debian/changelog

-bali-phy (3.1+dfsg-1) UNRELEASED; urgency=medium
+bali-phy (3.1.1+dfsg-1) UNRELEASED; urgency=medium
 
   [ Dylan Aïssi ]
   * Team upload.
@@ -9,7 +9,14 @@ bali-phy (3.1+dfsg-1) UNRELEASED; urgency=medium
   * New upstream version
   * Add quilt patch to not run external testiphy test suite.
 
- -- Benjamin Redelings <benjamin.redelings@gmail.com>  Wed, 02 May 2018 18:26:46 -0400
+  [ Andreas Tille ]
+  * New upstream version 3.1+dfsg
+
+  [ Benjamin Redelings ]
+  * New upstream version 3.1.1+dfsg
+  * Remove patches incorporated upstream.
+
+ -- Benjamin Redelings <benjamin.redelings@gmail.com>  Sat, 05 May 2018 08:05:07 -0400
 
 bali-phy (3.0.3+dfsg-1) unstable; urgency=medium
 

debian/patches/no_testiphy.diff

---- a/meson.build
-+++ b/meson.build
-@@ -135,9 +135,3 @@ test('bali-phy testsuite',
-      timeout: 600,
-      workdir: join_paths(meson.source_root(),'tests'),
-      args:[baliphy.full_path(), packagepath])
--
--test('testiphy (likelihood testsuite)',
--     find_program('testiphy/testiphy'),
--     timeout: 600,
--     workdir: join_paths(meson.source_root(),'testiphy'),
--     args:[baliphy.full_path(), packagepath])

debian/patches/series

-no_testiphy.diff

functions/gtr.json

 {
     "name": "gtr",
     "title":"The GTR exchangability matrix",
+    "deprecated-synonyms": ["GTR"],
     "result_type": "RevCTMC[a]",
     "call": "SModel.gtr'[sym,pi,a]",
     "citation":"Tavare, 1986",

functions/hky85.json

 {
     "name": "hky85",
     "title": "The Hasegawa-Kishino-Yano (1985) nucleotide rate matrix",
+    "deprecated-synonyms": ["HKY","hky","HKY85"],
     "result_type": "RevCTMC[a]",
     "constraints": ["Nucleotides[a]"],
     "citation":{"type": "article",

functions/tn93.json

 {
     "name": "tn93",
     "title": "The Tamura-Nei (1993) nucleotide rate matrix",
+    "deprecated-synonyms": ["TN","TrN","tn","TN93","trn"],
     "result_type": "RevCTMC[a]",
     "citation":{"type": "article",
 		"title": "Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.",

meson.build

 project('bali-phy', ['cpp','c'],
-	version: '3.1',
+	version: '3.1.1',
 	default_options : [
 	  'buildtype=release',
 	  'cpp_std=c++14'
@@ -130,14 +130,23 @@ subdir('src')
 
 subdir('doc')
 
+# Run internal tests
+run_tests = find_program(join_paths(meson.source_root(),'tests/run-tests.py'))
+
 test('bali-phy testsuite',
-     find_program('tests/run-tests.py'),
+     run_tests,
      timeout: 600,
      workdir: join_paths(meson.source_root(),'tests'),
      args:[baliphy.full_path(), packagepath])
 
+# Run external likelihood testsuite
+
+testiphy = find_program(join_paths(meson.source_root(),'testiphy/testiphy'), required: false)
+
+if testiphy.found()
   test('testiphy (likelihood testsuite)',
-     find_program('testiphy/testiphy'),
+       testiphy,
        timeout: 600,
        workdir: join_paths(meson.source_root(),'testiphy'),
        args:[baliphy.full_path(), packagepath])
+endif

src/models/rules.cc

@@ -190,7 +190,7 @@ optional<Rule> Rules::get_rule_for_func(const string& s) const
     else if (auto syn = it->second.get_optional<string>("synonym"))
 	return get_rule_for_func(*syn);
     else if (auto syn = it->second.get_optional<string>("deprecated-synonym"))
-	throw myexception()<<"Error: the function '"<<s<<"' is now called '"<<*syn<<"'";
+	throw myexception()<<"I don't recognize '"<<s<<"'.  Perhaps you meant '"<<*syn<<"'?";
     else
 	return it->second;
 }

src/models/setup.H

@@ -23,6 +23,8 @@ public:
     std::vector<pretty_model_t> terms;
 
     std::string show(const Rules& R, bool = true) const;
+    std::string show_main(const Rules&, bool = true) const;
+    std::string show_extracted(const Rules&) const;
 
     pretty_model_t(const ptree& m);
 };
@@ -40,6 +42,8 @@ public:
     std::string show(const Rules&, bool = true) const;
 
     std::string show_pretty(const Rules&, bool = true) const;
+    std::string show_main(const Rules&, bool = true) const;
+    std::string show_extracted(const Rules&) const;
 
     model_t() = default;
     model_t(const ptree&,const ptree&, const std::set<term_t>&, const expression_ref&);

src/models/setup.cc

@@ -118,6 +118,18 @@ string model_t::show_pretty(const Rules& rules, bool top) const
     return p.show(rules, not top);
 }
 
+string model_t::show_main(const Rules& rules, bool top) const
+{
+    auto p = pretty_model_t(description);
+    return p.show_main(rules, top);
+}
+
+string model_t::show_extracted(const Rules& rules) const
+{
+    auto p = pretty_model_t(description);
+    return p.show_extracted(rules);
+}
+
 model_t::model_t(const ptree& d, const ptree&t, const std::set<term_t>& c, const expression_ref& e)
     :description(d), type(t), constraints(c), expression(e)
 {
@@ -649,15 +661,11 @@ vector<pair<string, ptree>> extract_terms(ptree& m)
 
 #include "startup/help.hh"
 
-string pretty_model_t::show(const Rules& R, bool top) const
+string pretty_model_t::show_extracted(const Rules& R) const
 {
     const int indent = 4;
 
     string output;
-    if (top)
-	output = unparse(extract_value(main), R);
-    else
-	output = show_model(extract_value(main), R);
 
     for(int i=0; i<terms.size(); i++)
     {
@@ -668,6 +676,19 @@ string pretty_model_t::show(const Rules& R, bool top) const
     return output;
 }
 
+string pretty_model_t::show_main(const Rules& R, bool top) const
+{
+    if (top)
+	return unparse(extract_value(main), R);
+    else
+	return show_model(extract_value(main), R);
+}
+
+string pretty_model_t::show(const Rules& R, bool top) const
+{
+    return show_main(R,top) + show_extracted(R);
+}
+
 pretty_model_t::pretty_model_t(const ptree& m)
     :main(m)
 {

src/startup/A-T-model.cc

@@ -142,6 +142,13 @@ json optional_to_json(const boost::optional<T>& o)
 	return *o;
 }
 
+
+// FIXME - maybe we should try to make a single giant model so that we get S1/parameter
+//           exactly when this occurs for the logged parameter names, themselves.
+//
+//           This would also help it we have some variables that are outside of models, because
+//             they are shared between them.
+
 json log_summary(ostream& out_cache, ostream& out_screen,ostream& out_both,
 		 const vector<model_t>& IModels, const vector<model_t>& SModels,
 		 const vector<model_t>& ScaleModels,
@@ -151,30 +158,61 @@ json log_summary(ostream& out_cache, ostream& out_screen,ostream& out_both,
     json info;
     json partitions;
 
+    json tree;
+    if (P.t().n_branches() > 1)
+    {
+	out_both<<"T:topology ~ uniform on tree topologies\n";
+	tree["topology"] = "uniform";
+    }
+
+    if (P.t().n_branches() > 0)
+    {
+	out_both<<"T:lengths "<<branch_length_model.show(rules)<<endl<<endl;
+	tree["lengths"] = branch_length_model.show(rules, false);
+    }
+
     //-------- Log some stuff -----------//
     vector<string> filenames = args["align"].as<vector<string> >();
 
     for(int i=0;i<P.n_data_partitions();i++)
     {
-	string a_name = P[i].get_alphabet().name;
+	json partition;
 
-	out_cache<<"data"<<i+1<<" = "<<filenames[i]<<endl<<endl;
-	out_cache<<"alphabet"<<i+1<<" = "<<a_name<<endl<<endl;
-	out_cache<<"smodel-index"<<i+1<<" = "<<P.smodel_index_for_partition(i)<<endl;
-	out_cache<<"imodel-index"<<i+1<<" = "<<P.imodel_index_for_partition(i)<<endl;
-	out_cache<<"scale-index"<<i+1<<" = "<<P.scale_index_for_partition(i)<<endl;
+	// 1. filename 
+	out_cache<<"data"<<i+1<<" = "<<filenames[i]<<endl;
+	out_screen<<"#"<<i+1<<": file = "<<filenames[i]<<endl;
+	partition["filename"] = filenames[i];
 
-	json partition;
+	// 2. alphabet
+	string a_name = P[i].get_alphabet().name;
+	out_screen<<"#"<<i+1 <<": alphabet = "<<a_name<<"\n";
+	out_cache<<"alphabet"<<i+1<<" = "<<a_name<<endl;
+	partition["alphabet"] = a_name;
 
+	// 3. substitution model
+	auto s_index = P.smodel_index_for_partition(i);
+	out_screen<<"#"<<i+1<<": subst "<<indent_and_wrap(0,12,1000,SModels[*s_index].show_main(rules,false))<<" (S"<<*s_index+1<<")\n";
+	out_cache<<"smodel-index"<<i+1<<" = "<<P.smodel_index_for_partition(i)<<endl;
 	partition["smodel"] = optional_to_json( P.smodel_index_for_partition(i) );
+
+	// 4. indel model
+	if (auto i_index = P.imodel_index_for_partition(i))
+	    out_screen<<"#"<<i+1<<": indel "<<indent_and_wrap(0,12,1000,IModels[*i_index].show_main(rules, false))<<" (I"<<*i_index+1<<")\n";
+	else
+	    out_screen<<"#"<<i+1<<": indel = none\n";
+	out_cache<<"imodel-index"<<i+1<<" = "<<P.imodel_index_for_partition(i)<<endl;
 	partition["imodel"] = optional_to_json( P.imodel_index_for_partition(i) );
+
+	// 5. scale model
+	auto scale_index = P.scale_index_for_partition(i);
+	out_screen<<"#"<<i+1<<": scale "<<indent_and_wrap(0,12,1000,ScaleModels[*scale_index].show_main(rules,false))<<" (Scale"<<*scale_index+1<<")\n";
+	out_cache<<"scale-index"<<i+1<<" = "<<P.scale_index_for_partition(i)<<endl;
 	partition["scale"] = optional_to_json( P.scale_index_for_partition(i) );
-	partition["filename"] = filenames[i];
-	partition["alphabet"] = a_name;
 
+	out_screen<<endl;
+	out_cache<<endl;
 	partitions.push_back(partition);
     }
-    out_cache<<endl;
 
     json smodels = json::array();
     for(int i=0;i<P.n_smodels();i++)
@@ -182,6 +220,9 @@ json log_summary(ostream& out_cache, ostream& out_screen,ostream& out_both,
 	//    out_cache<<"subst model"<<i+1<<" = "<<P.SModel(i).name()<<endl<<endl;
 	out_cache<<"subst model"<<i+1<<" "<<SModels[i].show(rules)<<endl<<endl;
 	smodels.push_back(SModels[i].pretty_model());
+	string e = SModels[i].show_extracted(rules);
+	if (e.size())
+	    out_screen<<"Substitution model (S"<<i+1<<") -- priors:"<<e<<"\n\n";
     }
 
     json imodels = json::array();
@@ -189,6 +230,9 @@ json log_summary(ostream& out_cache, ostream& out_screen,ostream& out_both,
     {
 	out_cache<<"indel model"<<i+1<<" "<<IModels[i].show(rules)<<endl<<endl;
 	imodels.push_back(IModels[i].pretty_model());
+	string e = IModels[i].show_extracted(rules);
+	if (e.size())
+	    out_screen<<"Insertion/deletion model (I"<<i+1<<") -- priors:"<<e<<"\n\n";
     }
 
     json scales = json::array();
@@ -196,41 +240,9 @@ json log_summary(ostream& out_cache, ostream& out_screen,ostream& out_both,
     {
 	out_cache<<"scale model"<<i+1<<" "<<ScaleModels[i].show(rules)<<endl<<endl;
 	scales.push_back(ScaleModels[i].pretty_model());
-    }
-
-    json tree;
-    if (P.t().n_branches() > 1)
-    {
-	out_both<<"T:topology ~ uniform on tree topologies\n";
-	tree["topology"] = "uniform";
-    }
-
-    if (P.t().n_branches() > 0)
-    {
-	out_both<<"T:lengths "<<branch_length_model.show(rules)<<endl<<endl;
-	tree["lengths"] = branch_length_model.show(rules, false);
-    }
-
-    for(int i=0;i<P.n_data_partitions();i++)
-    {
-	auto s_index = P.smodel_index_for_partition(i);
-	//    out_screen<<"#"<<i+1<<": subst ~ "<<P.SModel(s_index).name()<<" ("<<s_index+1<<")    ";
-	out_screen<<"#"<<i+1 <<": alphabet = "<<P.get_data_partition(i).get_alphabet().name<<"\n";
-
-	out_screen<<"#"<<i+1<<": subst "<<indent_and_wrap(0,12,1000,SModels[*s_index].show_pretty(rules))<<" (S"<<*s_index+1<<")\n";
-
-	auto i_index = P.imodel_index_for_partition(i);
-	string i_name = "= none";
-	if (i_index)
-	    i_name = indent_and_wrap(0,12,1000,IModels[*i_index].show_pretty(rules));
-	out_screen<<"#"<<i+1<<": indel "<<i_name;
-	if (i_index and *i_index >= 0)
-	    out_screen<<" (I"<<*i_index+1<<")";
-	out_screen<<endl;
-
-	auto scale_index = P.scale_index_for_partition(i);
-	out_screen<<"#"<<i+1<<": scale "<<indent_and_wrap(0,12,1000,ScaleModels[*scale_index].show(rules))<<" (Scale"<<*scale_index+1<<")\n";
-	out_screen<<endl;
+	string e = ScaleModels[i].show_extracted(rules);
+	if (e.size())
+	    out_screen<<"Scale model (Scale"<<i+1<<") -- priors:"<<e<<"\n\n";
     }
 
     info["partitions"] = partitions;