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gnu: python-anndata: Update to 0.12.1.

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* gnu/packages/python-science.scm (python-anndata): Update to 0.12.1.
  [arguments] <test-flags>: Rework ignored and skipped tests.
  [propagated-inputs]: Remove python-exceptiongroup and
  python-numcodecs; add python-legacy-api-wrap.
  [native-inputs]: Remove python-pytest-doctestplus, python-toml, and
  python-flit.

Change-Id: I46c46c73f3a232345cc029d79b1018290505f5af
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Sharlatan Hellseher 2025-08-06 21:42:20 +01:00
parent 123ec7f705
commit b91c64a3a5
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1 changed files with 22 additions and 18 deletions
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@ -253,28 +253,36 @@ possibility to differentiate functions that contain matrix functions as
(define-public python-anndata (define-public python-anndata
(package (package
(name "python-anndata") (name "python-anndata")
(version "0.11.1") (version "0.12.1")
(source (source
(origin (origin
;; The tarball from PyPi doesn't include tests. ;; The tarball from PyPi doesn't include tests.
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
(url "https://github.com/theislab/anndata") (url "https://github.com/theislab/anndata")
(commit version))) (commit version)))
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32 "1pwqy1pxsiqf13kfshcbqah1a92x4044s6jyr94488ngpqkr275z"))))
"0skmjjvxk5gdsx6fkplszff92jsb4l45j23c6mhq1vdi3wqhqhcw"))))
(build-system pyproject-build-system) (build-system pyproject-build-system)
(arguments (arguments
(list (list
#:test-flags #:test-flags
#~(list "-k" #$(string-append #~(list "--numprocesses" (number->string (parallel-job-count))
;; This one test seemingly freezes ;; XXX: AttributeError: module 'pyarrow.lib' has no attribute
"not test_read_lazy_h5_cluster" ;; 'PyExtensionType
;; Fails with a numpy deprecation warning "--ignore=tests/test_awkward.py"
;; but not an actual failure "-k" (string-join
" and not test_read_write_X")) ;; 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"
;; Failed: DID NOT WARN. No warnings of type (<class
;; 'FutureWarning'>,) were emitted.
"test_readloom_deprecations")
" and not "))
#:phases #:phases
#~(modify-phases %standard-phases #~(modify-phases %standard-phases
;; Doctests require scanpy from (gnu packages bioinformatics) ;; Doctests require scanpy from (gnu packages bioinformatics)
@ -293,15 +301,14 @@ possibility to differentiate functions that contain matrix functions as
(setenv "NUMBA_CACHE_DIR" "/tmp")))))) (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
(propagated-inputs (propagated-inputs
(list python-array-api-compat (list python-array-api-compat
python-exceptiongroup ;only for Python <3.11
python-h5py python-h5py
python-importlib-metadata python-importlib-metadata
python-legacy-api-wrap
python-natsort python-natsort
python-numcodecs
python-packaging python-packaging
python-pandas python-pandas
python-scipy
python-scikit-learn python-scikit-learn
python-scipy
python-setuptools ; For pkg_resources. python-setuptools ; For pkg_resources.
python-zarr)) python-zarr))
(native-inputs (native-inputs
@ -309,17 +316,14 @@ possibility to differentiate functions that contain matrix functions as
python-boltons python-boltons
python-dask python-dask
python-distributed python-distributed
python-hatchling
python-hatch-vcs python-hatch-vcs
python-hatchling
python-joblib python-joblib
python-loompy python-loompy
python-matplotlib python-matplotlib
python-pytest python-pytest
python-pytest-mock python-pytest-mock
python-pytest-doctestplus
python-pytest-xdist python-pytest-xdist
python-toml
python-flit
python-setuptools-scm)) python-setuptools-scm))
(home-page "https://github.com/theislab/anndata") (home-page "https://github.com/theislab/anndata")
(synopsis "Annotated data for data analysis pipelines") (synopsis "Annotated data for data analysis pipelines")