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fix scope mismatch with zenodo data #1828

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Merged
atravitz merged 2 commits into from
Feb 4, 2026
Merged

fix scope mismatch with zenodo data #1828

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79c1921
fix scope mismatch with zenodo data
atravitz Feb 4, 2026
e33bb13
fix session scope
atravitz Feb 4, 2026
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11 changes: 4 additions & 7 deletions src/openfe/tests/protocols/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -311,17 +311,14 @@ def industry_benchmark_files():
)


@pytest.fixture
def t4_lysozyme_trajectory_universe():
# session scope for downstream reuse
@pytest.fixture(scope="session")
def t4_lysozyme_trajectory_dir():
zenodo_restraint_data.fetch("t4_lysozyme_trajectory.zip", processor=pooch.Unzip())
cache_dir = pathlib.Path(
POOCH_CACHE / "t4_lysozyme_trajectory.zip.unzip/t4_lysozyme_trajectory"
)
universe = mda.Universe(
str(cache_dir / "t4_toluene_complex.pdb"),
str(cache_dir / "t4_toluene_complex.xtc"),
)
return universe
return cache_dir


RFE_OUTPUT = pooch.create(
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8 changes: 6 additions & 2 deletions src/openfe/tests/protocols/restraints/test_geometry_boresch_host.py
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Expand Up @@ -332,8 +332,12 @@ class TestFindAnchorBondedTrajectory(TestFindAnchorMulti):
ref_h1h2_distance = 1.55881

@pytest.fixture(scope="class")
def universe(self, t4_lysozyme_trajectory_universe):
universe = t4_lysozyme_trajectory_universe
def universe(self, t4_lysozyme_trajectory_dir):
cache_dir = t4_lysozyme_trajectory_dir
universe = mda.Universe(
str(cache_dir / "t4_toluene_complex.pdb"),
str(cache_dir / "t4_toluene_complex.xtc"),
)
# guess bonds for the protein atoms
universe.select_atoms("protein").guess_bonds()
return universe
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10 changes: 10 additions & 0 deletions src/openfe/tests/protocols/restraints/test_geometry_utils.py
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Expand Up @@ -400,6 +400,16 @@ def test_atomgroup_has_bonds(eg5_protein_pdb):
assert _atomgroup_has_bonds(ag)


@pytest.fixture()
def t4_lysozyme_trajectory_universe(t4_lysozyme_trajectory_dir):
cache_dir = t4_lysozyme_trajectory_dir
universe = mda.Universe(
str(cache_dir / "t4_toluene_complex.pdb"),
str(cache_dir / "t4_toluene_complex.xtc"),
)
return universe


@pytest.mark.skipif(
not os.path.exists(POOCH_CACHE) and not HAS_INTERNET,
reason="Internet seems to be unavailable and test data is not cached locally.",
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