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| author | Ricardo Wurmus <rekado@elephly.net> | 2024-12-17 11:28:01 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2025-01-20 21:37:22 +0100 |
| commit | 6fa324e355495986d1aed90b6bbc3d87a3755baa (patch) | |
| tree | 21e57870b7b645552d4cfe5f48bd563f9e58d916 /gnu/packages/bioinformatics.scm | |
| parent | 89246206f0ffb984941f804fc4155bea1dac5940 (diff) | |
gnu: python-biom-format: Use pyproject-build-system.
* gnu/packages/bioinformatics.scm (python-biom-format)[build-system]: Use
pyproject-build-system.
[arguments]: Replace phase 'disable-broken-tests with #:test-flags; enable one
test; add phase 'build-extensions.
[native-inputs]: Remove python-nose.
Change-Id: I8399d9b05bdb6da89d8056d536ab7e25dc22f9c2
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 48 |
1 files changed, 15 insertions, 33 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f12019372c..86bd84ce15 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3502,48 +3502,30 @@ use-case, we encourage users to compose functions to achieve their goals.") ;; Delete generated C files. (snippet '(for-each delete-file (find-files "." "\\.c"))))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments (list + #:test-flags + '(list "-k" + (string-append ;; Unclear why this one fails. There is no backtrace. + "not test_to_dataframe_is_sparse" + ;; These need skbio, but that neeeds biom-format. + " and not test_align_tree_intersect_obs" + " and not test_align_tree_intersect_tips" + " and not test_align_tree_sample")) #:phases '(modify-phases %standard-phases (add-after 'unpack 'use-cython (lambda _ (setenv "USE_CYTHON" "1"))) + (add-before 'check 'build-extensions + (lambda _ + ;; Cython extensions have to be built before running the tests. + (invoke "python" "setup.py" "build_ext" "--inplace"))) (add-after 'unpack 'pandas-compatibility (lambda _ (substitute* "biom/tests/test_table.py" (("import pandas.util.testing") - "import pandas.testing")))) - (add-after 'unpack 'disable-broken-tests - (lambda _ - (substitute* "biom/tests/test_util.py" - (("^(.+)def test_biom_open_hdf5_no_h5py" m indent) - (string-append indent - "@npt.dec.skipif(True, msg='Guix')\n" - m))) - (substitute* "biom/tests/test_table.py" - (("^(.+)def test_from_hdf5_issue_731" m indent) - (string-append indent - "@npt.dec.skipif(True, msg='Guix')\n" - m)) - ;; Unclear why this one fails. There is no backtrace. - (("^(.+)def test_to_dataframe_is_sparse" m indent) - (string-append indent - "@npt.dec.skipif(True, msg='Guix')\n" - m)) - ;; These need skbio, but that neeeds biom-format. - (("^(.+)def test_align_tree_intersect_obs" m indent) - (string-append indent - "@npt.dec.skipif(True, msg='Guix')\n" - m)) - (("^(.+)def test_align_tree_intersect_tips" m indent) - (string-append indent - "@npt.dec.skipif(True, msg='Guix')\n" - m)) - (("^(.+)def test_align_tree_sample" m indent) - (string-append indent - "@npt.dec.skipif(True, msg='Guix')\n" - m)))))))) + "import pandas.testing"))))))) (propagated-inputs (list python-anndata python-click @@ -3555,7 +3537,7 @@ use-case, we encourage users to compose functions to achieve their goals.") ;;python-scikit-bio ;mutually recursive dependency python-scipy)) (native-inputs - (list python-cython python-pytest python-pytest-cov python-nose)) + (list python-cython python-pytest python-pytest-cov)) (home-page "https://www.biom-format.org") (synopsis "Biological Observation Matrix (BIOM) format utilities") (description |