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gnu: python-scanpy: Use pyproject-build-system.

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* gnu/packages/bioinformatics.scm (python-scanpy)[build-system]: Use
pyproject-build-system.
[arguments]: Remove custom 'build and 'install phases; move pytest arguments
to #:test-flags; add 'pretend-version phase; replace custom 'check phase with
'delete-bad-tests phase.
This commit is contained in:
Ricardo Wurmus 2022-12-18 15:28:20 +01:00
parent 6aebf864a7
commit 9cb42f725a
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GPG key ID: 197A5888235FACAC
1 changed files with 33 additions and 46 deletions
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79
gnu/packages/bioinformatics.scm
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@ -12802,32 +12802,35 @@ (define-public python-scanpy
(sha256
(base32
"0k524xnx3dvpz5yx65p316wghvi01zs17is8w2m3w2qywiswk0sl"))))
(build-system python-build-system)
(build-system pyproject-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$")))))
;; Numba needs a writable dir to cache functions.
(add-before 'check 'set-numba-cache-dir
(lambda _
(setenv "NUMBA_CACHE_DIR" "/tmp")))
(replace 'check
(lambda* (#:key tests? inputs #:allow-other-keys)
(when tests?
(list
#:test-flags
'(list "-k"
;; Plot tests that fail.
(string-append "not test_dotplot_matrixplot_stacked_violin"
" and not test_violin_without_raw"
" and not test_correlation"
" and not test_scatterplots"
" and not test_scatter_embedding_add_outline_vmin_vmax_norm"
" and not test_paga"
" and not test_paga_compare"
" and not test_clustermap"
;; These try to connect to the network
" and not test_scrublet_plots"
" and not test_plot_rank_genes_groups_gene_symbols"
" and not test_pca_n_pcs"
" and not test_pca_chunked"
" and not test_pca_sparse"
" and not test_pca_reproducible"))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'pretend-version
(lambda _
(setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)))
(add-after 'unpack 'delete-bad-tests
(lambda _
;; These tests require Internet access.
(delete-file-recursively "scanpy/tests/notebooks")
(delete-file "scanpy/tests/test_clustering.py")
@ -12854,27 +12857,11 @@ (define-public python-scanpy
(setenv "PYTHONPATH"
(string-append (getcwd) ":"
(assoc-ref inputs "python-anndata:source") ":"
(getenv "GUIX_PYTHONPATH")))
(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"
" 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"))))))))
#$(this-package-native-input "python-anndata:source") ":"
(getenv "GUIX_PYTHONPATH")))))
;; Numba needs a writable dir to cache functions.
(add-before 'check 'set-numba-cache-dir
(lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
(propagated-inputs
(list python-anndata
python-dask