relion (3.1.3-4) [PTS] [DDPO]

NEW: VCS has unreleased changes: 5.0.1-1 > 3.1.3-4

Git: https://salsa.debian.org/med-team/relion.git
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Branch: debian/master
Path: debian/changelog
Repo size: 1167360
Browser: https://salsa.debian.org/med-team/relion
Last scan: 2025-12-05 13:41:11+00
Next scan: 2025-12-14 05:46:00+00
CI pipeline status: success

Debian changelog in Git:

relion (5.0.1-1) unstable; urgency=medium

  * Team upload.
  * New upstream release:
    + Fixes FTBFS with GCC 15 (Closes: #1097784).
  * debian/patches/0001-Repair-wrong-comment-sign...patch: Delete; was
    cherry-picked from upstream.
  * debian/patches/typos.patch: Remove hunks applied upstream; fix more
    spelling errors.
  * debian/patches/format-security.patch: New; fix FTBFS
    with -Werror=format-security.
  * debian/patches/python3.patch: New; migrate the relion_it script from
    Python 2 to 3 as it's the core of on-the-fly processing.
  * debian/patches/system-eigen.patch: New; use the system Eigen library.
  * Run wrap-and-sort -ast.
  * debian/control (Build-Depends): Remove fluid (unnecessary).  Add
    libpng-dev, dh-sequence-python3, python3 and libeigen3-dev.
    (relion) <Depends>: Add ctffind (<< 5).
    <Recommends>: Add ghostscript (for generating PDF files), pbzip2,
    xz-utils and zstd (for reading compressed MRC movies).
    (relion-gui) <Depends>: Add ${python3:Depends} and python3-tk.
    (Breaks, Replaces): Remove; obsolete.
    (Rules-Requires-Root): Remove; it's the default.
    (Standards-Version): Claim compliance with 4.7.2; no changes needed.
  * debian/rules: Enable full hardening.
    (CONFIGURE_COMMON): Remove redundant flags that are already set by
    debhelper's cmake build system.  Fix FTBFS with CMake 4 by adding
    -DCMAKE_POLICY_VERSION_MINIMUM=3.5 (Closes: #1113466).
    Add -DPYTHON_EXE_PATH=/usr/bin/python3 to override upstream's test
    which relies on a Conda environment.
    (NUMJOBS, MAKE_-J): Remove; gymnastics no longer necessary.
    (override_dh_auto_configure): Run dh_auto_configure.
    (override_dh_auto_build): Remove; redundant.
    (override_dh_auto_clean): Likewise.
    (override_dh_auto_install): Run dh_auto_install --destdir.  Rename
    scripts with .py extension to fix W: script-with-language-extension.
    Delete Python/Bash scripts which will fail due to missing modules.
  * debian/relion-gui.install: Install schemes in /usr/share/relion.
  * debian/README.Debian: New file; document missing functionality.
  * debian/watch: Upgrade to version 5.
  * debian/salsa-ci.yml: Use the default recipe.
  * debian/copyright: Update copyright years, fix superfluous patterns,
    add EPL and MPL-2 licenses.

 -- Yavor Doganov <yavor@gnu.org>  Wed, 05 Nov 2025 09:20:46 +0200

This branch is 22 commits ahead of tag debian/3.1.3-4

Git log:

commit 141fba11f0f219b463f4b5dc7a3c545bf39f375a
Author: Yavor Doganov <yavor@gnu.org>
Date:   Wed Nov 5 09:21:00 2025 +0200

    Refresh changelog to trigger Salsa CI.

commit 2e5caa55272215b2d586454445ec8f5ee58949f4
Author: Yavor Doganov <yavor@gnu.org>
Date:   Wed Nov 5 09:19:04 2025 +0200

    salsa-ci.yml: Use the default recipe.

commit a6c60f185f1f070067c8f258b7566f8b79b1fa8d
Author: Yavor Doganov <yavor@gnu.org>
Date:   Wed Nov 5 09:00:47 2025 +0200

    Delete Python/Bash scripts which will fail due to missing modules.

commit e0888e56cb19ec3b0332d04ad499085ce17f9543
Author: Yavor Doganov <yavor@gnu.org>
Date:   Wed Nov 5 08:37:30 2025 +0200

    Use the system Eigen library instead of the bundled copy.

commit b50cf4a754b011e61f42b7245a45c58a9eaa6e23
Author: Yavor Doganov <yavor@gnu.org>
Date:   Wed Nov 5 08:08:47 2025 +0200

    copyright: Update years, fix superfluous patterns, add EPL and MPL-2.

commit 9aee694aa16c78e2613547a348740408e7db06dd
Author: Yavor Doganov <yavor@gnu.org>
Date:   Tue Nov 4 19:04:15 2025 +0200

    (Depends): Add ctffind (<< 5).

commit de877310e5a4b8bfad468d4d60927aafe8bf5e13
Author: Yavor Doganov <yavor@gnu.org>
Date:   Tue Nov 4 19:01:47 2025 +0200

    (Recommends): Add ghostscript, pbzip2, xz-utils and zstd.

commit 04f3b37775e23df2577c35e2ab7ba4c5303e7cb8
Author: Yavor Doganov <yavor@gnu.org>
Date:   Tue Nov 4 18:41:25 2025 +0200

    watch: Upgrade to version 5.

commit c4e23b42e9fca831401fb4364543b76e5d3a3f1d
Author: Yavor Doganov <yavor@gnu.org>
Date:   Tue Nov 4 18:36:14 2025 +0200

    (Standards-Version): Claim compliance with 4.7.2; no changes needed.

commit 7fe3445cb7732e7d02d2fd92bf838924ccee1c85
Author: Yavor Doganov <yavor@gnu.org>
Date:   Tue Nov 4 18:35:40 2025 +0200

    (Rules-Requires-Root): Remove; it's the default.

commit fba7c263dd8b37db8493260030d4d7b76a35c1b3
Author: Yavor Doganov <yavor@gnu.org>
Date:   Tue Nov 4 18:35:09 2025 +0200

    (Breaks, Replaces): Remove; obsolete.

commit 0db2f17d8e16e5e20188a4bf398c876ba505354e
Author: Yavor Doganov <yavor@gnu.org>
Date:   Tue Nov 4 18:32:29 2025 +0200

    Python-related fixes so that relion_it/relion_schemegui work.

commit 38edb3853164821a3bac125cb764d08109d8f279
Author: Yavor Doganov <yavor@gnu.org>
Date:   Tue Nov 4 16:32:30 2025 +0200

    rules: Fix FTBFS with CMake 4 (#1113466).

commit 56f7ff73afd94947afbb17ed68e0ec8eb38ed1d7
Author: Yavor Doganov <yavor@gnu.org>
Date:   Tue Nov 4 16:15:42 2025 +0200

    rules: Simplify; use standard dh_* commands where possible.

commit e509ba62841159662e582b038bdd8409ecc5cb2d
Author: Yavor Doganov <yavor@gnu.org>
Date:   Tue Nov 4 15:38:08 2025 +0200

    rules: Enable full hardening.

commit a874da796f413b5f0dffe02c2bde5b35536bed4f
Author: Yavor Doganov <yavor@gnu.org>
Date:   Tue Nov 4 15:31:27 2025 +0200

    (Build-Depends): Remove fluid (unnecessary); add libpng-dev.

commit ed30ac73076c87cc7b0766520c2d8f4edead0c33
Author: Yavor Doganov <yavor@gnu.org>
Date:   Tue Nov 4 15:29:47 2025 +0200

    Run wrap-and-sort -ast.

commit 7c28f97299c1716526299e49432744e0a7cb1406
Author: Yavor Doganov <yavor@gnu.org>
Date:   Tue Nov 4 15:26:47 2025 +0200

    format-security.patch: New; fix FTBFS with -Werror=format-security.

commit bea70bb703a529c0955d602900e1586c9790ce13
Author: Yavor Doganov <yavor@gnu.org>
Date:   Tue Nov 4 15:24:00 2025 +0200

    typos.patch: Remove hunks applied upstream; fix more spelling errors.

commit 5512eecb8ddfd3170ae9efedfdb7a79862b18c67
Author: Yavor Doganov <yavor@gnu.org>
Date:   Tue Nov 4 14:10:57 2025 +0200

    0001-Repair-wrong-comment-sign-pointed-out-by-Alexey-Roma.patch: Delete.

commit 056457ae65fb378cdcbcd7e90e69cc608dc0c49e
Merge: 4485256 d983f8a
Author: Yavor Doganov <yavor@gnu.org>
Date:   Tue Nov 4 14:04:33 2025 +0200

    Update upstream source from tag 'upstream/5.0.1'
    
    Update to upstream version '5.0.1'
    with Debian dir 796f5edf1d5fe6d7edc2cc2ea484c7dbf0e51b43

commit d983f8a301a6ac2e013333fc1eeebf74db361b95
Author: Yavor Doganov <yavor@gnu.org>
Date:   Tue Nov 4 14:04:17 2025 +0200

    New upstream version 5.0.1