guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit 1f4e1e0014d2f24bb4bb4171a79d7abd392e7080
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Mon Dec 29 22:40:17 2025 +0000
gnu: python-circe: Update to 0.3.9.
* gnu/packages/bioinformatics.scm (python-circe): Update to 0.3.9.
[source] <uri>: Use direct URL string.
[arguments] <tests?, test-flags>: Enable them.
[inputs]: Add python-numpy-1.
[propagated-inputs]: Remove python-numpy; add python-attrs.
[native-inputs]: Add python-pytest.
[home-page]: Move above synopsis.
Change-Id: Ia4e7a18c3225b1134b71ba33c369429bc4c01305
---
gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++------------------
1 file changed, 25 insertions(+), 20 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7d1942d5d6..f47208a883 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4930,43 +4930,48 @@ long-read sequencing data.")
(define-public python-circe
(package
(name "python-circe")
- (version "0.3.8")
- (home-page "https://github.com/cantinilab/circe";)
+ (version "0.3.9")
(source
(origin
(method git-fetch)
(uri (git-reference
- (url home-page)
+ (url "https://github.com/cantinilab/circe";)
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32
- "050zwg6qvd6sa4xd41sn4gigwmyfn0v6r93j5kvpbxklq4144q15"))))
+ (base32 "0psqfkxjvfj3h23xmski0c2h8dx118zr4xshz2dbk2i3hk50ljvr"))))
(build-system pyproject-build-system)
+ (arguments
+ (list
+ ;; tests: 19 passed, 1 deselected, 3 warnings
+ #:test-flags
+ ;; Network access is required to reach data from <www.ensembl.org>.
+ #~(list
"--deselect=tests/test_network/test_network.py::test_network_atac")
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; Numba needs a writable dir to cache functions.
+ (add-before 'build 'set-numba-cache-dir
+ (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
+ (native-inputs
+ (list python-cython
+ python-pybiomart
+ python-pytest
+ python-setuptools))
+ (inputs
+ (list lapack
+ openblas
+ python-numpy-1)) ;avoid propagating @1 to user profile
(propagated-inputs
(list python-anndata
+ python-attrs
python-dask
python-distributed
python-joblib
- python-numpy
python-pandas
python-rich
python-scanpy
python-scikit-learn))
- (inputs
- (list lapack openblas))
- (native-inputs
- (list python-cython
- python-pybiomart
- python-setuptools))
- (arguments
- (list
- #:tests? #f ;XXX: tests hangs during collection
- #:phases
- '(modify-phases %standard-phases
- ;; Numba needs a writable dir to cache functions.
- (add-before 'build 'set-numba-cache-dir
- (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
+ (home-page "https://github.com/cantinilab/circe";)
(synopsis "Cis-regulatory interactions between chromatin regions")
(description "Circe is a Python package for inferring co-accessibility
networks from single-cell ATAC-seq data, using skggm for the graphical lasso
