guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit 0716b82aa3817a37d3eedd8547350c84bd6a5c6f
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Sun Jan 4 20:08:01 2026 +0000
gnu: scvelo: Update to 0.3.3.
* gnu/packages/bioinformatics.scm (scvelo): Update to 0.3.3.
[source]: Switch to git-fetch.
[arguments] <test-flags>: Run all tests in "tests/core"
<phases>: Remove 'matplotlib-compatibility; add 'set-version.
Change-Id: Iea4f9e9b7d385033b1131644c0145a5fdc3a7db7
---
gnu/packages/bioinformatics.scm | 62 +++++++++++++++++++++--------------------
1 file changed, 32 insertions(+), 30 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8358ba801d..8092d36bd4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -24291,39 +24291,40 @@ aligner.")
(define-public scvelo
(package
(name "scvelo")
- (version "0.2.4")
+ (version "0.3.3")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "scvelo" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/theislab/scvelo";)
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
- (base32 "0h5ha1459ljs0qgpnlfsw592i8dxqn6p9bl08l1ikpwk36baxb7z"))))
+ (base32 "0xsi0bdsk24mf7zifizshlc3arc6fn2blmvjzbl21k66hc2xd2z9"))))
(build-system pyproject-build-system)
(arguments
(list
- #:test-flags
- '(list "--pyargs" "scvelo/core"
- ;; XXX: these two tests fail for unknown reasons
- "-k"
- "not test_perfect_fit and not test_perfect_fit_2d")
- #:phases
- #~(modify-phases %standard-phases
- (add-after 'unpack 'matplotlib-compatibility
- (lambda _
- (substitute* "scvelo/settings.py"
- (("warnings.filterwarnings\\(\"ignore\",
category=cbook.mplDeprecation\\)")
- ""))))
- ;; Numba needs a writable dir to cache functions.
- (add-before 'check 'set-numba-cache-dir
- (lambda _
- (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
+ ;; tests: 173 passed, 1707 warnings
+ #:test-flags
+ ;; Run only core tests as other fail a lot in: datasets, preprocessing
+ ;; and tools.
+ #~(list "tests/core")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'build 'set-version
+ (lambda _
+ (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)))
+ ;; Numba needs a writable dir to cache functions.
+ (add-before 'check 'set-numba-cache-dir
+ (lambda _
+ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
+ (native-inputs
+ (list python-pytest
+ python-setuptools
+ python-setuptools-scm))
(propagated-inputs
- (list pybind11 ;XXX: marked as install requirement
- python-anndata
- python-hnswlib
- python-igraph
+ (list python-anndata
python-loompy
- python-louvain
python-matplotlib
python-numba
python-numpy
@@ -24331,11 +24332,12 @@ aligner.")
python-scanpy
python-scikit-learn
python-scipy
- python-umap-learn))
- (native-inputs
- (list python-pytest
- python-setuptools
- python-setuptools-scm))
+ python-umap-learn
+ ;; [optional]
+ pybind11
+ python-hnswlib
+ python-igraph
+ python-louvain))
(home-page "https://scvelo.org";)
(synopsis "RNA velocity generalized through dynamical modeling")
(description "ScVelo is a scalable toolkit for RNA velocity analysis in
