[Debian-med-packaging] Bug#1006667: python-biopython - build-dependencies unsatisfiable on most architectures.

[peter green]

source: python-biopython
version: 1.79+dfsg-1
severity: serious
tags: patch

muscle was recently removed from most architectures[1], leaving
python-biopython's build-dependencies unsatisfiable on those
architectures. The build-dependency is already marked as
nocheck so presumably is only used for tests.

I added an architecture restriction to the dependency and was able
to perform a successfully test build in an environment without muscle
installed. Note that I used python3-fonttools from testing for the
test build as unstable's version is currently uninstallable. A
debdiff is attached.

The recent upload of python-biopython 1.79+dfsg-2 also moved
w3-dtd-mathml from Suggests to Depends. Unfortunately
w3-dtd-mathml is rc buggy[2] and not in testing. There is a patch
available for the rc bug, but discussion in the bug report
suggests that it may be better to migrate to w3c-sgml-lib
which has a newer version of the mathml dtd.

[1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1006161
[2] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=994795
-------------- next part --------------
diff -Nru python-biopython-1.79+dfsg/debian/changelog python-biopython-1.79+dfsg/debian/changelog
--- python-biopython-1.79+dfsg/debian/changelog	2022-02-17 19:15:09.000000000 +0000
+++ python-biopython-1.79+dfsg/debian/changelog	2022-03-01 20:39:50.000000000 +0000
@@ -1,3 +1,11 @@
+python-biopython (1.79+dfsg-2.1) UNRELEASED; urgency=medium
+
+  * Non-maintainer upload.
+  * Restrict architecture list of muscle build-dependency to reflect
+    architectures where the current version of muscle is available.
+
+ -- Peter Michael Green <plugwash at debian.org>  Tue, 01 Mar 2022 20:39:50 +0000
+
 python-biopython (1.79+dfsg-2) unstable; urgency=medium
 
   * Move w3-dtd-mathml from Suggests to Depends to avoid dangling symlink
diff -Nru python-biopython-1.79+dfsg/debian/control python-biopython-1.79+dfsg/debian/control
--- python-biopython-1.79+dfsg/debian/control	2022-02-17 19:15:09.000000000 +0000
+++ python-biopython-1.79+dfsg/debian/control	2022-03-01 20:39:50.000000000 +0000
@@ -25,7 +25,7 @@
                emboss <!nocheck>,
                fasttree <!nocheck>,
                mafft <!nocheck>,
-               muscle <!nocheck>,
+               muscle [i386 amd64 x32] <!nocheck>,
                ncbi-blast+ <!nocheck>,
                phylip <!nocheck>,
                phyml [any-amd64 any-i386] <!nocheck>,