guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit 7962f8312cf0f48f740c9c00b8ce7f36172e2ca8
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Sun Jan 4 21:07:57 2026 +0000
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
---
gnu/packages/bioinformatics.scm | 44 ++++++++++++++++++++++-------------------
1 file changed, 24 insertions(+), 20 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4f16239805..0ce2ce1eea 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -20436,42 +20436,46 @@ 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
