guix_mirror_bot pushed a commit to branch master
in repository guix.
commit 317dbfb54124c6fa26a181431e05af6964ad20bc
Author: Hugo Buddelmeijer <[email protected]>
AuthorDate: Mon Oct 6 18:18:13 2025 +0200
gnu: cwltool: Update to 3.1.20250925164626.
* gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20250925164626.
[arguments] <#:test-flags>: Update tests to skip.
<#:phases>: Use SETUPTOOLS_SCM_PRETEND_VERSION. Allow tests to multithread.
[inputs]: Remove python-shellescape and python-typing-extensions; add
python-rich-argparse.
[native-inputs]: Remove python-humanfriendly, python-pytest-cov,
python-pytest-runner and python-wheel; add python-pytest-xdist.
Change-Id: I6a224606887346e160b11916ef7b25cb2120bf1d
Signed-off-by: Sharlatan Hellseher <[email protected]>
---
gnu/packages/bioinformatics.scm | 42 +++++++++++++++++++----------------------
1 file changed, 19 insertions(+), 23 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b62f250b8c..862eb31364 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7116,7 +7116,7 @@ documents.")
(define-public cwltool
(package
(name "cwltool")
- (version "3.1.20240112164112")
+ (version "3.1.20250925164626")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -7125,21 +7125,25 @@ documents.")
(file-name (git-file-name name version))
(sha256
(base32
- "1fpc5kqgpbn48g5vlvy64p297x2wm3gfz8casgpk15ap593wwh33"))))
+ "13mv7qcl64gng8bq0y9garp0vvn9851n98vzi75ppl16pjkkziks"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
;; These tests try to connect to the internet.
- '(list "--ignore=tests/test_content_type.py"
- "--ignore=tests/test_udocker.py"
- "--ignore=tests/test_http_input.py"
- "-k"
- (string-append
- "not test_env_filtering"
- " and not test_load_graph_fragment_from_packed"
- ;; Tries to use cwl-runners.
- " and not test_v1_0_arg_empty_prefix_separate_false"))
+ #~(list "--ignore=tests/test_content_type.py"
+ "--ignore=tests/test_udocker.py"
+ "--ignore=tests/test_http_input.py"
+ "-k"
+ (string-append
+ ;; Causes
+ ;; INTERNALERROR> RuntimeError: Unexpectedly no active
+ ;; workers available
+ "not test_env_filtering"
+ ;; Tries to write to /tmp/guix-build-cwltool-3.fastq
+ " and not test_iwdr_writable_secondaryfiles"
+ ;; Tries to use cwl-runners.
+ " and not test_v1_0_arg_empty_prefix_separate_false"))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'loosen-version-restrictions
@@ -7149,13 +7153,9 @@ documents.")
(add-after 'unpack 'set-version
(lambda _
;; Set exact version.
- (substitute* "setup.py"
- (("use_scm_version=True")
- (string-append "version=\"" #$version "\"")))))
+ (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)))
(add-after 'unpack 'patch-tests
(lambda _
- (substitute* "tox.ini"
- (("-n auto") ""))
(substitute* '("tests/subgraph/env-tool2.cwl"
"tests/subgraph/env-tool2_req.cwl"
"tests/subgraph/env-wf2_subwf-packed.cwl"
@@ -7172,23 +7172,19 @@ documents.")
python-psutil
python-rdflib-6
python-requests
+ python-rich-argparse
python-ruamel.yaml
python-schema-salad
- python-setuptools ; For pkg_resources.
- python-shellescape
+ python-setuptools
python-spython
- python-typing-extensions
;; Not listed as needed but still necessary:
node-lts))
(native-inputs
(list python-arcp
- python-humanfriendly
python-mock
python-pytest
- python-pytest-cov
python-pytest-mock
- python-pytest-runner
- python-wheel))
+ python-pytest-xdist))
(home-page
"https://github.com/common-workflow-language/common-workflow-language";)
(synopsis "Common Workflow Language reference implementation")
