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gnu: snakemake-7: Update to 7.32.4.

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* 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
This commit is contained in:
Ricardo Wurmus 2025-03-18 13:39:28 +01:00 • committed by Andreas Enge
parent bcf4ab7511
commit 1dc317fbbd
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1 changed files with 17 additions and 20 deletions
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37
gnu/packages/python-xyz.scm
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@ -15402,7 +15402,7 @@ Python style, together with a fast and comfortable execution environment.")
(package (package
(inherit snakemake-6) (inherit snakemake-6)
(name "snakemake") (name "snakemake")
(version "7.7.0") (version "7.32.4")
(source (source
(origin (origin
(method git-fetch) (method git-fetch)
@ -15411,10 +15411,20 @@ Python style, together with a fast and comfortable execution environment.")
(commit (string-append "v" version)))) (commit (string-append "v" version))))
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 "1qrqbmx4cbis0wxr6dl2rdjv9v627sbirsz6v5c31vlbqwkvs04q")))) (base32 "1d5hizai89k1glfqfkvf1ghj0l7wm8il6gl5pfwk2gkza87yka6d"))))
(build-system pyproject-build-system) (build-system pyproject-build-system)
(arguments (arguments
(list (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 #:phases
#~(modify-phases %standard-phases #~(modify-phases %standard-phases
;; For cluster execution Snakemake will call Python. Since there is ;; 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 (string-append
"tibanna_args.command = command.replace('" "tibanna_args.command = command.replace('"
#$output "/bin/snakemake', 'python3 -m snakemake')"))))) #$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 (add-after 'unpack 'patch-version
(lambda _ (lambda _
(substitute* "setup.py" (substitute* "setup.py"
@ -15457,17 +15461,8 @@ Python style, together with a fast and comfortable execution environment.")
(substitute* '("snakemake/_version.py" (substitute* '("snakemake/_version.py"
"versioneer.py") "versioneer.py")
(("0\\+unknown") #$version)))) (("0\\+unknown") #$version))))
(replace 'check (add-before 'check 'pre-check
(lambda* (#:key tests? #:allow-other-keys) (lambda _ (setenv "HOME" "/tmp"))))))
(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")))))))
(propagated-inputs (propagated-inputs
(list python-appdirs (list python-appdirs
python-configargparse python-configargparse
@ -15476,6 +15471,7 @@ Python style, together with a fast and comfortable execution environment.")
python-docutils python-docutils
python-filelock python-filelock
python-gitpython python-gitpython
python-humanfriendly
python-jinja2 python-jinja2
python-jsonschema python-jsonschema
python-nbformat python-nbformat
@ -15484,12 +15480,13 @@ Python style, together with a fast and comfortable execution environment.")
python-pulp python-pulp
python-pyyaml python-pyyaml
python-py-tes python-py-tes
python-ratelimiter
python-requests python-requests
python-retry python-retry
python-reretry
python-smart-open python-smart-open
python-stopit python-stopit
python-tabulate python-tabulate
python-throttler
python-toposort python-toposort
python-wrapt python-wrapt
python-yte)) python-yte))