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gnu: python-scanpy: Use more test-flags.

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* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Remove phase
'delete-bad-tests and use #:test-flags instead; add phase 'discover-anndata.

Change-Id: Idb5bd59a2bba968fbec820603938802cf9443bad
This commit is contained in:
Ricardo Wurmus 2025-01-01 19:53:32 +01:00
parent 333b5b1fae
commit 9ce6e9f94a
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GPG key ID: 197A5888235FACAC
1 changed files with 23 additions and 22 deletions
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45
gnu/packages/bioinformatics.scm
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@ -18789,34 +18789,35 @@ (define-public python-scanpy
" and not test_pca_n_pcs"
" and not test_pca_chunked"
" and not test_pca_sparse"
" and not test_pca_reproducible"))
" 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_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")
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'pretend-version
(lambda _
(setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)))
(add-after 'unpack 'delete-bad-tests
(add-after 'unpack 'discover-anndata
(lambda _
;; These tests require Internet access.
(delete-file-recursively "scanpy/tests/notebooks")
(delete-file "scanpy/tests/test_clustering.py")
(delete-file "scanpy/tests/test_datasets.py")
(delete-file "scanpy/tests/test_normalization.py")
(delete-file "scanpy/tests/test_score_genes.py")
(delete-file "scanpy/tests/test_highly_variable_genes.py")
;; TODO: I can't get the plotting tests to work, even with Xvfb.
(delete-file "scanpy/tests/test_embedding_plots.py")
(delete-file "scanpy/tests/test_preprocessing.py")
(delete-file "scanpy/tests/test_read_10x.py")
;; These two fail with "ValueError: I/O operation on closed file."
(delete-file "scanpy/tests/test_neighbors_key_added.py")
;; The following tests requires 'scanorama', which isn't
;; packaged yet.
(delete-file "scanpy/tests/external/test_scanorama_integrate.py")
(setenv "PYTHONPATH"
(string-append (getcwd) ":"
#$(this-package-native-input "python-anndata:source") ":"