[med-svn] [Git][med-team/python-biopython][master] 2 commits: Cherry-pick upstream patch to fix problems with numpy 1.24 (Closes: #1027253)

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / python-biopython


Commits:
5ffdbd23 by Nilesh Patra at 2022-12-29T18:52:03+05:30
Cherry-pick upstream patch to fix problems with numpy 1.24 (Closes: #1027253)

- - - - -
8a5c5ae5 by Nilesh Patra at 2022-12-29T18:52:21+05:30
Upload to unstable

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/numpy-1.24.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+python-biopython (1.80+dfsg-4) unstable; urgency=medium
+
+  * Team Upload.
+  * Cherry-pick upstream patch to fix problems with
+    numpy 1.24 (Closes: #1027253)
+
+ -- Nilesh Patra <nilesh at debian.org>  Thu, 29 Dec 2022 18:52:07 +0530
+
 python-biopython (1.80+dfsg-3) unstable; urgency=medium
 
   * muscle3.patch: ensure muscle3 is default even if unavailable.


=====================================
debian/patches/numpy-1.24.patch
=====================================
@@ -0,0 +1,64 @@
+From: Adam Vandergriff <adam.vandergriff at 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)


=====================================
debian/patches/series
=====================================
@@ -6,3 +6,4 @@ reproduciblebuild.patch
 croak-on-muscle5.patch
 muscle3.patch
 port_tutorial_to_muscle3.patch
+numpy-1.24.patch



View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/03f0adf4e58d4820a678b4a17bc13323fd1e780c...8a5c5ae55b6e4612d5a8549639c9a28ac1ea040f

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/03f0adf4e58d4820a678b4a17bc13323fd1e780c...8a5c5ae55b6e4612d5a8549639c9a28ac1ea040f
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