Bug#1108185: bookworm-pu: package prody/2.3.1+dfsg-3+deb12u1

[Santiago Vila <sanvila@debian.org>]

On Tue, Aug 26, 2025 at 06:39:36AM +0100, Adam D. Barratt wrote:

> I'm afraid that once the package is in (o-)p-u we can't reject it, so
> it would need to be a new +deb12u2 upload.

Ok, I've just uploaded 2.3.1+dfsg-3+deb12u2, with the attached debdiff
relative to the +deb12u1 version which was already approved.

I've tested the i386 build in Salsa CI and I believe it should now work
in the buildds.

Note: There was a bug reported regarding this i386 build (#1058454)
which I've documented in the Bug-Debian header of the patch but have
decided not to close in the changelog yet because it's not
in the "main trunk" (i.e. unstable).

In fact, this package is not present in trixie (or forky) and upstream
will have to release a new version which supports python3.13 before
the team can continue to work on it again in unstable.

Thanks.

diff --git a/debian/changelog b/debian/changelog
index 5197b8d..cc0a9f5 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+prody (2.3.1+dfsg-3+deb12u2) bookworm; urgency=medium
+
+  * Team upload.
+  * Add tolerance to some tests which now fail on i386.
+
+ -- Santiago Vila <sanvila@debian.org>  Tue, 26 Aug 2025 13:50:00 +0200
+
 prody (2.3.1+dfsg-3+deb12u1) bookworm; urgency=medium
 
   * Team upload.
diff --git a/debian/patches/fix-tests-on-i386.patch b/debian/patches/fix-tests-on-i386.patch
new file mode 100644
index 0000000..787f78f
--- /dev/null
+++ b/debian/patches/fix-tests-on-i386.patch
@@ -0,0 +1,40 @@
+Description: Add tolerance to some tests which now fail on i386
+Author: Santiago Vila <sanvila@debian.org>
+Bug-Debian: https://bugs.debian.org/1058454
+
+--- a/prody/tests/dynamics/test_enms.py
++++ b/prody/tests/dynamics/test_enms.py
+@@ -120,7 +120,9 @@
+ 
+     def testHessianSymmetry(self):
+         hessian = anm._getHessian()
+-        assert_equal(hessian, hessian.T, 'hessian is not symmetric')
++        assert_allclose(hessian, hessian.T,
++                rtol=1e-14, atol=1e-14,
++                err_msg='hessian is not symmetric')
+ 
+     def testHessianSums(self):
+         hessian = anm._getHessian()
+@@ -171,7 +173,9 @@
+ 
+     def testHessianSymmetry(self):
+         hessian = exanm._getHessian()
+-        assert_equal(hessian, hessian.T, 'hessian is not symmetric')
++        assert_allclose(hessian, hessian.T,
++                rtol=1e-14, atol=1e-14,
++                err_msg='hessian is not symmetric')
+ 
+     def testHessianSums(self):
+         hessian = exanm._getHessian()
+@@ -285,8 +289,9 @@
+         """Test output when  *coords* is an array."""
+ 
+         self.buildMatrix(COORDS)
+-        assert_equal(self.getMatrix(), self.getExpected(),
+-                     'failed to get correct matrix')
++        assert_allclose(self.getMatrix(), self.getExpected(),
++                rtol=1e-14, atol=1e-14,
++                err_msg='failed to get correct matrix')
+ 
+     def testBuildMatrixCutoffWrongType(self):
+         """Test response to cutoff of wrong type."""
diff --git a/debian/patches/series b/debian/patches/series
index 83274d7..2171dbb 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,3 +2,4 @@ no-network-access.patch
 add-missing-test-files.patch
 numpy-1.24.patch
 skip-equals-on-vector.patch
+fix-tests-on-i386.patch