guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit c3123fcd60df053608fb533091c842a103249285
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Sat Jan 3 22:28:27 2026 +0000
gnu: python-drep: Update to 3.6.2-0.7b4b8fb.
* gnu/packages/bioinformatics.scm (python-drep): Update to
7b4b8fbf9dfdfef61caf949f1aa1d4fc3be61d5a commit.
[source]: Switch to git-fetch providing tests.
[arguments] <test-flags>: Skip some tests requiring not available
optional packages.
[build-system]: Switch to pyproject-build-system.
[propagated-inputs]: Remove python-pytest; add python-networkx.
[native-inputs]: Add mash, python-pytest, and python-setuptools.
Change-Id: I5e22f7c142e267592b2ed74cf1c1d37a02472992
---
gnu/packages/bioinformatics.scm | 77 +++++++++++++++++++++++++++++++++++++----
1 file changed, 70 insertions(+), 7 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1d4f957f45..e90d94ad1d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -19990,21 +19990,84 @@ altering the counts or PCA space.")
(define-public python-drep
(package
(name "python-drep")
- (version "3.2.0")
+ ;; PyPI has no tests, Git does not tag the latest version.
+ (properties '((commit . "7b4b8fbf9dfdfef61caf949f1aa1d4fc3be61d5a")
+ (revision . "0")))
+ (version (git-version "3.6.2"
+ (assoc-ref properties 'revision)
+ (assoc-ref properties 'commit)))
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "drep" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/MrOlm/drep";)
+ (commit (assoc-ref properties 'commit))))
+ (file-name (git-file-name name version))
(sha256
- (base32
- "08vk0x6v5c5n7afgd5pcjhsvb424absypxy22hw1cm1n9kirbi77"))))
- (build-system python-build-system)
+ (base32 "0rys4r9mmknzayvqcsdpgqi9sigl1x0a1nh0x8h2sjz13qqmklly"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ ;; tests: 27 passed, 12 skipped, 39 deselected, 1 warning
+ #:test-flags
+ ;; Tests depend on "near essential" and "optional" dependencies.
+ #~(list #$@(map (lambda (test) (string-append "--deselect="
+ "tests/tests/"
+ test))
+ (list "test_analyze.py::test_plot_5_1"
+ "test_analyze.py::test_plot_5_2"
+ "test_analyze.py::test_plot_6_1"
+ "test_analyze.py::test_plotting_functional_1"
+ "test_bonus.py::test_drep_scaffold_level"
+ "test_bonus.py::test_drep_scaffold_level_2"
+ "test_bonus.py::test_drep_scaffold_level_3"
+ "test_bonus.py::test_drep_scaffold_level_4"
+ "test_bonus.py::test_drep_scaffold_level_5"
+ "test_bonus.py::test_parse_stb_2"
+ "test_choose.py::test_centrality_1"
+ "test_choose.py::test_centrality_2"
+ "test_choose.py::test_choose_2"
+ "test_choose.py::test_choose_3"
+ "test_cluster.py::test_cluster_functional_1"
+ "test_cluster.py::test_cluster_functional_3"
+ "test_cluster.py::test_cluster_functional_4"
+ "test_cluster.py::test_cluster_functional_5"
+ "test_cluster.py::test_compare_genomes"
+ "test_cluster.py::test_fastANI"
+ "test_cluster.py::test_goANI"
+ "test_cluster.py::test_goANI2"
+ "test_cluster.py::test_list_genome_load"
+ "test_cluster.py::test_low_ram_primary_clustering"
+ "test_cluster.py::test_skani"
+ "test_dereplicate.py::test_dereplicate_10"
+ "test_dereplicate.py::test_dereplicate_2"
+ "test_dereplicate.py::test_dereplicate_3"
+ "test_dereplicate.py::test_dereplicate_6"
+ "test_evaluate.py::test_tertiary_clustering_1"
+ "test_evaluate.py::test_tertiary_clustering_2"
+ "test_filter.py::test_filer_functional_3"
+
"test_greedy.py::test_greedy_secondary_clustering_1"
+
"test_greedy.py::test_greedy_secondary_clustering_2"
+
"test_greedy.py::test_multiround_primary_clustering_1"
+
"test_greedy.py::test_multiround_primary_clustering_2"
+ "test_rerun.py::test_unit_1"
+ "test_rerun.py::test_unit_3"
+ "test_rerun.py::test_unit_4")))))
+ (native-inputs
+ (list mash
+ ;; nsimscan
+ ;; mummer ;https://github.com/mummer4/mummer, asl2.0
+ ;; fastani ;https://github.com/ParBLiSS/FastANI, asl2.0
+ ;; checkm ;https://ecogenomics.github.io/CheckM/, gpl3
+ ;; skani
+ python-pytest
+ python-setuptools))
(propagated-inputs
(list python-biopython
python-matplotlib
+ python-networkx
python-numpy
python-pandas
- python-pytest
python-scikit-learn
python-seaborn
python-tqdm))
