@@ -5235,7 +5235,7 @@ (define-public python-cwl-utils
(define-public cwltool
(package
(name "cwltool")
- (version "3.1.20220119140128")
+ (version "3.1.20240112164112")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -5244,56 +5244,51 @@ (define-public cwltool
(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
@@ -5303,6 +5298,7 @@ (define-public cwltool
python-ruamel.yaml
python-schema-salad
python-shellescape
+ python-spython
python-typing-extensions
;; Not listed as needed but still necessary:
node))
@@ -5313,7 +5309,8 @@ (define-public cwltool
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")