Andreas Tille pushed to branch upstream at Debian Med / bali-phy
Commits: b0671c74 by Andreas Tille at 2026-02-10T08:20:09+01:00 New upstream version 4.1+dfsg - - - - - 114 changed files: - .github/workflows/release.yml - NEWS → NEWS.md - + bindings/functions/sort.json - 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/-/commit/b0671c74f931931b56ca8a92f5a750415ecaabaf -- View it on GitLab: https://salsa.debian.org/med-team/bali-phy/-/commit/b0671c74f931931b56ca8a92f5a750415ecaabaf You're receiving this email because of your account on salsa.debian.org.
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