rekado pushed a commit to branch master
in repository guix.
commit d731ec09837fb500fcbe073ec4e8796c8f7725c8
Author: Ricardo Wurmus <[email protected]>
AuthorDate: Wed Jan 8 10:23:57 2025 +0100
gnu: python-scanpy: Update to 1.10.4.
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.10.4.
[arguments]: Update list of disabled tests; rename phase 'discover-anndata
to
'add-anndata-source.
[native-inputs]: Add python-pytest-mock.
Change-Id: I409678c67d15f3d3e4147be68c7a987c0e095d23
---
gnu/packages/bioinformatics.scm | 66 ++++++++++++++++++++---------------------
1 file changed, 33 insertions(+), 33 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0482faf948..c94e87fe61 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014-2024 Ricardo Wurmus <[email protected]>
+;;; Copyright © 2014-2025 Ricardo Wurmus <[email protected]>
;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <[email protected]>
;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins
<[email protected]>
;;; Copyright © 2015 Andreas Enge <[email protected]>
@@ -18814,7 +18814,7 @@ implementation differs in these ways:
(define-public python-scanpy
(package
(name "python-scanpy")
- (version "1.9.6")
+ (version "1.10.4")
(source
(origin
(method git-fetch)
@@ -18824,12 +18824,33 @@ implementation differs in these ways:
(file-name (git-file-name name version))
(sha256
(base32
- "12rz0a9151fkry6ws1a8p5wnc4n5qbjl6xlynj7kxy223iz8isds"))))
+ "139d6fsdbhg1hqqq5yyl8hr3cqz2mj70i0i8r1mq6z6a8qmq1p4z"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
- '(list "-k"
+ '(list "-m" "not gpu"
+ ;; These tests require Internet access.
+ "--ignore-glob=tests/notebooks/*"
+ "--ignore=tests/test_clustering.py"
+ "--ignore=tests/test_datasets.py"
+ "--ignore=tests/test_normalization.py"
+ "--ignore=tests/test_score_genes.py"
+ "--ignore=tests/test_highly_variable_genes.py"
+ "--ignore=tests/test_aggregated.py"
+ "--ignore=get/_aggregated.py"
+ ;; TODO: I can't get the plotting tests to work, even with Xvfb.
+ ;; Some of them also require Internet access because they want to
+ ;; download a dataset.
+ "--ignore=tests/test_plotting.py"
+ "--ignore=tests/test_embedding_plots.py"
+ "--ignore=tests/test_preprocessing.py"
+ "--ignore=tests/test_read_10x.py"
+ "--ignore=plotting/_tools/scatterplots.py"
+ ;; The following tests requires 'scanorama', which isn't
+ ;; packaged yet.
+ "--ignore=tests/external/test_scanorama_integrate.py"
+ "-k"
;; Plot tests that fail.
(string-append "not test_clustermap"
" and not test_dotplot_matrixplot_stacked_violin"
@@ -18840,48 +18861,26 @@ implementation differs in these ways:
" and not test_violin"
" and not test_scatter_no_basis_per_obs"
- ;; Type mismatch
- " and not test_obs_df"
- " and not test_var_df"
-
- ;; Minor accuracy problem
- " and not test_consistency[morans_i-allclose]"
+ ;; These are doctests that fail because of missing
+ ;; datasets.
+ " and not scanpy.get._aggregated.aggregate"
+ " and not
scanpy.plotting._tools.scatterplots.spatial"
;; These try to connect to the network
" and not test_scrublet_plots"
" and not test_plot_rank_genes_groups_gene_symbols"
" and not test_pca_n_pcs"
" and not test_pca_chunked"
+ " and not test_pca_layer"
" and not test_pca_sparse"
" and not test_pca_reproducible"
-
- ;; File is missing
- " and not test_pbmc3k")
- ;; TODO: I can't get the plotting tests to work, even with Xvfb.
- "--ignore=scanpy/tests/test_plotting.py"
- "--ignore=scanpy/tests/test_embedding_plots.py"
- "--ignore=scanpy/tests/test_preprocessing.py"
- "--ignore=scanpy/tests/test_read_10x.py"
-
- ;; These two fail with "ValueError: I/O operation on closed file."
- "--ignore=scanpy/tests/test_neighbors_key_added.py"
-
- ;; These tests require Internet access.
- "--ignore-glob=scanpy/tests/notebooks.*"
- "--ignore=scanpy/tests/test_clustering.py"
- "--ignore=scanpy/tests/test_datasets.py"
- "--ignore=scanpy/tests/test_normalization.py"
- "--ignore=scanpy/tests/test_score_genes.py"
- "--ignore=scanpy/tests/test_highly_variable_genes.py"
- ;; The following tests requires 'scanorama', which isn't packaged
- ;; yet.
- "--ignore=scanpy/tests/external/test_scanorama_integrate.py")
+ " and not test_clip"))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'pretend-version
(lambda _
(setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)))
- (add-after 'unpack 'discover-anndata
+ (add-after 'unpack 'add-anndata-source
(lambda _
(setenv "PYTHONPATH"
(string-append (getcwd) ":"
@@ -18924,6 +18923,7 @@ implementation differs in these ways:
("python-hatch-vcs" ,python-hatch-vcs)
("python-leidenalg" ,python-leidenalg)
("python-pytest" ,python-pytest)
+ ("python-pytest-mock" ,python-pytest-mock)
("python-pytest-nunit" ,python-pytest-nunit)
("python-setuptools-scm" ,python-setuptools-scm)))
(home-page "https://github.com/theislab/scanpy";)
