diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 79 |
1 files changed, 33 insertions, 46 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1d3c5d6312..c41cdfbd86 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12802,32 +12802,35 @@ implementation differs in these ways: (sha256 (base32 "0k524xnx3dvpz5yx65p316wghvi01zs17is8w2m3w2qywiswk0sl")))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'build - (lambda _ - (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" ,version) - ;; ZIP does not support timestamps before 1980. - (setenv "SOURCE_DATE_EPOCH" "315532800") - (invoke "flit" "build"))) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (let ((out (assoc-ref outputs "out"))) - (for-each (lambda (wheel) - (format #true wheel) - (invoke "python" "-m" "pip" "install" - wheel (string-append "--prefix=" out))) - (find-files "dist" "\\.whl$"))))) - ;; Numba needs a writable dir to cache functions. - (add-before 'check 'set-numba-cache-dir - (lambda _ - (setenv "NUMBA_CACHE_DIR" "/tmp"))) - (replace 'check - (lambda* (#:key tests? inputs #:allow-other-keys) - (when tests? + (list + #:test-flags + '(list "-k" + ;; Plot tests that fail. + (string-append "not test_dotplot_matrixplot_stacked_violin" + " and not test_violin_without_raw" + " and not test_correlation" + " and not test_scatterplots" + " and not test_scatter_embedding_add_outline_vmin_vmax_norm" + " and not test_paga" + " and not test_paga_compare" + " and not test_clustermap" + + ;; These try to connect to the network + " and not test_scrublet_plots" + " and not test_plot_rank_genes_groups_gene_symbols" + " and not test_pca_n_pcs" + " and not test_pca_chunked" + " and not test_pca_sparse" + " and not test_pca_reproducible")) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'pretend-version + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version))) + (add-after 'unpack 'delete-bad-tests + (lambda _ ;; These tests require Internet access. (delete-file-recursively "scanpy/tests/notebooks") (delete-file "scanpy/tests/test_clustering.py") @@ -12854,27 +12857,11 @@ implementation differs in these ways: (setenv "PYTHONPATH" (string-append (getcwd) ":" - (assoc-ref inputs "python-anndata:source") ":" - (getenv "GUIX_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" - " and not test_clustermap" - - ;; These try to connect to the network - " and not test_scrublet_plots" - " and not test_plot_rank_genes_groups_gene_symbols" - " and not test_pca_n_pcs" - " and not test_pca_chunked" - " and not test_pca_sparse" - " and not test_pca_reproducible")))))))) + #$(this-package-native-input "python-anndata:source") ":" + (getenv "GUIX_PYTHONPATH"))))) + ;; Numba needs a writable dir to cache functions. + (add-before 'check 'set-numba-cache-dir + (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp")))))) (propagated-inputs (list python-anndata python-dask |