diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2025-03-18 13:39:28 +0100 |
|---|---|---|
| committer | Andreas Enge <andreas@enge.fr> | 2025-04-16 11:46:16 +0200 |
| commit | 1dc317fbbd887f5bc80a433151d2805af844c74e (patch) | |
| tree | e95bd44f0dbd02fc68b8a332fa79cadbda53dd86 /gnu/packages/python-xyz.scm | |
| parent | bcf4ab75111cfa0ea60b0c906ec5270ec18cb838 (diff) | |
gnu: snakemake-7: Update to 7.32.4.
* gnu/packages/python-xyz.scm (snakemake-7): Update to 7.32.4.
[arguments]: Use #:test-flags instead of a custom 'check phase; remove
'tabulate-compatibility phase; add 'pre-check phase.
[propagated-inputs]: Add python-humanfriendly, python-reretry, and
python-throttler; remove python-ratelimiter.
Change-Id: Iea7f17559b19098ca5a589d164355f3918f4bb3e
Diffstat (limited to 'gnu/packages/python-xyz.scm')
| -rw-r--r-- | gnu/packages/python-xyz.scm | 37 |
1 files changed, 17 insertions, 20 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 6bdfd27321..e0851455a2 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15402,7 +15402,7 @@ Python style, together with a fast and comfortable execution environment.") (package (inherit snakemake-6) (name "snakemake") - (version "7.7.0") + (version "7.32.4") (source (origin (method git-fetch) @@ -15411,10 +15411,20 @@ Python style, together with a fast and comfortable execution environment.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1qrqbmx4cbis0wxr6dl2rdjv9v627sbirsz6v5c31vlbqwkvs04q")))) + (base32 "1d5hizai89k1glfqfkvf1ghj0l7wm8il6gl5pfwk2gkza87yka6d")))) (build-system pyproject-build-system) (arguments (list + #:test-flags + ;; This test attempts to change S3 buckets on AWS and fails + ;; because there are no AWS credentials. + '(list "--ignore=tests/test_tibanna.py" + ;; It's a similar story with this test, which requires access to + ;; the Google Storage service. + "--ignore=tests/test_google_lifesciences.py" + "--ignore-glob=tests/test_conda_python_3_7_script/*" + ;; We don't have a slurm installation in the build environment + "--ignore=tests/test_slurm.py") #:phases #~(modify-phases %standard-phases ;; For cluster execution Snakemake will call Python. Since there is @@ -15443,12 +15453,6 @@ Python style, together with a fast and comfortable execution environment.") (string-append "tibanna_args.command = command.replace('" #$output "/bin/snakemake', 'python3 -m snakemake')"))))) - ;; No longer needed with 7.15.2+ - (add-after 'unpack 'tabulate-compatibility - (lambda _ - (substitute* "snakemake/dag.py" - (("\"job\": rule,") - "\"job\": rule.name,")))) (add-after 'unpack 'patch-version (lambda _ (substitute* "setup.py" @@ -15457,17 +15461,8 @@ Python style, together with a fast and comfortable execution environment.") (substitute* '("snakemake/_version.py" "versioneer.py") (("0\\+unknown") #$version)))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (setenv "HOME" "/tmp") - ;; This test attempts to change S3 buckets on AWS and fails - ;; because there are no AWS credentials. - (delete-file "tests/test_tibanna.py") - ;; It's a similar story with this test, which requires access - ;; to the Google Storage service. - (delete-file "tests/test_google_lifesciences.py") - (invoke "pytest"))))))) + (add-before 'check 'pre-check + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list python-appdirs python-configargparse @@ -15476,6 +15471,7 @@ Python style, together with a fast and comfortable execution environment.") python-docutils python-filelock python-gitpython + python-humanfriendly python-jinja2 python-jsonschema python-nbformat @@ -15484,12 +15480,13 @@ Python style, together with a fast and comfortable execution environment.") python-pulp python-pyyaml python-py-tes - python-ratelimiter python-requests python-retry + python-reretry python-smart-open python-stopit python-tabulate + python-throttler python-toposort python-wrapt python-yte)) |