[med-svn] [Git][med-team/relion][debian/master] 12 commits: Slight change on d/watch and mark changelog part from Pierre Gruet

[Andreas Tille (@tille)]

Andreas Tille pushed to branch debian/master at Debian Med / relion


Commits:
1c328b27 by Andreas Tille at 2026-09-24T10:02:52+02:00
Slight change on d/watch and mark changelog part from Pierre Gruet

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92ff9695 by Andreas Tille at 2026-09-24T10:03:37+02:00
New upstream version 5.1.0+dfsg
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7189e371 by Andreas Tille at 2026-09-24T10:03:37+02:00
New upstream version

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c569c1b8 by Andreas Tille at 2026-09-24T10:03:43+02:00
Update upstream source from tag 'upstream/5.1.0+dfsg'

Update to upstream version '5.1.0+dfsg'
with Debian dir 0b4e18b3b91e32db14c5f5eee391f030b55ac9d9
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d1ea87d0 by Andreas Tille at 2026-09-24T10:03:43+02:00
Standards-Version: 4.7.4 (routine-update)

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44beb4a0 by Andreas Tille at 2026-09-24T10:03:48+02:00
Changes made by cme

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f9dde9ad by Andreas Tille at 2026-09-24T10:04:24+02:00
Build-Depends: pybuild-plugin-pyproject (routine-update)

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5e2ca142 by Andreas Tille at 2026-09-24T09:04:31+01:00
Add missing build-dependency on python3-setuptools.

This is necessary for build-backend setuptools.build_meta in pyproject.toml

Changes-By: lintian-brush
Fixes: lintian: relion source: missing-prerequisite-for-pyproject-backend setuptools.build_meta (does not satisfy python3-setuptools)
See-also: https://lintian.debian.org/tags/missing-prerequisite-for-pyproject-backend.html

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9729c932 by Andreas Tille at 2026-09-24T09:04:32+01:00
Remove unnecessary Team Upload line in changelog.

Changes-By: lintian-brush
Fixes: lintian: source: unnecessary-team-upload [debian/changelog:1]
See-also: https://lintian.debian.org/tags/unnecessary-team-upload.html

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107889f6 by Andreas Tille at 2026-09-24T10:04:38+02:00
debputy lint --auto-fix (routine-update)

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189c0793 by Andreas Tille at 2026-09-24T10:10:19+02:00
d/copyright:

   - Do not mention removed src/Eigen
   - Use link to /usr/share/common-licenses/MPL-2.0 instead of full text

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796ce5bb by Andreas Tille at 2026-09-24T10:14:02+02:00
Rebase patches to latest upstream version

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88 changed files:

- CMakeLists.txt
- cmake/BuildTypes.cmake
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/system-eigen.patch
- debian/patches/typos.patch
- debian/watch
- environment.yml
- environment_blackwell.yml → environment_pascal.yml
- + scripts/Schemes/amyprep/autopick_fom/job.star
- + scripts/Schemes/amyprep/ctffind/job.star
- + scripts/Schemes/amyprep/import/job.star
- + scripts/Schemes/amyprep/motioncorr/job.star
- + scripts/Schemes/amyprep/scheme.star
- + scripts/Schemes/amyprep/select_mics/job.star
- + scripts/Schemes/amyproc/autopick_trace/job.star
- + scripts/Schemes/amyproc/class2d/job.star
- + scripts/Schemes/amyproc/extract/job.star
- + scripts/Schemes/amyproc/scheme.star
- + scripts/Schemes/amyproc/split/job.star
- scripts/Schemes/proc/extract/job.star
- scripts/python_fetch_weights.in
- + scripts/python_trace_amyloids.in
- scripts/schemegui.py → scripts/schemegui.in
- + scripts/trace_amyloids.py
- src/CPlot2D.cpp
- src/acc/acc_ml_optimiser_impl.h
- src/align_tiltseries_runner.cpp
- src/align_tiltseries_runner.h
- + src/amyloid_finder.cpp
- + src/amyloid_finder.h
- + src/amyloid_finder_mpi.cpp
- + src/amyloid_finder_mpi.h
- src/apps/CMakeLists.txt
- + src/apps/find_amyloid.cpp
- + src/apps/find_amyloid_mpi.cpp
- src/apps/image_handler.cpp
- src/apps/import.cpp
- src/apps/maingui.cpp
- src/apps/particle_symmetry_expand.cpp
- src/apps/project.cpp
- src/apps/pseudotomo_expansion.cpp
- src/apps/star_handler.cpp
- src/autopicker.cpp
- src/backprojector.cpp
- src/backprojector.h
- src/ctffind_runner.cpp
- src/ctffind_runner.h
- src/displayer.cpp
- src/displayer.h
- src/exp_model.cpp
- src/gui_background.xpm
- src/gui_entries.h
- src/gui_jobwindow.cpp
- src/gui_jobwindow.h
- src/gui_mainwindow.cpp
- src/helix.cpp
- src/helix.h
- src/jaz/tomography/programs/align.cpp
- src/jaz/tomography/programs/reconstruct_tomogram.cpp
- src/jaz/tomography/programs/reconstruct_tomogram.h
- src/jaz/tomography/programs/subtomo.cpp
- src/jaz/tomography/programs/subtomo.h
- src/jaz/tomography/programs/subtomo_mpi.cpp
- src/jaz/tomography/tomogram_set.cpp
- src/jaz/tomography/tomogram_set.h
- src/local_symmetry.cpp
- src/local_symmetry.h
- src/local_symmetry_mpi.cpp
- src/macros.h
- src/manualpicker.cpp
- src/metadata_label.h
- src/metadata_table.cpp
- src/metadata_table.h
- src/ml_optimiser.cpp
- src/ml_optimiser.h
- src/ml_optimiser_mpi.cpp
- src/motioncorr_runner.cpp
- src/particle_subtractor.cpp
- src/pipeline_jobs.cpp
- src/pipeline_jobs.h
- src/preprocessing.cpp
- src/preprocessing.h
- src/reconstructor.cpp
- src/reconstructor.h
- src/tomography_python_programs/get_particle_poses/filaments.py
- tests/CMakeLists.txt


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/relion/-/compare/bd62d44268a9c3f492b76cf76e8dd81d09057fd9...796ce5bb31c5772463c4a68e9b2de5f035f6b108

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View it on GitLab: https://salsa.debian.org/med-team/relion/-/compare/bd62d44268a9c3f492b76cf76e8dd81d09057fd9...796ce5bb31c5772463c4a68e9b2de5f035f6b108
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