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Support PyRosetta initialization options in actions/pyrosettacluster/assert_coordinates.py #13

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Merged
klimaj merged 3 commits into from
Feb 3, 2026
Merged

Support PyRosetta initialization options in actions/pyrosettacluster/assert_coordinates.py #13

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3bf54b0
Support PyRosetta initialization options
klimaj Feb 2, 2026
4059a48
Fix self.pyrosetta_init_flags
klimaj Feb 2, 2026
d6122f9
Test pyrosetta.init flags
klimaj Feb 2, 2026
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9 changes: 9 additions & 0 deletions actions/pyrosettacluster/assert_coordinates.py
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Original file line number Diff line number Diff line change
Expand Up @@ -76,6 +76,8 @@ def assert_total_score(self, pose1, pose2):
self.assertEqual(scorefxn(pose1), scorefxn(pose2))

def test_coordinates(self):
if not pyrosetta.rosetta.basic.was_init_called():
pyrosetta.init(options="", extra_options=self.pyrosetta_init_flags, silent=True)
original_pose = io.pose_from_file(self.original_output_file).pose
reproduce_pose = io.pose_from_file(self.reproduce_output_file).pose
self.assert_atom_coordinates(original_pose, reproduce_pose)
Expand All @@ -88,9 +90,16 @@ def test_coordinates(self):
parser = argparse.ArgumentParser()
parser.add_argument('--original_output_file', type=str, required=True)
parser.add_argument('--reproduce_output_file', type=str, required=True)
parser.add_argument(
"--pyrosetta_init_flags",
type=str,
required=False,
default="-run:constant_seed 1 -out:level 200",
)
args, remaining_argv = parser.parse_known_args()
# Inject args into the class before running test
TestAtomCoordinates.original_output_file = args.original_output_file
TestAtomCoordinates.reproduce_output_file = args.reproduce_output_file
TestAtomCoordinates.pyrosetta_init_flags = args.pyrosetta_init_flags
# Run test
unittest.main(argv=[__file__] + remaining_argv)
4 changes: 4 additions & 0 deletions actions/pyrosettacluster/test_env_reproducibility.py
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Original file line number Diff line number Diff line change
Expand Up @@ -300,23 +300,27 @@ def recreate_environment_test(
reproduce_output_file = reproduce_record["metadata"]["output_file"]
assert_coordinates_script = os.path.join(os.path.dirname(__file__), "assert_coordinates.py")
module = os.path.splitext(os.path.basename(assert_coordinates_script))[0]
pyrosetta_init_flags = "-run:constant_seed 1 -out:level 300"
if environment_manager == "pixi":
cmd = (
f"pixi run python -u -m {module} "
f"--original_output_file '{original_output_file}' "
f"--reproduce_output_file '{reproduce_output_file}' "
f"--pyrosetta_init_flags '{pyrosetta_init_flags}'"
)
elif environment_manager == "uv":
cmd = (
f"uv run --project {reproduce_env_dir} python -u -m {module} "
f"--original_output_file '{original_output_file}' "
f"--reproduce_output_file '{reproduce_output_file}' "
f"--pyrosetta_init_flags '{pyrosetta_init_flags}'"
)
elif environment_manager in ("conda", "mamba"):
cmd = (
f"conda run -p {reproduce_env_dir} python -u -m {module} "
f"--original_output_file '{original_output_file}' "
f"--reproduce_output_file '{reproduce_output_file}' "
f"--pyrosetta_init_flags '{pyrosetta_init_flags}'"
)
returncode = TestEnvironmentReproducibility.run_subprocess(
cmd,
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