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

Author: klimaj

actions/pyrosettacluster/assert_coordinates.py

@@ -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)
@@ -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)

actions/pyrosettacluster/test_env_reproducibility.py

@@ -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,