Fixed some deprecation warnings from numpy 1.20

crystals/affine.py

@@ -262,8 +262,8 @@ def change_basis_mesh(xx, yy, zz, basis1, basis2):
     XX, YY, ZZ : `~numpy.ndarray`
     """
     # Build coordinate array row-wise
-    changed = np.empty(shape=(3, xx.size), dtype=np.float)
-    linearized = np.empty(shape=(3, xx.size), dtype=np.float)
+    changed = np.empty(shape=(3, xx.size), dtype=np.float64)
+    linearized = np.empty(shape=(3, xx.size), dtype=np.float64)
     linearized[0, :] = xx.ravel()
     linearized[1, :] = yy.ravel()
     linearized[2, :] = zz.ravel()
@@ -295,7 +295,7 @@ def minimum_image_distance(xx, yy, zz, lattice):
             Minimum image distance over the lattice
     """
     COB = change_of_basis(np.eye(3), lattice)
-    linearized = np.empty(shape=(3, xx.size), dtype=np.float)  # In the standard basis
+    linearized = np.empty(shape=(3, xx.size), dtype=np.float64)  # In the standard basis
     ulinearized = np.empty_like(linearized)  # In the unitcell basis
 
     linearized[0, :] = xx.ravel()

crystals/indexing/common.py

@@ -34,7 +34,7 @@ def ratio_indexed(lattice, reflections):
     ratio : float
         Ratio of reflections that are indexed correctly, in the [0, 1] range.
     """
-    reflections = np.asarray(reflections, dtype=np.float)
+    reflections = np.asarray(reflections, dtype=np.float64)
 
     hkl = lattice.miller_indices(reflections)
     return (

crystals/indexing/dirax.py

@@ -159,7 +159,7 @@ def _find_basis(vectors, reflections):
     # The best way to find the last vector is to iterate through the remaining
     # vectors, from shortest to longest, until a matrix with the candidate
     # basis as rows has rank 3
-    m = np.empty(shape=(3, 3), dtype=np.float)
+    m = np.empty(shape=(3, 3), dtype=np.float64)
     m[0, :] = a1
     m[1, :] = a2
     for v in vectors:

crystals/lattice.py

@@ -65,9 +65,9 @@ class Lattice:
 
     def __init__(self, lattice_vectors, **kwargs):
         a1, a2, a3 = lattice_vectors
-        self.a1 = np.asarray(a1, dtype=np.float)
-        self.a2 = np.asarray(a2, dtype=np.float)
-        self.a3 = np.asarray(a3, dtype=np.float)
+        self.a1 = np.asarray(a1, dtype=np.float64)
+        self.a2 = np.asarray(a2, dtype=np.float64)
+        self.a3 = np.asarray(a3, dtype=np.float64)
         super().__init__(**kwargs)
 
     def __repr__(self):

crystals/parsers.py

@@ -418,7 +418,7 @@ def symmetry_operators(self):
             if op_num not in sym_ops:
                 sym_ops[op_num] = {"rotation": list(), "translation": list()}
 
-            r1, r2, r3, t = np.fromstring(line[23:], dtype=np.float, count=4, sep=" ")
+            r1, r2, r3, t = np.fromstring(line[23:], dtype=np.float64, count=4, sep=" ")
             sym_ops[op_num]["rotation"].append([r1, r2, r3])
             sym_ops[op_num]["translation"].append(t)
 
@@ -429,7 +429,7 @@ def symmetry_operators(self):
 
         operators = list()
         for op in sym_ops.values():
-            mat = np.eye(4, dtype=np.float)
+            mat = np.eye(4, dtype=np.float64)
             mat[:3, :3] = np.array(op["rotation"])
             mat[:3, 3] = np.array(op["translation"])
             operators.append(mat)
@@ -1051,7 +1051,7 @@ def lattice_vectors_alat(self):
 
     def reciprocal_vectors_alat(self):
         """
-        Returns the reciprocal lattice vectors associated to a structure, in units of :math:`2 \pi / alat`.
+        Returns the reciprocal lattice vectors associated to a structure, in units of :math:`2 \\pi / alat`.
 
         Returns
         -------

crystals/tests/test_lattice.py

@@ -51,7 +51,7 @@ def test_lattice_array_dtype():
     """ Test that the data-type of array(Lattice(...)) is respected """
     arr = np.random.random(size=(3, 3))
     lattice = Lattice(arr)
-    assert np.array(lattice, dtype=np.int).dtype, np.int
+    assert np.array(lattice, dtype=np.int32).dtype, np.int32
 
 
 def test_lattice_frac_mesh():