mirror/guix
mirror/guix
1
Fork 0
mirror of https://https.git.savannah.gnu.org/git/guix.git/ synced 2025-07-13 18:40:57 +02:00
Code Releases Activity

gnu: python-scanpy: Update to 1.10.4.

Browse source 
* 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
This commit is contained in:
Ricardo Wurmus 2025-01-08 10:23:57 +01:00
parent 9179247361
commit d731ec0983
No known key found for this signature in database
GPG key ID: 197A5888235FACAC
1 changed files with 33 additions and 33 deletions
Download patch file Download diff file Expand all files Collapse all files

66
gnu/packages/bioinformatics.scm
View file

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014-2024 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2014-2025 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
@ -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")