guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit 2bed4ac3251cf2619472c0c551d9fb9668abc184
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Mon Dec 29 11:37:58 2025 +0000
gnu: python-anndata: Update to 0.12.7.
* gnu/packages/python-science.scm (python-anndata): Update to 0.12.7.
[arguments] <test-flags>: Skip CUDA dependent tests.
[phases]{set-version}: Remove setting zip timestamp logic.
[propagated-inputs]: Remove python-importlib-metadata,
python-scikit-learn, and python-setuptools; add python-numpy.
[native-inputs]: Add hdf5, python-openpyxl, python-pyarrow,
python-pytest-randomly, and python-scikit-learn.
Change-Id: I8e68cf85d435a13db995ea966ed5ff9edac3d672
---
gnu/packages/python-science.scm | 88 ++++++++++++++++++++++++++++-------------
1 file changed, 60 insertions(+), 28 deletions(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 99cb89d388..ed72ff8b46 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -258,35 +258,66 @@ possibility to differentiate functions that contain
matrix functions as
(define-public python-anndata
(package
(name "python-anndata")
- (version "0.12.1")
+ (version "0.12.7")
(source
(origin
- ;; The tarball from PyPi doesn't include tests.
(method git-fetch)
(uri (git-reference
(url "https://github.com/theislab/anndata";)
(commit version)))
(file-name (git-file-name name version))
(sha256
- (base32 "1pwqy1pxsiqf13kfshcbqah1a92x4044s6jyr94488ngpqkr275z"))))
+ (base32 "1404x0z37z7xfdzkkafh62amchikrz0ssyc83rn6pv3dd4nn8nid"))))
(build-system pyproject-build-system)
(arguments
(list
+ ;; tests: 4167 passed, 1208 skipped, 12 xfailed, 2225 warnings
#:test-flags
- #~(list "--numprocesses" (number->string (parallel-job-count))
+ #~(list "--numprocesses" (number->string (min 8 (parallel-job-count)))
;; XXX: AttributeError: module 'pyarrow.lib' has no attribute
- ;; 'PyExtensionType
+ ;; '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: read_text() takes from 1 to 2 positional
- ;; arguments but 4 were given
- (list "not test_read_csv"
- ;; TypeError: _fix_co_filename() argument 2 must be
- ;; str, not PosixPath
- "test_hints"
+ ;; 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_readloom_deprecations")
+ "test_old_format_warning_thrown")
" and not "))
#:phases
#~(modify-phases %standard-phases
@@ -297,27 +328,14 @@ possibility to differentiate functions that contain
matrix functions as
(("--doctest-modules") ""))))
(add-before 'build 'set-version
(lambda _
- (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)
- ;; ZIP does not support timestamps before 1980.
- (setenv "SOURCE_DATE_EPOCH" "315532800")))
+ (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"))))))
- (propagated-inputs
- (list python-array-api-compat
- python-h5py
- python-importlib-metadata
- python-legacy-api-wrap
- python-natsort
- python-packaging
- python-pandas
- python-scikit-learn
- python-scipy
- python-setuptools ; For pkg_resources.
- python-zarr))
(native-inputs
- (list python-awkward
+ (list hdf5 ;for h5diff, tests/test_io_backwards_compat.py
+ python-awkward
python-boltons
python-dask
python-distributed
@@ -327,10 +345,24 @@ possibility to differentiate functions that contain
matrix functions as
python-joblib
python-loompy
python-matplotlib
+ python-openpyxl
+ python-pyarrow
python-pytest
python-pytest-mock
+ python-pytest-randomly
python-pytest-xdist
+ python-scikit-learn
python-setuptools-scm))
+ (propagated-inputs
+ (list python-array-api-compat
+ python-h5py
+ python-legacy-api-wrap
+ python-natsort
+ python-numpy
+ python-packaging
+ python-pandas
+ python-scipy
+ python-zarr))
(home-page "https://github.com/theislab/anndata";)
(synopsis "Annotated data for data analysis pipelines")
(description "Anndata is a package for simple (functional) high-level APIs
