diff options
| author | Sharlatan Hellseher <sharlatanus@gmail.com> | 2026-01-04 21:07:57 +0000 |
|---|---|---|
| committer | Rutherther <rutherther@ditigal.xyz> | 2026-01-25 21:21:38 +0100 |
| commit | 40b416e4dbd581d0599188b26f4a17833d5d30f5 (patch) | |
| tree | 1eda68f0a295d29940551abe807a5c9f70796482 /gnu/packages | |
| parent | c5671bbd442aa466f9516b031d05df40d162181d (diff) | |
gnu: python-pygenometracks: Update to 3.9.
* gnu/packages/bioinformatics.scm (python-pygenometracks): Update to 3.9.
[source]: Switch to git-fetch.
[arguments] <tests?, test-flags>: Enable them.
<phases>: Remove 'remove-invalid-syntax; adjust 'relax-requirements.
[propagated-inputs]: Add python-bx-python, python-pybedtools, and
python-pyfaidx.
[native-inputs]: Remove python-wheel; add python-setuptools.
Change-Id: I364255a3e4d072535a871340588cdff0f30b83ff
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 44 |
1 files changed, 24 insertions, 20 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6d2b5076673..7b6db6e9085 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -20441,42 +20441,46 @@ the HiCExplorer and pyGenomeTracks packages.") (define-public python-pygenometracks (package (name "python-pygenometracks") - (version "3.5") + (version "3.9") (source (origin - (method url-fetch) - (uri (pypi-uri "pyGenomeTracks" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/deeptools/pyGenomeTracks") + (commit version))) + (file-name (git-file-name name version)) (sha256 - (base32 - "1l7smg2gc1vm2181lzmdnywb11gp6s6z6j444dbsigv65car8z8p")))) + (base32 "1xaw0yjdqnxd1d1aww1x2kkfydrmbdvpvma2ahmax68f5a68b0yk")))) (build-system pyproject-build-system) (arguments (list - #:tests? #f ;there are none + ;; tests: 1 failed, 205 passed, 4 skipped, 229 warnings + #:test-flags + ;; AttributeError: module 'bx.seq' has no attribute 'DNA_COMP' + #~(list "--deselect=pygenometracks/tests/test_maf.py::test_first_maf_seq_zoom_dec") #:phases - '(modify-phases %standard-phases - (add-after 'unpack 'relax-requirements - (lambda _ - (substitute* "setup.py" - (("matplotlib ==3.1.1") - "matplotlib >=3.1.1")))) - (add-after 'unpack 'remove-invalid-syntax - (lambda _ - (substitute* "setup.py" - ((".\\*,") ","))))))) + #~(modify-phases %standard-phases + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "pyproject.toml" + (("matplotlib >=3.1.1,<3.9") + "matplotlib >=3.1.1"))))))) + (native-inputs + (list python-pytest + python-setuptools)) (propagated-inputs - (list python-future + (list python-bx-python + python-future python-gffutils python-hicmatrix python-intervaltree python-matplotlib python-numpy + python-pybedtools python-pybigwig + python-pyfaidx python-pysam python-tqdm)) - (native-inputs - (list python-pytest - python-wheel)) (home-page "https://pygenometracks.readthedocs.io") (synopsis "Program and library to plot beautiful genome browser tracks") (description |