segfaulting test

MDAnalysis · Sep 6, 2024 · 2fe6b65 · 2fe6b65
1 parent e13a092
commit 2fe6b65
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Showing 2 changed files with 13 additions and 10 deletions.
diff --git a/distopia/_distopia.pyx b/distopia/_distopia.pyx
@@ -987,8 +987,8 @@ def calc_self_distance_array_triclinic(
 @cython.wraparound(False)
 def calc_bonds_no_box_idx(
      floating[:, ::1] coords,
-     integral[::1] a_idx,
-     integral[::1] b_idx,
+     int[::1] a_idx,
+     int[::1] b_idx,
      floating[::1] results=None):
     """Calculate pairwise distances between coords[a_idx] and coords[b_idx] with no periodic boundary conditions
 
@@ -1013,6 +1013,7 @@ def calc_bonds_no_box_idx(
 
     _check_shapes(a_idx, b_idx)
 
+
     if results is None:
         if floating is float:
             results = cnp.PyArray_EMPTY(1, dims, cnp.NPY_FLOAT32, 0)
@@ -1033,8 +1034,8 @@ def calc_bonds_no_box_idx(
 @cython.wraparound(False)
 def calc_bonds_ortho_idx(
      floating[:, ::1] coords,
-     integral[::1] a_idx,
-     integral[::1] b_idx,
+     int[::1] a_idx,
+     int[::1] b_idx,
      floating[::1] box,
      floating[::1] results=None):
     """Calculate pairwise distances between coords[a_idx] and coords[b_idx] under orthorhombic boundary conditions
@@ -1062,6 +1063,7 @@ def calc_bonds_ortho_idx(
 
     _check_shapes(a_idx, b_idx)
 
+
     if results is None:
         if floating is float:
             results = cnp.PyArray_EMPTY(1, dims, cnp.NPY_FLOAT32, 0)
@@ -1082,8 +1084,8 @@ def calc_bonds_ortho_idx(
 @cython.wraparound(False)
 def calc_bonds_triclinic_idx(
      floating[:, ::1] coords,
-     integral[::1] a_idx,
-     integral[::1] b_idx,
+     int[::1] a_idx,
+     int[::1] b_idx,
      floating[:, ::1] box,
      floating[::1] results=None):
     """Calculate pairwise distances between coords[a_idx] and coords[b_idx] under triclinic boundary conditions
@@ -1111,6 +1113,7 @@ def calc_bonds_triclinic_idx(
 
     _check_shapes(a_idx, b_idx)
 
+
     if results is None:
         if floating is float:
             results = cnp.PyArray_EMPTY(1, dims, cnp.NPY_FLOAT32, 0)

diff --git a/distopia/tests/test_distopia.py b/distopia/tests/test_distopia.py
@@ -253,13 +253,13 @@ def result_shim(self, make_arr, N, dtype):
 
 
     @pytest.mark.parametrize("dtype", (np.float32, np.float64))
-    @pytest.mark.parametrize("N", (0, 10, 1000, 10000))
+    @pytest.mark.parametrize("N", (10, 1000, 10000))
     @pytest.mark.parametrize("use_result_buffer", (True, False))
     def test_calc_bonds_no_box_idx(self, N, use_result_buffer, dtype):
         c = self.arange_input(N, dtype)
-        a_idx = np.asarray([0, 1, 2, 3, 4, 5])
-        b_idx = np.asarray([6, 7, 8, 9, 10, 11])
-        result_buffer = self.result_shim(use_result_buffer, N, dtype)
+        a_idx = np.asarray(np.arange(N -3)).astype(np.int32)
+        b_idx = np.asarray(np.arange(N -3)).astype(np.int32)
+        result_buffer = self.result_shim(use_result_buffer, len(a_idx), dtype)
         result = distopia.calc_bonds_no_box_idx(
             c, a_idx, b_idx, results=result_buffer
         )