guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit a4f1aa657b083e8e70fa6b3a5fc10d0eed2f4fcb
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Mon Dec 29 22:50:54 2025 +0000
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
---
gnu/packages/bioinformatics.scm | 36 ++++++++++++++++++++++--------------
1 file changed, 22 insertions(+), 14 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f47208a883..64466765a5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -20183,17 +20183,18 @@ 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
@@ -20202,29 +20203,36 @@ 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")
