rekado pushed a commit to branch master
in repository guix.
commit 64acec341bf279e9be92f3a1955922d404746c12
Author: Ricardo Wurmus <[email protected]>
AuthorDate: Wed Jan 15 21:19:44 2025 +0100
gnu: python-fanc: Update to 0.9.28.
* gnu/packages/bioinformatics.scm (python-fanc): Update to 0.9.28.
[arguments]: Remove custom 'check phase; disable tests that seemingly
freeze.
[propagated-inputs]: Add python-imageio, python-pywavelets, and
python-tifffile; remove python-pytest.
[native-inputs]: Add python-pytest, python-setuptools, and python-wheel.
Change-Id: Ia83f5fe1d0cbbf56840061feb9561e439380e965
---
gnu/packages/bioinformatics.scm | 33 ++++++++++++++-------------------
1 file changed, 14 insertions(+), 19 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0dca040570..6aae5b7f7b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -16328,33 +16328,26 @@ lowly expressed transcripts.")
(define-public python-fanc
(package
(name "python-fanc")
- (version "0.9.25")
+ (version "0.9.28")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/vaquerizaslab/fanc";)
;; There are no tags. This commit corresponds to
- ;; version 0.9.25.
- (commit "e2205346c13ea5349681dff21adeb271d4ea5261")))
+ ;; version 0.9.28.
+ (commit "d5d86085c920a4dca6e5f6be4857129d718243cc")))
(file-name (git-file-name name version))
(sha256
(base32
- "0rxq24p852iiayi0083fyigvc30as695rha71q6xd4s2ij1k9mqi"))))
+ "0pfl35ancd0izw9w2dp85lznq9rsyv2nv5f5la6dnbvj20d1m06d"))))
(build-system pyproject-build-system)
(arguments
(list
- #:phases
- '(modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "pytest" "-vv"
- "-k"
- ;; XXX: These all fail because they fail to read
- ;; the included test_{cooler,juicer}.hic files.
- (string-append "not test_edges_iter"
- " and not test_get_edges_uncorrected"
- " and not test_get_edges"))))))))
+ #:test-flags
+ '(list "-m" "not longrunning"
+ ;; XXX: some of the tests here just take forever
+ "--ignore=fanc/test/test_matrix.py"
+ "--ignore=fanc/test/test_pairs.py")))
(propagated-inputs
(list python-biopython
python-cooler
@@ -16363,6 +16356,7 @@ lowly expressed transcripts.")
python-genomic-regions
python-gridmap
python-h5py
+ python-imageio
python-intervaltree
python-matplotlib
python-msgpack
@@ -16374,15 +16368,16 @@ lowly expressed transcripts.")
python-pybedtools
python-pybigwig
python-pysam
- python-pytest
+ python-pywavelets
python-pyyaml
python-scikit-image
python-scikit-learn
python-scipy
python-seaborn
- python-tables))
+ python-tables
+ python-tifffile))
(native-inputs
- (list python-cython))
+ (list python-cython python-pytest python-setuptools python-wheel))
(home-page "https://github.com/vaquerizaslab/fanc";)
(synopsis "Framework for the analysis of C-data")
(description
