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| author | Ricardo Wurmus <rekado@elephly.net> | 2025-01-01 19:53:32 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2025-01-01 19:53:32 +0100 |
| commit | 9ce6e9f94a532c22622cd972f0aeff5983743b7f (patch) | |
| tree | c48c19b75b22cb456bfa90801c2acdf285a9a436 /gnu/packages/bioinformatics.scm | |
| parent | 333b5b1faee1a7da979d99d7ad75887c6b19b6a2 (diff) | |
gnu: python-scanpy: Use more test-flags.
* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Remove phase
'delete-bad-tests and use #:test-flags instead; add phase 'discover-anndata.
Change-Id: Idb5bd59a2bba968fbec820603938802cf9443bad
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 45 |
1 files changed, 23 insertions, 22 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5c118aed07..ccf284d18f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -18789,34 +18789,35 @@ implementation differs in these ways: " 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") ":" |