Replace atomic trajectory cython version with numpy implementation

.gitignore

@@ -9,6 +9,7 @@
 .vscode
 *.pyc
 mdanse_env/
+.venv/
 sandbox/
 
 # Distribution / packaging

MDANSE/Src/MDANSE/Trajectory/AtomicTrajectory.py

@@ -2,12 +2,10 @@
 
 
 def atomic_trajectory(config, cell, rcell, box_coordinates=False):
-    trajectory = np.empty((config.shape[0], 3), dtype=np.float64)
-    trajectory = np.einsum("ij,ikj->ik", config, rcell[: config.shape[0]])
-    sdxyz = trajectory[:-1, :] - trajectory[1:, :]
-    sdxyz -= np.round(sdxyz)
+    trajectory = np.einsum("ij,ikj->ik", config, rcell)
+    sdxyz = trajectory[1:, :] - trajectory[:-1, :]
+    sdxyz -= np.cumsum(np.round(sdxyz), axis=0)
     trajectory[1:, :] = trajectory[:-1, :] + sdxyz
-
     if not box_coordinates:
-        trajectory = np.einsum("ij,ikj->ik", trajectory, cell[: config.shape[0]])
+        trajectory = np.einsum("ij,ikj->ik", trajectory, cell)
     return trajectory

MDANSE/Src/MDANSE/Trajectory/MdanseTrajectory.py

@@ -365,8 +365,18 @@ def read_atomic_trajectory(
         coords = grp["coordinates"][first:last:step, index, :].astype(np.float64)
 
         if self._unit_cells is not None:
-            direct_cells = np.array([uc.transposed_direct for uc in self._unit_cells])
-            inverse_cells = np.array([uc.transposed_inverse for uc in self._unit_cells])
+            direct_cells = np.array(
+                [
+                    self._unit_cells[nf].transposed_direct
+                    for nf in range(first, last, step)
+                ]
+            )
+            inverse_cells = np.array(
+                [
+                    self._unit_cells[nf].transposed_inverse
+                    for nf in range(first, last, step)
+                ]
+            )
             atomic_traj = atomic_trajectory(
                 coords, direct_cells, inverse_cells, box_coordinates
             )

MDANSE/Tests/UnitTests/test_atomic_trajectory.py

@@ -0,0 +1,26 @@
+import numpy as np
+import pytest
+from MDANSE.Trajectory.AtomicTrajectory import atomic_trajectory
+# from MDANSE.Extensions import atomic_trajectory
+
+cells = np.array([np.eye(3)]*5)
+
+def test_constant():
+    coords = np.zeros((5, 3)) + 0.5
+    atomic_traj = atomic_trajectory(coords, cells, cells, False)
+    assert np.allclose(atomic_traj, 0.5)
+
+
+def test_one_big_jump():
+    coords = np.zeros((5, 3)) + 3.2
+    coords[0, 0] = 0.1
+    atomic_traj = atomic_trajectory(coords, cells, cells, False)
+    result = np.zeros((5, 3)) + 3.2
+    result[0, 0] = 0.1
+    result[1:, 0] = 0.2
+    assert np.allclose(atomic_traj, result)
+
+
+
+
+