[Debian-med-packaging] Bug#1036761: unblock: kleborate/2.3.1-2

[Étienne Mollier]

Package: release.debian.org
Severity: normal
User: release.debian.org at packages.debian.org
Usertags: unblock
X-Debbugs-Cc: kleborate at packages.debian.org
Control: affects -1 + src:kleborate

Please unblock package kleborate

[ Reason ]
kleborate is affected by the release critical upgrade bug
#1036743 identified by Andreas Beckmann (Thanks for QA tests!).

[ Impact ]
If the unblock is not granted, the package may have inconsistent
blast databases when ncbi-blast+ is upgraded after kleborate.

[ Tests ]
I ran manually the upgrade paths described in #1036743, comment
#30, to make sure the initial issue was reproducible somehow and
actually fixed by the changes.  For extra safety, I also ran a
few more basic piuparts runs since some prerm modification was
involved.

I would have hoped to point to Salsa CI results, but they have a
long standing issues at their build steps.  Other automated
tests were the build time checks and an autopkgtest manually run
on amd64.

Autobuilders look to have managed to get kleborate to build
anywhere where its build dependencies are already available.
Debci autopkgtests are pending; I don't expect difficulties on
this front as changes would have little risk to break in an
architecture specific way anyway.

[ Risks ]
Little risks are identified: changes involve a change in
maintainer script but they should be covered by the piuparts
tests already done, otherwise this is a leaf package so the area
of effect of any mishap should be limited to the package.

[ Checklist ]
  [*] all changes are documented in the d/changelog
  [*] I reviewed all changes and I approve them
  [*] attach debdiff against the package in testing

[ Other info ]
Thanks for your work on putting together the bookworm release!

unblock kleborate/2.3.1-2

Have a nice day,  :)
Étienne.
-------------- next part --------------
diff -Nru kleborate-2.3.1/debian/changelog kleborate-2.3.1/debian/changelog
--- kleborate-2.3.1/debian/changelog	2023-02-06 07:37:51.000000000 +0100
+++ kleborate-2.3.1/debian/changelog	2023-05-25 14:48:18.000000000 +0200
@@ -1,3 +1,18 @@
+kleborate (2.3.1-2) unstable; urgency=medium
+
+  * d/{rules,*.prerm}: cleanup .fasta.{ndb,ntf} files
+    kleborate binary package  used to embed autogenerated files depending
+    on makeblastdb version at both build time and postinst time.  When
+    there is a discrepancy of makeblastdb version between the package
+    build and the package installation, for instance during a major
+    operating system upgrade, there can be a mismatch of int the
+    .fasta.ndb and .fasta.ntf files produced and expected.  This change
+    gets rid of the build time artifacts to solely rely on the
+    post-installation artifacts, which will be more consistent and won't
+    break the package consistency. (Closes: #1036743)
+
+ -- Étienne Mollier <emollier at debian.org>  Thu, 25 May 2023 14:48:18 +0200
+
 kleborate (2.3.1-1) unstable; urgency=medium
 
   * New upstream version
diff -Nru kleborate-2.3.1/debian/kleborate.prerm kleborate-2.3.1/debian/kleborate.prerm
--- kleborate-2.3.1/debian/kleborate.prerm	2023-02-06 07:37:51.000000000 +0100
+++ kleborate-2.3.1/debian/kleborate.prerm	2023-05-25 14:48:18.000000000 +0200
@@ -5,6 +5,8 @@
 case "$1" in
     remove|purge|upgrade|deconfigure)
 	rm -f /usr/lib/python3/dist-packages/kleborate/data/*.fasta.nin
+	rm -f /usr/lib/python3/dist-packages/kleborate/data/*.fasta.ndb
+	rm -f /usr/lib/python3/dist-packages/kleborate/data/*.fasta.ntf
     ;;
     failed-upgrade)
     ;;
diff -Nru kleborate-2.3.1/debian/rules kleborate-2.3.1/debian/rules
--- kleborate-2.3.1/debian/rules	2023-02-06 07:37:51.000000000 +0100
+++ kleborate-2.3.1/debian/rules	2023-05-25 14:48:18.000000000 +0200
@@ -7,8 +7,14 @@
 
 override_dh_install:
 	dh_install
-	# fasta.nin files will be (re)build at package installation time to not contain build path
+	# fasta.nin files will be (re)build at package installation time to not
+	# contain build path.  Other fasta.* are rebuilt by makeblastdb and may
+	# cause inconsistencies in the package itself when makeblastdb is
+	# upgraded and changes format, e.g. during a major operating system
+	# upgrade.  See Bug#1036743.
 	find debian -name "*.fasta.nin" -delete
+	find debian -name "*.fasta.ndb" -delete
+	find debian -name "*.fasta.ntf" -delete
 
 override_dh_fixperms:
 	dh_fixperms
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 833 bytes
Desc: not available
URL: <http://alioth-lists.debian.net/pipermail/debian-med-packaging/attachments/20230525/f91f9c58/attachment.sig>