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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.
master
Ricardo Wurmus 2023-04-26 22:53:26 +02:00
parent 4ea332cd50
commit bb385f2472
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GPG Key ID: 197A5888235FACAC
1 changed files with 22 additions and 19 deletions
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@ -3897,26 +3897,29 @@ CWL descriptions.")
(sha256 (sha256
(base32 (base32
"0lrfzjqzbpk1rrra9vd7z2j7q09jy9w1ss7wn2rd85i4k5y3xz8l")))) "0lrfzjqzbpk1rrra9vd7z2j7q09jy9w1ss7wn2rd85i4k5y3xz8l"))))
(build-system python-build-system) (build-system pyproject-build-system)
(arguments (arguments
`(#:phases (list
(modify-phases %standard-phases #:test-flags
(add-after 'unpack 'skip-broken-tests '(list "-k"
(lambda _ (string-join
;; These tests fail because we have no "paup" executable. ;; These tests fail because we have no "paup" executable.
(substitute* "tests/test_datamodel_split_bitmasks.py" (list "not test_group1"
(((format #false "(~{~a~^|~})"
'("test_group1"
"test_basic_split_counting_under_different_rootings" "test_basic_split_counting_under_different_rootings"
"test_basic_split_count_with_incorrect_weight_treatment_raises_error" "test_basic_split_count_with_incorrect_weight_treatment_raises_error"
"test_basic_split_count_with_incorrect_rootings_raises_error")) m) "test_basic_split_count_with_incorrect_rootings_raises_error"
(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 ;; Assert error for unknown reasons
(substitute* "tests/test_protractedspeciation.py" "test_by_num_lineages")
(("test_by_num_lineages" m) " and not "))
(string-append "_skip_" m)))))))) #: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/") (home-page "https://dendropy.org/")
(synopsis "Library for phylogenetics and phylogenetic computing") (synopsis "Library for phylogenetics and phylogenetic computing")
(description (description