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gnu: snakemake-7: Fix version reporting.

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* gnu/packages/python-xyz.scm (snakemake-7)[arguments]: Add phase
'patch-version and use G-exp.
[build-system]: Use pyproject-build-system.
This commit is contained in:
Ricardo Wurmus 2023-08-01 08:18:36 +02:00
parent 896b40d2ca
commit f872482043
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GPG key ID: 197A5888235FACAC
1 changed files with 34 additions and 25 deletions
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59
gnu/packages/python-xyz.scm
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@ -11519,32 +11519,41 @@ (define-public snakemake-7
(file-name (git-file-name name version))
(sha256
(base32 "1qrqbmx4cbis0wxr6dl2rdjv9v627sbirsz6v5c31vlbqwkvs04q"))))
(build-system python-build-system)
(build-system pyproject-build-system)
(arguments
'(#:phases
(modify-phases %standard-phases
;; For cluster execution Snakemake will call Python. Since there is
;; no suitable GUIX_PYTHONPATH set, cluster execution will fail. We
;; fix this by calling the snakemake wrapper instead.
(add-after 'unpack 'call-wrapper-not-wrapped-snakemake
(lambda* (#:key outputs #:allow-other-keys)
(substitute* "snakemake/executors/__init__.py"
(("self\\.get_python_executable\\(\\),")
"")
(("\"-m snakemake\"")
(string-append "\"" (assoc-ref outputs "out")
"/bin/snakemake" "\"")))))
(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")))))))
(list
#:phases
#~(modify-phases %standard-phases
;; For cluster execution Snakemake will call Python. Since there is
;; no suitable GUIX_PYTHONPATH set, cluster execution will fail. We
;; fix this by calling the snakemake wrapper instead.
(add-after 'unpack 'call-wrapper-not-wrapped-snakemake
(lambda* (#:key outputs #:allow-other-keys)
(substitute* "snakemake/executors/__init__.py"
(("self\\.get_python_executable\\(\\),")
"")
(("\"-m snakemake\"")
(string-append "\"" #$output
"/bin/snakemake" "\"")))))
(add-after 'unpack 'patch-version
(lambda _
(substitute* "setup.py"
(("version=versioneer.get_version\\(\\)")
(format #f "version=~s" #$version)))
(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")))))))
(propagated-inputs
(list python-appdirs
python-configargparse