diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 63 |
1 files changed, 48 insertions, 15 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1974978700..ac918eac8f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11452,38 +11452,53 @@ implementation differs in these ways: (define-public python-scanpy (package (name "python-scanpy") - (version "1.7.2") + (version "1.8.1") (source (origin - (method url-fetch) - (uri (pypi-uri "scanpy" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/theislab/scanpy") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "0c66adnfizsyk0h8bv2yhmay876z0klpxwpn4z6m71wly7yplpmd")))) + "0w1qmv3djqi8q0sn5hv34ivzs157fwjjb9nflfnagnhpxmw8vx5g")))) (build-system python-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$"))))) (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_plotting.py") + (delete-file "scanpy/tests/test_embedding_plots.py") (delete-file "scanpy/tests/test_preprocessing.py") (delete-file "scanpy/tests/test_read_10x.py") - ;; The following tests need anndata.tests, which aren't included - ;; in the final python-anndata package. - (delete-file "scanpy/tests/test_combat.py") - (delete-file "scanpy/tests/test_embedding_plots.py") - (delete-file "scanpy/tests/test_normalization.py") - (delete-file "scanpy/tests/test_pca.py") - (delete-file "scanpy/tests/external/test_scrublet.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. @@ -11491,9 +11506,24 @@ implementation differs in these ways: (setenv "PYTHONPATH" (string-append (getcwd) ":" + (assoc-ref inputs "python-anndata:source") ":" (getenv "PYTHONPATH"))) - (invoke "pytest") - #t))))) + (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) @@ -11517,7 +11547,10 @@ implementation differs in these ways: ("python-tqdm" ,python-tqdm) ("python-umap-learn" ,python-umap-learn))) (native-inputs - `(("python-leidenalg" ,python-leidenalg) + `(;; This package needs anndata.tests, which is not installed. + ("python-anndata:source" ,(package-source python-anndata)) + ("python-flit" ,python-flit) + ("python-leidenalg" ,python-leidenalg) ("python-pytest" ,python-pytest) ("python-setuptools-scm" ,python-setuptools-scm) ("python-sinfo" ,python-sinfo))) |