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| author | Sharlatan Hellseher <sharlatanus@gmail.com> | 2026-01-03 00:33:06 +0000 |
|---|---|---|
| committer | Rutherther <rutherther@ditigal.xyz> | 2026-01-25 21:21:03 +0100 |
| commit | 4a9ba2e094024a8ab20f847e7e35cc0cb9cfdf3c (patch) | |
| tree | 2194bfd086af048d2441d19611d7329281e52e51 /gnu | |
| parent | 5bddbae69318d8789166b02b327f35d1c91ac1f9 (diff) | |
gnu: python-pyfaidx: Update to 0.9.0.3.
* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.9.0.3.
[arguments] <tests?>: Disable for now.
<phases>: Remove 'fix-version; add 'set-version.
[propagated-inputs]: Remove python-setuptools; add python-packaging.
[native-inputs]: Remove libc-utf8-locales-for-target; add
python-biopython, python-fsspec, python-numpy, python-pytest,
python-setuptools, and python-setuptools-scm.
Change-Id: I49e95f8e1b19a181d4d1b2e344cf1a00b055eefd
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 26 |
1 files changed, 12 insertions, 14 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0ac4db0544..baa3014188 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -20191,35 +20191,33 @@ bgzipped text file that contains a pair of genomic coordinates per line.") (define-public python-pyfaidx (package (name "python-pyfaidx") - (version "0.7.2.1") + (version "0.9.0.3") (source (origin (method url-fetch) (uri (pypi-uri "pyfaidx" version)) (sha256 (base32 - "182ia2zg026lgphv68agxm9imw7649z9pdhfn8zkalrxkq5d5w1h")))) + "0yaa64n5m4wxc02lxw6j9dzjk65rxdbak21dlvwhdjwdv4l4p2v4")))) (build-system pyproject-build-system) (arguments (list - #:test-flags - ;; These tests require the download of large fasta.gz files. - '(list "--ignore=tests/test_Fasta_bgzip.py") + ;; tests: 107 failed, 54 passed, 8 skipped, 7 xfailed, 14 errors + #:tests? #f ;most of them need remote data #:phases #~(modify-phases %standard-phases - (add-after 'unpack 'fix-version + (add-before 'build 'set-version (lambda _ - (substitute* "pyproject.toml" - (("dynamic = \\[\"version\"\\]") - (string-append "version = \"" #$version "\"")))))))) + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)))))) (native-inputs - (list (libc-utf8-locales-for-target) ;tests need "en_US.utf8" + (list python-biopython python-fsspec - python-mock python-numpy + ;; python-pyfasta python-pytest - python-pytest-cov - python-wheel)) - (propagated-inputs (list python-setuptools)) + python-setuptools + python-setuptools-scm)) + (propagated-inputs + (list python-packaging)) (home-page "http://mattshirley.com") (synopsis "Random access to fasta subsequences") (description |