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| author | Ricardo Wurmus <rekado@elephly.net> | 2023-07-03 16:37:45 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2023-07-03 16:37:45 +0200 |
| commit | c66e5ef5f9b184b0abb882b0cce7c7d19e02f30d (patch) | |
| tree | abdaf4a62de08762ae9388b26a56148af4a62ba4 /gnu/packages/bioinformatics.scm | |
| parent | cb15c60d35f33133a194daff8bd1303fcdbea2f0 (diff) | |
| download | guix-c66e5ef5f9b184b0abb882b0cce7c7d19e02f30d.tar guix-c66e5ef5f9b184b0abb882b0cce7c7d19e02f30d.tar.gz | |
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.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 38 |
1 files changed, 25 insertions, 13 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 28c9edcc14..62bb0074b2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3945,28 +3945,40 @@ annotations of the genome.") (define-public cutadapt (package (name "cutadapt") - (version "2.1") + (version "4.0") (source (origin (method url-fetch) (uri (pypi-uri "cutadapt" version)) (sha256 (base32 - "1vqmsfkm6llxzmsz9wcfcvzx9a9f8iabvwik2rbyn7nc4wm25z89")))) - (build-system python-build-system) + "0xgsv88mrlw2b1radmd1104y7bg8hvv54ay7xfdpnjiw2jgkrha9")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'always-cythonize - (lambda _ - (delete-file "src/cutadapt/_align.c") - ;; If PKG-INFO exists, setup.py decides not to run Cython. - (substitute* "setup.py" - (("os.path.exists\\('PKG-INFO'\\):") - "os.path.exists('totally-does-not-exist'):"))))))) + (list + #:test-flags + '(list "-k" "not test_no_read_only_comment_fasta_input") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-test + (lambda _ + (let ((site (string-append + #$output "/lib/python" + #$(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 (list python-dnaio python-xopen)) (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/") (synopsis "Remove adapter sequences from nucleotide sequencing reads") (description |