Merge pull request #1217 from sys-bio/develop

Release 2.7.0

CMakeLists.txt

@@ -8,7 +8,7 @@ cmake_minimum_required(VERSION 3.16)
 # Version information and include modules
 
 set(ROADRUNNER_VERSION_MAJOR 2)
-set(ROADRUNNER_VERSION_MINOR 6)
+set(ROADRUNNER_VERSION_MINOR 7)
 set(ROADRUNNER_VERSION_PATCH 0)
 
 set(ROADRUNNER_VERSION "${ROADRUNNER_VERSION_MAJOR}.${ROADRUNNER_VERSION_MINOR}.${ROADRUNNER_VERSION_PATCH}")

README.md

@@ -15,7 +15,7 @@
 
 # Summary
 
-libRoadRunner is a C/C++ library that supports simulation of SBML based models. It uses LLVM) to generate extremely high performance code and is the fastest SBML-based simulator currently available (ref). Its main purpose is for use as a reusable library that can be hosted by other applications, particularly on large compute clusters for doing parameter optimization where performance is critical. It also has a set of python bindings that allow it to be easily used from python. 
+libRoadRunner is a C/C++ library that supports simulation of SBML based models. It uses LLVM to generate extremely high performance code and is the fastest SBML-based simulator currently available (ref). Its main purpose is for use as a reusable library that can be hosted by other applications, particularly on large compute clusters for doing parameter optimization where performance is critical. It also has a set of python bindings that allow it to be easily used from python. 
 
 We provide C/C++, Python and Julia bindings.
 
@@ -133,7 +133,7 @@ Endre T. Somogyi, Jean-Marie Bouteiller, James A. Glazier, Matthias König, J. K
 
 This work is funded by NIGMS grant: GM081070
 
-## Licence
+## License
 
 Licensed under the Apache License, Version 2.0 (the License); you may not use this 
 file except in compliance with the License. You may obtain a copy of the License at

docs/docs-build/C++APIReference/CVODEIntegrator.html

@@ -438,7 +438,7 @@ <h1>CVODEIntegrator<a class="headerlink" href="#cvodeintegrator" title="Permalin
 
 <dl class="cpp function">
 <dt class="sig sig-object cpp" id="_CPPv4N2rr15CVODEIntegrator26getAbsoluteToleranceVectorEv">
-<span id="_CPPv3N2rr15CVODEIntegrator26getAbsoluteToleranceVectorEv"></span><span id="_CPPv2N2rr15CVODEIntegrator26getAbsoluteToleranceVectorEv"></span><span id="rr::CVODEIntegrator::getAbsoluteToleranceVector"></span><span class="target" id="classrr_1_1CVODEIntegrator_1a623435278b083018cc05780ace8922f1"></span><span class="k"><span class="pre">virtual</span></span><span class="w"> </span><span class="n"><span class="pre">std</span></span><span class="p"><span class="pre">::</span></span><span class="n"><span class="pre">vector</span></span><span class="p"><span class="pre">&lt;</span></span><span class="kt"><span class="pre">double</span></span><span class="p"><span class="pre">&gt;</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">getAbsoluteToleranceVector</span></span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv4N2rr15CVODEIntegrator26getAbsoluteToleranceVectorEv" title="Permalink to this definition"></a><br /></dt>
+<span id="_CPPv3N2rr15CVODEIntegrator26getAbsoluteToleranceVectorEv"></span><span id="_CPPv2N2rr15CVODEIntegrator26getAbsoluteToleranceVectorEv"></span><span id="rr::CVODEIntegrator::getAbsoluteToleranceVector"></span><span class="target" id="classrr_1_1CVODEIntegrator_1a061679b9a025e15a6457efc8cd8806e4"></span><span class="k"><span class="pre">virtual</span></span><span class="w"> </span><span class="n"><span class="pre">std</span></span><span class="p"><span class="pre">::</span></span><span class="n"><span class="pre">vector</span></span><span class="p"><span class="pre">&lt;</span></span><span class="kt"><span class="pre">double</span></span><span class="p"><span class="pre">&gt;</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">getAbsoluteToleranceVector</span></span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><span class="w"> </span><span class="k"><span class="pre">override</span></span><a class="headerlink" href="#_CPPv4N2rr15CVODEIntegrator26getAbsoluteToleranceVectorEv" title="Permalink to this definition"></a><br /></dt>
 <dd><p>Get the absolute tolerance vector for the solver. </p>
 <p>The absolute tolerance vector is either set directly by the user as a vector, or is generated from the single absolute tolerance value (either default or set by the user) multiplied by the initial value of every element in the state vector (independent floating species, and elements controlled by rate rules). If that initial value is zero, the corresponding element of the absolute tolerance vector is the single value multiplied by the compartment volume for species, or by one for all other values. </p>
 </dd></dl>
@@ -634,8 +634,8 @@ <h1>CVODEIntegrator<a class="headerlink" href="#cvodeintegrator" title="Permalin
 <dd></dd></dl>
 
 <dl class="cpp function">
-<dt class="sig sig-object cpp" id="_CPPv4N2rr15CVODEIntegrator12cvodeRootFcnEd8N_VectorPdPv">
-<span id="_CPPv3N2rr15CVODEIntegrator12cvodeRootFcnEd8N_VectorPdPv"></span><span id="_CPPv2N2rr15CVODEIntegrator12cvodeRootFcnEd8N_VectorPdPv"></span><span id="rr::CVODEIntegrator::cvodeRootFcn__double.N_Vector.doubleP.voidP"></span><span class="target" id="classrr_1_1CVODEIntegrator_1a00e587898c84d96c26d10292fd820975"></span><span class="k"><span class="pre">friend</span></span><span class="w"> </span><span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">cvodeRootFcn</span></span></span><span class="sig-paren">(</span><span class="kt"><span class="pre">double</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">t</span></span>, <span class="n"><span class="pre">N_Vector</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">y</span></span>, <span class="kt"><span class="pre">double</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">gout</span></span>, <span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">g_data</span></span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv4N2rr15CVODEIntegrator12cvodeRootFcnEd8N_VectorPdPv" title="Permalink to this definition"></a><br /></dt>
+<dt class="sig sig-object cpp" id="_CPPv4N2rr15CVODEIntegrator29cvodeEventAndPiecewiseRootFcnEd8N_VectorPdPv">
+<span id="_CPPv3N2rr15CVODEIntegrator29cvodeEventAndPiecewiseRootFcnEd8N_VectorPdPv"></span><span id="_CPPv2N2rr15CVODEIntegrator29cvodeEventAndPiecewiseRootFcnEd8N_VectorPdPv"></span><span id="rr::CVODEIntegrator::cvodeEventAndPiecewiseRootFcn__double.N_Vector.doubleP.voidP"></span><span class="target" id="classrr_1_1CVODEIntegrator_1ad10146c594a7ed17810eacc1adb7e0c5"></span><span class="k"><span class="pre">friend</span></span><span class="w"> </span><span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">cvodeEventAndPiecewiseRootFcn</span></span></span><span class="sig-paren">(</span><span class="kt"><span class="pre">double</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">t</span></span>, <span class="n"><span class="pre">N_Vector</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">y</span></span>, <span class="kt"><span class="pre">double</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">gout</span></span>, <span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">g_data</span></span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv4N2rr15CVODEIntegrator29cvodeEventAndPiecewiseRootFcnEd8N_VectorPdPv" title="Permalink to this definition"></a><br /></dt>
 <dd></dd></dl>
 
 </div>

docs/docs-build/C++APIReference/GillespieIntegrator.html

@@ -332,13 +332,8 @@ <h1>GillespieIntegrator<a class="headerlink" href="#gillespieintegrator" title="
 <dd></dd></dl>
 
 <dl class="cpp function">
-<dt class="sig sig-object cpp" id="_CPPv4N2rr19GillespieIntegrator13setEngineSeedENSt8uint64_tE">
-<span id="_CPPv3N2rr19GillespieIntegrator13setEngineSeedENSt8uint64_tE"></span><span id="_CPPv2N2rr19GillespieIntegrator13setEngineSeedENSt8uint64_tE"></span><span id="rr::GillespieIntegrator::setEngineSeed__std::uint64_t"></span><span class="target" id="classrr_1_1GillespieIntegrator_1aefe7409a15c083899ff595498f0b17cd"></span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">setEngineSeed</span></span></span><span class="sig-paren">(</span><span class="n"><span class="pre">std</span></span><span class="p"><span class="pre">::</span></span><span class="n"><span class="pre">uint64_t</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">seed</span></span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv4N2rr19GillespieIntegrator13setEngineSeedENSt8uint64_tE" title="Permalink to this definition"></a><br /></dt>
-<dd></dd></dl>
-
-<dl class="cpp function">
-<dt class="sig sig-object cpp" id="_CPPv4NK2rr19GillespieIntegrator7getSeedEv">
-<span id="_CPPv3NK2rr19GillespieIntegrator7getSeedEv"></span><span id="_CPPv2NK2rr19GillespieIntegrator7getSeedEv"></span><span id="rr::GillespieIntegrator::getSeedC"></span><span class="target" id="classrr_1_1GillespieIntegrator_1a708d408bfc8c93d3db30e245d15d8303"></span><span class="n"><span class="pre">std</span></span><span class="p"><span class="pre">::</span></span><span class="n"><span class="pre">uint64_t</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">getSeed</span></span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><span class="w"> </span><span class="k"><span class="pre">const</span></span><a class="headerlink" href="#_CPPv4NK2rr19GillespieIntegrator7getSeedEv" title="Permalink to this definition"></a><br /></dt>
+<dt class="sig sig-object cpp" id="_CPPv4N2rr19GillespieIntegrator13setEngineSeedE7Setting">
+<span id="_CPPv3N2rr19GillespieIntegrator13setEngineSeedE7Setting"></span><span id="_CPPv2N2rr19GillespieIntegrator13setEngineSeedE7Setting"></span><span id="rr::GillespieIntegrator::setEngineSeed__Setting"></span><span class="target" id="classrr_1_1GillespieIntegrator_1a3642b6ff632ad240604499aaa7039343"></span><span class="kt"><span class="pre">void</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">setEngineSeed</span></span></span><span class="sig-paren">(</span><span class="n"><span class="pre">Setting</span></span><span class="w"> </span><span class="n sig-param"><span class="pre">seedSetting</span></span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv4N2rr19GillespieIntegrator13setEngineSeedE7Setting" title="Permalink to this definition"></a><br /></dt>
 <dd></dd></dl>
 
 <dl class="cpp function">
@@ -411,21 +406,6 @@ <h1>GillespieIntegrator<a class="headerlink" href="#gillespieintegrator" title="
 <span id="_CPPv3N2rr19GillespieIntegrator15stateVectorRateE"></span><span id="_CPPv2N2rr19GillespieIntegrator15stateVectorRateE"></span><span id="rr::GillespieIntegrator::stateVectorRate__doubleP"></span><span class="target" id="classrr_1_1GillespieIntegrator_1ac87ff4fe8008c062e1c7f2573ece23ce"></span><span class="kt"><span class="pre">double</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="sig-name descname"><span class="n"><span class="pre">stateVectorRate</span></span></span><a class="headerlink" href="#_CPPv4N2rr19GillespieIntegrator15stateVectorRateE" title="Permalink to this definition"></a><br /></dt>
 <dd></dd></dl>
 
-<dl class="cpp var">
-<dt class="sig sig-object cpp" id="_CPPv4N2rr19GillespieIntegrator10stoichRowsE">
-<span id="_CPPv3N2rr19GillespieIntegrator10stoichRowsE"></span><span id="_CPPv2N2rr19GillespieIntegrator10stoichRowsE"></span><span id="rr::GillespieIntegrator::stoichRows__i"></span><span class="target" id="classrr_1_1GillespieIntegrator_1a73aa49ae624f2eff1872e275f083733b"></span><span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">stoichRows</span></span></span><a class="headerlink" href="#_CPPv4N2rr19GillespieIntegrator10stoichRowsE" title="Permalink to this definition"></a><br /></dt>
-<dd></dd></dl>
-
-<dl class="cpp var">
-<dt class="sig sig-object cpp" id="_CPPv4N2rr19GillespieIntegrator10stoichColsE">
-<span id="_CPPv3N2rr19GillespieIntegrator10stoichColsE"></span><span id="_CPPv2N2rr19GillespieIntegrator10stoichColsE"></span><span id="rr::GillespieIntegrator::stoichCols__i"></span><span class="target" id="classrr_1_1GillespieIntegrator_1adeca1a671e321f9c3c7fe12647876972"></span><span class="kt"><span class="pre">int</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">stoichCols</span></span></span><a class="headerlink" href="#_CPPv4N2rr19GillespieIntegrator10stoichColsE" title="Permalink to this definition"></a><br /></dt>
-<dd></dd></dl>
-
-<dl class="cpp var">
-<dt class="sig sig-object cpp" id="_CPPv4N2rr19GillespieIntegrator10stoichDataE">
-<span id="_CPPv3N2rr19GillespieIntegrator10stoichDataE"></span><span id="_CPPv2N2rr19GillespieIntegrator10stoichDataE"></span><span id="rr::GillespieIntegrator::stoichData__doubleP"></span><span class="target" id="classrr_1_1GillespieIntegrator_1ae394922712ee63181b3584471993708a"></span><span class="kt"><span class="pre">double</span></span><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="sig-name descname"><span class="n"><span class="pre">stoichData</span></span></span><a class="headerlink" href="#_CPPv4N2rr19GillespieIntegrator10stoichDataE" title="Permalink to this definition"></a><br /></dt>
-<dd></dd></dl>
-
 <dl class="cpp var">
 <dt class="sig sig-object cpp" id="_CPPv4N2rr19GillespieIntegrator11eventStatusE">
 <span id="_CPPv3N2rr19GillespieIntegrator11eventStatusE"></span><span id="_CPPv2N2rr19GillespieIntegrator11eventStatusE"></span><span id="rr::GillespieIntegrator::eventStatus__std::vector:unsigned-c:"></span><span class="target" id="classrr_1_1GillespieIntegrator_1a2ad59189650fbd78f0845f45ef4f7980"></span><span class="n"><span class="pre">std</span></span><span class="p"><span class="pre">::</span></span><span class="n"><span class="pre">vector</span></span><span class="p"><span class="pre">&lt;</span></span><span class="kt"><span class="pre">unsigned</span></span><span class="w"> </span><span class="kt"><span class="pre">char</span></span><span class="p"><span class="pre">&gt;</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">eventStatus</span></span></span><a class="headerlink" href="#_CPPv4N2rr19GillespieIntegrator11eventStatusE" title="Permalink to this definition"></a><br /></dt>

docs/docs-build/C++APIReference/RoadRunnerMap.html

@@ -334,7 +334,7 @@ <h1>RoadRunnerMap<a class="headerlink" href="#roadrunnermap" title="Permalink to
 
 <dl class="cpp function">
 <dt class="sig sig-object cpp" id="_CPPv4N2rr13RoadRunnerMap5beginEv">
-<span id="_CPPv3N2rr13RoadRunnerMap5beginEv"></span><span id="_CPPv2N2rr13RoadRunnerMap5beginEv"></span><span id="rr::RoadRunnerMap::begin"></span><span class="target" id="classrr_1_1RoadRunnerMap_1a6cc2faaac1c5ee045a5a42ea9aa17394"></span><span class="n"><span class="pre">ThreadSafeUnorderedMap</span></span><span class="p"><span class="pre">::</span></span><span class="n"><span class="pre">iterator</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">begin</span></span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv4N2rr13RoadRunnerMap5beginEv" title="Permalink to this definition"></a><br /></dt>
+<span id="_CPPv3N2rr13RoadRunnerMap5beginEv"></span><span id="_CPPv2N2rr13RoadRunnerMap5beginEv"></span><span id="rr::RoadRunnerMap::begin"></span><span class="target" id="classrr_1_1RoadRunnerMap_1a34903c378ab7ac40ccc656bf4d0dac9d"></span><span class="n"><span class="pre">ThreadSafeUnorderedMap</span></span><span class="p"><span class="pre">::</span></span><span class="n"><span class="pre">iterator</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">begin</span></span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv4N2rr13RoadRunnerMap5beginEv" title="Permalink to this definition"></a><br /></dt>
 <dd><p>map iterator </p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="k">for</span> <span class="p">(</span><span class="n">auto</span><span class="o">&amp;</span><span class="p">[</span><span class="n">modelName</span><span class="p">,</span> <span class="n">rr</span><span class="p">]:</span> <span class="n">rrm</span><span class="p">)</span> <span class="p">{</span>
    <span class="o">...</span>
@@ -357,7 +357,7 @@ <h1>RoadRunnerMap<a class="headerlink" href="#roadrunnermap" title="Permalink to
 
 <dl class="cpp function">
 <dt class="sig sig-object cpp" id="_CPPv4N2rr13RoadRunnerMap3endEv">
-<span id="_CPPv3N2rr13RoadRunnerMap3endEv"></span><span id="_CPPv2N2rr13RoadRunnerMap3endEv"></span><span id="rr::RoadRunnerMap::end"></span><span class="target" id="classrr_1_1RoadRunnerMap_1a6807a3ec91489b43298a17ea0f117e0c"></span><span class="n"><span class="pre">ThreadSafeUnorderedMap</span></span><span class="p"><span class="pre">::</span></span><span class="n"><span class="pre">iterator</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">end</span></span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv4N2rr13RoadRunnerMap3endEv" title="Permalink to this definition"></a><br /></dt>
+<span id="_CPPv3N2rr13RoadRunnerMap3endEv"></span><span id="_CPPv2N2rr13RoadRunnerMap3endEv"></span><span id="rr::RoadRunnerMap::end"></span><span class="target" id="classrr_1_1RoadRunnerMap_1a32cd8895262727088f335c25ae813e98"></span><span class="n"><span class="pre">ThreadSafeUnorderedMap</span></span><span class="p"><span class="pre">::</span></span><span class="n"><span class="pre">iterator</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">end</span></span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv4N2rr13RoadRunnerMap3endEv" title="Permalink to this definition"></a><br /></dt>
 <dd><div class="highlight-default notranslate"><div class="highlight"><pre><span></span> <span class="k">for</span> <span class="p">(</span><span class="n">auto</span> <span class="n">it</span> <span class="o">=</span> <span class="n">rrm</span><span class="o">.</span><span class="n">begin</span><span class="p">();</span> <span class="n">it</span> <span class="o">!=</span> <span class="n">rrm</span><span class="o">.</span><span class="n">end</span><span class="p">();</span> <span class="o">++</span><span class="n">it</span><span class="p">)</span> <span class="p">{</span>
     <span class="n">auto</span><span class="o">&amp;</span><span class="p">[</span><span class="n">modelName</span><span class="p">,</span> <span class="n">rr</span><span class="p">]</span> <span class="o">=</span> <span class="o">*</span><span class="n">it</span><span class="p">;</span>
     <span class="n">i</span><span class="o">++</span><span class="p">;</span>