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gnu: cutadapt: Update to 4.0.
* 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.
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@ -3945,28 +3945,40 @@ (define-public python-deeptools
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(define-public cutadapt
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(package
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(name "cutadapt")
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(version "2.1")
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(version "4.0")
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(source (origin
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(method url-fetch)
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(uri (pypi-uri "cutadapt" version))
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(sha256
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(base32
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"1vqmsfkm6llxzmsz9wcfcvzx9a9f8iabvwik2rbyn7nc4wm25z89"))))
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(build-system python-build-system)
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"0xgsv88mrlw2b1radmd1104y7bg8hvv54ay7xfdpnjiw2jgkrha9"))))
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(build-system pyproject-build-system)
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'always-cythonize
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(lambda _
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(delete-file "src/cutadapt/_align.c")
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;; If PKG-INFO exists, setup.py decides not to run Cython.
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(substitute* "setup.py"
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(("os.path.exists\\('PKG-INFO'\\):")
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"os.path.exists('totally-does-not-exist'):")))))))
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(list
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#:test-flags
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'(list "-k" "not test_no_read_only_comment_fasta_input")
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'fix-test
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(lambda _
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(let ((site (string-append
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#$output "/lib/python"
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#$(version-major+minor
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(package-version python))
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"/site-packages")))
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(substitute* "tests/test_command.py"
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(("env=\\{\"LC_CTYPE\": \"C\"\\},")
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(string-append "env={\"LC_CTYPE\": \"C\", \"GUIX_PYTHONPATH\": \""
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(getenv "GUIX_PYTHONPATH") ":" site
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"\"},")))))))))
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(inputs
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(list python-dnaio python-xopen))
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(native-inputs
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(list python-cython python-pytest python-setuptools-scm))
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(list python-cython
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python-pytest
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python-pytest-mock
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python-pytest-timeout
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python-setuptools-scm))
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(home-page "https://cutadapt.readthedocs.io/en/stable/")
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(synopsis "Remove adapter sequences from nucleotide sequencing reads")
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(description
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