[med-svn] [Git][med-team/bali-phy][upstream] New upstream version 4.0
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Fri Feb 28 21:19:53 GMT 2025
Étienne Mollier pushed to branch upstream at Debian Med / bali-phy
Commits:
58c8f1d3 by Étienne Mollier at 2025-02-28T21:54:30+01:00
New upstream version 4.0
- - - - -
350 changed files:
- .github/workflows/build.yml
- .github/workflows/release.yml
- .gitignore
- .vscode/launch.json
- NEWS
- README.md
- + bindings/distributions/dirichlet.json
- + bindings/distributions/dirichlet_on.json
- + bindings/distributions/dirichlet_on_dirichlet.json
- bindings/distributions/fixed_topology_tree.json
- bindings/distributions/symmetric_dirichlet.json
- bindings/distributions/symmetric_dirichlet_on.json
- + bindings/functions/branch_length.json
- bindings/functions/branches.json
- + bindings/functions/branches_list.json
- + bindings/functions/convertDiscrete.json
- + bindings/functions/identity.json
- + bindings/functions/lookup.json
- + bindings/functions/nodes.json
- bindings/functions/num_branches.json
- + bindings/functions/pow.json
- + bindings/functions/scaleBy.json
- + bindings/functions/scaleTo.json
- bindings/models/Covarion/galtier01.json
- bindings/models/Covarion/gtr.json
- bindings/models/Covarion/huelsenbeck02.json
- bindings/models/Covarion/huelsenbeck02_test.json
- + bindings/models/Covarion/multi_freq.json
- bindings/models/Covarion/ts98.json
- bindings/models/Rates/free.json
- bindings/models/Rates/gamma.json
- bindings/models/branch_site.json
- + bindings/models/branch_site_mixture.json
- + bindings/models/busted.json
- + bindings/models/busted_s.json
- bindings/models/f81.json
- bindings/models/gy94.json
- bindings/models/gy94_ext.json
- bindings/models/m2a_test.json
- bindings/models/m3_test.json
- bindings/models/m8a_test.json
- bindings/models/mg94.json
- bindings/models/mg94k.json
- + bindings/models/mnm.json
- + bindings/models/multi_freq.json
- bindings/models/multi_rate.json
- bindings/models/parameter_mixture.json
- bindings/models/rna_16a.json
- − bindings/models/scaled_mixture.json
- bindings/models/x3.json
- doc/GNUmakefile
- doc/README.itex.xml
- + doc/Tutorial7.tut.xml
- doc/man/alignment-consensus.md
- doc/man/alignment-draw.md
- doc/man/alignment-gild.md
- doc/man/alignment-info.md
- doc/man/alignment-max.md
- doc/man/alignment-smc.md
- doc/man/alignment-thin.md
- doc/man/bali-phy.md
- doc/man/cut-range.md
- doc/man/help_to_man
- doc/man/mcon-tool.md
- doc/man/summarize-ancestors.md
- doc/man/tree-tool.md
- doc/man/trees-distances.md
- examples/lrRNA/NOTES.txt
- haskell/Bio/Alignment.hs
- haskell/Bio/Alignment/Matrix.hs
- haskell/Bio/Alphabet.hs
- haskell/Bio/Sequence.hs
- haskell/Compiler/IO.hs
- haskell/Control/Applicative.hs
- haskell/Control/Monad.hs
- haskell/Data/Array.hs
- haskell/Data/BitVector.hs
- haskell/Data/CSV.hs
- haskell/Data/Floating/Types.hs
- haskell/Data/Foldable.hs
- haskell/Data/IntMap.hs
- haskell/Data/IntSet.hs
- haskell/Data/JSON.hs
- haskell/Data/Matrix.hs
- haskell/Data/Text.hs
- + haskell/EigenExp.hs
- haskell/Foreign/CList.hs
- haskell/Foreign/Maybe.hs
- haskell/Foreign/String.hs
- haskell/Foreign/Vector.hs
- haskell/Forest.hs
- haskell/Graph.hs
- haskell/MCMC/Moves/Tree.hs
- haskell/Markov.hs
- haskell/Parse.hs
- haskell/PopGen.hs
- haskell/PopGen/Deploid.hs
- haskell/Probability.hs
- haskell/Probability/Distribution/Dirichlet.hs
- haskell/Probability/Distribution/DirichletProcess.hs
- haskell/Probability/Distribution/Discrete.hs
- haskell/Probability/Distribution/Geometric.hs
- haskell/Probability/Distribution/List.hs
- haskell/Probability/Distribution/Multinomial.hs
- haskell/Probability/Distribution/PhyloCTMC/FixedA.hs
- haskell/Probability/Distribution/PhyloCTMC/Properties.hs
- haskell/Probability/Distribution/PhyloCTMC/VariableA.hs
- haskell/Probability/Distribution/Tree.hs
- + haskell/Probability/Distribution/Tree/BirthDeath2.hs
- haskell/Probability/Distribution/Tree/UniformTimeTree.hs
- + haskell/Probability/Distribution/UniqueDist.hs
- haskell/Probability/Logger.hs
- haskell/Probability/Random.hs
- haskell/SMC.hs
- haskell/SModel.hs
- + haskell/SModel/ASRV.hs
- haskell/SModel/BranchModel.hs
- + haskell/SModel/BranchSiteMixture.hs
- haskell/SModel/Codons.hs
- haskell/SModel/Doublets.hs
- − haskell/SModel/EigenExp.hs
- haskell/SModel/Empirical.hs
- haskell/SModel/Frequency.hs
- haskell/SModel/Likelihood/FixedA.hs
- haskell/SModel/Likelihood/VariableA.hs
- haskell/SModel/Markov.hs
- haskell/SModel/MarkovModulated.hs
- haskell/SModel/MixtureModel.hs
- haskell/SModel/MixtureModels.hs
- haskell/SModel/MultiFrequency.hs
- haskell/SModel/MutSel.hs
- haskell/SModel/NonReversibleMarkov.hs
- haskell/SModel/Nucleotides.hs
- haskell/SModel/Parsimony.hs
- + haskell/SModel/PosSelection.hs
- haskell/SModel/RNAEdit.hs
- haskell/SModel/Rate.hs
- haskell/SModel/ReversibleMarkov.hs
- haskell/SModel/Simple.hs
- haskell/System/Environment.hs
- haskell/Tree.hs
- meson.build
- scripts/make_winroot.sh
- src/alignment/index-matrix.cc
- src/bali-phy/A-T-model.cc
- src/bali-phy/bali-phy.cc
- src/bali-phy/cmd_line.cc
- src/bali-phy/files.cc
- src/bali-phy/help.cc
- src/bali-phy/meson.build
- src/builtins/Alignment.cc
- src/builtins/File.cc
- src/builtins/Foreign.cc
- src/builtins/Likelihood.cc
- src/builtins/LikelihoodSEV.cc
- src/builtins/Matrix.cc
- src/builtins/Parsimony.cc
- src/builtins/Real.cc
- src/builtins/SModel.cc
- src/computation/haskell/core2.H → src/computation/core/ast.H
- + src/computation/core/func.H
- + src/computation/core/func.cc
- + src/computation/core/wrap.H
- + src/computation/core/wrap.cc
- src/computation/data_con_info.H
- src/computation/desugar/desugar-case.cc
- src/computation/desugar/desugar.H
- src/computation/desugar/desugar.cc
- src/computation/expression/convert.H
- src/computation/expression/convert.cc
- src/computation/expression/indexify.H
- src/computation/expression/indexify.cc
- src/computation/expression/var.H
- src/computation/fresh_vars.H
- src/computation/fresh_vars.cc
- src/computation/haskell/core.H
- src/computation/haskell/core.cc
- src/computation/haskell/coretype.H
- src/computation/haskell/coretype.cc
- − src/computation/haskell/desugar_type.H
- src/computation/haskell/extensions.H
- src/computation/haskell/extensions.cc
- src/computation/haskell/haskell.H
- src/computation/haskell/haskell.cc
- src/computation/haskell/pattern.H
- src/computation/haskell/type.H
- src/computation/haskell/type.cc
- src/computation/haskell/var.H
- src/computation/instance_info.H
- src/computation/loader.H
- src/computation/loader.cc
- src/computation/machine/graph_register.H
- src/computation/meson.build
- src/computation/message.H
- src/computation/message.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/inliner.cc
- src/computation/optimization/occurrence.H
- src/computation/optimization/occurrence.cc
- src/computation/optimization/occurrence_info.H
- src/computation/optimization/set-levels.H
- src/computation/optimization/set-levels.cc
- src/computation/optimization/simplifier.H
- src/computation/optimization/simplifier.cc
- src/computation/optimization/substitution.H
- 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/rename/decls.cc
- src/computation/rename/expression.cc
- src/computation/rename/pattern.cc
- src/computation/rename/rename.H
- src/computation/rename/rename.cc
- src/computation/rename/types.cc
- src/computation/typecheck/alphabetize.cc
- src/computation/typecheck/binds.cc
- src/computation/typecheck/class.cc
- src/computation/typecheck/constraints.H
- src/computation/typecheck/constraints.cc
- src/computation/typecheck/context.H
- + src/computation/typecheck/data.cc
- src/computation/typecheck/default.cc
- src/computation/typecheck/env.H
- src/computation/typecheck/env.cc
- src/computation/typecheck/errors.cc
- src/computation/typecheck/expression.cc
- src/computation/typecheck/instance.cc
- src/computation/typecheck/kind.H
- src/computation/typecheck/kind.cc
- src/computation/typecheck/kindcheck.H
- src/computation/typecheck/kindcheck.cc
- src/computation/typecheck/match.H
- src/computation/typecheck/pattern.cc
- src/computation/typecheck/quals.cc
- src/computation/typecheck/solver.H
- src/computation/typecheck/solver.cc
- src/computation/typecheck/solver/canonicalize.cc
- src/computation/typecheck/solver/rewrite.cc
- src/computation/typecheck/substitution.cc
- src/computation/typecheck/tidy.H
- src/computation/typecheck/tidy.cc
- src/computation/typecheck/type_groups.cc
- src/computation/typecheck/typecheck.H
- src/computation/typecheck/typecheck.cc
- src/computation/typecheck/types.H
- src/computation/typecheck/types.cc
- src/computation/typecheck/unify.cc
- src/dp/2way.cc
- src/dp/4way.cc
- src/dp/5way.cc
- src/dp/alignment-sums.cc
- − src/math/eigenvalue.H
- − src/math/eigenvalue.cc
- src/math/exponential.H
- src/math/exponential.cc
- src/mcmc/result.cc
- src/mcmc/sample-alignment.cc
- src/mcmc/sample-topology-SPR.cc
- src/mcon/mcon.cc
- src/meson.build
- src/models/A-T-prog.H
- src/models/A-T-prog.cc
- src/models/TreeInterface.H
- src/models/TreeInterface.cc
- src/models/code-generation.cc
- src/models/compile.cc
- src/models/driver.cc
- src/models/lexer.cc
- src/models/lexer.l
- src/models/parameters.H
- src/models/parameters.cc
- src/models/parse.cc
- src/models/parser.cc
- src/models/parser.hh
- src/models/parser.y
- src/models/rules.cc
- src/models/typecheck.cc
- src/models/unification.H
- src/models/unification.cc
- src/substitution/cache.H
- + src/substitution/cache.cc
- src/substitution/likelihood.H
- src/substitution/likelihood.cc
- src/substitution/likelihoodSEV.H
- src/substitution/likelihoodSEV.cc
- src/tools/draw-tree.cc
- src/tree/tree.H
- src/util/graph.cc
- src/util/include/util/range.H
- src/util/include/util/text.H
- src/util/ptree.cc
- src/util/text.cc
- tests/PartialSelfing/diploid.andro.multi_theta.BP.hs
- tests/PartialSelfing/diploid.andro.multi_theta.TCb.hs
- tests/PartialSelfing/diploid.multi_theta.TC.hs
- tests/PartialSelfing/diploid.multi_theta.menziesii.hs
- tests/PartialSelfing/diploid.null.multi_theta.TCb.hs
- tests/PartialSelfing/diploid.pure_herm.multi_theta.BP.hs
- tests/PartialSelfing/diploid.pure_herm.multi_theta.DC.hs
- tests/PartialSelfing/diploid.pure_herm.multi_theta.NNKB.hs
- tests/PartialSelfing/diploid.pure_herm.multi_theta.TC.hs
- tests/PartialSelfing/diploid.pure_herm.multi_theta.TCa.hs
- tests/PartialSelfing/diploid.pure_herm.multi_theta.TCb.hs
- tests/PartialSelfing/diploid.pure_herm.single_theta.BP.hs
- tests/PartialSelfing/diploid.pure_herm.single_theta.DC.hs
- tests/PartialSelfing/diploid.pure_herm.single_theta.NNKB2.hs
- tests/PartialSelfing/diploid.pure_herm.single_theta.NNKB3.hs
- tests/PartialSelfing/firstallele.pure_herm.multi_theta.BP.hs
- tests/haskell/Types/11/error
- tests/haskell/Types/2/error
- tests/haskell/Types/4/error
- tests/haskell/Types/6/error
- tests/haskell/Types/8/error
- tests/haskell/Types/9/error
- tests/haskell/Types/GADT/4/error
- + tests/haskell/Types/TypeFamilies/5/Main.hs
- + tests/haskell/Types/TypeFamilies/5/command.txt
- + tests/haskell/Types/TypeFamilies/5/error
- + tests/haskell/Types/TypeFamilies/5/exit
- tests/mcmc/fixed-scale/command.txt
- tests/mcmc/no-imodel/command.txt
- tests/mcmc/with-imodel/command.txt
- tests/parse/5/command.txt
- tests/parse/error/2/command.txt
- tests/parse/let/1/command.txt
- tests/parse/partitions/link/3/command.txt
- tests/parse/partitions/link/4/command.txt
- tests/parse/partitions/link/5/command.txt
- tests/parse/partitions/link/6/command.txt
- tests/parse/partitions/link/7/command.txt
- + tests/parse/rates/1/command.txt
- + tests/parse/rates/1/dna.fasta
- tests/prob_prog/cluster/1/command.txt
- tests/prob_prog/infer_tree/1/Model.hs
- tests/prob_prog/infer_tree/1/command.txt
- tests/prob_prog/infer_tree/4/command.txt
- tests/prob_prog/infer_tree/5/Model.hs
- tests/prob_prog/infer_tree/6/Model.hs
- tests/prob_prog/infer_tree/coalescent/2/Model.hs
- + tests/prob_prog/infer_tree/m7/Model.hs
- + tests/prob_prog/infer_tree/m7/bglobin.fasta
- + tests/prob_prog/infer_tree/m7/command.txt
- tests/run-tests.py
The diff was not included because it is too large.
View it on GitLab: https://salsa.debian.org/med-team/bali-phy/-/commit/58c8f1d304ac83471746d17d13ba1d9d3260ec33
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View it on GitLab: https://salsa.debian.org/med-team/bali-phy/-/commit/58c8f1d304ac83471746d17d13ba1d9d3260ec33
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