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| author | Ricardo Wurmus <rekado@elephly.net> | 2022-05-30 23:07:52 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2022-05-30 23:09:46 +0200 |
| commit | 0bcd28e58cb8f06bc6d0e47da22cef3d834a6da7 (patch) | |
| tree | 2f92b39f286d356f7a54056a2916538aad783e45 /gnu/packages/bioinformatics.scm | |
| parent | ca2516f0653c33494701ad02638bf5d7c5c74f25 (diff) | |
| download | guix-patches-0bcd28e58cb8f06bc6d0e47da22cef3d834a6da7.tar guix-patches-0bcd28e58cb8f06bc6d0e47da22cef3d834a6da7.tar.gz | |
gnu: python-scanpy: Update to 1.9.1.
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.9.1.
[arguments]: Add phase 'set-numba-cache-dir; disable more broken tests.
[propagated-inputs]: Add python-dask and python-session-info; replace
python-louvain-0.7 with python-louvain.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 18 |
1 files changed, 15 insertions, 3 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1d8397c1aa..23c0024e52 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12248,7 +12248,7 @@ implementation differs in these ways: (define-public python-scanpy (package (name "python-scanpy") - (version "1.8.2") + (version "1.9.1") (source (origin (method git-fetch) @@ -12258,7 +12258,7 @@ implementation differs in these ways: (file-name (git-file-name name version)) (sha256 (base32 - "14zax23lqinv7xyv3491vpl3ydi38naiwaxg5mkfs5zk2406cqdr")))) + "0k524xnx3dvpz5yx65p316wghvi01zs17is8w2m3w2qywiswk0sl")))) (build-system python-build-system) (arguments `(#:phases @@ -12278,6 +12278,10 @@ implementation differs in these ways: (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? @@ -12285,6 +12289,7 @@ implementation differs in these ways: (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") @@ -12293,6 +12298,9 @@ implementation differs in these ways: (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") + ;; TODO: these fail with TypingError and "Use of unsupported ;; NumPy function 'numpy.split'". (delete-file "scanpy/tests/test_metrics.py") @@ -12318,17 +12326,20 @@ implementation differs in these ways: " 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")))))))) (propagated-inputs (list python-anndata + python-dask python-h5py python-igraph python-joblib python-legacy-api-wrap - python-louvain-0.7 + python-louvain python-matplotlib python-natsort python-networkx @@ -12339,6 +12350,7 @@ implementation differs in these ways: python-scikit-learn python-scipy python-seaborn + python-session-info python-sinfo python-statsmodels python-tables |