.travis.yml

@@ -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

debian/changelog

+bali-phy (3.4.1+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream version 3.4.1+dfsg
+  * Update Standards-Version to 4.3.0
+
+ -- Benjamin Redelings <benjamin.redelings@gmail.com>  Tue, 22 Jan 2019 14:04:09 -0500
+
 bali-phy (3.4+dfsg-1) unstable; urgency=medium
 
   * New upstream version

debian/control

@@ -15,7 +15,7 @@ Build-Depends: debhelper (>= 11),
                libboost-system-dev,
                libboost-filesystem-dev,
                libboost-chrono-dev
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/bali-phy
 Vcs-Git: https://salsa.debian.org/med-team/bali-phy.git
 Homepage: http://www.bali-phy.org

meson.build

 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

@@ -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

+#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

@@ -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;
 }

src/startup/help.cc

@@ -408,7 +408,7 @@ void help_topics(std::ostream& o, const ptree& help)
     auto subtopics = get_subtopics(help);
     subtopics.push_back("functions");
     
-    o<<"To help on one of the following topics, run `bali-phy help "<<underline("topic")<<"`\n\n";
+    o<<"To see help on one of the following topics, run `bali-phy help "<<underline("topic")<<"`\n\n";
     o<<show_options(subtopics);
     o<<"\n";
     o<<"\n";
@@ -440,15 +440,17 @@ void show_help(const string& topic, const vector<fs::path>& package_paths)
     Rules R(package_paths);
     if (topic == "functions")
     {
+	vector<string> func_names;
+
 	for(auto& rule: R.get_rules())
 	{
 	    if (rule.second.get_child_optional("name"))
 	    {
 		string name = rule.second.get_child("name").get_value<string>();
-		string result_type = unparse_type(rule.second.get_child("result_type"));
-		std::cout<<name<<" :: "<<result_type << std::endl;
+		func_names.push_back(name);
 	    }
 	}
+	std::cout<<show_options(func_names)<<std::endl;
 	return;
     }
 

src/tools/draw-tree.cc

@@ -23,6 +23,10 @@
 #include <vector>
 #include <fstream>
 
+#ifndef M_PI
+#define M_PI 3.14159265358979323846
+#endif
+
 // FIXME - Add a command-line option to turn on clouds.
 //       - Actually draw arrows on type 2 edges.
 //       - Figure out how to use boost's Kamada-Kawai layout.

src/tools/stats-table.cc

@@ -28,7 +28,10 @@
 #include <boost/optional.hpp>
 
 using boost::optional;
-using namespace std;
+
+using std::string;
+using std::vector;
+using std::pair;
 
 using boost::dynamic_bitset;
 
@@ -68,7 +71,7 @@ void write_header(std::ostream& o, const vector<string>& headers)
 {
     for(int i=0;i<headers.size();i++) 
     {
-	cout<<headers[i];
+	std::cout<<headers[i];
       
 	if (i == headers.size()-1)
 	    o<<"\n";
@@ -102,8 +105,8 @@ optional<pair<unsigned,unsigned>> is_numeric_range(const string& s, unsigned n)
 	    return boost::none;
     }
 
-    start = max(1U,start);
-    end = min(n,end);
+    start = std::max(1U,start);
+    end = std::min(n,end);
     return pair<unsigned,unsigned>{start,end};
 }
 
@@ -172,7 +175,7 @@ bool read_entries(const string& line, const vector<int>& indices, char delim, ve
 
 
 template<> 
-void Table<string>::load_file(istream& file,int skip,int subsample, int max,
+void Table<string>::load_file(std::istream& file,int skip,int subsample, int max,
 			      const vector<string>& ignore, const vector<string>& select)
 {
     // Read in headers from file

src/tools/trees-distances.cc

@@ -40,9 +40,16 @@
 namespace po = boost::program_options;
 using po::variables_map;
 
-using namespace std;
 using namespace statistics;
 
+using std::vector;
+using std::valarray;
+using std::string;
+
+using std::endl;
+using std::cout;
+using std::cerr;
+
 using boost::optional;
 
 template <typename T>
@@ -739,7 +746,7 @@ int main(int argc,char* argv[])
 	    // set the window size
 	    int max_lag = int( double(trees.size()/10.0 + 1.0 ) );
 	    if (args.count("max-lag"))
-		max_lag = min(max_lag,args["max-lag"].as<int>());
+		max_lag = std::min(max_lag,args["max-lag"].as<int>());
       
 	    // bound the max_lag
 	    if (max_lag >= trees.size()/2)
@@ -875,7 +882,7 @@ int main(int argc,char* argv[])
 	    for(;t<trees1.size() and required_hits;t++) 
 	    {
 		double d = distance(trees1[t],trees2,metric_fn);
-		closest = min(closest,d);
+		closest = std::min(closest,d);
 
 		if (direction == 0 and d < x1) {
 		    if (required_hits ==4)

src/tools/trees-to-SRQ.cc

@@ -31,7 +31,6 @@
 #include "tree/tree-util.H"
 #include "statistics.H"
 
-using namespace std;
 #include <boost/program_options.hpp>
 
 namespace po = boost::program_options;
@@ -40,7 +39,10 @@ using po::variables_map;
 using std::cout;
 using std::cerr;
 using std::endl;
+
 using std::string;
+using std::vector;
+using std::valarray;
 
 using boost::optional;
 

src/tree/tree.H

@@ -725,4 +725,6 @@ void remove_sub_branches(Tree& T);
 
 bool same_topology_and_node_and_branch_numbers(const Tree& T1, const Tree& T2);
 
+std::string escape_for_newick(const std::string& s);
+std::string unescape_from_newick(const std::string& s);
 #endif

tests/optimizer/10/error

 size = 1   Test.#0 = Foreign.Vector.listFromString Test.#11
-size = 1   Test.#10 = Test.#4:Test.#3
+size = 1   Test.#10 = Test.#8:Test.#3
 size = 1   Test.#11 = "case: failed pattern match"
-size = 1   Test.#1145 = Test.#13:Test.#10
+size = 1   Test.#1145 = Test.#7:Test.#10
 size = 1   Test.#1151 = 10
 size = 1   Test.#1153 = 2
-size = 1   Test.#13 = 'y'
 size = 1   Test.#2 = '!'
 size = 1   Test.#3 = Test.#2:[]
-size = 1   Test.#4 = 'o'
-size = 1   Test.#5 = Prelude:error Test.#1145
-size = 1   Test.#6 = Prelude:error Test.#0
-size = 1   Test.f = \#8 -> case #8 of {#1148:#1149 -> #1148,[] -> Test.#5,_ -> Test.#6}
-size = 3   Test.g = \#1149 -> let {#1150 = 10} in let {#1152 = case #1149 of {#1148:#1153 -> #1148,[] -> Test.#5,_ -> Test.#6}} in Prelude:add #1150 #1152
+size = 1   Test.#4 = Prelude:error Test.#0
+size = 1   Test.#7 = 'y'
+size = 1   Test.#8 = 'o'
+size = 1   Test.#9 = Prelude:error Test.#1145
+size = 1   Test.f = \#6 -> case #6 of {#1148:#1149 -> #1148,[] -> Test.#9,_ -> Test.#4}
+size = 3   Test.g = \#1149 -> let {#1150 = 10} in let {#1152 = case #1149 of {#1148:#1153 -> #1148,[] -> Test.#9,_ -> Test.#4}} in Prelude:add #1150 #1152
 size = 1   Test.h = Prelude:add Test.#1151 Test.#1153

tests/optimizer/13/error

-size = 2   Test.f = \#9 -> let {#1 = case #9 of {#166:#167 -> #166,[] -> Data.List.#22,_ -> Data.List.#23}} in \#10 #11 -> case #1 of {Data.Bool.True -> #10,_ -> #11}
-size = 2   Test.g = \#13 #14 #15 -> case #15 of {#166:#167 -> case #166 of {Data.Bool.True -> #13,_ -> #14},[] -> case Data.List.#22 of {Data.Bool.True -> #13,_ -> #14},_ -> case Data.List.#23 of {Data.Bool.True -> #13,_ -> #14}}
+size = 2   Test.f = \#7 -> let {#1 = case #7 of {#166:#167 -> #166,[] -> Data.List.#55,_ -> Data.List.#17}} in \#8 #9 -> case #1 of {Data.Bool.True -> #8,_ -> #9}
+size = 2   Test.g = \#10 #11 #12 -> case #12 of {#166:#167 -> case #166 of {Data.Bool.True -> #10,_ -> #11},[] -> case Data.List.#55 of {Data.Bool.True -> #10,_ -> #11},_ -> case Data.List.#17 of {Data.Bool.True -> #10,_ -> #11}}

tests/optimizer/14/error

-size = 1   Main.#0 = Main.#18:[]
+size = 1   Main.#0 = Main.#25:[]
 size = 1   Main.#1 = 'f'
-size = 1   Main.#1141 = Foreign.Vector.listFromString Main.#17
-size = 1   Main.#1144 = Foreign.Vector.listFromString Main.#33
+size = 1   Main.#1141 = Foreign.Vector.listFromString Main.#12
+size = 1   Main.#1144 = Foreign.Vector.listFromString Main.#24
 size = 1   Main.#1148 = Main.#1:[]
 size = 1   Main.#1151 = "Main.f3: pattern match failure"
 size = 1   Main.#1152 = Foreign.Vector.listFromString Main.#1151
-size = 1   Main.#13 = Prelude:error Main.#1141
-size = 1   Main.#17 = "case: failed pattern match"
-size = 1   Main.#18 = 'f'
-size = 1   Main.#33 = "case: failed pattern match"
-size = 1   Main.#45 = Prelude:error Main.#1148
-size = 1   Main.#59 = Prelude:error Main.#1152
-size = 1   Main.#6 = Prelude:error Main.#1144
-size = 7   Main.f = \#29 #30 -> let {fail1 = case #29 of {[] -> Main.fail2#0,#10:#11 -> case #30 of {[] -> #10:[],#3:#4 -> Main.fail2#0,_ -> Main.#6},_ -> Main.#13}} in case #29 of {#24:#25 -> case #30 of {#1151:#1152 -> Data.List.++ #25 #1152,_ -> fail1},_ -> fail1}
-size = 4   Main.f2 = \#1150 #1151 -> case #1150 of {#35:#36 -> case #1151 of {#37:#38 -> Data.List.++ #36 #38,[] -> #35:[],_ -> Main.#45},_ -> Main.#45}
-size = 4   Main.f3 = \#47 #48 -> case #47 of {#49:#50 -> case #48 of {#51:#52 -> Data.List.++ #50 #52,[] -> #49:[],_ -> Main.#59},_ -> Main.#59}
+size = 1   Main.#12 = "case: failed pattern match"
+size = 1   Main.#24 = "case: failed pattern match"
+size = 1   Main.#25 = 'f'
+size = 1   Main.#33 = Prelude:error Main.#1148
+size = 1   Main.#4 = Prelude:error Main.#1144
+size = 1   Main.#45 = Prelude:error Main.#1152
+size = 1   Main.#9 = Prelude:error Main.#1141
+size = 7   Main.f = \#21 #22 -> let {fail1 = case #21 of {[] -> Main.fail2#0,#7:#8 -> case #22 of {[] -> #7:[],#1151:#3 -> Main.fail2#0,_ -> Main.#4},_ -> Main.#9}} in case #21 of {#17:#18 -> case #22 of {#1151:#1152 -> Data.List.++ #18 #1152,_ -> fail1},_ -> fail1}
+size = 4   Main.f2 = \#1150 #1151 -> case #1150 of {#1152:#26 -> case #1151 of {#27:#28 -> Data.List.++ #26 #28,[] -> #1152:[],_ -> Main.#33},_ -> Main.#33}
+size = 4   Main.f3 = \#35 #36 -> case #35 of {#37:#38 -> case #36 of {#39:#40 -> Data.List.++ #38 #40,[] -> #37:[],_ -> Main.#45},_ -> Main.#45}
 size = 1   Main.fail2#0 = Prelude:error Main.#0

tests/optimizer/15/error

-size = 1   Test.#0 = Foreign.Vector.listFromString Test.#9
-size = 1   Test.#5 = Prelude:error Test.#0
-size = 1   Test.#9 = "case: failed pattern match"
-size = 2   Test.f = \#7 -> case #7 of {(#1142, #3) -> 2,_ -> Test.#5}
+size = 1   Test.#0 = Foreign.Vector.listFromString Test.#7
+size = 1   Test.#4 = Prelude:error Test.#0
+size = 1   Test.#7 = "case: failed pattern match"
+size = 2   Test.f = \#6 -> case #6 of {(#1142, #3) -> 2,_ -> Test.#4}

tests/optimizer/3/error

 size = 1   Test.#0 = 10
 size = 1   Test.#1142 = 3
-size = 1   Test.#4 = Prelude:add Test.#0 Test.#1142
-size = 0   Test.f = \#3 -> Test.#4
+size = 1   Test.#3 = Prelude:add Test.#0 Test.#1142
+size = 0   Test.f = \#2 -> Test.#3

tests/optimizer/4/error

 size = 1   Test.#0 = Foreign.Vector.listFromString Test.#12
 size = 1   Test.#12 = "case: failed pattern match"
-size = 1   Test.#8 = Prelude:error Test.#0
-size = 2   Test.f = \#10 -> case #10 of {0 -> 1,2 -> 3,_ -> Test.#8}
+size = 1   Test.#5 = Prelude:error Test.#0
+size = 2   Test.f = \#7 -> case #7 of {0 -> 1,2 -> 3,_ -> Test.#5}

tests/optimizer/5/error

-size = 1   Test.#0 = Foreign.Vector.listFromString Test.#18
-size = 1   Test.#12 = Prelude:error Test.#0
-size = 1   Test.#18 = "case: failed pattern match"
-size = 2   Test.f = \#14 -> case #14 of {#8:#9 -> #9,[] -> [],_ -> Test.#12}
+size = 1   Test.#0 = Foreign.Vector.listFromString Test.#13
+size = 1   Test.#13 = "case: failed pattern match"
+size = 1   Test.#9 = Prelude:error Test.#0
+size = 2   Test.f = \#11 -> case #11 of {#7:#8 -> #8,[] -> [],_ -> Test.#9}