Dear Maintainer,

mdtraj is failing to build from source with the error:

dh_numpy3
	mv debian/python3-mdtraj.substvars.new debian/python3-mdtraj.substvars
	mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars
# setup.py builds the static lib libtheobald.a for each python version
# but dh_python3 can't tell the difference between the different builds,
# since py3.11 compiles libtheobald.o with -fwrapv, where py3.12 uses -fno-strict-overflow
# So clean up manually (assume the binary difference is not an issue)
rm -f debian/python3-mdtraj/usr/lib/python3.*/dist-packages/mdtraj/core/lib/libtheobald.a
rmdir -p --ignore-fail-on-non-empty debian/python3-mdtraj/usr/lib/python3.*/dist-packages/mdtraj/core/lib
rmdir: failed to remove 'debian/python3-mdtraj/usr/lib/python3.*/dist-packages/mdtraj/core/lib': No such file or directory
make[1]: *** [debian/rules:59: execute_after_dh_python3] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:11: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2


The latest log can be seen at https://buildd.debian.org/status/fetch.php?pkg=mdtraj&arch=amd64&ver=1.10.0-2%2Bb1&stamp=1720720921&raw=0

Control: tags -1 patch
--

The attached patch will fix the build.

Thanks, but that patch is no good.  It deletes libtheobald.a and
core/lib completely, which is not what we want.

The error arises since it's not building for python 3.11 anymore.

We believe that the bug you reported is fixed in the latest version of
mdtraj, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1076166@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Drew Parsons <dparsons@debian.org> (supplier of updated mdtraj package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Sun, 14 Jul 2024 12:37:33 +0200
Source: mdtraj
Architecture: source
Version: 1.10.0-3
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Changed-By: Drew Parsons <dparsons@debian.org>
Closes: 1076166
Changes:
 mdtraj (1.10.0-3) unstable; urgency=medium
 .
   * only remove python3-specific mdtraj/core/lib (from libtheobald.a)
     if the excess dir exists (it's only left over if there is more
     than one supported python version). Closes: #1076166.
Checksums-Sha1:
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 4b546334338f9452a56b7588acbc2209d962edc5 301160 mdtraj_1.10.0-3.debian.tar.xz
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 d07e934e5fbc55b34630a703774044e8d2e07903c363aeb3d18bcd9e39b83208 2635 mdtraj_1.10.0-3.dsc
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 5b68dd90c3b67950a3316dc8526658c8 301160 python optional mdtraj_1.10.0-3.debian.tar.xz
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