From: Adam Vandergriff <adam.vandergriff@gmail.com>
Date: Tue, 20 Dec 2022 11:48:13 -0800
Subject: [PATCH] fixing numpy type issues - replaced `np.int` with `np.int64`
 - replaced `np.bool` with `bool`

---
 Bio/PDB/SASA.py            | 2 +-
 Bio/PDB/internal_coords.py | 8 ++++----
 Tests/test_Cluster.py      | 2 +-
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/Bio/PDB/SASA.py b/Bio/PDB/SASA.py
index 4fa76a0..4add82c 100644
--- a/Bio/PDB/SASA.py
+++ b/Bio/PDB/SASA.py
@@ -203,7 +203,7 @@ class ShrakeRupley:
         twice_maxradii = np.max(radii) * 2
 
         # Calculate ASAs
-        asa_array = np.zeros((n_atoms, 1), dtype=np.int)
+        asa_array = np.zeros((n_atoms, 1), dtype=np.int64)
         ptset = set(range(self.n_points))
         for i in range(n_atoms):
 
diff --git a/Bio/PDB/internal_coords.py b/Bio/PDB/internal_coords.py
index 0acc43d..4750976 100644
--- a/Bio/PDB/internal_coords.py
+++ b/Bio/PDB/internal_coords.py
@@ -749,7 +749,7 @@ class IC_Chain:
         self.dCoordSpace: np.ndarray = np.empty(
             (2, self.dihedraLen, 4, 4), dtype=np.float64
         )
-        self.dcsValid: np.ndarray = np.zeros((self.dihedraLen), dtype=np.bool)
+        self.dcsValid: np.ndarray = np.zeros((self.dihedraLen), dtype=bool)
 
         # hedra atoms
         self.hAtoms: np.ndarray = np.zeros((self.hedraLen, 3, 4), dtype=np.float64)
@@ -786,10 +786,10 @@ class IC_Chain:
         # dihedra forward/reverse data
         a2da_map = {}
         a2d_map = [[[], []] for _ in range(self.AAsiz)]
-        self.dRev: np.ndarray = np.zeros((self.dihedraLen), dtype=np.bool)
+        self.dRev: np.ndarray = np.zeros((self.dihedraLen), dtype=bool)
 
-        self.dH1ndx = np.empty(self.dihedraLen, dtype=np.int)
-        self.dH2ndx = np.empty(self.dihedraLen, dtype=np.int)
+        self.dH1ndx = np.empty(self.dihedraLen, dtype=np.int64)
+        self.dH2ndx = np.empty(self.dihedraLen, dtype=np.int64)
         self.h1d_map = [[] for _ in range(self.hedraLen)]
 
         self.id3_dh_index = {k[0:3]: [] for k in self.dihedraNdx.keys()}
diff --git a/Tests/test_Cluster.py b/Tests/test_Cluster.py
index a0fe913..3796b6d 100644
--- a/Tests/test_Cluster.py
+++ b/Tests/test_Cluster.py
@@ -251,7 +251,7 @@ class TestCluster(unittest.TestCase):
                 [4.1, 2.2, 0.6, 5.5, 0.6],
                 [2.7, 2.5, 0.4, 5.7, 0.2],
             ],
-            numpy.float,
+            float,
         )
         try:
             treecluster(data, mask1)