Merge pull request #1097 from sys-bio/develop

Update to 2.4.0

CMakeLists.txt

@@ -8,8 +8,8 @@ cmake_minimum_required(VERSION 3.16)
 # Version information and include modules
 
 set(ROADRUNNER_VERSION_MAJOR 2)
-set(ROADRUNNER_VERSION_MINOR 3)
-set(ROADRUNNER_VERSION_PATCH 2)
+set(ROADRUNNER_VERSION_MINOR 4)
+set(ROADRUNNER_VERSION_PATCH 0)
 
 set(ROADRUNNER_VERSION "${ROADRUNNER_VERSION_MAJOR}.${ROADRUNNER_VERSION_MINOR}.${ROADRUNNER_VERSION_PATCH}")
 

azure-pipelines.yml

@@ -38,10 +38,10 @@ stages:
           matrix:
             64-bit Mac Release:
               BuildType: Release
-              LLVM_DOWNLOAD_LINK: 'https://github.com/sys-bio/llvm-13.x/releases/download/llvmorg-13.0.0/llvm-13.x-clang13-universal-binaries-rel.zip'
+              LLVM_DOWNLOAD_LINK: 'https://github.com/sys-bio/llvm-13.x/releases/download/llvmorg-13.0.0/llvm-13.x-macosx_11_7_x86_64.zip'
             64-bit Mac Debug:
               BuildType: Debug
-              LLVM_DOWNLOAD_LINK: 'https://github.com/sys-bio/llvm-13.x/releases/download/llvmorg-13.0.0/llvm-13.x-clang13-universal-binaries-rel.zip'
+              LLVM_DOWNLOAD_LINK: 'https://github.com/sys-bio/llvm-13.x/releases/download/llvmorg-13.0.0/llvm-13.x-macosx_11_7_x86_64.zip'
         variables:
           LLVM_CACHE: 'false'
           PythonName: 'py39'
@@ -159,7 +159,7 @@ stages:
               mkdir $(BUILD_DIR)
               echo "CD to build dir: $(BUILD_DIR)"
               cd $(BUILD_DIR)
-              cmake -DLLVM_INSTALL_PREFIX=$(LLVM_INSTALL_PREFIX) -DRR_DEPENDENCIES_INSTALL_PREFIX=$(DEPS_INSTALL_PREFIX) -DBUILD_TESTS=ON -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIR) -DBUILD_RR_PLUGINS=ON -DBUILD_RR_CAPI=ON -DCMAKE_BUILD_TYPE=$(BuildType) -DCMAKE_OSX_ARCHITECTURES="x86_64;arm64" ..
+              cmake -DLLVM_INSTALL_PREFIX=$(LLVM_INSTALL_PREFIX) -DRR_DEPENDENCIES_INSTALL_PREFIX=$(DEPS_INSTALL_PREFIX) -DBUILD_TESTS=ON -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIR) -DBUILD_RR_PLUGINS=ON -DBUILD_RR_CAPI=ON -DCMAKE_BUILD_TYPE=$(BuildType) -DCMAKE_OSX_ARCHITECTURES="x86_64" ..
             displayName: Run CMake Configure Command
           - script: |
               echo "less -N $(BUILD_DIR)/source/CMakeFiles/roadrunner.dir/build.make"
@@ -218,7 +218,7 @@ stages:
           SWIG_CACHE: 'false'
           MINICONDA_CACHE: 'false'
           LLVM_CACHE: 'false'
-          LLVM_DOWNLOAD_LINK: 'https://github.com/sys-bio/llvm-13.x/releases/download/llvmorg-13.0.0/llvm-13.x-clang13-universal-binaries-rel.zip'
+          LLVM_DOWNLOAD_LINK: 'https://github.com/sys-bio/llvm-13.x/releases/download/llvmorg-13.0.0/llvm-13.x-macosx_11_7_x86_64.zip'
         steps:
           - checkout: self
             submodules: recursive
@@ -343,7 +343,7 @@ stages:
               cd $(BUILD_DIR)
               ls
               export LD_LIBRARY_PATH=$(PythonLibDir)
-              cmake -DLLVM_INSTALL_PREFIX=$(LLVM_INSTALL_PREFIX) -DRR_DEPENDENCIES_INSTALL_PREFIX=$(DEPS_INSTALL_PREFIX) -DBUILD_TESTS=ON -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIR) -DBUILD_RR_PLUGINS=ON -DBUILD_RR_CAPI=ON -DCMAKE_BUILD_TYPE=Release -DBUILD_PYTHON=ON -DPython_ROOT_DIR=$(PythonRoot) -DSWIG_EXECUTABLE=$(SWIG_EXECUTABLE) -DCMAKE_OSX_ARCHITECTURES="x86_64;arm64" ..
+              cmake -DLLVM_INSTALL_PREFIX=$(LLVM_INSTALL_PREFIX) -DRR_DEPENDENCIES_INSTALL_PREFIX=$(DEPS_INSTALL_PREFIX) -DBUILD_TESTS=ON -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIR) -DBUILD_RR_PLUGINS=ON -DBUILD_RR_CAPI=ON -DCMAKE_BUILD_TYPE=Release -DBUILD_PYTHON=ON -DPython_ROOT_DIR=$(PythonRoot) -DSWIG_EXECUTABLE=$(SWIG_EXECUTABLE) -DCMAKE_OSX_ARCHITECTURES="x86_64" ..
               cmake --build . --target install --config Release -j 12
             displayName: BuildRoadrunnerWithPython
           - script: |
@@ -842,7 +842,7 @@ stages:
               echo "g++ $(g++ --version)"
               sudo add-apt-repository ppa:ubuntu-toolchain-r/test
               sudo apt-get update
-              sudo apt-get install -y gcc-10 g++-10 doxygen dvipng texlive texlive-font-utils textlive-latex-extra
+              sudo apt-get install -y gcc-10 g++-10 doxygen dvipng texlive texlive-font-utils texlive-latex-extra
               sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-10 1
             displayName: Install g++10 and doxygen
           - script: |
@@ -1089,7 +1089,7 @@ stages:
 
               echo "cd'ing to build dir $(BUILD_DIR)"
               cd $(BUILD_DIR)
-              ctest --tests-regex python_tests_RunStochasticTestSuite .
+              ctest --extra-verbose --output-on-failure --tests-regex python_tests_RunStochasticTestSuite .
             displayName: Run Stochastic test suite
 
           - script: |

cmake/ImportRoadrunnerAndDependencies.cmake

@@ -1,4 +1,3 @@
-##############################################################
 # CMake module for importing roadrunner targets with dependencies
 # into consuming libraries cmake system.
 #
@@ -10,17 +9,18 @@ find_package(Threads) # for libxml2, FindThreads.cmake is shipped with cmake
 find_package(LibLZMA) # for libxml2, LibLZMA.cmake is shipped with cmake
 find_package(zlib CONFIG REQUIRED)
 find_package(bzip2 CONFIG REQUIRED)
-find_package(iconv CONFIG REQUIRED)
-find_package(LibXml2 CONFIG REQUIRED)
-find_package(libsbml-static CONFIG REQUIRED)
+#find_package(iconv CONFIG REQUIRED)
+#find_package(LibXml2 CONFIG REQUIRED)
+find_package(expat CONFIG REQUIRED)
+find_package(sbml-static CONFIG REQUIRED)
 find_package(rr-libstruct CONFIG REQUIRED)
 find_package(clapack CONFIG REQUIRED)
 find_package(nleq1 CONFIG REQUIRED)
 find_package(nleq2 CONFIG REQUIRED)
 find_package(PocoFoundation CONFIG REQUIRED)
 find_package(PocoNet CONFIG REQUIRED)
 find_package(PocoXML CONFIG REQUIRED)
-find_package(Sundials CONFIG REQUIRED)
+find_package(SUNDIALS CONFIG REQUIRED)
 find_package(LLVM REQUIRED)
 find_package(roadrunner-static CONFIG REQUIRED)
 find_package(roadrunner CONFIG REQUIRED)

docs/docs-build/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 4fdea462f19561a75feef109d8a885cd
+config: eeeea70bbadf2ed570191302c1060714
 tags: 645f666f9bcd5a90fca523b33c5a78b7

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

@@ -12,10 +12,9 @@
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
         <script src="../_static/jquery.js"></script>
-        <script src="../_static/underscore.js"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
         <script src="../_static/doctools.js"></script>
         <script src="../_static/sphinx_highlight.js"></script>
     <script src="../_static/js/theme.js"></script>
@@ -215,7 +214,7 @@ <h1>CVODEIntegrator<a class="headerlink" href="#cvodeintegrator" title="Permalin
 </p>
 <div class="admonition note">
 <p class="admonition-title">Note</p>
-<p>Delegates to <a class="reference internal" href="#classrr_1_1CVODEIntegrator_1aa889b08549036792918c41e88e2097f4"><span class="std std-ref">getName</span></a> </p>
+<p>Delegates to <a class="reference internal" href="#classrr_1_1CVODEIntegrator_1aa889b08549036792918c41e88e2097f4"><span class="std std-ref">getName</span></a></p>
 </div>
 </dd></dl>
 
@@ -230,7 +229,7 @@ <h1>CVODEIntegrator<a class="headerlink" href="#cvodeintegrator" title="Permalin
 </p>
 <div class="admonition note">
 <p class="admonition-title">Note</p>
-<p>Delegates to <a class="reference internal" href="#classrr_1_1CVODEIntegrator_1a1c6a393504cc85f2dc236abd0cb5577a"><span class="std std-ref">getDescription</span></a> </p>
+<p>Delegates to <a class="reference internal" href="#classrr_1_1CVODEIntegrator_1a1c6a393504cc85f2dc236abd0cb5577a"><span class="std std-ref">getDescription</span></a></p>
 </div>
 </dd></dl>
 
@@ -245,7 +244,7 @@ <h1>CVODEIntegrator<a class="headerlink" href="#cvodeintegrator" title="Permalin
 </p>
 <div class="admonition note">
 <p class="admonition-title">Note</p>
-<p>Delegates to <a class="reference internal" href="#classrr_1_1CVODEIntegrator_1addde67b3639fe1347efc2a37bbfdd60e"><span class="std std-ref">getHint</span></a> </p>
+<p>Delegates to <a class="reference internal" href="#classrr_1_1CVODEIntegrator_1addde67b3639fe1347efc2a37bbfdd60e"><span class="std std-ref">getHint</span></a></p>
 </div>
 </dd></dl>
 

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

@@ -12,10 +12,9 @@
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
         <script src="../_static/jquery.js"></script>
-        <script src="../_static/underscore.js"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
         <script src="../_static/doctools.js"></script>
         <script src="../_static/sphinx_highlight.js"></script>
     <script src="../_static/js/theme.js"></script>
@@ -151,13 +150,12 @@ <h1>Dictionary<a class="headerlink" href="#dictionary" title="Permalink to this
 <span id="_CPPv3N2rr10Dictionary7setItemERKNSt6stringERKN2rr7SettingE"></span><span id="_CPPv2N2rr10Dictionary7setItemERKNSt6stringERKN2rr7SettingE"></span><span id="rr::Dictionary::setItem__ssCR.rr::SettingCR"></span><span class="target" id="classrr_1_1Dictionary_1a4708fee12ec4cd5e879df9bf5570c02a"></span><span class="k"><span class="pre">virtual</span></span><span class="w"> </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">setItem</span></span></span><span class="sig-paren">(</span><span class="k"><span class="pre">const</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">string</span></span><span class="w"> </span><span class="p"><span class="pre">&amp;</span></span><span class="n sig-param"><span class="pre">key</span></span>, <span class="k"><span class="pre">const</span></span><span class="w"> </span><span class="n"><span class="pre">rr</span></span><span class="p"><span class="pre">::</span></span><span class="n"><span class="pre">Setting</span></span><span class="w"> </span><span class="p"><span class="pre">&amp;</span></span><span class="n sig-param"><span class="pre">value</span></span><span class="sig-paren">)</span><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="m"><span class="pre">0</span></span><a class="headerlink" href="#_CPPv4N2rr10Dictionary7setItemERKNSt6stringERKN2rr7SettingE" title="Permalink to this definition"></a><br /></dt>
 <dd><p>Set the value for an arbitrary key. </p>
 <p>The Setting object has a large number of creation operators so you only have to give the value as native C++ object i.e.</p>
-<p><div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Dictionary</span><span class="o">*</span><span class="n">d</span> <span class="o">=</span> <span class="p">(</span><span class="o">...</span><span class="p">);</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Dictionary</span><span class="o">*</span><span class="n">d</span> <span class="o">=</span> <span class="p">(</span><span class="o">...</span><span class="p">);</span>
 <span class="n">d</span><span class="o">-&gt;</span><span class="n">setItem</span><span class="p">(</span><span class="s2">&quot;someIntKey&quot;</span><span class="p">,</span> <span class="mi">1</span><span class="p">);</span>
 <span class="n">d</span><span class="o">-&gt;</span><span class="n">setItem</span><span class="p">(</span><span class="s2">&quot;someStrKey&quot;</span><span class="p">,</span> <span class="n">std</span><span class="p">::</span><span class="n">string</span><span class="p">(</span><span class="s2">&quot;some std::string&quot;</span><span class="p">));</span>
 <span class="n">d</span><span class="o">-&gt;</span><span class="n">setItem</span><span class="p">(</span><span class="s2">&quot;someFloatVal, 0.123);</span>
 </pre></div>
 </div>
- </p>
 </dd></dl>
 
 <dl class="cpp function">
@@ -166,13 +164,12 @@ <h1>Dictionary<a class="headerlink" href="#dictionary" title="Permalink to this
 <dd><p>Get a value. </p>
 <p>Variants are POD. If the key does not exist, an std::exception will be thrown.</p>
 <p>The Setting object has the assigment operator overloaded so it will automatically convert to any native C++ object. If the Setting can not be converted, it will raise an exception, i.e.</p>
-<p><div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Dictionary</span><span class="o">*</span> <span class="n">d</span> <span class="o">=</span> <span class="o">...</span><span class="p">;</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Dictionary</span><span class="o">*</span> <span class="n">d</span> <span class="o">=</span> <span class="o">...</span><span class="p">;</span>
 <span class="nb">int</span> <span class="n">a</span> <span class="o">=</span> <span class="n">d</span><span class="o">-&gt;</span><span class="n">getItem</span><span class="p">(</span><span class="s2">&quot;someIntKey&quot;</span><span class="p">);</span>
 <span class="n">std</span><span class="p">::</span><span class="n">string</span> <span class="n">s</span> <span class="o">=</span> <span class="n">d</span><span class="o">-&gt;</span><span class="n">getItem</span><span class="p">(</span><span class="s2">&quot;someStrVal&quot;</span><span class="p">);</span>
 <span class="n">double</span> <span class="n">val</span> <span class="o">=</span> <span class="n">d</span><span class="o">-&gt;</span><span class="n">getItem</span><span class="p">(</span><span class="s2">&quot;someDoubleVal&quot;</span><span class="p">);</span>
 </pre></div>
 </div>
- </p>
 </dd></dl>
 
 <dl class="cpp function">

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

@@ -12,10 +12,9 @@
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
         <script src="../_static/jquery.js"></script>
-        <script src="../_static/underscore.js"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
         <script src="../_static/doctools.js"></script>
         <script src="../_static/sphinx_highlight.js"></script>
     <script src="../_static/js/theme.js"></script>
@@ -146,7 +145,7 @@ <h1>EulerIntegrator<a class="headerlink" href="#eulerintegrator" title="Permalin
 <p>This integrator should not really be used in practice as the forward Euler algorithm is highly unstable and will seldomly yield numerically correct values.</p>
 <p>This class also has two dummy variables, exampleParameter1 and exampleParameter2. These serve as examples of how to use the <a class="reference internal" href="Dictionary.html#classrr_1_1Dictionary"><span class="std std-ref">Dictionary</span></a> interface to get/set various tuning paramters that an <a class="reference internal" href="Integrator.html#classrr_1_1Integrator"><span class="std std-ref">Integrator</span></a> might have. These values will be displayed when the toString method is called, typically by Python.</p>
 <p>An example of calling simulate in Python, and the results of specifying the parameters as keyword arguments is</p>
-<p><div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">r</span><span class="o">.</span><span class="n">simulate</span><span class="p">(</span><span class="n">integrator</span><span class="o">=</span><span class="s1">&#39;euler&#39;</span><span class="p">,</span> <span class="n">exampleParameter1</span><span class="o">=</span><span class="mi">123456</span><span class="p">,</span> <span class="n">exampleParameter2</span><span class="o">=</span><span class="s1">&#39;some value&#39;</span><span class="p">);</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">r</span><span class="o">.</span><span class="n">simulate</span><span class="p">(</span><span class="n">integrator</span><span class="o">=</span><span class="s1">&#39;euler&#39;</span><span class="p">,</span> <span class="n">exampleParameter1</span><span class="o">=</span><span class="mi">123456</span><span class="p">,</span> <span class="n">exampleParameter2</span><span class="o">=</span><span class="s1">&#39;some value&#39;</span><span class="p">);</span>
 
 <span class="nb">print</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">integrator</span><span class="p">)</span>
 <span class="o">&lt;</span> <span class="n">roadrunner</span><span class="o">.</span><span class="n">EulerIntegrator</span><span class="p">()</span>
@@ -156,7 +155,6 @@ <h1>EulerIntegrator<a class="headerlink" href="#eulerintegrator" title="Permalin
 <span class="p">}</span><span class="o">&gt;</span>
 </pre></div>
 </div>
- </p>
 <div class="breathe-sectiondef docutils container">
 <p class="breathe-sectiondef-title rubric" id="breathe-section-title-public-functions">Public Functions</p>
 <dl class="cpp function">
@@ -220,7 +218,7 @@ <h1>EulerIntegrator<a class="headerlink" href="#eulerintegrator" title="Permalin
 <dl class="cpp function">
 <dt class="sig sig-object cpp" id="_CPPv4NK2rr15EulerIntegrator8toStringEv">
 <span id="_CPPv3NK2rr15EulerIntegrator8toStringEv"></span><span id="_CPPv2NK2rr15EulerIntegrator8toStringEv"></span><span id="rr::EulerIntegrator::toStringC"></span><span class="target" id="classrr_1_1EulerIntegrator_1a65fed1a29701ddcfb6d0d3f023550bc8"></span><span class="k"><span class="pre">inline</span></span><span class="w"> </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">string</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">toString</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><span class="w"> </span><span class="k"><span class="pre">override</span></span><a class="headerlink" href="#_CPPv4NK2rr15EulerIntegrator8toStringEv" title="Permalink to this definition"></a><br /></dt>
-<dd><p>get a description of this object, compatable with python <strong>str</strong> </p>
+<dd><p>get a description of this object, compatable with python <strong>str</strong></p>
 </dd></dl>
 
 <dl class="cpp function">
@@ -246,7 +244,7 @@ <h1>EulerIntegrator<a class="headerlink" href="#eulerintegrator" title="Permalin
 </p>
 <div class="admonition note">
 <p class="admonition-title">Note</p>
-<p>Delegates to <a class="reference internal" href="#classrr_1_1EulerIntegrator_1a5c3fe76e2ab79a6bf9dfa5b1f382308a"><span class="std std-ref">getDescription</span></a> </p>
+<p>Delegates to <a class="reference internal" href="#classrr_1_1EulerIntegrator_1a5c3fe76e2ab79a6bf9dfa5b1f382308a"><span class="std std-ref">getDescription</span></a></p>
 </div>
 </dd></dl>
 
@@ -261,7 +259,7 @@ <h1>EulerIntegrator<a class="headerlink" href="#eulerintegrator" title="Permalin
 </p>
 <div class="admonition note">
 <p class="admonition-title">Note</p>
-<p>Delegates to <a class="reference internal" href="#classrr_1_1EulerIntegrator_1a915c7662fbab3e2c39a67826f70495fa"><span class="std std-ref">getHint</span></a> </p>
+<p>Delegates to <a class="reference internal" href="#classrr_1_1EulerIntegrator_1a915c7662fbab3e2c39a67826f70495fa"><span class="std std-ref">getHint</span></a></p>
 </div>
 </dd></dl>