Control: tags -1 confirmed moreinfo On 2021-03-30 17:57:16, Andrius Merkys wrote: > 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.
ACK, please remove the moreinfo tag once the version is available in unstable. Cheers > > [ 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 -- Sebastian Ramacher