Commit aed48311 authored by Benjamin Redelings's avatar Benjamin Redelings
Browse files

New upstream version 3.4.1+dfsg

parent 0bc915a8

.travis.yml

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@@ -58,7 +58,7 @@ before_install: 
  - if [ -n "${C_COMPILER}" ]; then export CC="${C_COMPILER}"; fi

  - if [ -n "${CXX_COMPILER}" ]; then export CXX="${CXX_COMPILER}"; fi

  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update && brew install meson; fi

  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then wget https://github.com/ninja-build/ninja/releases/download/v1.8.2/ninja-linux.zip && unzip -q ninja-linux.zip -d ~/bin && pyenv local 3.6 && pip3 install meson; fi

  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then wget https://github.com/ninja-build/ninja/releases/download/v1.8.2/ninja-linux.zip && unzip -q ninja-linux.zip -d ~/bin && pyenv local 3.7 && pip3 install meson; fi



script:

  - meson build --prefix=$HOME/local

meson.build

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project('bali-phy', ['cpp','c'],

	version: '3.4',

	version: '3.4.1',

	default_options : [

	  'buildtype=release',

	  'cpp_std=c++14'

src/alignment/index-matrix.H

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@@ -35,7 +35,7 @@ struct Edge 
};



struct edge_comp {

  bool operator()(const Edge& E1, const Edge& E2) {

  bool operator()(const Edge& E1, const Edge& E2) const {

    return E1.p  > E2.p;

  }

};

src/models/TreeInterface.cc

+7 −3
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#include "tree/tree.H"

#include "TreeInterface.H"

#include "models/parameters.H"
@@ -482,7 +483,7 @@ std::string write(const TreeInterface& T, int root, const std::vector<double>& L 
    for(int b: branches)

    {

	int n = T.target(b);

	names2[n] = "'" + names2[n] + "':" + std::to_string(L[T.undirected(b)]);

	names2[n] = names2[n] +":" + std::to_string(L[T.undirected(b)]);

    }

    return write(T, root, names2);

}
@@ -491,15 +492,18 @@ std::string write(const TreeInterface& T, int root, const std::vector<double>& L 
std::string write(const TreeInterface& T, const std::vector<std::string>& names, bool print_lengths)

{

    int root = 0; // T.target(0);

    vector<string> names2;

    for(auto& name: names)

	names2.push_back(escape_for_newick(name));

    if (print_lengths)

    {

	vector<double> L;

	for(int i=0;i<T.n_branches();i++)

	    L.push_back(T.branch_length(i));

	return write(T, root, L, names);

	return write(T, root, L, names2);

    }

    else

	return write(T, root, names);

	return write(T, root, names2);

}



vector<int> edges_connecting_to_node(const Tree& T, int n);

src/parser/desugar-case.cc

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@@ -289,7 +289,7 @@ failable_expression desugar_state::match_empty(const vector<expression_ref>& x, 
    failable_expression E = fail_identity();



    for(auto& e: std::reverse(equations))

	E = combine(E, e.rhs);

	E = combine(e.rhs, E);



    return E;

}