Package: guix-patches;
Reported by: Arun Isaac <arunisaac <at> systemreboot.net>
Date: Sun, 22 Oct 2023 22:29:02 UTC
Severity: normal
Tags: moreinfo, patch
Done: Arun Isaac <arunisaac <at> systemreboot.net>
Bug is archived. No further changes may be made.
Message #26 received at 66690 <at> debbugs.gnu.org (full text, mbox):
From: Arun Isaac <arunisaac <at> systemreboot.net> To: 66690 <at> debbugs.gnu.org Cc: Arun Isaac <arunisaac <at> systemreboot.net> Subject: [PATCH 7/7] gnu: cwltool: Update to 3.1.20230601100705. Date: Mon, 23 Oct 2023 09:09:46 +0100
* gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20230601100705.
[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.
[inputs]: Add python-cwl-utils.
---
gnu/packages/bioinformatics.scm | 88 ++++++++++++++++-----------------
1 file changed, 43 insertions(+), 45 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2deec5368e..b4ac896a0d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4583,7 +4583,7 @@ (define-public python-cwl-utils
(define-public cwltool
(package
(name "cwltool")
- (version "3.1.20220119140128")
+ (version "3.1.20231020140205")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -4592,56 +4592,54 @@ (define-public cwltool
(file-name (git-file-name name version))
(sha256
(base32
- "1jmrm0qrqgka79avc1kq63fgh20gx6g07fc8p3iih4k85vhdyl3f"))))
+ "045n594k7zhm5qnf7mippldmm43wj3x0wnizhhpd1n2ak2iiky88"))))
(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") "\"")))
+ ;; Pytest doesn't know what to do with "-n auto"
+ (substitute* "tox.ini"
+ (("-n auto") "")))))))
(inputs
(list python-argcomplete
python-bagit
python-coloredlogs
+ python-cwl-utils
python-mypy-extensions
python-prov
python-pydot
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