bartronx7/guix
1
0
Fork 0
mirror of https://codeberg.org/guix/guix.git synced 2026-01-29 04:01:28 -06:00
Code Issues Projects Releases Packages Wiki Activity Actions

gnu: cwltool: Update to 3.1.20250925164626.

Browse source 
* 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 <sharlatanus@gmail.com>
This commit is contained in:
Hugo Buddelmeijer 2025-10-06 18:18:13 +02:00 • committed by Sharlatan Hellseher
parent 060cfe93e9
commit 317dbfb541
No known key found for this signature in database
GPG key ID: 76D727BFF62CD2B5
1 changed files with 19 additions and 23 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

42
gnu/packages/bioinformatics.scm
View file

@ -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")