guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit 5ff7e522808f66448d1e5822340149921d39c23e
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Sat Jun 27 23:20:39 2026 +0100
gnu: python-anndata: Update to 0.13.0rc3.
* gnu/packages/python-science.scm (python-anndata): Update to 0.13.0rc3.
[arguments] <test-flags> Simplify skipped tests by utilizing "not gpu"
marker to ignore all tests requiring CUDA.
[propagated-inputs]: Add python-scverse-misc and python-typing-extensions.
[native-inputs]: Add python-jsonschema.
---
gnu/packages/python-science.scm | 57 ++++++++---------------------------------
1 file changed, 10 insertions(+), 47 deletions(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index a9301b3e3a..91361b63af 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -272,7 +272,7 @@ possibility to differentiate functions that contain matrix
functions as
(define-public python-anndata
(package
(name "python-anndata")
- (version "0.12.7")
+ (version "0.13.0rc3")
(source
(origin
(method git-fetch)
@@ -281,58 +281,18 @@ possibility to differentiate functions that contain
matrix functions as
(commit version)))
(file-name (git-file-name name version))
(sha256
- (base32 "1404x0z37z7xfdzkkafh62amchikrz0ssyc83rn6pv3dd4nn8nid"))))
+ (base32 "0hbnp4pw8wpn2lcds0wa92kb8x4bdkiv76dijg7g4pj0v86qm034"))))
(build-system pyproject-build-system)
(arguments
(list
- ;; tests: 4167 passed, 1208 skipped, 12 xfailed, 2225 warnings
+ ;; tests: 6677 passed, 1842 skipped, 195 xfailed, 4842 warnings, 98
+ ;; subtests passed
#:test-flags
- #~(list "--numprocesses" (number->string (min 8 (parallel-job-count)))
+ #~(list "-m" "not gpu"
+ "--numprocesses" (number->string (min 8 (parallel-job-count)))
;; XXX: AttributeError: module 'pyarrow.lib' has no attribute
;; 'PyExtensionType'
- "--ignore=tests/test_awkward.py"
- ;; These tests require CUDA backed package:
- ;; <https://github.com/cupy/cupy>.
- "--deselect=sts/test_views.py::test_view_of_view"
- #$@(map (lambda (test) (string-append "--deselect="
- "tests/"
- test))
- (list "test_concatenate.py::test_concatenate_layers"
-
"test_concatenate.py::test_concat_different_types_dask"
-
"test_concatenate.py::test_concat_on_var_outer_join"
-
"test_concatenate.py::test_concatenate_layers_misaligned"
-
"test_concatenate.py::test_concatenate_layers_outer"
- "test_concatenate.py::test_concatenate_roundtrip"
- "test_concatenate.py::test_error_on_mixed_device"
- "test_concatenate.py::test_nan_merge"
- "test_concatenate.py::test_pairwise_concat"
- "test_concatenate.py::test_transposed_concat"
- "test_dask.py::test_dask_to_disk_view"
- "test_dask.py::test_dask_to_memory_unbacked"
- "test_gpu.py::test_adata_raw_gpu"
- "test_gpu.py::test_gpu"
- "test_gpu.py::test_raw_gpu"
- "test_helpers.py::test_as_cupy_dask"
- "test_helpers.py::test_as_dask_functions"
- "test_io_elementwise.py::test_io_spec_cupy"
- "test_obsmvarm.py::test_1d_declaration"
- "test_obsmvarm.py::test_1d_set"
- "test_views.py::test_ellipsis_index"
- "test_views.py::test_modify_view_component"
- "test_views.py::test_set_scalar_subset_X"
- "test_views.py::test_view_different_type_indices"
- "test_views.py::test_view_of_view"))
- "-k" (string-join
- ;; TypeError: _fix_co_filename() argument 2 must be str,
- ;; not PosixPath
- (list "not test_hints"
- ;; ValueError: Cannot convert. CSC format must be
- ;; 2D. Got 1D
- "test_backed_modification_sparse[csc_matrix]"
- ;; Failed: DID NOT WARN. No warnings of type (<class
- ;; 'FutureWarning'>,) were emitted.
- "test_old_format_warning_thrown")
- " and not "))
+ "--ignore=tests/test_awkward.py")
#:phases
#~(modify-phases %standard-phases
;; Doctests require scanpy from (gnu packages bioinformatics)
@@ -354,6 +314,7 @@ possibility to differentiate functions that contain matrix
functions as
python-hatch-vcs
python-hatchling
python-joblib
+ python-jsonschema
python-loompy
python-matplotlib
python-openpyxl
@@ -373,6 +334,8 @@ possibility to differentiate functions that contain matrix
functions as
python-packaging
python-pandas
python-scipy
+ python-scverse-misc
+ python-typing-extensions ;Python version < 3.13
python-zarr))
(home-page "https://github.com/theislab/anndata";)
(synopsis "Annotated data for data analysis pipelines")
