guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit 88ca99c4fb9715d724d7ee795e25bed3c2fc73f0
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Mon Dec 29 21:18:31 2025 +0000
gnu: python-scanpy: Update to 1.11.5.
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.11.5.
[arguments] <test-flags>: Rework skipped tests.
<phases>: Remove 'patch-version-check and 'add-anndata-source.
[propagated-inputs]: Remove python-pytoml, python-sinfo,
and python-tables; add python-numpy, python-pynndescent, and
python-typing-extensions.
[native-inputs]: Remove (package-source python-anndata), python-flaky,
python-flit, python-leidenalg, python-pytest-nunit, and
python-scanorama; add python-dependency-groups, python-pytest-randomly,
and python-pytest-rerunfailures.
Change-Id: I7a9a18434ddf3cca4d34a7909cce22ef86ffa054
---
gnu/packages/bioinformatics.scm | 216 +++++++++++++++++-----------------------
1 file changed, 94 insertions(+), 122 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 051966e44a..7d1942d5d6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -19681,158 +19681,130 @@ implementation differs in these ways:
(define-public python-scanpy
(package
(name "python-scanpy")
- (version "1.11.2")
+ (version "1.11.5")
(source
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/theislab/scanpy";)
- (commit version)))
+ (url "https://github.com/theislab/scanpy";)
+ (commit version)))
(file-name (git-file-name name version))
(sha256
(base32
- "18ddb3jkyjan87f5kymyq951sa5955z41f10h6z954map8dy2136"))))
+ "07brcdwpzy2qa950jgiw38qax1xd0yi1zh7jrp1k4s8jksl7axhs"))))
(build-system pyproject-build-system)
(arguments
(list
- ;; 736 passed, 95 skipped, 20 xfailed, 148 warnings
+ ;; tests: 537 passed, 118 skipped, 15 xfailed, 89 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"
- "--ignore=tests/test_datasets.py"
- "--ignore=tests/test_normalization.py"
- "--ignore=tests/test_score_genes.py"
- "--ignore=tests/test_highly_variable_genes.py"
- "--ignore=tests/test_aggregated.py"
- "--ignore=get/_aggregated.py"
- ;; TODO: I can't get the plotting tests to work, even with Xvfb.
- ;; Some of them also require Internet access because they want to
- ;; download a dataset.
- "--ignore=tests/test_plotting.py"
- "--ignore=tests/test_embedding_plots.py"
- "--ignore=tests/test_preprocessing.py"
- "--ignore=tests/test_read_10x.py"
- "--ignore=plotting/_tools/scatterplots.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"
- " and not test_dotplot_matrixplot_stacked_violin"
- " and not test_paga_compare"
- " and not test_paga_path"
- " and not test_paga_pie"
- " 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.
- " and not scanpy.get._aggregated.aggregate"
- " and not
scanpy.plotting._tools.scatterplots.spatial"
-
- ;; One difference in a long array.
- " and not test_cell_demultiplexing"
-
- ;; These try to connect to the network
- " and not test_scrublet_plots"
- " and not test_plot_rank_genes_groups_gene_symbols"
- " and not test_pca_n_pcs"
- " and not test_pca_chunked"
- " and not test_pca_layer"
- " and not test_pca_sparse"
- " and not test_pca_reproducible"
- " 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
- ;; python-metacells that the anndata version check fails, resulting
- ;; in the wrong module name to be loaded from anndata. I cannot
- ;; reproduce this in an interactive Python session. We patch this
- ;; here to ensure that the appropriate module name is used.
- (add-after 'unpack 'patch-version-check
- (lambda _
- (substitute* "src/scanpy/_utils/__init__.py"
- (("Version\\(anndata_version\\) < Version\\(\"0.6.10\"\\):")
- "False:")
- (("Version\\(anndata_version\\) >= Version\\(\"0.10.0\"\\):")
- "True:"))))
- (add-after 'unpack 'pretend-version
- (lambda _
- (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)))
- (add-after 'unpack 'add-anndata-source
- (lambda _
- (setenv "PYTHONPATH"
- (string-append (getcwd) ":"
- #$(this-package-native-input
"python-anndata:source") ":"
- (getenv "GUIX_PYTHONPATH")))))
- (add-before 'check 'pre-check
- (lambda _
- ;; Numba needs a writable dir to cache functions.
- (setenv "NUMBA_CACHE_DIR" "/tmp")
- ;; For Matplotlib.
- (setenv "HOME" "/tmp"))))))
+ #~(list "-m" "not gpu"
+ "--numprocesses" (number->string (min 8 (parallel-job-count)))
+ ;; Network access is required.
+ #$@(map (lambda (file) (string-append "--ignore=tests/" file))
+ (list "test_aggregated.py"
+ "test_highly_variable_genes.py"
+ "test_normalization.py"
+ "test_pca.py"
+ "test_plotting.py"
+ "test_plotting_embedded/test_embeddings.py"
+ "test_preprocessing.py"
+ "test_scaling.py"
+ "test_score_genes.py"))
+ "--deselect=tests/test_datasets.py::test_download_failure"
+ "--deselect=tests/test_paga.py::test_paga_compare"
+ ;; AssertionError: Image files did not match.
+ #$@(map (lambda (test) (string-append "--deselect=tests/"
+ "test_plotting_embedded/"
+ "test_spatial.py::"
+ test))
+ (list "test_spatial_general"
+ "test_spatial_external_img"
+ "test_visium_empty_img_key"))
+ (string-append "--deselect=plotting/_tools/scatterplots.py::"
+ "scanpy.plotting._tools.scatterplots.spatial")
+ "--deselect=get/_aggregated.py::scanpy.get._aggregated.aggregate"
+ ;; XXX: When python-dask is added some tests fail with error:
+ ;; ImportError: cannot import name 'as_sparse_dask_array' from
+ ;; 'anndata.tests.helpers'.
+ ;;
+ ;; That functionality was removed from anndata: see
+ ;; <https://github.com/scverse/anndata/pull/2201>.
+ #$@(map (lambda (test) (string-append "--deselect=tests/"
+ "test_utils.py::"
+ test))
+ (list "test_axis_sum[dask_array_sparse]"
+
"test_check_nonnegative_integers[middle-dask_array_sparse]"
+
"test_check_nonnegative_integers[normal-dask_array_sparse]"
+
"test_check_nonnegative_integers[poisson-float64-dask_array_sparse]"
+
"test_check_nonnegative_integers[poisson-uint32-dask_array_sparse]"
+ "test_divide_by_zero[dask_array_sparse]"
+ "test_elem_mul[dask_array_sparse]"
+ "test_scale_column[mul-dask_array_sparse]"
+ "test_scale_column[truediv-dask_array_sparse]"
+
"test_scale_out_with_dask_or_sparse_raises[dask_array_sparse]"
+ "test_scale_rechunk[mul-0-dask_array_sparse]"
+ "test_scale_rechunk[mul-1-dask_array_sparse]"
+ "test_scale_rechunk[truediv-0-dask_array_sparse]"
+ "test_scale_rechunk[truediv-1-dask_array_sparse]"
+ "test_scale_row[mul-dask_array_sparse]"
+ "test_scale_row[truediv-dask_array_sparse]"))
+ #$@(map (lambda (test) (string-append "--deselect=tests/"
+ "test_qc_metrics.py::"
+ test))
+ (list "test_dask_against_in_memory[log1p]"
+ "test_dask_against_in_memory[no_log1p]"
+ "test_qc_metrics[dask_array_sparse]"
+ "test_qc_metrics_idempotent[dask_array_sparse]"
+ "test_qc_metrics_no_log1p[dask_array_sparse]")))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'set-version
+ (lambda _
+ (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)))
+ (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
python-h5py
- python-igraph
python-joblib
python-legacy-api-wrap
- python-louvain
python-matplotlib
python-natsort
python-networkx
python-numba
+ python-numpy
python-packaging
python-pandas
python-patsy
- python-pytoml
+ python-pynndescent
python-scikit-learn
python-scipy
python-seaborn
python-session-info2
- python-setuptools ; For pkg_resources.
- python-sinfo
python-statsmodels
- python-tables
python-tqdm
- python-umap-learn))
+ python-typing-extensions
+ python-umap-learn
+ ;; [optional]
+ python-dask
+ python-igraph
+ python-louvain
+ python-setuptools)) ;for pkg_resources
(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-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)))
+ (list python-dependency-groups
+ python-hatch-vcs
+ python-hatchling
+ python-pytest
+ python-pytest-mock
+ python-pytest-randomly
+ python-pytest-rerunfailures
+ python-pytest-xdist
+ python-setuptools-scm
+ #;python-tuna)) ;no packaged in Guix yet
(home-page "https://github.com/theislab/scanpy";)
(synopsis "Single-Cell Analysis in Python")
(description "Scanpy is a scalable toolkit for analyzing single-cell gene
