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gnu: python-scanpy: Update to 1.9.1.

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* 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.
This commit is contained in:
Ricardo Wurmus 2022-05-30 23:07:52 +02:00
parent ca2516f065
commit 0bcd28e58c
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GPG key ID: 197A5888235FACAC
1 changed files with 15 additions and 3 deletions
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gnu/packages/bioinformatics.scm
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@ -12248,7 +12248,7 @@ (define-public fit-sne
(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 @@ (define-public python-scanpy
(file-name (git-file-name name version))
(sha256
(base32
"14zax23lqinv7xyv3491vpl3ydi38naiwaxg5mkfs5zk2406cqdr"))))
"0k524xnx3dvpz5yx65p316wghvi01zs17is8w2m3w2qywiswk0sl"))))
(build-system python-build-system)
(arguments
`(#:phases
@ -12278,6 +12278,10 @@ (define-public python-scanpy
(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 @@ (define-public python-scanpy
(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 @@ (define-public python-scanpy
(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 @@ (define-public python-scanpy
" 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 @@ (define-public python-scanpy
python-scikit-learn
python-scipy
python-seaborn
python-session-info
python-sinfo
python-statsmodels
python-tables