guix_mirror_bot pushed a commit to branch master
in repository guix.
commit b91c64a3a538726a560526f9496191b33ef1ddb5
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Wed Aug 6 21:42:20 2025 +0100
gnu: python-anndata: Update to 0.12.1.
* 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
---
gnu/packages/python-science.scm | 40 ++++++++++++++++++++++------------------
1 file changed, 22 insertions(+), 18 deletions(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index b71f693538..24c56d14a2 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -253,28 +253,36 @@ possibility to differentiate functions that contain
matrix functions as
(define-public python-anndata
(package
(name "python-anndata")
- (version "0.11.1")
+ (version "0.12.1")
(source
(origin
;; The tarball from PyPi doesn't include tests.
(method git-fetch)
(uri (git-reference
- (url "https://github.com/theislab/anndata";)
- (commit version)))
+ (url "https://github.com/theislab/anndata";)
+ (commit version)))
(file-name (git-file-name name version))
(sha256
- (base32
- "0skmjjvxk5gdsx6fkplszff92jsb4l45j23c6mhq1vdi3wqhqhcw"))))
+ (base32 "1pwqy1pxsiqf13kfshcbqah1a92x4044s6jyr94488ngpqkr275z"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
- #~(list "-k" #$(string-append
- ;; This one test seemingly freezes
- "not test_read_lazy_h5_cluster"
- ;; Fails with a numpy deprecation warning
- ;; but not an actual failure
- " and not test_read_write_X"))
+ #~(list "--numprocesses" (number->string (parallel-job-count))
+ ;; XXX: AttributeError: module 'pyarrow.lib' has no attribute
+ ;; 'PyExtensionType
+ "--ignore=tests/test_awkward.py"
+ "-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"
+ ;; Failed: DID NOT WARN. No warnings of type (<class
+ ;; 'FutureWarning'>,) were emitted.
+ "test_readloom_deprecations")
+ " and not "))
#:phases
#~(modify-phases %standard-phases
;; 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"))))))
(propagated-inputs
(list python-array-api-compat
- python-exceptiongroup ;only for Python <3.11
python-h5py
python-importlib-metadata
+ python-legacy-api-wrap
python-natsort
- python-numcodecs
python-packaging
python-pandas
- python-scipy
python-scikit-learn
+ python-scipy
python-setuptools ; For pkg_resources.
python-zarr))
(native-inputs
@@ -309,17 +316,14 @@ possibility to differentiate functions that contain
matrix functions as
python-boltons
python-dask
python-distributed
- python-hatchling
python-hatch-vcs
+ python-hatchling
python-joblib
python-loompy
python-matplotlib
python-pytest
python-pytest-mock
- python-pytest-doctestplus
python-pytest-xdist
- python-toml
- python-flit
python-setuptools-scm))
(home-page "https://github.com/theislab/anndata";)
(synopsis "Annotated data for data analysis pipelines")
