fixed mdpath testing

wolberlab · Jul 30, 2024 · 9861b63 · 9861b63
1 parent d507916
commit 9861b63
Showing 1 changed file with 33 additions and 17 deletions.
diff --git a/mdpath/tests/test_mdpath.py b/mdpath/tests/test_mdpath.py
@@ -1176,34 +1176,50 @@ def test_bootstrap_analysis():
 
 
 def test_mdpath_output_files():
-
     script_dir = os.path.dirname(os.path.abspath(__file__))
+    project_root = os.path.dirname(script_dir)
+    mdpath_dir = os.path.join(project_root, 'mdpath')
+
     topology = os.path.join(script_dir, "test_topology.pdb")
     trajectory = os.path.join(script_dir, "test_trajectory.dcd")
-    numpath = "50"
+    numpath = "25"
 
     assert os.path.exists(topology), f"Topology file {topology} does not exist."
     assert os.path.exists(trajectory), f"Trajectory file {trajectory} does not exist."
 
     expected_files = [
-        "first_frame.pdb",
-        "mi_diff_df.csv",
-        "output.txt",
-        "path_confidence_intervals.txt",
-        "residue_coordinates.pkl",
-        "cluster_pathways_dict.pkl",
-        "clusters_paths.json",
-        "precomputed_clusters_paths.json",
-        "quick_precomputed_clusters_paths.json",
+        os.path.join(script_dir, "first_frame.pdb"),
+        os.path.join(script_dir, "mi_diff_df.csv"),
+        os.path.join(script_dir, "output.txt"),
+        os.path.join(script_dir, "residue_coordinates.pkl"),
+        os.path.join(script_dir, "cluster_pathways_dict.pkl"),
+        os.path.join(script_dir, "clusters_paths.json"),
+        os.path.join(script_dir, "precomputed_clusters_paths.json"),
+        os.path.join(script_dir, "quick_precomputed_clusters_paths.json")
     ]
 
-    result = subprocess.run(
-        ["mdpath", "-top", topology, "-traj", trajectory, "-numpath", numpath],
-        capture_output=True,
-        text=True,
-    )
+    sys.path.insert(0, mdpath_dir)
+
+    try:
+        import mdpath
+    except ImportError as e:
+        raise ImportError(f"Error importing mdpath: {e}")
 
+    original_cwd = os.getcwd()
+    os.chdir(script_dir)
+
+    sys.argv = [
+        "mdpath",  
+        "-top", topology,
+        "-traj", trajectory,
+        "-numpath", numpath
+    ]
+
+    mdpath.mdpath.main()
+
     for file in expected_files:
         assert os.path.exists(file), f"Expected output file {file} not found."
+
     for file in expected_files:
-        os.remove(file)
+        if os.path.exists(file):
+            os.remove(file)