guix_mirror_bot pushed a commit to branch master
in repository guix.
commit 6e38e8ab54c8ef0b906753423a2b6ca470864245
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Thu Aug 7 14:55:05 2025 +0100
gnu: python-scanpy: Update to 1.11.2.
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.11.2.
[arguments] <test-flags>: Run tests in parallel, supported
upstream. Skipp some more problematic tests.
<phases>: Remove 'set-numba-cache-dir; add combined 'pre-check.
[propagated-inputs]: Remove python-session-info; add python-session-info2.
[native-inputs]: Add python-flaky, python-pytest-xdist, and
python-scanorama.
Change-Id: I6a13a7c3449b0d60801daf49e40e6f1fcc48f0c0
---
gnu/packages/bioinformatics.scm | 51 ++++++++++++++++++++++++++++++-----------
1 file changed, 38 insertions(+), 13 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a326cf40ee..1332a1b68d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -19730,7 +19730,7 @@ implementation differs in these ways:
(define-public python-scanpy
(package
(name "python-scanpy")
- (version "1.10.4")
+ (version "1.11.2")
(source
(origin
(method git-fetch)
@@ -19740,12 +19740,14 @@ implementation differs in these ways:
(file-name (git-file-name name version))
(sha256
(base32
- "139d6fsdbhg1hqqq5yyl8hr3cqz2mj70i0i8r1mq6z6a8qmq1p4z"))))
+ "18ddb3jkyjan87f5kymyq951sa5955z41f10h6z954map8dy2136"))))
(build-system pyproject-build-system)
(arguments
(list
+ ;; 736 passed, 95 skipped, 20 xfailed, 148 warnings
#:test-flags
'(list "-m" "not gpu"
+ "--numprocesses" (number->string (parallel-job-count))
;; These tests require Internet access.
"--ignore-glob=tests/notebooks/*"
"--ignore=tests/test_clustering.py"
@@ -19763,9 +19765,10 @@ implementation differs in these ways:
"--ignore=tests/test_preprocessing.py"
"--ignore=tests/test_read_10x.py"
"--ignore=plotting/_tools/scatterplots.py"
- ;; The following tests requires 'scanorama', which isn't
- ;; packaged yet.
- "--ignore=tests/external/test_scanorama_integrate.py"
+ ;; Adding additional options does not help to resolve the
+ ;; faileur: TypeError: _FlakyPlugin._make_test_flaky() got an
+ ;; unexpected keyword argument 'reruns'.
+ "--ignore=tests/test_backed.py"
"-k"
;; Plot tests that fail.
(string-append "not test_clustermap"
@@ -19776,6 +19779,8 @@ implementation differs in these ways:
" and not test_paga_plots"
" and not test_violin"
" and not test_scatter_no_basis_per_obs"
+ " and not test_spatial_general"
+ " and not test_visium_empty_img_key"
;; These are doctests that fail because of missing
;; datasets.
@@ -19793,7 +19798,21 @@ implementation differs in these ways:
" and not test_pca_layer"
" and not test_pca_sparse"
" and not test_pca_reproducible"
- " and not test_clip"))
+ " and not test_clip"
+
+ ;; Missing test data.
+ " and not test_covariance_eigh_impls"
+ " and not test_embedding_colorbar_location"
+ " and not test_sparse_dask_input_errors"
+ " and not test_sparse_dask_input_errors"
+ " and not test_spatial_external_img"
+
+ ;; Somehow broken tests.
+ " and not test_sim_toggleswitch"
+ " and not scanpy.datasets._datasets.krumsiek11"
+ " and not scanpy.datasets._datasets.toggleswitch"
+ " and not
scanpy.external.pp._scanorama_integrate.scanorama_integrate"
+ " and not
scanpy.preprocessing._simple.filter_cells"))
#:phases
#~(modify-phases %standard-phases
;; XXX This should not be necessary, but I noticed while building
@@ -19817,9 +19836,12 @@ implementation differs in these ways:
(string-append (getcwd) ":"
#$(this-package-native-input
"python-anndata:source") ":"
(getenv "GUIX_PYTHONPATH")))))
- ;; Numba needs a writable dir to cache functions.
- (add-before 'check 'set-numba-cache-dir
- (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
+ (add-before 'check 'pre-check
+ (lambda _
+ ;; Numba needs a writable dir to cache functions.
+ (setenv "NUMBA_CACHE_DIR" "/tmp")
+ ;; For Matplotlib.
+ (setenv "HOME" "/tmp"))))))
(propagated-inputs
(list python-anndata
python-dask
@@ -19835,27 +19857,30 @@ implementation differs in these ways:
python-packaging
python-pandas
python-patsy
+ python-pytoml
python-scikit-learn
python-scipy
- python-setuptools ; For pkg_resources.
python-seaborn
- python-session-info
+ python-session-info2
+ python-setuptools ; For pkg_resources.
python-sinfo
python-statsmodels
python-tables
- python-pytoml
python-tqdm
python-umap-learn))
(native-inputs
`(;; This package needs anndata.tests, which is not installed.
("python-anndata:source" ,(package-source python-anndata))
+ ("python-flaky" ,python-flaky)
("python-flit" ,python-flit)
- ("python-hatchling" ,python-hatchling)
("python-hatch-vcs" ,python-hatch-vcs)
+ ("python-hatchling" ,python-hatchling)
("python-leidenalg" ,python-leidenalg)
("python-pytest" ,python-pytest)
("python-pytest-mock" ,python-pytest-mock)
("python-pytest-nunit" ,python-pytest-nunit)
+ ("python-pytest-xdist" ,python-pytest-xdist)
+ ("python-scanorama" ,python-scanorama)
("python-setuptools-scm" ,python-setuptools-scm)))
(home-page "https://github.com/theislab/scanpy";)
(synopsis "Single-Cell Analysis in Python")
