- Package:
- src:python-gffutils
- Source:
- src:python-gffutils
- Submitter:
- Chris Lamb
- Date:
- 2026-08-13 15:35:01 UTC
- Severity:
- normal
- Tags:
Hi, Whilst working on the Reproducible Builds effort [0], we noticed that python-gffutils could not be built reproducibly. This is because it generates different content in the binary file depending on whether the tests are run. In particular, the tests leave around this file: /usr/lib/python3/dist-packages/gffutils/test/data/FBgn0031208.gtf.db Patch attached that expands the existing cleanup after calling dh_install, but there are likely other solutions. [0] https://reproducible-builds.org/ Regards,
Hi Chris, Chris Lamb, on 2025-11-04: Thanks for your patch, I initially considered applying it, but got reminded by autopkgtest that the file is needed by the test suite, so will focus on preserving the original version from the upstream tarball instead. In any case, thank you for having identified the cause of the reproducibility issue and paved the way to its resolution! Have a nice day, :)
We believe that the bug you reported is fixed in the latest version of
python-gffutils, 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 1120066@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-gffutils 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 20:54:03 +0100
Source: python-gffutils
Architecture: source
Version: 0.13-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Closes: 1120066
Changes:
python-gffutils (0.13-4) unstable; urgency=medium
.
* d/rules: preserve original FBgn0031208.gtf.db.
Thanks to Chris Lamb (Closes: #1120066)
* d/watch: convert to PyPI watch file v5.
* pytest8.4.patch: file the dep3 header.
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found 1120066 0.13-4 thanks Hey Étienne, Thanks for caring about reproducibility! Unfortunately, I don't think your patch works just yet — I'm still seeing a difference between two test runs in the FBgn0031208.gtf.db file. Can you easily spot the issue...? You seem to be making a .orig copy which should just work, but maybe the directory is not quite right? Hope you can spot it quickly. Best wishes,
Hi Chris, Chris Lamb, on 2026-04-24: Uuuh, right, the preservation starts fine, but the restoration should occur from the .pybuild directory, as that's what gets installed afterwards. I suppose I should move the restoration stanza out of the execute_before_dh_auto_install target in favor of the PYBUILD_BEFORE_INSTALL environment variable. Let's see… Thanks for spotting this! Have a nice day, :)
Hello, Bug #1120066 in python-gffutils reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/python-gffutils/-/commit/b790f4c95778d21bb901227ee14aa44ab899a8e8 ------------------------------------------------------------------------ d/rules: fix original test data restoration. Closes: #1120066 ------------------------------------------------------------------------ (this message was generated automatically) -- Greetings https://bugs.debian.org/1120066
We believe that the bug you reported is fixed in the latest version of python-gffutils, 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 1120066@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-gffutils 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: Fri, 24 Apr 2026 23:17:07 +0200 Source: python-gffutils Architecture: source Version: 0.13-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> Changed-By: Étienne Mollier <emollier@debian.org> Closes: 1120066 Changes: python-gffutils (0.13-5) unstable; urgency=medium . * d/rules: fix original test data restoration. (Closes: #1120066) * d/control: drop redundant Priority: optional. * d/control: declare compliance to standards version 4.7.4. Checksums-Sha1: 370716e381e043f46297d030be0e449caf3846ef 2455 python-gffutils_0.13-5.dsc ae600f1ffce6dcd1e36dafa49c7206f4f60e1321 5708 python-gffutils_0.13-5.debian.tar.xz Checksums-Sha256: 7f8f4973c428d21fff7ef24c1bc7024d67056858f4238682bb66ba5401e8381d 2455 python-gffutils_0.13-5.dsc a75a25ae300d4da654be4f7626ff613d3572f46330d281dab072dde440833515 5708 python-gffutils_0.13-5.debian.tar.xz Files: fc2cdb7c04eb086a8aa3aef06c657547 2455 science optional python-gffutils_0.13-5.dsc c32b08140ce81a3bf835ec7ad94acd86 5708 science optional python-gffutils_0.13-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmnr3/YUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdoTOA/+LmiF3NH2ShVR1YdGPrNxMNzGo3U8 qd9S7VJllOv5tpxSKfwNFbrVw9gArN5UrJvRypBKfQ8nkb2yCUjkT4K1NzLfYrCo bhcMlO0Lje4aeNVAJLdzFmohQ7rkWrM9IZLC58r4UbvZ5ud/BWDHvzJ9ymHaKp53 UeT0ANFg+0631nM5/gvmGtYEY3oaIsu94DNiEpmlbQEZZX62KgbD1j+u9os1Zpf/ mE/orA5203yZQN5d+cZgXwtW7Qrlj7fINdTEpJnpwiToxQeXZNFUSuz51qdKF9Mz mYNh2oWro16KoAwVQ9BuJEK74L7vkU97nogGjl8s2A8EnsxTHOoegGqleBB3wsva xly77KuaVOWWTw7BB8ngXPXScKKz2af84MPprY5SMq1Sw0aRoqSRxB28z35VsNy7 Ij+4VdgB3eduWZ7GTM6D8SghE7jsVSaWXUMgdUKFzKF2voIc8r12bG/H1YMlESpU k0v8Jh23ZXl5DhpRVEB02Hby2bGqDbhJJcvFhMNlQobs6JxaOwy2LdVXkK1nAa/c n/woVMBjfxreIgaa07Bph4B5TZRnKb0HPT2NAeZ283omoc0CGGslj8S9L/kR3obv gSc3Vy0RgayhQXZNfyq+7mkPe/xXeNFUQOTTpT6pk7Winht+/OQ66VlRHgz8y5nY OP3cexb+Fer42xA= =FLE7 -----END PGP SIGNATURE-----
found 1120066 0.13-5 thanks Hey Étienne, Nearly there…! The important bit is that the restoration should also occur *to* the installation directory, otherwise the mv in PYBUILD_AFTER_INSTALL is not restoring the directory that will ultimately be used to construct the .deb file. Patch attached to make it clearer. Regards,
Hello, Bug #1120066 in python-gffutils reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/python-gffutils/-/commit/4401eb6f6bdc1f8c3160d7fb8779ae5fc225eeef (this message was generated automatically) -- Greetings https://bugs.debian.org/1120066
We believe that the bug you reported is fixed in the latest version of
python-gffutils, 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 1120066@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated python-gffutils 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: Thu, 13 Aug 2026 16:48:08 +0200
Source: python-gffutils
Architecture: source
Version: 0.14-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Closes: 1120066
Changes:
python-gffutils (0.14-1) unstable; urgency=medium
.
* Team upload.
.
[ Chris Lamb ]
* Make the build reproducible
Closes: #1120066
.
[ Andreas Tille ]
* New upstream version
* Reflow Uploaders field (cme)
* Remove trailing whitespace in debian/changelog (routine-update)
* Build-Depends: pybuild-plugin-pyproject (routine-update)
* Set upstream metadata fields: Repository-Browse.
* debputy lint --auto-fix (routine-update)
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