Merge pull request #117 from N720720/strong_type_numpy_fix

problems with strong typing and numpy

lindemann/index/per_atoms.py

@@ -65,7 +65,8 @@ def lindemann_per_frames(frames: np.ndarray) -> np.ndarray:
     return lindex_array
 
 
-def calculate(indices: np.ndarray) -> np.ndarray:
+# def calculate(indices: np.ndarray) -> np.ndarray:
+def calculate(indices):
     """
     Small helper function, since numba has not implemented the np.nanmean with axis parameter 
     I cant implemnet this in the jit function for now.

lindemann/index/per_frames.py

@@ -64,7 +64,8 @@ def lindemann_per_frames_for_each_atom(frames: np.ndarray) -> np.ndarray:
     return lindex_array
 
 
-def calculate(indices: np.ndarray) -> np.ndarray:
+# def calculate(indices: np.ndarray) -> np.ndarray:
+def calculate(indices):
     """
     Small helper function, since numba has not implemented the np.nanmean with axis parameter 
     I cant implemnet this in the jit function for now.

lindemann/index/per_trj.py

@@ -3,7 +3,8 @@
 
 
 @nb.njit(fastmath=True)  # , cache=True)
-def lindemann_per_atom(frames: np.ndarray) -> np.ndarray:
+# def lindemann_per_atom(frames: np.ndarray) -> np.ndarray:
+def lindemann_per_atom(frames):
 
     """Calculates the lindemann index for """
     natoms = len(frames[0])
@@ -51,7 +52,8 @@ def lindemann_per_atom(frames: np.ndarray) -> np.ndarray:
     return lindemann_indices
 
 
-def calculate(frames: np.ndarray) -> np.float64:
+# def calculate(frames: np.ndarray) -> float:
+def calculate(frames):
     """
     Small helper function, since numba has not implemented the np.nanmean with axis parameter 
     I cant implemnet this in the jit function for now.

lindemann/trajectory/plt_plot.py

@@ -11,7 +11,7 @@ def lindemann_vs_frames(indices: np.ndarray) -> str:
     plt.xlabel("Frames")
     plt.ylabel("Lindemann index")
     plt.plot(np.arange(0, len(indices)), indices, "+")
-    plt.tight_layout()
+    # plt.tight_layout()
     # plt.show()
     plt.savefig("lindemann_per_frame.pdf")
     return "lindemann_per_frame.pdf"

tests/test_example/test_hello.py

@@ -13,15 +13,15 @@
     [
         (
             "tests/test_example/459_01.lammpstrj",
-            np.round(np.float(0.025923892565654555), 12),
+            np.round(float(0.025923892565654555), 12),
         ),
         (
             "tests/test_example/459_02.lammpstrj",
-            np.round(np.float(0.026426709832984754), 12),
+            np.round(float(0.026426709832984754), 12),
         ),
     ],
 )
-# def test_setup(trajectory: str, lindemannindex: np.float) -> bool:
+# def test_setup(trajectory: str, lindemannindex: float) -> bool:
 
 
 def test_tra(trajectory, lindemannindex):
@@ -35,11 +35,11 @@ def test_tra(trajectory, lindemannindex):
     [
         (
             "tests/test_example/459_01.lammpstrj",
-            np.round(np.float(0.025923892565654555), 12),
+            np.round(float(0.025923892565654555), 12),
         ),
         (
             "tests/test_example/459_02.lammpstrj",
-            np.round(np.float(0.026426709832984754), 12),
+            np.round(float(0.026426709832984754), 12),
         ),
     ],
 )
@@ -55,11 +55,11 @@ def test_frames(trajectory, lindemannindex):
     [
         (
             "tests/test_example/459_01.lammpstrj",
-            np.round(np.float(0.025923892565654555), 12),
+            np.round(float(0.025923892565654555), 12),
         ),
         (
             "tests/test_example/459_02.lammpstrj",
-            np.round(np.float(0.026426709832984754), 12),
+            np.round(float(0.026426709832984754), 12),
         ),
     ],
 )