diff options
| author | Sharlatan Hellseher <sharlatanus@gmail.com> | 2025-12-29 22:50:54 +0000 |
|---|---|---|
| committer | Rutherther <rutherther@ditigal.xyz> | 2026-01-25 21:19:55 +0100 |
| commit | 44efd7c77b56bd7e843744e2985d88a41d411633 (patch) | |
| tree | c9735b43ae48c71026575a6795205691bcdae0f4 /gnu/packages | |
| parent | ac2544a69d26becc6884f7f4cf1e98da9aca0ac5 (diff) | |
gnu: python-cooler: Update to 0.10.4.
* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.10.4.
[arguments] <phases>: Add 'fix-pytest-config.
[propagated-inputs]: Remove python-pypairix; add python-ipywidgets,
python-matplotlib, and python-psutil.
[native-inputs]: Remove python-coverage, python-isort, and
python-pytest-cov.
Change-Id: I61157064630416c599f05639ddcd21c6ace8cefb
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 36 |
1 files changed, 22 insertions, 14 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 254920a8c2e..221faa529ad 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -20108,17 +20108,18 @@ fasta subsequences.") (define-public python-cooler (package (name "python-cooler") - (version "0.9.3") + (version "0.10.4") (source (origin (method url-fetch) (uri (pypi-uri "cooler" version)) (sha256 (base32 - "0qqb0i5449r6w871klsbjzxsjhdkpsaas3hvs9f1hc7ssrkf1vi1")))) + "1fh5wjffbl5j8fdkc3c3lybscwvhv4v6r5jiyqgxvkkhb5nn498w")))) (build-system pyproject-build-system) (arguments (list + ;; tests: 141 passed, 4 skipped, 2 deselected, 268 warnings #:test-flags '(list "-k" (string-append @@ -20127,29 +20128,36 @@ fasta subsequences.") " and not test_roundtrip" ;; This test depends on ipytree, which contains a lot of ;; minified JavaScript. - " and not test_print_trees")))) + " and not test_print_trees")) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-pytest-config + (lambda _ + (substitute* "pyproject.toml" + ((".*--cov.*") ""))))))) + (native-inputs + (list python-hatchling + python-pytest)) (propagated-inputs (list python-asciitree - python-biopython python-click python-cytoolz - python-dask python-h5py python-multiprocess python-numpy python-pandas python-pyfaidx - python-pypairix - python-pysam python-pyyaml python-scipy - python-simplejson)) - (native-inputs - (list python-coverage - python-hatchling - python-isort - python-pytest - python-pytest-cov)) + python-simplejson + ;; [optional] + python-biopython + python-dask + ;; python-ipytree ;no packaged in Guix + python-ipywidgets + python-matplotlib + python-psutil + python-pysam)) ;; Almost all the projects of the Mirnylab are moved under Open2C umbrella (home-page "https://github.com/open2c/cooler") (synopsis "Sparse binary format for genomic interaction matrices") |