Hi,

Whilst working on the Reproducible Builds effort [0], we noticed that
python-biom-format could not be built reproducibly.

This is because it generates different content whether the tests are
run, and, relatedly, it installs an "examples/" directory directly
under dist-packages.

I believe it is this line that is the 'cause':

   export PYBUILD_BEFORE_TEST=cp -r {dir}/examples {build_dir}

... and a patch is attached that cleans up with:

   export PYBUILD_AFTER_TEST=rm -rf {build_dir}/examples


 [0] https://reproducible-builds.org/


Regards,

We believe that the bug you reported is fixed in the latest version of
python-biom-format, 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 1120068@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Étienne Mollier <emollier@debian.org> (supplier of updated python-biom-format 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: Tue, 04 Nov 2025 21:39:49 +0100
Source: python-biom-format
Architecture: source
Version: 2.1.17-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Closes: 1102990 1120068
Changes:
 python-biom-format (2.1.17-1) unstable; urgency=medium
 .
   [ Étienne Mollier ]
   * New upstream version 2.1.17
   * d/watch: converto to v5 Github template.
   * d/copyright: bump upstream copyright year.
   * d/control: drop redundant Rules-Requires-Root: no.
   * d/control: declare compliance to standards version 4.7.2.
   * d/copyright: remove reference to the old fsf address.
   * d/patches/*: normalize Last-Update timestamps.
   * d/{rules,control}: streamline dh_numpy3 integration.
     This addresses supplemental comments in #1102990.
 .
   [ Chris Lamb ]
   * d/rules: remove examples from dist-packages.
     This makes the build reproducible.  (Closes: #1120068, #1102990)
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 8f0e04e2bb41dd0cf03845367e05a146b2dcf6a3 11894239 python-biom-format_2.1.17.orig.tar.gz
 d82352fcea9665d7b843b45cd2dc3fa3637fa624 11596 python-biom-format_2.1.17-1.debian.tar.xz
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found 1120068 2.1.17-1
found 1102990 2.1.17-1
thanks

Unfortunately, I think that the interaction of some of the changes
to this bug with the changes made for #1102990 have meant that neither
is actually fixed. As in, the package remains unreproducible, and I
think the examples/ are still shipped under dist-packages.

(Probably related, but is it right that you are installing examples
via the debian/python3-biom-format.examples file? Should that not be
debian/python-biom-format-doc.examples? :)


Regards,