diff options
| author | Sharlatan Hellseher <sharlatanus@gmail.com> | 2025-12-29 23:49:48 +0000 |
|---|---|---|
| committer | Rutherther <rutherther@ditigal.xyz> | 2026-01-25 21:19:56 +0100 |
| commit | 0d78581ee6482cda8b27cf37c2259f4f650d1772 (patch) | |
| tree | 8368f7429782b3b43adccdc41d89a4bbdd6fbf51 /gnu | |
| parent | 44efd7c77b56bd7e843744e2985d88a41d411633 (diff) | |
gnu: python-coolbox: Update to 0.3.9.
* gnu/packages/bioinformatics.scm (python-coolbox): Update to 0.3.9.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments] <tests?, test-flags>: Enable them.
<phases>: Delete 'sanity-check.
[inputs]: Remove pybind11.
[propagated-inputs]: Remove python-pybbi, python-pytest, and
python-termcolor.
[native-inputs]: Add pybind11, python-pytest, python-pypairix,
python-pybbi, python-setuptools, and samtools.
Change-Id: I356fa043a18e7901e50b15f2815f84178cf4e969
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 50 |
1 files changed, 36 insertions, 14 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 221faa529ad..7f72ddf6ad3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -23950,38 +23950,60 @@ e.g. from GenBank or Gff files, or Biopython SeqRecords.") (define-public python-coolbox (package (name "python-coolbox") - (version "0.3.8") + ;; TODO: Newer versions depend on python-polars, see + ;; <https://codeberg.org/guix/guix/pulls/2570>. + (version "0.3.9") (source (origin - (method url-fetch) - (uri (pypi-uri "coolbox" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/GangCaoLab/CoolBox") + (commit version))) + (file-name (git-file-name name version)) (sha256 - (base32 - "0gqp76285w9klswr47y6kxbzwhv033b26jfa179kccfhiaq5p2xa")))) - (build-system python-build-system) - (arguments '(#:tests? #false)) ; there are none - (inputs - (list pybind11)) + (base32 "1a9h0xrg7issgprzm6awabfw73ddm2910rqcvcfg5v0cfn599aws")))) + (build-system pyproject-build-system) + (arguments + (list + ;; tests: 29 passed, 7 deselected, 17 warnings + #:test-flags + ;; XXX: Maybe there is a build problem with python-pypairix? + ;; FileNotFoundError: [Errno 2] No such file or directory: 'pairix' + #~(list "--deselect=tests/test_browser.py::test_browser" + "--deselect=tests/test_coverage.py::test_arcs_coverage" + "--deselect=tests/test_frame.py::test_frame" + "--deselect=tests/test_track.py::test_bedpe" + "--deselect=tests/test_track.py::test_pairs" + "--deselect=tests/test_track.py::test_arcs") + #:phases + #~(modify-phases %standard-phases + ;; FIXME: Some issue with checking the correct versions of Jupyter + ;; dependencies. + (delete 'sanity-check)))) + (native-inputs + (list pybind11 + python-pytest + python-pypairix + python-pybbi + python-setuptools + samtools)) (propagated-inputs - (list python-cooler + (list jupyter + python-cooler python-dna-features-viewer python-fire python-h5py python-intervaltree python-ipywidgets - jupyter python-matplotlib python-nbformat python-numpy python-numpydoc python-pandas - python-pybbi - python-pytest python-scipy python-statsmodels python-strawc python-svgutils - python-termcolor python-voila)) (home-page "https://github.com/GangCaoLab/CoolBox") (synopsis "Genomic data visualization toolkit") |