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| author | Sharlatan Hellseher <sharlatanus@gmail.com> | 2025-12-29 22:40:17 +0000 |
|---|---|---|
| committer | Rutherther <rutherther@ditigal.xyz> | 2026-01-25 21:19:54 +0100 |
| commit | ac2544a69d26becc6884f7f4cf1e98da9aca0ac5 (patch) | |
| tree | f6ae9bc467b8d686ac126267f23edc2e7d36c8f6 | |
| parent | 65a250d35f04e2518423b412e853281b8fc380d1 (diff) | |
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
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 45 |
1 files changed, 25 insertions, 20 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d458cda8ee1..254920a8c2e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4931,43 +4931,48 @@ 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 |