[Debichem-devel] Bug#1027233: prody: autopkgtest fail with numpy/1.24.1

[Sebastiaan Couwenberg]

Control: tags -1 patch

The attached patch resolves the issue.

Kind Regards,

Bas

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diff -Nru prody-2.3.1+dfsg/debian/changelog prody-2.3.1+dfsg/debian/changelog
--- prody-2.3.1+dfsg/debian/changelog	2022-12-06 08:32:42.000000000 +0100
+++ prody-2.3.1+dfsg/debian/changelog	2023-01-11 19:47:52.000000000 +0100
@@ -1,3 +1,11 @@
+prody (2.3.1+dfsg-2.1) UNRELEASED; urgency=medium
+
+  * Non-maintainer upload.
+  * Add patch to fix test failure with Numpy 1.24.
+    (closes: #1027233)
+
+ -- Bas Couwenberg <sebastic at debian.org>  Wed, 11 Jan 2023 19:47:52 +0100
+
 prody (2.3.1+dfsg-2) unstable; urgency=medium
 
   * python3-prody-tests: add missing Breaks+Replaces: python3-prody (<< 2.3.1)
diff -Nru prody-2.3.1+dfsg/debian/patches/numpy-1.24.patch prody-2.3.1+dfsg/debian/patches/numpy-1.24.patch
--- prody-2.3.1+dfsg/debian/patches/numpy-1.24.patch	1970-01-01 01:00:00.000000000 +0100
+++ prody-2.3.1+dfsg/debian/patches/numpy-1.24.patch	2023-01-11 19:47:43.000000000 +0100
@@ -0,0 +1,19 @@
+Description: Fix test failure with Numpy 1.24.
+Author: Bas Couwenberg <sebastic at debian.org>
+Bug-Debian: https://bugs.debian.org/1027233
+
+--- a/prody/compounds/pdbligands.py
++++ b/prody/compounds/pdbligands.py
+@@ -158,9 +158,9 @@ def fetchPDBLigand(cci, filename=None):
+     resnums = np.ones(n_atoms, dtype=ATOMIC_FIELDS['charge'].dtype)
+ 
+     alternate_atomnames = np.zeros(n_atoms, dtype=ATOMIC_FIELDS['name'].dtype)
+-    leaving_atom_flags = np.zeros(n_atoms, np.bool)
+-    aromatic_flags = np.zeros(n_atoms, np.bool)
+-    stereo_configs = np.zeros(n_atoms, np.bool)
++    leaving_atom_flags = np.zeros(n_atoms, bool)
++    aromatic_flags = np.zeros(n_atoms, bool)
++    stereo_configs = np.zeros(n_atoms, bool)
+     ordinals = np.zeros(n_atoms, int)
+ 
+     name2index = {}
diff -Nru prody-2.3.1+dfsg/debian/patches/series prody-2.3.1+dfsg/debian/patches/series
--- prody-2.3.1+dfsg/debian/patches/series	2022-12-01 12:35:56.000000000 +0100
+++ prody-2.3.1+dfsg/debian/patches/series	2023-01-11 19:46:50.000000000 +0100
@@ -1,2 +1,3 @@
 no-network-access.patch
 add-missing-test-files.patch
+numpy-1.24.patch