branch master updated: gnu: python-scanpy: Run tests conditionally.

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     new 616bcc9  gnu: python-scanpy: Run tests conditionally.
616bcc9 is described below

commit 616bcc9c0b71de1cae271fa37ef8829872c92773
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Mon Nov 15 15:12:50 2021 +0000

    gnu: python-scanpy: Run tests conditionally.
    
    * gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Respect TESTS?
    argument.
---
 gnu/packages/bioinformatics.scm | 81 +++++++++++++++++++++--------------------
 1 file changed, 41 insertions(+), 40 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c5a1215..2ffe7f7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11996,47 +11996,48 @@ implementation differs in these ways:
                                    wheel (string-append "--prefix=" out)))
                          (find-files "dist" "\\.whl$")))))
          (replace 'check
-           (lambda* (#:key inputs #:allow-other-keys)
-             ;; 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_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")
-
-             ;; 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")
+           (lambda* (#:key tests? inputs #:allow-other-keys)
+             (when tests?
+               ;; 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_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")
+
+               ;; 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")
 
-             (setenv "PYTHONPATH"
-                     (string-append (getcwd) ":"
-                                    (assoc-ref inputs "python-anndata:source") 
":"
-                                    (getenv "PYTHONPATH")))
-             (invoke "pytest" "-vv"
-                     "-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"
-                                    " and not test_paga_compare"
-
-                                    ;; These try to connect to the network
-                                    " and not 
test_plot_rank_genes_groups_gene_symbols"
-                                    " and not test_pca_chunked"
-                                    " and not test_pca_sparse"
-                                    " and not test_pca_reproducible")))))))
+               (setenv "PYTHONPATH"
+                       (string-append (getcwd) ":"
+                                      (assoc-ref inputs 
"python-anndata:source") ":"
+                                      (getenv "PYTHONPATH")))
+               (invoke "pytest" "-vv"
+                       "-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"
+                                      " and not test_paga_compare"
+
+                                      ;; These try to connect to the network
+                                      " and not 
test_plot_rank_genes_groups_gene_symbols"
+                                      " and not test_pca_chunked"
+                                      " and not test_pca_sparse"
+                                      " and not test_pca_reproducible"))))))))
     (propagated-inputs
      `(("python-anndata" ,python-anndata)
        ("python-h5py" ,python-h5py)