diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2023-04-26 22:53:26 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2023-04-26 22:53:26 +0200 |
| commit | bb385f247292d3162b27afa7ac48a1bf404c8e37 (patch) | |
| tree | 572c9af164de4fe05ed6306d6f2ceed1734b7622 | |
| parent | 4ea332cd5068df74e4bfff52e84cf128b510e221 (diff) | |
gnu: python-dendropy: Fix build.
* gnu/packages/bioinformatics.scm (python-dendropy)[native-inputs]: Add
python-pytest.
[arguments]: Add phase 'python-compatibility; remove 'skip-broken-tests; add
#:test-flags; do not delete test files.
[build-system]: Use pyproject-build-system.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 41 |
1 files changed, 22 insertions, 19 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2bf00e14ca..ef84e65ed7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3897,26 +3897,29 @@ CWL descriptions.") (sha256 (base32 "0lrfzjqzbpk1rrra9vd7z2j7q09jy9w1ss7wn2rd85i4k5y3xz8l")))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'skip-broken-tests - (lambda _ - ;; These tests fail because we have no "paup" executable. - (substitute* "tests/test_datamodel_split_bitmasks.py" - (((format #false "(~{~a~^|~})" - '("test_group1" - "test_basic_split_counting_under_different_rootings" - "test_basic_split_count_with_incorrect_weight_treatment_raises_error" - "test_basic_split_count_with_incorrect_rootings_raises_error")) m) - (string-append "_skip_" m))) - (delete-file "tests/test_paup.py") - (delete-file "tests/test_dataio_nexml_reader_tree_list.py") - ;; Assert error for unknown reasons - (substitute* "tests/test_protractedspeciation.py" - (("test_by_num_lineages" m) - (string-append "_skip_" m)))))))) + (list + #:test-flags + '(list "-k" + (string-join + ;; These tests fail because we have no "paup" executable. + (list "not test_group1" + "test_basic_split_counting_under_different_rootings" + "test_basic_split_count_with_incorrect_weight_treatment_raises_error" + "test_basic_split_count_with_incorrect_rootings_raises_error" + + ;; Assert error for unknown reasons + "test_by_num_lineages") + " and not ")) + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'python-compatibility + (lambda _ + (substitute* "tests/test_datamodel_taxon.py" + (("collections.Iterable") + "collections.abc.Iterable"))))))) + (native-inputs (list python-pytest)) (home-page "https://dendropy.org/") (synopsis "Library for phylogenetics and phylogenetic computing") (description |