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rename openfecli fixture to avoid duplication with openfe fixture #1755

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Merged
atravitz merged 4 commits into from
Jan 7, 2026
Merged

rename openfecli fixture to avoid duplication with openfe fixture #1755

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c8c91bd
rename openfecli fixture to avoid duplication with openfe fixture
atravitz Dec 16, 2025
47c6398
Merge branch 'main' into fix/duplicate_fixture_names
atravitz Dec 17, 2025
c3fcc8a
Merge branch 'main' into fix/duplicate_fixture_names
IAlibay Jan 3, 2026
ae5ab63
Merge branch 'main' into fix/duplicate_fixture_names
atravitz Jan 7, 2026
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18 changes: 9 additions & 9 deletions openfecli/tests/commands/test_atommapping.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ def mapper_args():


@pytest.fixture
def mols(molA_args, molB_args):
def mols_AB(molA_args, molB_args):
return MOL.get(molA_args[1]), MOL.get(molB_args[1])


Expand Down Expand Up @@ -89,8 +89,8 @@ def test_atommapping_missing_mapper(molA_args, molB_args):


@pytest.mark.parametrize("n_mappings", [0, 1, 2])
def test_generate_mapping(n_mappings, mols):
molA, molB = mols
def test_generate_mapping(n_mappings, mols_AB):
molA, molB = mols_AB
mappings = [
LigandAtomMapping(molA, molB, {i: i for i in range(7)}),
LigandAtomMapping(molA, molB, {i: (i + 1) % 7 for i in range(7)}),
Expand All @@ -104,8 +104,8 @@ def test_generate_mapping(n_mappings, mols):
generate_mapping(mapper, molA, molB)


def test_atommapping_print_dict_main(capsys, mols):
molA, molB = mols
def test_atommapping_print_dict_main(capsys, mols_AB):
molA, molB = mols_AB
mapper = LomapAtomMapper
mapping = LigandAtomMapping(molA, molB, {i: i for i in range(7)})
with mock.patch("openfecli.commands.atommapping.generate_mapping", mock.Mock(return_value=mapping)): # fmt: skip
Expand All @@ -114,14 +114,14 @@ def test_atommapping_print_dict_main(capsys, mols):
assert captured.out == str(mapping.componentA_to_componentB) + "\n"


def test_atommapping_visualize_main(mols, tmpdir):
molA, molB = mols
def test_atommapping_visualize_main(mols_AB, tmpdir):
molA, molB = mols_AB
mapper = LomapAtomMapper
pytest.skip() # TODO: probably with a smoke test


def test_atommapping_visualize_main_bad_extension(mols, tmpdir):
molA, molB = mols
def test_atommapping_visualize_main_bad_extension(mols_AB, tmpdir):
molA, molB = mols_AB
mapper = LomapAtomMapper
mapping = LigandAtomMapping(molA, molB, {i: i for i in range(7)})
with mock.patch("openfecli.commands.atommapping.generate_mapping", mock.Mock(return_value=mapping)): # fmt: skip
Expand Down