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gnu: cutadapt: Update to 4.0.

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* gnu/packages/bioinformatics.scm (cutadapt): Update to 4.0.
[build-system]: Use pyproject-build-system.
[arguments]: Disable a single test; remove 'always-cythonize build phase; add
phase 'fix-test.
[native-inputs]: Add python-pytest-mock and python-pytest-timeout.
This commit is contained in:
Ricardo Wurmus 2023-07-03 16:37:45 +02:00
parent cb15c60d35
commit c66e5ef5f9
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GPG key ID: 197A5888235FACAC
1 changed files with 25 additions and 13 deletions
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gnu/packages/bioinformatics.scm
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@ -3945,28 +3945,40 @@ (define-public python-deeptools
(define-public cutadapt (define-public cutadapt
(package (package
(name "cutadapt") (name "cutadapt")
(version "2.1") (version "4.0")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (pypi-uri "cutadapt" version)) (uri (pypi-uri "cutadapt" version))
(sha256 (sha256
(base32 (base32
"1vqmsfkm6llxzmsz9wcfcvzx9a9f8iabvwik2rbyn7nc4wm25z89")))) "0xgsv88mrlw2b1radmd1104y7bg8hvv54ay7xfdpnjiw2jgkrha9"))))
(build-system python-build-system) (build-system pyproject-build-system)
(arguments (arguments
`(#:phases (list
(modify-phases %standard-phases #:test-flags
(add-after 'unpack 'always-cythonize '(list "-k" "not test_no_read_only_comment_fasta_input")
(lambda _ #:phases
(delete-file "src/cutadapt/_align.c") #~(modify-phases %standard-phases
;; If PKG-INFO exists, setup.py decides not to run Cython. (add-after 'unpack 'fix-test
(substitute* "setup.py" (lambda _
(("os.path.exists\\('PKG-INFO'\\):") (let ((site (string-append
"os.path.exists('totally-does-not-exist'):"))))))) #$output "/lib/python"
#$(version-major+minor
(package-version python))
"/site-packages")))
(substitute* "tests/test_command.py"
(("env=\\{\"LC_CTYPE\": \"C\"\\},")
(string-append "env={\"LC_CTYPE\": \"C\", \"GUIX_PYTHONPATH\": \""
(getenv "GUIX_PYTHONPATH") ":" site
"\"},")))))))))
(inputs (inputs
(list python-dnaio python-xopen)) (list python-dnaio python-xopen))
(native-inputs (native-inputs
(list python-cython python-pytest python-setuptools-scm)) (list python-cython
python-pytest
python-pytest-mock
python-pytest-timeout
python-setuptools-scm))
(home-page "https://cutadapt.readthedocs.io/en/stable/") (home-page "https://cutadapt.readthedocs.io/en/stable/")
(synopsis "Remove adapter sequences from nucleotide sequencing reads") (synopsis "Remove adapter sequences from nucleotide sequencing reads")
(description (description