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gnu: python-scanpy: Update to 1.8.1.

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* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.8.1.
[arguments]: Bulid with flit; update list of broken tests.
[native-inputs]: Add python-flit and python-anndata:source.
This commit is contained in:
Ricardo Wurmus 2021-08-30 18:25:09 +02:00
parent 105d8196be
commit b105655670
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1 changed files with 48 additions and 15 deletions
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63
gnu/packages/bioinformatics.scm
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@ -11452,38 +11452,53 @@ (define-public fit-sne
(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 @@ (define-public python-scanpy
(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 @@ (define-public python-scanpy
("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)))