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