[med-svn] [Git][med-team/bali-phy][master] 5 commits: New upstream version

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / bali-phy


Commits:
436aaf48 by Andreas Tille at 2026-02-10T08:20:08+01:00
New upstream version

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b0671c74 by Andreas Tille at 2026-02-10T08:20:09+01:00
New upstream version 4.1+dfsg
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7ecb0321 by Andreas Tille at 2026-02-10T08:20:13+01:00
Update upstream source from tag 'upstream/4.1+dfsg'

Update to upstream version '4.1+dfsg'
with Debian dir d7294d6a055d8546e9ba8dbfd9cd10f29dad723e
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0c743e9d by Andreas Tille at 2026-02-10T08:20:14+01:00
Standards-Version: 4.7.3 (routine-update)

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191a4db4 by Andreas Tille at 2026-02-10T08:20:18+01:00
Remove Priority field to comply with Debian Policy 4.7.3 (routine- update)

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116 changed files:

- .github/workflows/release.yml
- NEWS → NEWS.md
- + bindings/functions/sort.json
- debian/changelog
- debian/control
- doc/GNUmakefile
- doc/Instructions8.tut.xml → doc/Instructions.tut.xml
- doc/README.itex.xml
- doc/Tutorial.tut.xml
- − doc/Tutorial7.tut.xml
- doc/add_screen.pl
- haskell/Bio/Sequence.hs
- haskell/Data/IntMap.hs
- haskell/Data/OldList.hs
- haskell/Foreign/IntMap.hs
- haskell/Forest.hs
- haskell/Probability/Distribution/PhyloCTMC/FixedA.hs
- haskell/Probability/Distribution/Tree/Coalescent.hs
- haskell/Probability/Distribution/Tree/Moves.hs
- haskell/Probability/Logger.hs
- haskell/SModel/Likelihood/FixedA.hs
- haskell/SModel/MixtureModels.hs
- meson.build
- scripts/bp-analyze
- src/alignment/alignment-util.H
- src/alignment/alignment-util.cc
- src/alignment/alignment.H
- src/alignment/alignment.cc
- src/alignment/index-matrix.H
- src/alignment/index-matrix.cc
- src/bali-phy/A-T-model.cc
- src/bali-phy/bali-phy.cc
- src/builtins/Alignment.cc
- src/builtins/IntMap.cc
- src/builtins/LikelihoodSEV.cc
- src/builtins/MCMC.cc
- + src/builtins/TreeDist.cc
- src/builtins/meson.build
- src/computation/context.cc
- src/computation/core/ast.H
- src/computation/core/func.H
- src/computation/data_con_info.H
- src/computation/expression/convert.H
- src/computation/expression/convert.cc
- src/computation/expression/indexify.cc
- src/computation/fresh_vars.H
- src/computation/fresh_vars.cc
- src/computation/haskell/Integer.H
- src/computation/haskell/core.cc
- + src/computation/haskell/integer_container.H
- src/computation/instance_info.H
- src/computation/machine/evaluate.cc
- src/computation/machine/graph_register.H
- src/computation/machine/graph_register.cc
- src/computation/machine/show_graph.cc
- src/computation/module.H
- src/computation/module.cc
- src/computation/optimization/float-out.H
- src/computation/optimization/float-out.cc
- src/computation/optimization/free-vars.H
- src/computation/optimization/free-vars.cc
- − src/computation/optimization/free_vars.H
- src/computation/optimization/occurrence.H
- src/computation/optimization/occurrence.cc
- src/computation/optimization/set-levels.H
- src/computation/optimization/set-levels.cc
- src/computation/optimization/simplifier.cc
- src/computation/parser/parser.cc
- src/computation/parser/parser.hh
- src/computation/parser/parser.y
- src/computation/preprocess.cc
- src/computation/program.cc
- src/computation/typecheck/constraints.H
- src/computation/varinfo.H
- src/mcmc/moves.cc
- src/mcmc/sample-alignment.cc
- src/mcmc/sample-branch-lengths.cc
- src/mcmc/sample-topology-SPR.cc
- src/mcmc/slice-sampling.cc
- src/models/A-T-prog.H
- src/models/A-T-prog.cc
- src/models/TreeInterface.cc
- src/models/compile.cc
- src/models/parameters.cc
- src/sequence/alphabet.cc
- src/sequence/sequence.cc
- src/substitution/likelihoodSEV.H
- src/substitution/likelihoodSEV.cc
- src/tools/alignment-cat.cc
- src/tools/alignment-compare.cc
- src/tools/alignment-consensus.cc
- src/tools/alignment-distances.cc
- src/tools/alignment-gild.cc
- src/tools/alignment-indices.cc
- src/tools/alignment-max.cc
- src/tools/alignment-smc.cc
- src/tools/alignment-thin.cc
- src/tools/alignments-diff.cc
- src/tools/findroot.cc
- src/tools/optimize.H
- src/tools/optimize.cc
- src/tools/partition.cc
- src/tools/tree-tool.cc
- src/util/include/util/string/split.H
- src/util/string/split.cc
- tests/haskell/Types/TypeFamilies/5/error
- tests/prob_prog/infer_tree/1/Model.hs
- tests/prob_prog/infer_tree/2/Model.hs
- tests/prob_prog/infer_tree/3/Model.hs
- tests/prob_prog/infer_tree/4/Model.hs
- tests/prob_prog/infer_tree/5/Model.hs
- tests/prob_prog/infer_tree/6/Model.hs
- tests/prob_prog/infer_tree/coalescent/1/Model.hs
- tests/prob_prog/infer_tree/coalescent/2/Model.hs
- tests/prob_prog/infer_tree/m7/Model.hs
- tests/prob_prog/infer_tree/yule/1/Model.hs


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/bali-phy/-/compare/b3bb7169002348e74320e6379e1f6eb3e1483bad...191a4db45c460318d18d033383377f6492823cfc

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View it on GitLab: https://salsa.debian.org/med-team/bali-phy/-/compare/b3bb7169002348e74320e6379e1f6eb3e1483bad...191a4db45c460318d18d033383377f6492823cfc
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