g5vlvy64p297x2wm3gfz8casgpk15ap593wwh33"))))
(build-system pyproject-build-system) (build-system pyproject-build-system)
(arguments (arguments
`(#:phases (list
(modify-phases %standard-phases #:phases
(add-after 'unpack 'loosen-version-restrictions #~(modify-phases %standard-phases
(lambda _ (add-after 'unpack 'loosen-version-restrictions
(substitute* "setup.py" (lambda _
(("== 1.5.1") ">=1.5.1")))) ; prov (substitute* "setup.py"
(add-after 'unpack 'dont-use-git (("== 1.5.1") "> 1.5.1")))) ; prov
(lambda _ (add-after 'unpack 'set-version
(substitute* "gittaggers.py" (lambda _
(("self.git_timestamp_tag\\(\\)") ;; Set exact version.
(string-append "time.strftime('.%Y%m%d%H%M%S', time.gmtime(int(" (substitute* "setup.py"
(string-drop ,version 4) ")))"))))) (("use_scm_version=True")
(add-after 'unpack 'modify-tests (string-append "version=\"" #$version "\"")))))
(lambda _ (add-after 'unpack 'modify-tests
;; Tries to connect to the internet. (lambda _
(delete-file "tests/test_content_type.py") ;; Tries to connect to the internet.
(delete-file "tests/test_udocker.py") (delete-file "tests/test_content_type.py")
(delete-file "tests/test_http_input.py") (delete-file "tests/test_udocker.py")
(substitute* "tests/test_load_tool.py" (delete-file "tests/test_http_input.py")
(("def test_load_graph_fragment_from_packed") (substitute* "tests/test_load_tool.py"
(string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" (("def test_load_graph_fragment_from_packed")
"def test_load_graph_fragment_from_packed"))) (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
(substitute* "tests/test_examples.py" "def test_load_graph_fragment_from_packed")))
(("def test_env_filtering") (substitute* "tests/test_examples.py"
(string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" (("def test_env_filtering")
"def test_env_filtering"))) (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
;; Tries to use cwl-runners. "def test_env_filtering")))
(substitute* "tests/test_examples.py" ;; Tries to use cwl-runners.
(("def test_v1_0_arg_empty_prefix_separate_false") (substitute* "tests/test_examples.py"
(string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" (("def test_v1_0_arg_empty_prefix_separate_false")
"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" (substitute* '("tests/subgraph/env-tool2.cwl"
"cwltool/schemas/v1.1/tests/env-tool2.cwl" "tests/subgraph/env-tool2_req.cwl"
"cwltool/schemas/v1.1/tests/imported-hint.cwl" "tests/subgraph/env-wf2_subwf-packed.cwl"
"tests/subgraph/env-tool2.cwl" "tests/subgraph/env-tool2_no_env.cwl")
"tests/subgraph/env-tool2_req.cwl" (("\"/bin/sh\"") (string-append "\"" (which "sh") "\""))))))))
"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") "")))))))
(inputs (inputs
(list python-argcomplete (list python-argcomplete
python-bagit python-bagit
python-coloredlogs python-coloredlogs
python-cwl-utils
python-mypy-extensions python-mypy-extensions
python-prov python-prov
python-pydot python-pydot
@ -5296,6 +5291,7 @@ (define-public cwltool
python-ruamel.yaml python-ruamel.yaml
python-schema-salad python-schema-salad
python-shellescape python-shellescape
python-spython
python-typing-extensions python-typing-extensions
;; Not listed as needed but still necessary: ;; Not listed as needed but still necessary:
node)) node))
@ -5306,7 +5302,8 @@ (define-public cwltool
python-pytest python-pytest
python-pytest-cov python-pytest-cov
python-pytest-mock python-pytest-mock
python-pytest-runner)) python-pytest-runner
python-pytest-xdist))
(home-page (home-page
"https://github.com/common-workflow-language/common-workflow-language") "https://github.com/common-workflow-language/common-workflow-language")
(synopsis "Common Workflow Language reference implementation") (synopsis "Common Workflow Language reference implementation")