Commit 6d3ce2e5 authored by Benjamin Redelings's avatar Benjamin Redelings
Browse files

New upstream version 3.1.1+dfsg

parent c52ec75e

functions/gtr.json

+1 −0
Original line number Diff line number Diff line 
{

    "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

+1 −0
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{

    "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

+1 −0
Original line number Diff line number Diff line 
{

    "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

+16 −7
Original line number Diff line number Diff line 
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

+1 −1
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@@ -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;

}