63/105: gnu: python-biom-format: Use pyproject-build-system.
rekado pushed a commit to branch python-team in repository guix. commit f14cd2968de31ca66d462bbabbff88b27f223498 Author: Ricardo Wurmus AuthorDate: Tue Dec 17 11:28:01 2024 +0100 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 --- gnu/packages/bioinformatics.scm | 48 + 1 file changed, 15 insertions(+), 33 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c10983cc2d..1a551dfdc7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3479,48 +3479,30 @@ 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 @@ -3532,7 +3514,7 @@ 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
63/105: gnu: python-biom-format: Use pyproject-build-system.
rekado pushed a commit to branch python-team in repository guix. commit b45f3f4318efcdf398a8d98868cb4bb2f80fd4cf Author: Ricardo Wurmus AuthorDate: Tue Dec 17 11:28:01 2024 +0100 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 --- gnu/packages/bioinformatics.scm | 48 + 1 file changed, 15 insertions(+), 33 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c10983cc2d..1a551dfdc7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3479,48 +3479,30 @@ 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 @@ -3532,7 +3514,7 @@ 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