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gnu: python-scanpy: Update to 1.9.6.

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* 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
This commit is contained in:
Ricardo Wurmus 2024-01-08 23:34:03 +01:00
parent 6a2f1863e7
commit 447876fa0d
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GPG key ID: 197A5888235FACAC
1 changed files with 19 additions and 13 deletions
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32
gnu/packages/bioinformatics.scm
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@ -16449,7 +16449,7 @@ (define-public fit-sne
(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 @@ (define-public python-scanpy
(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 @@ (define-public python-scanpy
;; 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 @@ (define-public python-scanpy
`(;; 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")