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 -- View it on GitLab: https://salsa.debian.org/med-team/bali-phy/-/commit/58c8f1d304ac83471746d17d13ba1d9d3260ec33 You're receiving this email because of your account on salsa.debian.org.
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