Minimal reader and corresponding test-suite clean up

Author: amruthesht

imdclient/tests/minimalReader.py

@@ -24,14 +24,12 @@ class minimalReader:
         keyword arguments passed to the constructed :class:`IMDClient`
     """
 
-    def __init__(self, filename, n_atoms=None, process_stream=False, **kwargs):
+    def __init__(self, filename, **kwargs):
 
         self.imd_frame = None
 
         # a trajectory of imd frames
-        self.trajectory = None
-
-        self.n_atoms = n_atoms
+        self.trajectory = []
 
         host, port = parse_host_port(filename)
 
@@ -42,8 +40,7 @@ def __init__(self, filename, n_atoms=None, process_stream=False, **kwargs):
 
         self._frame = -1
 
-        if process_stream:
-            self._process_stream()
+        self._process_stream()
 
     def _read_next_frame(self):
         try:
@@ -56,20 +53,15 @@ def _read_next_frame(self):
 
         logger.debug(f"minimalReader: Loaded frame {self._frame}")
 
-    def _add_frame_to_trajectory(self):
-        # Add the current frame to the trajectory
-        if self.trajectory is None:
-            self.trajectory = []
-        self.trajectory.append(self.imd_frame)
-        logger.debug(
-            f"minimalReader: Added frame {self._frame} to trajectory"
-        )
-        
+        return imd_frame
+
     def _process_stream(self):
         # Process the stream of frames
         while True:
             try:
-                self._read_next_frame()
-                self._add_frame_to_trajectory()
+                self.trajectory.append(self._read_next_frame().copy())
+                logger.debug(
+                    f"minimalReader: Added frame {self._frame} to trajectory"
+                )
             except EOFError:
                 break

imdclient/tests/test_lammps.py

@@ -67,4 +67,4 @@ def true_u(self, topol, traj, imd_u, tmp_path):
 
     @pytest.fixture()
     def imd_u(self, docker_client, topol, tmp_path, port):
-        u = minimalReader(f"imd://localhost:{port}", process_stream=True)
+        u = minimalReader(f"imd://localhost:{port}")

imdclient/tests/test_manual.py

@@ -90,7 +90,7 @@ def load_true_universe(topol_path, traj_path):
 
 def load_imd_universe(topol_path, tmp_path):
     # Pass atom_style (ignored if not using LAMMPS topol)
-    tmp_u = minimalReader(f"imd://localhost:8888", process_stream=True)
+    tmp_u = minimalReader(f"imd://localhost:8888")
     return tmp_u
 
 

imdclient/tests/test_namd.py

@@ -104,6 +104,7 @@ def test_compare_imd_to_true_traj(self, imd_u, true_u, first_frame):
                 atol=1e-03,
             )
 
+    # Since NAMD does not write velocities, forces to the DCD file, we need to do so seperately by extracting that info from theri respective DCD files
     # Compare velocities
     def test_compare_imd_to_true_traj_vel(self, imd_u, true_u_vel, first_frame):
         for i in range(first_frame, len(true_u_vel.trajectory)):