guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit 5167449be684e4c19d4c464ef83eadf00160ae1d
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Tue Jul 14 09:53:12 2026 +0100
gnu: python-scanpy: Update to 1.12.2.
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.12.2.
[arguments] <#:test-flags>: Run more tests, exclude only networking
tests; rework skipped tests.
[phases]{fix-pytest-config}: New phase.
[propagated-inputs]: Add python-certifi, python-fast-array-utils,
python-scverse-misc, python-harmonypy, python-leidenalg,
python-magic-impute, and python-scikit-misc.
[native-inputs]: Remove python-setuptools-scm; add nss-certs-for-test.
---
gnu/packages/bioinformatics.scm | 215 ++++++++++++++++++++++++++++------------
1 file changed, 150 insertions(+), 65 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7dbe3c13e6..4468617fa8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -19654,7 +19654,7 @@ implementation differs in these ways:
(define-public python-scanpy
(package
(name "python-scanpy")
- (version "1.11.5")
+ (version "1.12.2")
(source
(origin
(method git-fetch)
@@ -19664,75 +19664,153 @@ implementation differs in these ways:
(file-name (git-file-name name version))
(sha256
(base32
- "07brcdwpzy2qa950jgiw38qax1xd0yi1zh7jrp1k4s8jksl7axhs"))))
+ "02mmsz267zyx1ndw9qqsrccxhjr65xpyyqbf5i1j761y7mm4aayh"))))
(build-system pyproject-build-system)
(arguments
(list
- ;; tests: 537 passed, 117 skipped, 15 xfailed, 77 warnings
+ ;; tests: 2052 passed, 101 skipped, 100 xfailed, 12 warnings, 34
+ ;; subtests passed
#:test-flags
+ ;; XXX: There is an "internet" marker but it has no effect when
+ ;; deselected, forcing to download data from Internet during tests
+ ;; anyway.
#~(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]"))
- ;; XXX: Not equal to tolerance rtol=1e-07, atol=0
-
"--deselect=tests/test_neighbors.py::test_connectivities_euclidean[umap]")
+ #$@(map (lambda (ls) (string-append "--deselect=tests/"
+ (string-join ls "::")))
+ ;; Tests requiring Internet access.
+ '(("test_pca.py" "test_pca_rep")
+ ("test_scaling.py" "test_clip")
+ ("test_pca.py" "test_pca_n_pcs")
+ ("test_pca.py" "test_pca_sparse")
+ ("test_pca.py" "test_pca_chunked")
+ ("test_paga.py" "test_paga_compare")
+ ("test_pca.py" "test_pca_reproducible")
+ ("test_plotting.py" "test_string_mask")
+ ("notebooks/test_pbmc3k.py" "test_pbmc3k")
+ ("test_plotting.py" "test_scrublet_plots")
+ ("test_metrics.py" "test_modularity_adata")
+ ("test_plotting.py" "test_umap_mask_equal")
+ ("test_aggregated.py" "test_aggregate_axis")
+ ("test_datasets.py" "test_download_failure")
+ ("test_pca.py" "test_covariance_eigh_impls")
+ ("test_plotting.py" "test_highest_expr_genes")
+ ("test_pca.py" "test_sparse_dask_input_errors")
+ ("test_plotting.py" "test_umap_mask_mult_plots")
+ ("test_plotting.py" "test_violin_scale_warning")
+ ("test_preprocessing.py" "test_regress_out_int")
+ ("test_aggregated.py" "test_aggregate_arraytype")
+ ("test_aggregated.py" "test_aggregate_vs_pandas")
+ ("test_highly_variable_genes.py" "test_keep_layer")
+ ("test_score_genes.py" "test_score_with_reference")
+ ("test_highly_variable_genes.py" "test_cutoff_info")
+ ("test_aggregated.py" "test_aggregate_incorrect_dim")
+ ("test_plotting.py" "test_umap_mask_no_modification")
+ ("test_aggregated.py"
+ "test_aggregate_bad_dask_array")
+ ("test_highly_variable_genes.py"
+ "test_no_filter_genes")
+ ("test_highly_variable_genes.py"
+ "test_dask_consistency")
+ ("test_highly_variable_genes.py"
+ "test_seurat_v3_warning")
+ ("test_highly_variable_genes.py"
+ "test_compare_to_seurat_v3")
+ ("external/test_harmony_integrate.py"
+ "test_harmony_integrate")
+ ("test_plotting.py"
+ "test_plot_rank_genes_groups_gene_symbols")
+ ("test_highly_variable_genes.py"
+ "test_pearson_residuals_batch")
+ ("test_normalization.py"
+ "test_normalize_pearson_residuals_pca")
+ ("test_highly_variable_genes.py"
+ "test_pearson_residuals_general")
+ ("test_highly_variable_genes.py"
+ "test_subset_inplace_consistency")
+ ("test_normalization.py"
+ "test_normalize_pearson_residuals_errors")
+ ("test_normalization.py"
+ "test_normalize_pearson_residuals_recipe")
+ ("test_normalization.py"
+ "test_normalize_pearson_residuals_warnings")
+ ("test_highly_variable_genes.py"
+ "test_pearson_residuals_inputchecks")
+ ("test_plotting_embedded/test_embeddings.py"
+ "test_raise_save_future_warning")
+ ("test_highly_variable_genes.py"
+ "test_seurat_v3_mean_var_output_with_batchkey")
+ ("test_plotting_embedded/test_embeddings.py"
+ "test_embedding_colorbar_location")))
+ (string-append "--deselect=tests/test_plotting.py"
+ "::test_umap_categories_change_"
+ "when_rerun_with_more_categories")
+ (string-append "--deselect=tests/test_plotting.py"
+ "::test_umap_categories_dont_change_"
+ "when_rerun_with_fewer_categories")
+ (string-append "--deselect=get/_aggregated.py"
+ "::scanpy.get._aggregated.aggregate")
+ (string-append "--deselect=external/pp/_magic.py"
+ "::scanpy.external.pp._magic.magic")
+ (string-append "--deselect=external/pp/_harmony_integrate.py"
+ "::scanpy.external.pp."
+ "_harmony_integrate.harmony_integrate")
+ #$@(map (lambda (ls) (string-append "--deselect=tests/"
+ (string-join ls "::")))
+ ;; Tests failing with error: Image files did not match.
+ '(("test_plotting.py" "test_rankings")
+ ("test_plotting.py" "test_dotplot_obj")
+ ("test_plotting.py" "test_stacked_violin_obj")
+ ("test_plotting.py" "test_dotplot_add_totals")
+ ("test_plotting.py" "test_rank_genes_group_axes")
+ ("test_plotting.py" "test_scatter_no_basis_per_obs")
+ ("test_plotting.py"
+ "test_dotplot_matrixplot_stacked_violin")
+ ("test_plotting_embedded/test_spatial.py"
+ "test_spatial_general")
+ ("test_plotting_embedded/test_spatial.py"
+ "test_visium_empty_img_key")
+ ("test_plotting_embedded/test_spatial.py"
+ "test_spatial_external_img")))
+ #$@(map (lambda (ls) (string-append "--deselect=tests/"
+ (string-join ls "::")))
+ ;; Failed on deprecation warnings.
+ '(("external/test_magic.py" "test_magic_copy")
+ ("external/test_magic.py" "test_magic_default")
+ ("external/test_magic.py" "test_magic_pca_only")
+ ("test_preprocessing.py"
+ "test_regress_out_constants")
+ ("test_preprocessing.py"
+ "test_regress_out_reproducible")
+ ("test_preprocessing.py"
+ "test_regress_out_constants_equivalent")))
+ #$@(map (lambda (ls) (string-append "--deselect=tests/"
+ (string-join ls "::")))
+ ;; TypeError: deprecate_kwarg() missing 1 required
+ ;; positional argument: 'new_arg_name'
+ '(("test_preprocessing.py"
"test_regress_out_categorical")
+ ;; TypeError: Cannot interpret
+ ;; '<StringDtype(na_value=nan)>' as a data type
+ ("test_combat.py" "test_norm")
+ ;; TypeError: only integer scalar arrays can be
+ ;; converted to a scalar index
+ ("test_combat.py" "test_covariates")
+ ("test_combat.py" "test_combat_obs_names")
+ ("test_combat.py" "test_silhouette")
+ ;; [XPASS(strict)] seaborn violin plot is
+ ;; incompatible with pandas 3
+ ("test_plotting.py" "test_rank_genes_groups")
+ ;; pytest.PytestUnhandledThreadExceptionWarning:
+ ;; Exception in thread ExecutorManagerThread
+ ("test_preprocessing.py"
+ "test_regress_out_categorical"))))
#:phases
#~(modify-phases %standard-phases
+ (add-after 'unpack 'fix-pytest-config
+ (lambda _
+ (substitute* "pyproject.toml"
+ ;; ModuleNotFoundError: No module named 'pyparsing.warnings'
+ ((".*pyparsing.warnings.*") ""))))
(add-before 'check 'pre-check
(lambda _
;; Numba needs a writable dir to cache functions.
@@ -19741,6 +19819,8 @@ implementation differs in these ways:
(setenv "HOME" "/tmp"))))))
(propagated-inputs
(list python-anndata
+ python-certifi
+ python-fast-array-utils
python-h5py
python-joblib
python-legacy-api-wrap
@@ -19755,19 +19835,25 @@ implementation differs in these ways:
python-pynndescent
python-scikit-learn
python-scipy
+ python-scverse-misc
python-seaborn
python-session-info2
python-statsmodels
python-tqdm
- python-typing-extensions
+ python-typing-extensions ;Python version <3.13
python-umap-learn
;; [optional]
python-dask
+ python-harmonypy
python-igraph
+ python-leidenalg
python-louvain
+ python-magic-impute
+ python-scikit-misc
python-setuptools)) ;for pkg_resources
(native-inputs
- (list python-dependency-groups
+ (list nss-certs-for-test
+ python-dependency-groups
python-hatch-vcs
python-hatchling
python-pytest
@@ -19775,7 +19861,6 @@ implementation differs in these ways:
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")
