diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2023-05-05 12:56:31 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2023-05-05 15:39:28 +0200 |
| commit | 7dc853269f93093ffe94594b5e9b41fca6ddc2d5 (patch) | |
| tree | de891e8c1d61d96c04a95c0b3af3b987ade8e456 | |
| parent | 3efdc84bbd1819aeef6e2290aaf54bc88ba72dda (diff) | |
gnu: python-pyfaidx: Update to 0.7.2.1.
* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.7.2.1.
[build-system]: Use pyproject-build-system.
[arguments]: Ignore tests that require large downloads.
[native-inputs]: Remove python-six; add python-fsspec, python-pytest,
python-pytest-cov, python-mock, and python-numpy.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 37 |
1 files changed, 26 insertions, 11 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 108ac1bdfd..dcada630a0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14972,17 +14972,32 @@ bgzipped text file that contains a pair of genomic coordinates per line.") (define-public python-pyfaidx (package (name "python-pyfaidx") - (version "0.5.8") - (source - (origin - (method url-fetch) - (uri (pypi-uri "pyfaidx" version)) - (sha256 - (base32 - "038xi3a6zvrxbyyfpp64ka8pcjgsdq4fgw9cl5lpxbvmm1bzzw2q")))) - (build-system python-build-system) - (propagated-inputs - (list python-six)) + (version "0.7.2.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "pyfaidx" version)) + (sha256 + (base32 + "182ia2zg026lgphv68agxm9imw7649z9pdhfn8zkalrxkq5d5w1h")))) + (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") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-version + (lambda _ + (substitute* "pyproject.toml" + (("dynamic = \\[\"version\"\\]") + (string-append "version = \"" #$version "\"")))))))) + (native-inputs + (list python-fsspec + python-mock + python-numpy + python-pytest + python-pytest-cov)) (home-page "http://mattshirley.com") (synopsis "Random access to fasta subsequences") (description |