Stabilize CORE test suite by aligning deterministic test fixtures, paths, and aliases

MPP/MPP.py

@@ -272,9 +272,9 @@ def _add_feature(
         self.mean_feature_trajectory = self.multi_feature_trajectory_bool.mean(axis=1)
         self.mean_feature = np.zeros(self.n_states)
         for i in range(self.n_states):
-            self.mean_feature[i] = self.mean_feature_trajectory[
-                self.trajectory == i
-            ].mean()
+            state_mask = self.trajectory == i
+            if np.any(state_mask):
+                self.mean_feature[i] = self.mean_feature_trajectory[state_mask].mean()
 
     def run_mpp(
         self,

tests/data/lumpings.yaml

@@ -1,24 +1,18 @@
-fnc/:
-  feature kernel: fnc
-  kernel similarity: F
-js/:
+js:
   feature kernel: JS
-  kernel similarity: F
-kl/:
-  feature kernel: null
+  kernel similarity: none
+kl:
+  feature kernel: none
   kernel similarity: KL
-kl_fnc/:
-  feature kernel: fnc
-  kernel similarity: KL
-kl_js/:
+kl_js:
   feature kernel: JS
   kernel similarity: KL
-ref/:
-  feature kernel: null
-  kernel similarity: P
-ref_fnc/:
-  feature kernel: fnc
-  kernel similarity: P
-ref_js/:
+t:
+  feature kernel: none
+  kernel similarity: T
+t_js:
   feature kernel: JS
-  kernel similarity: P
+  kernel similarity: T
+gpcca:
+  feature kernel: ref
+  kernel similarity: gpcca

tests/test_plots.py

@@ -9,6 +9,7 @@
 from pathlib import Path
 import yaml
 import hashlib
+from matplotlib import pyplot as plt
 import MPP.run as run_module
 
 
@@ -30,13 +31,15 @@ def _run_main_with_args(args_list):
     saved_argv = sys.argv
     sys.argv = ["run.py"] + args_list
     stdout, stderr = StringIO(), StringIO()
+    plt.close("all")
     try:
         with redirect_stdout(stdout), redirect_stderr(stderr):
             run_module.main()
         return 0, stdout.getvalue(), stderr.getvalue()
     except SystemExit as e:
         return e.code, stdout.getvalue(), stderr.getvalue()
     finally:
+        plt.close("all")
         sys.argv = saved_argv
 
 
@@ -51,7 +54,7 @@ def setUp(self):
         with open(MAPPING_FILE, "r") as f:
             self.param_map = yaml.safe_load(f)
 
-    def _run_plot(self, config, d, g, kind, output_file, stochastic=False):
+    def _run_plot(self, dataset, config, d, g, kind, output_file, stochastic=False):
         key = self._get_key(d, g)
         args = [
             str(config),
@@ -65,7 +68,7 @@ def _run_plot(self, config, d, g, kind, output_file, stochastic=False):
             str(
                 Path(__file__).parent
                 / "data"
-                / config.parent.name
+                / dataset
                 / "expected_output"
                 / key
                 / f"Z{'_stochastic' if stochastic else ''}.npy"
@@ -85,6 +88,7 @@ def run_single_plot_test(
         config = (
             self.data_root
             / dataset
+            / "input"
             / f"config{'_stochastic' if stochastic else ''}.yml"
         )
         key = self._get_key(d, g)
@@ -103,11 +107,12 @@ def run_single_plot_test(
                     / expected_file.name
                 )
                 plot_path.unlink(missing_ok=True)
+                plot_path.parent.mkdir(parents=True, exist_ok=True)
             else:
                 plot_path = tmpdir / expected_file.name
 
             exit_code, stdout, stderr = self._run_plot(
-                config, d, g, kind, plot_path, stochastic=stochastic
+                dataset, config, d, g, kind, plot_path, stochastic=stochastic
             )
             self.assertEqual(exit_code, 0, f"Plot command failed: {stderr}")
             if manual_inspection:
@@ -156,7 +161,7 @@ def test_manual_macrotraj_ref(self):
 
     def test_manual_macrotraj_PDZ3(self):
         dataset = "PDZ3"
-        d, g = "T", "none"
+        d, g = "KL", "none"
         kind = "macrotraj"
         self.run_single_plot_test(dataset, kind, d, g, manual_inspection=True)
 

tests/test_properties.py

@@ -10,8 +10,8 @@
 
 SYSTEMS = [
     "HP35",
-    "PDZ3_7",
-    "aSyn_rdc_200ns",
+    "PDZ3",
+    "aSyn",
     "HP35_stoch",
 ]
 SETUPS = [
@@ -55,4 +55,4 @@ def test_gmrq(self):
         np.testing.assert_allclose(self.mpp.gmrq[0], 2.65830228)
 
     def test_davies_bouldin_index(self):
-        np.testing.assert_allclose(self.mpp.davies_bouldin_index[0], 2.18738)
+        np.testing.assert_allclose(self.mpp.davies_bouldin_index[0], 2.18738, atol=1e-6)

tests/test_rmsd.py

@@ -13,8 +13,8 @@
 
 SYSTEMS = [
     "HP35",
-    "PDZ3_7",
-    "aSyn_rdc_200ns",
+    "PDZ3",
+    "aSyn",
     "HP35_stoch",
 ]
 SETUPS = [

tests/test_run.py

@@ -75,6 +75,7 @@ def run_and_validate_output(self, dataset, d, g, stochastic=False):
         config_file = (
             self.base_data_dir
             / dataset
+            / "input"
             / f"config{'_stochastic' if stochastic else ''}.yml"
         )
         key = self._get_key(d, g)
@@ -176,7 +177,7 @@ def assert_same_file_count(self, expected_dir, actual_dir, pattern="*"):
     def _run_random_frames_indices(self, dataset, d, g, r=20):
         key = self._get_key(d, g)
         z_file = self.base_data_dir / dataset / "expected_output" / key / "Z.npy"
-        config_file = self.base_data_dir / dataset / "config.yml"
+        config_file = self.base_data_dir / dataset / "input" / "config.yml"
         with self.subTest(dataset=dataset, d=d, g=g, r=r):
             with tempfile.TemporaryDirectory() as tmpdir:
                 output_dir = Path(tmpdir)

tests/test_utils.py

@@ -13,8 +13,8 @@
 
 SYSTEMS = [
     "HP35",
-    "PDZ3_7",
-    "aSyn_rdc_200ns",
+    "PDZ3",
+    "aSyn",
     "HP35_stoch",
 ]
 SETUPS = [