From 917b81c8b0e80a3bfd7fbf891ccf9448b41ebb42 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Mon, 29 Dec 2025 11:37:58 +0000 Subject: [PATCH] gnu: python-anndata: Update to 0.12.7. * gnu/packages/python-science.scm (python-anndata): Update to 0.12.7. [arguments] : 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 Signed-off-by: Rutherther --- 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 99cb89d388e0b113711eb93f7ddc22341cfa1452..ed72ff8b46e8248451d9adc896531f28808fd119 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: + ;; . + "--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 (,) 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