Package: release.debian.org
Severity: normal
User: release.debian....@packages.debian.org
Usertags: unblock
Dear release-team,
I am seeking pre-approval to upload libchemistry-opensmiles-perl/0.4.3-2.
[ Reason ]
libchemistry-opensmiles-perl/0.4.3-1 has a bug which has been fixed
upstream (also by me). The bug is in code logic detecting aromatic bonds
in chemical compounds, and as such is not specific to Debian. Fix has
been released in 0.4.5. libchemistry-opensmiles-perl/0.4.3-2 fixes this
bug in unstable via patch.
[ Impact ]
Without the fix, users of libchemistry-opensmiles-perl will observe
false-negatives in aromatic bond detection.
[ Tests ]
* Built on clean sid chroot;
* Upstream regression test for the bug passes.
[ Risks ]
Changes are minimal and are unlikely to affect other packages
negatively. Currently libchemistry-opensmiles-perl is a leaf package in
Debian.
[ Checklist ]
[*] all changes are documented in the d/changelog
[*] I reviewed all changes and I approve them
[*] attach debdiff against the package in testing
unblock libchemistry-opensmiles-perl/0.4.3-2
Best,
Andrius
diff -Nru libchemistry-opensmiles-perl-0.4.3/debian/changelog
libchemistry-opensmiles-perl-0.4.3/debian/changelog
--- libchemistry-opensmiles-perl-0.4.3/debian/changelog 2021-01-28
05:16:40.000000000 -0500
+++ libchemistry-opensmiles-perl-0.4.3/debian/changelog 2021-03-30
07:23:23.000000000 -0400
@@ -1,3 +1,10 @@
+libchemistry-opensmiles-perl (0.4.3-2) unstable; urgency=medium
+
+ * Applying upstream commit 6b8267f0bbc87d877bce87bfd28d4538c3f95ee5 as
+ a patch fixing detection of aromatic bonds.
+
+ -- Andrius Merkys <mer...@debian.org> Tue, 30 Mar 2021 07:23:23 -0400
+
libchemistry-opensmiles-perl (0.4.3-1) unstable; urgency=medium
* New upstream version 0.4.3
diff -Nru
libchemistry-opensmiles-perl-0.4.3/debian/patches/6b8267f0bbc87d877bce87bfd28d4538c3f95ee5.patch
libchemistry-opensmiles-perl-0.4.3/debian/patches/6b8267f0bbc87d877bce87bfd28d4538c3f95ee5.patch
---
libchemistry-opensmiles-perl-0.4.3/debian/patches/6b8267f0bbc87d877bce87bfd28d4538c3f95ee5.patch
1969-12-31 19:00:00.000000000 -0500
+++
libchemistry-opensmiles-perl-0.4.3/debian/patches/6b8267f0bbc87d877bce87bfd28d4538c3f95ee5.patch
2021-03-30 07:19:40.000000000 -0400
@@ -0,0 +1,36 @@
+From 6b8267f0bbc87d877bce87bfd28d4538c3f95ee5 Mon Sep 17 00:00:00 2001
+From: Andrius Merkys <andrius.mer...@gmail.com>
+Date: Thu, 25 Mar 2021 13:28:22 +0200
+Subject: [PATCH] Fixing a bug due to incorrectly identified aromatic bond.
+
+---
+ lib/Chemistry/OpenSMILES/Parser.yp | 2 +-
+ t/06_write.t | 2 ++
+ 2 files changed, 3 insertions(+), 1 deletion(-)
+
+diff --git a/lib/Chemistry/OpenSMILES/Parser.yp
b/lib/Chemistry/OpenSMILES/Parser.yp
+index 8094826..f0e0a13 100644
+--- a/lib/Chemistry/OpenSMILES/Parser.yp
++++ b/lib/Chemistry/OpenSMILES/Parser.yp
+@@ -60,7 +60,7 @@ chain: atom
+
+ $_[2]->{graph}->add_edge( $_[1]->{last}, $_[2] );
+
+- if( is_aromatic $_[1]->{last} && is_aromatic $_[1]->{last} ) {
++ if( is_aromatic $_[1]->{last} && is_aromatic $_[2] ) {
+ $_[2]->{graph}->set_edge_attribute( $_[1]->{last},
+ $_[2],
+ 'bond',
+diff --git a/t/06_write.t b/t/06_write.t
+index aee54c5..c0f4656 100644
+--- a/t/06_write.t
++++ b/t/06_write.t
+@@ -19,6 +19,8 @@ my @cases = (
+ # Chirality information is preserved:
+ [ 'N[C@](Br)(O)C', 'N([C@](Br)(O)(C))' ],
+ [ 'N[C@@](Br)(O)C', 'N([C@@](Br)(O)(C))' ],
++ # A regression test for previously incorrectly identified aromatic bond:
++ [ 'c1(c(cccc1)F)C(=O)[O-]', 'c:1(:c(:c(:c(:c(:c:1))))(F))(C(=O)([O-]))' ],
+ );
+
+ plan tests => 2 * scalar @cases;
diff -Nru libchemistry-opensmiles-perl-0.4.3/debian/patches/series
libchemistry-opensmiles-perl-0.4.3/debian/patches/series
--- libchemistry-opensmiles-perl-0.4.3/debian/patches/series 1969-12-31
19:00:00.000000000 -0500
+++ libchemistry-opensmiles-perl-0.4.3/debian/patches/series 2021-03-30
07:19:55.000000000 -0400
@@ -0,0 +1 @@
+6b8267f0bbc87d877bce87bfd28d4538c3f95ee5.patch
