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23/59: gnu: python-scanpy: Update to 1.9.6.
From: |
guix-commits |
Subject: |
23/59: gnu: python-scanpy: Update to 1.9.6. |
Date: |
Tue, 16 Jan 2024 05:24:28 -0500 (EST) |
rekado pushed a commit to branch wip-python-science
in repository guix.
commit c3531f79900764795480b66ee602f7d0ea38104d
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 f75254ed9f..1f707a31c1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -16449,7 +16449,7 @@ 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)
@@ -16459,21 +16459,28 @@ 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"
@@ -16505,10 +16512,6 @@ 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")
@@ -16549,8 +16552,11 @@ 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")
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- 32/59: gnu: python-plastid: Update to 0.6.1., guix-commits, 2024/01/16
- 35/59: gnu: python-demuxem: Disable tests., guix-commits, 2024/01/16
- 29/59: gnu: python-pegasusio: Disable tests., guix-commits, 2024/01/16
- 41/59: gnu: python-hicexplorer: Make compatible with latest scipy., guix-commits, 2024/01/16
- 28/59: gnu: python-pyani: Disable tests., guix-commits, 2024/01/16
- 59/59: gnu: gourmet: Add missing input., guix-commits, 2024/01/16
- 58/59: gnu: python-pyrdfa3: Update to 3.6.2., guix-commits, 2024/01/16
- 33/59: gnu: python-cooler: Update to 0.9.1., guix-commits, 2024/01/16
- 39/59: gnu: python-scikit-optimize: Make compatible with latest sklearn., guix-commits, 2024/01/16
- 23/59: gnu: python-scanpy: Update to 1.9.6.,
guix-commits <=
- 30/59: gnu: python-reportlab: Update to 4.0.8., guix-commits, 2024/01/16
- 08/59: gnu: python-tifffile: Update to 2023.12.9., guix-commits, 2024/01/16
- 22/59: gnu: Add python-pytest-nunit., guix-commits, 2024/01/16
- 43/59: gnu: python-metpy: Update to 1.6.0., guix-commits, 2024/01/16
- 49/59: gnu: python-adjusttext: Disable tests., guix-commits, 2024/01/16
- 46/59: gnu: python-click-default-group: Update to 1.2.4., guix-commits, 2024/01/16
- 44/59: gnu: Add python-asyncinject., guix-commits, 2024/01/16
- 31/59: gnu: cnvkit: Update to 0.9.10., guix-commits, 2024/01/16
- 38/59: gnu: python-fit-nbinom: Disable tests., guix-commits, 2024/01/16
- 34/59: gnu: python-pint: Update to 0.23., guix-commits, 2024/01/16