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23/53: gnu: python-scanpy: Update to 1.9.6.
From: |
guix-commits |
Subject: |
23/53: gnu: python-scanpy: Update to 1.9.6. |
Date: |
Thu, 11 Jan 2024 09:43:00 -0500 (EST) |
rekado pushed a commit to branch wip-python-science
in repository guix.
commit 248bf373d777115cc2c552af3f6553889e8a947e
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Mon Jan 8 23:34:03 2024 +0100
gnu: python-scanpy: Update to 1.9.6.
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.9.6.
[arguments]: Update test flags.
[native-inputs]: Add python-hatchling, python-hatch-vcs, and
python-pytest-nunit.
Change-Id: I6d4dcd267a076c5697ed103650841f520dc9917f
---
gnu/packages/bioinformatics.scm | 32 +++++++++++++++++++-------------
1 file changed, 19 insertions(+), 13 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f574fea0e9..a279b8b993 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -16390,7 +16390,7 @@ implementation differs in these ways:
(define-public python-scanpy
(package
(name "python-scanpy")
- (version "1.9.1")
+ (version "1.9.6")
(source
(origin
(method git-fetch)
@@ -16400,21 +16400,28 @@ implementation differs in these ways:
(file-name (git-file-name name version))
(sha256
(base32
- "0k524xnx3dvpz5yx65p316wghvi01zs17is8w2m3w2qywiswk0sl"))))
+ "12rz0a9151fkry6ws1a8p5wnc4n5qbjl6xlynj7kxy223iz8isds"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
'(list "-k"
;; Plot tests that fail.
- (string-append "not test_dotplot_matrixplot_stacked_violin"
- " and not test_violin_without_raw"
- " and not test_correlation"
- " and not test_scatterplots"
- " and not
test_scatter_embedding_add_outline_vmin_vmax_norm"
- " and not test_paga"
+ (string-append "not test_clustermap"
+ " and not test_dotplot_matrixplot_stacked_violin"
" and not test_paga_compare"
- " and not test_clustermap"
+ " and not test_paga_path"
+ " and not test_paga_pie"
+ " and not test_paga_plots"
+ " 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 try to connect to the network
" and not test_scrublet_plots"
@@ -16446,10 +16453,6 @@ implementation differs in these ways:
;; These two fail with "ValueError: I/O operation on closed
file."
(delete-file "scanpy/tests/test_neighbors_key_added.py")
- ;; TODO: these fail with TypingError and "Use of unsupported
- ;; NumPy function 'numpy.split'".
- (delete-file "scanpy/tests/test_metrics.py")
-
;; The following tests requires 'scanorama', which isn't
;; packaged yet.
(delete-file
"scanpy/tests/external/test_scanorama_integrate.py")
@@ -16490,8 +16493,11 @@ implementation differs in these ways:
`(;; This package needs anndata.tests, which is not installed.
("python-anndata:source" ,(package-source python-anndata))
("python-flit" ,python-flit)
+ ("python-hatchling" ,python-hatchling)
+ ("python-hatch-vcs" ,python-hatch-vcs)
("python-leidenalg" ,python-leidenalg)
("python-pytest" ,python-pytest)
+ ("python-pytest-nunit" ,python-pytest-nunit)
("python-setuptools-scm" ,python-setuptools-scm)))
(home-page "https://github.com/theislab/scanpy")
(synopsis "Single-Cell Analysis in Python")
- 26/53: gnu: python-captum: Update to 0.7.0., (continued)
- 26/53: gnu: python-captum: Update to 0.7.0., guix-commits, 2024/01/11
- 38/53: gnu: python-fit-nbinom: Disable tests., guix-commits, 2024/01/11
- 40/53: gnu: python-hicmatrix: Update to 17.1., guix-commits, 2024/01/11
- 47/53: gnu: python-pandas: Update to 1.5.3., guix-commits, 2024/01/11
- 11/53: gnu: python-scikit-image: Update to 0.22.0., guix-commits, 2024/01/11
- 19/53: gnu: Add python-contourpy., guix-commits, 2024/01/11
- 41/53: gnu: python-hicexplorer: Make compatible with latest scipy., guix-commits, 2024/01/11
- 10/53: gnu: python-imageio: Update to 2.33.1., guix-commits, 2024/01/11
- 13/53: gnu: python-matplotx: Disable test_png test., guix-commits, 2024/01/11
- 17/53: gnu: Add python-cppy., guix-commits, 2024/01/11
- 23/53: gnu: python-scanpy: Update to 1.9.6.,
guix-commits <=
- 04/53: gnu: Add python-pyproject-metadata-0.7., guix-commits, 2024/01/11
- 07/53: gnu: python-scipy: Update to 1.11.4., guix-commits, 2024/01/11
- 14/53: gnu: python-scikit-learn: Update to 1.3.2., guix-commits, 2024/01/11
- 37/53: gnu: scvelo: Make compatible with latest matplotlib., guix-commits, 2024/01/11
- 35/53: gnu: python-demuxem: Disable tests., guix-commits, 2024/01/11
- 27/53: gnu: tadbit: Add missing input., guix-commits, 2024/01/11
- 46/53: gnu: python-click-default-group: Update to 1.2.4., guix-commits, 2024/01/11
- 50/53: gnu: python-mysql-connector-python: Defuse time bomb., guix-commits, 2024/01/11
- 29/53: gnu: python-pegasusio: Disable tests., guix-commits, 2024/01/11
- 34/53: gnu: python-pint: Update to 0.23., guix-commits, 2024/01/11