Small updates

Author: joseph-hellerstein

data/linear_predictor_scores_1.csv

@@ -574,17 +574,20 @@ class TestTrajectoryCollectionPlotPrediction(unittest.TestCase):
     num_species: int
     NUM_POINT: int = 50
     tc: TrajectoryCollection
-    END_TIME: float = 1.5
+    END_TIME: float = 0.1
+    MODEL_NUM: int = 2
+    MODEL_NAME: str = makeBiomdName(MODEL_NUM)
 
     @classmethod
     def setUpClass(cls) -> None:
         #if IGNORE_TESTS:
         #    return
-        if not os.path.exists(BIOMD153_PATH):
-            raise unittest.SkipTest(f"{makeBiomdName(153)} not found at {BIOMD153_PATH}")
+        path = makeBiomdPath(cls.MODEL_NUM)
+        if not os.path.exists(path):
+            raise unittest.SkipTest(f"{cls.MODEL_NAME} not found at {path}")
         cls.trajectory = Trajectory.makeBiomodel(
-                path=BIOMD153_PATH, end_time=cls.END_TIME, num_point=cls.NUM_POINT)
-        cls.tc = TrajectoryCollection.split(cls.trajectory, [0.5])
+                path=path, end_time=cls.END_TIME, num_point=cls.NUM_POINT)
+        cls.tc = TrajectoryCollection.split(cls.trajectory, [cls.END_TIME/2])
         if IGNORE_TESTS:
             print(pd.DataFrame(cls.trajectory.jacobian_median_arr))
             print(pd.DataFrame(cls.tc.trajectories[0].jacobian_median_arr))
@@ -605,8 +608,8 @@ def test_jacobian_collection_sizes(self) -> None:
     def test_plot(self):
         if IGNORE_TESTS:
             return
-        self.trajectory.plotPrediction(title="BIOMD153")
-        self.tc.plotPrediction(title="BIOMD153")
+        self.trajectory.plotPrediction(title=self.MODEL_NAME, ylim=(0.0, 1e-5))
+        self.tc.plotPrediction(title=self.MODEL_NAME, ylim=(0.0, 1e-5))
         if IS_PLOT:
             plt.show()
 

data/linear_predictor_scores_2.csv

@@ -7,11 +7,11 @@
 
 def makeBiomdName(model_num: int) -> str:
     """Construct the model name"""
-    return f"{model_num:04d}"
+    return f"BIOMD000000{model_num:04d}"
 
 def makeBiomdPath(model_num: int) -> str:
     """Construct the file path for a BioModel SBML file given its model number."""
-    model_str = makeBiomdName(model_num)
+    model_name = makeBiomdName(model_num)
     return os.path.join(
-        cn.BIOMODELS_DIR, f"BIOMD000000{model_str}", f"BIOMD000000{model_str}_url.xml"
+        cn.BIOMODELS_DIR, model_name, f"{model_name}_url.xml"
     )