[med-svn] [Git][med-team/vienna-rna][master] 13 commits: New upstream version

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / vienna-rna


Commits:
b0c7de36 by Andreas Tille at 2026-08-31T13:54:29+02:00
New upstream version

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76316924 by Andreas Tille at 2026-08-31T13:54:30+02:00
New upstream version 2.7.2+dfsg
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2983b38c by Andreas Tille at 2026-08-31T13:54:40+02:00
Update upstream source from tag 'upstream/2.7.2+dfsg'

Update to upstream version '2.7.2+dfsg'
with Debian dir a46c716108ad2d67e8c792233d372c134c8e4cdc
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8b5f95d6 by Andreas Tille at 2026-08-31T13:54:41+02:00
Standards-Version: 4.7.4 (routine-update)

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f2d5029d by Andreas Tille at 2026-08-31T13:55:55+02:00
Changes made by cme

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ff64b42b by Andreas Tille at 2026-08-31T13:58:13+02:00
Remove trailing whitespace in debian/copyright (routine-update)

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67d261cc by Andreas Tille at 2026-08-31T13:58:13+02:00
Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)

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a7889c34 by Andreas Tille at 2026-08-31T12:58:19+01:00
Remove patch add_shared_library that is missing from debian/patches/series.

Changes-By: lintian-brush
Fixes: lintian: source: patch-file-present-but-not-mentioned-in-series [debian/patches/add_shared_library]
See-also: https://lintian.debian.org/tags/patch-file-present-but-not-mentioned-in-series.html

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1582bfd3 by Andreas Tille at 2026-08-31T12:58:20+01:00
Reformat the Last-Update date as ISO YYYY-MM-DD.

Changes-By: lintian-brush
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/g2.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/use_debian_packaged_dlib.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/python3.11.patch]
See-also: https://lintian.debian.org/tags/invalid-dep3-format-patch-wrong-last-update.html

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339eaab1 by Andreas Tille at 2026-08-31T12:58:20+01:00
Remove listed license files (src/RNAforester/g2-0.72/COPYING) from copyright.

Changes-By: lintian-brush
Fixes: lintian: source: license-file-listed-in-debian-copyright src/RNAforester/g2-0.72/COPYING [debian/copyright]
See-also: https://lintian.debian.org/tags/license-file-listed-in-debian-copyright.html

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1214ff79 by Andreas Tille at 2026-08-31T12:58:21+01:00
Replace FSF postal address with a reference to https://www.gnu.org/licenses/.

Changes-By: lintian-brush
Fixes: lintian: source: old-fsf-address-in-copyright-file
See-also: https://lintian.debian.org/tags/old-fsf-address-in-copyright-file.html

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1a3c406e by Andreas Tille at 2026-08-31T14:31:53+02:00
Adapt patches to new upstream version

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21e07832 by Andreas Tille at 2026-08-31T14:50:38+02:00
Team upload to unstable

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448 changed files:

- .github/workflows/build_python_package.yaml
- .github/workflows/dist_archives.yaml
- .github/workflows/dist_check.yaml
- .github/workflows/dist_osx.yaml
- .github/workflows/release.yaml
- .readthedocs.yaml
- CHANGELOG.md
- MANIFEST.in
- README.md
- configure.ac
- debian/changelog
- debian/control
- debian/copyright
- − debian/patches/add_shared_library
- debian/patches/build-with-swig-4.5.0.patch
- debian/patches/g2.patch
- debian/patches/gcc-15.patch
- debian/patches/python3.11.patch
- debian/patches/use_debian_packaged_dlib.patch
- debian/rules
- doc/breathe/.github/FUNDING.yml
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- interfaces/.gitignore
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- + src/ViennaRNA/constraints/wrap_hairpin_hc.inc
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- + src/ViennaRNA/math/fun_bin.c
- + src/ViennaRNA/math/fun_chain.c
- + src/ViennaRNA/math/fun_gaussian.c
- + src/ViennaRNA/math/fun_kde.c
- + src/ViennaRNA/math/fun_linear.c
- + src/ViennaRNA/math/fun_log.c
- + src/ViennaRNA/math/fun_logistic.c
- + src/ViennaRNA/math/functions.h
- src/ViennaRNA/mfe/gquad.h
- src/ViennaRNA/mfe/mfe.c
- src/ViennaRNA/mfe/mfe_exterior.c
- src/ViennaRNA/mfe/mfe_exterior_window.c
- src/ViennaRNA/mfe/mfe_internal.c
- src/ViennaRNA/mfe/mfe_multibranch.c
- src/ViennaRNA/mfe/mfe_window.c
- src/ViennaRNA/mfe/mfe_wrappers.c
- src/ViennaRNA/model.h
- src/ViennaRNA/params/io.c
- src/ViennaRNA/params/params.c
- src/ViennaRNA/partfunc/partfunc.c
- src/ViennaRNA/partfunc/pf_exterior.c
- src/ViennaRNA/partfunc/pf_gquad.c
- src/ViennaRNA/partfunc/pf_internal.c
- src/ViennaRNA/partfunc/pf_multibranch.c
- src/ViennaRNA/partfunc/pf_multifold.c
- src/ViennaRNA/plex_functions.c
- src/ViennaRNA/probabilities/equilibrium_probs.c
- src/ViennaRNA/probing/SHAPE.c
- src/ViennaRNA/probing/SHAPE.h
- src/ViennaRNA/probing/basic.h
- src/ViennaRNA/probing/probing.c
- + src/ViennaRNA/probing/strategy_chain.c
- + src/ViennaRNA/probing/strategy_deigan.c
- + src/ViennaRNA/probing/strategy_deigan.h
- + src/ViennaRNA/probing/strategy_eddy.c
- + src/ViennaRNA/probing/strategy_eddy.h
- + src/ViennaRNA/probing/strategy_nlogp.c
- + src/ViennaRNA/probing/strategy_nlogp.h
- + src/ViennaRNA/probing/strategy_zarringhalam.c
- + src/ViennaRNA/probing/strategy_zarringhalam.h
- src/ViennaRNA/sampling/boltzmann_sampling.c
- src/ViennaRNA/static/.gitignore
- src/ViennaRNA/static/Makefile.am
- + src/ViennaRNA/static/probing_data_priors.h.in
- src/ViennaRNA/structures/benchmark.h
- src/ViennaRNA/structures/mea.c
- src/ViennaRNA/structures/structure_benchmark.c
- src/ViennaRNA/structures/structure_pairtable.c
- src/ViennaRNA/structures/structure_problist.c
- src/ViennaRNA/subopt/subopt.c
- src/ViennaRNA/utils/string_utils.c
- src/ViennaRNA/utils/strings.h
- src/ViennaRNA/utils/utils.c
- src/ViennaRNA/wrap_dlib.h
- src/bin/Makefile.am
- src/bin/RNALalifold.c
- src/bin/RNALfold.c
- src/bin/RNAalifold.c
- src/bin/RNAalifold.ggo
- src/bin/RNAcofold.c
- src/bin/RNAeval.c
- src/bin/RNAfold.c
- src/bin/RNAfold.ggo
- src/bin/RNAmultifold.c
- src/bin/RNAplfold.c
- src/bin/RNAsubopt.c
- src/bin/RNAsubopt.ggo
- src/bin/gengetopt_helpers.h
- + src/bin/probing_data_helpers.c
- + src/bin/probing_data_helpers.h
- src/cephes/expn.c
- src/cephes/kn.c
- src/cephes/mtherr.c
- tests/RNAfold/special
- tests/constraints.ts
- tests/python/test_RNA-utils.py
- tests/python/test_RNA.py
- tests/python2/test-RNA-boltzmann-sampling.py2
- tests/python2/test-RNA-combinatorics.py2
- tests/python2/test-RNA-constraints-SHAPE.py2
- tests/python2/test-RNA-constraints-soft.py2
- tests/python2/test-RNA-constraints-special.py2
- tests/python2/test-RNA-constraints.py2
- tests/python2/test-RNA-ensemble_defect.py2
- tests/python2/test-RNA-file-formats.py2
- tests/python2/test-RNA-mfe_eval.py2
- tests/python2/test-RNA-mfe_window.py2
- tests/python2/test-RNA-pf_window.py2
- tests/python2/test-RNA-sc-callbacks.py2
- tests/python2/test-RNA-subopt.py2
- tests/python2/test-RNA-utils.py2
- tests/python2/test-RNA.py2


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/vienna-rna/-/compare/5bd00c2989ed9366d6cc3ecc5a90d7aa7caa58fb...21e07832fab4f28bfaf2bc6365a622fa57810cba

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