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authorRicardo Wurmus <rekado@elephly.net>2022-05-30 23:07:52 +0200
committerRicardo Wurmus <rekado@elephly.net>2022-05-30 23:09:46 +0200
commit0bcd28e58cb8f06bc6d0e47da22cef3d834a6da7 (patch)
tree2f92b39f286d356f7a54056a2916538aad783e45 /gnu/packages/bioinformatics.scm
parentca2516f0653c33494701ad02638bf5d7c5c74f25 (diff)
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.scm18
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