Merge pull request #1131 from sys-bio/develop

Latest docs.
sys-bio · May 11, 2023 · ea600f8 · ea600f8
2 parents 9151189 + fe07ab9
commit ea600f8
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Showing 3,194 changed files with 235,407 additions and 253,842 deletions.
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -792,6 +792,8 @@ stages:
           - script: |
               echo "SOURCE_DIR $(SOURCE_DIR)"
               echo "BUILD_DIR $(BUILD_DIR)"
+              echo "BuildType $(BuildType)"
+              echo "BuildDocs $(BuildDocs)"
               echo "INSTALL_DIR $(INSTALL_DIR)"
               echo "LLVM_INSTALL_PREFIX $(LLVM_INSTALL_PREFIX)"
               echo "DEPS_INSTALL_PREFIX $(DEPS_INSTALL_PREFIX)"
@@ -842,14 +844,18 @@ stages:
               echo "g++ $(g++ --version)"
               sudo add-apt-repository ppa:ubuntu-toolchain-r/test
               sudo apt-get update
-              sudo apt-get install -y gcc-10 g++-10 doxygen dvipng texlive texlive-font-utils texlive-latex-extra
+              sudo apt-get install -y gcc-10 g++-10 doxygen dvipng texlive texlive-font-utils texlive-latex-extra graphviz
               sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-10 1
             displayName: Install g++10 and doxygen
           - script: |
               eval "$(conda shell.bash hook)"
               conda create -y --name $(PythonName) python=$(PythonVersion)
               $(PipExecutable) install requests
             displayName: "Install Python via conda"
+          - script: |
+              echo "pip install dependencies"
+              $(PipExecutable) install -r $(SOURCE_DIR)/docs/requirements.txt
+            displayName: "Install doc requirements"
           - script: |
               $(PythonExecutable) ./.azurepipelines/getLLVM.py $(LLVM_DOWNLOAD_LINK) $(LLVM_INSTALL_PREFIX)
               echo "give execute permissions to llvm-config using chmod 777"
@@ -886,8 +892,22 @@ 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=$(BuildType) -DBUILD_DOCS=${BuildDocs} ..
+              echo "cmake -DLLVM_INSTALL_PREFIX=$(LLVM_INSTALL_PREFIX) -DRR_DEPENDENCIES_INSTALL_PREFIX=$(DEPS_INSTALL_PREFIX) -DBUILD_TESTS=ON -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIR) -DBUILD_RR_PLUGINS=ON -DBUILD_RR_CAPI=ON -DBUILD_DOCS=$(BuildDocs) -DCMAKE_BUILD_TYPE=$(BuildType) -DSPHINX_EXECUTABLE=$(SphinxExecutable) .."
+              cmake -DLLVM_INSTALL_PREFIX=$(LLVM_INSTALL_PREFIX) -DRR_DEPENDENCIES_INSTALL_PREFIX=$(DEPS_INSTALL_PREFIX) -DBUILD_TESTS=ON -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIR) -DBUILD_RR_PLUGINS=ON -DBUILD_RR_CAPI=ON -DBUILD_DOCS=$(BuildDocs) -DCMAKE_BUILD_TYPE=$(BuildType) -DSPHINX_EXECUTABLE=$(SphinxExecutable) ..
             displayName: Run CMake Configure Command
+          - script: |
+              echo "cd to docs dir"
+              cd $(SOURCE_DIR)/docs/
+              rm -r -f docs-build doxygen-output
+            displayName: Remove roadrunner docs before re-building
+            condition: eq(variables.BuildType, 'Release')
+          - script: |
+              echo "cd to build dir"
+              cd $(BUILD_DIR)
+              make roadrunner-docs-doxygen
+              make roadrunner-docs-sphinx
+            displayName: Build roadrunner docs
+            condition: eq(variables.BuildType, 'Release')
           - script: |
               export CC=/usr/bin/gcc-10
               export CXX=/usr/bin/g++-10
@@ -920,20 +940,9 @@ stages:
             displayName: Clear staging area
             condition: eq(variables.BuildType, 'Release')
           - script: |
-              echo "cd to docs dir"
-              cd $(SOURCE_DIR)/docs/
-              echo "pip install dependencies"
-              $(PipExecutable) install -r requirements.txt
-              export SPHINXBUILD=$(SphinxExecutable)
-              echo "make html"
-              make html
-              echo "list build/html"
-              ls build/html
               echo "move docs to installation"
-              cd
-              pwd
               mkdir $(INSTALL_DIR)/docs
-              mv $(SOURCE_DIR)/docs/build/html '$(INSTALL_DIR)/docs/docs-build'
+              mv $(SOURCE_DIR)/docs/docs-build '$(INSTALL_DIR)/docs/docs-build'
               mv $(SOURCE_DIR)/docs/doxygen-output '$(INSTALL_DIR)/docs/doxygen-output'
               ls '$(INSTALL_DIR)/docs'
             displayName: Make Docs

diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt
@@ -1,7 +1,7 @@
 ##################################################################
 # Usage
 # -----
-# Build the roadrunner-docs-sphinx target
+# Build the roadrunner-docs-doxygen and roadrunner-docs-sphinx targets
 #
 
 ##################################################################
@@ -17,15 +17,14 @@
 # when you configure the cmake project. This defines two cmake targets
 #    1) roadrunner-docs-doxygen
 #    2) roadrunner-docs-sphinx
-# Building the roadrunner-docs-sphinx target will execute all commands necessary, since it depends
-# on roadruner-docs-doxygen target.
+# You need to build the first and then build the second.  At one point, the second was dependent on the first, but that seems to have broken at some point, but building them both explicitly does work.
 #
 
 ##################################################################
 # Dependencies
 # ------------
-# You will need Sphinx and some python packages
-#   - pip install sphinx breathe sphinxcontrib-bibtex sphinx-tabs sphinx_rtd_theme
+# You will need Sphinx and some python packages, all listed in docs/requirements.txt
+#   - pip install -r docs/requirements.txt
 # and doxygen. Make sure you either install doxygen in a default location, so that
 # cmake can find it or add the path to the doxygen executable to the PATH environment
 # variable so cmake can find it.

diff --git a/docs/docs-build/.doctrees/C++APIReference/CVODEIntegrator.doctree b/docs/docs-build/.doctrees/C++APIReference/CVODEIntegrator.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/Dictionary.doctree b/docs/docs-build/.doctrees/C++APIReference/Dictionary.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/EulerIntegrator.doctree b/docs/docs-build/.doctrees/C++APIReference/EulerIntegrator.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/ExecutableModelFactory.doctree b/docs/docs-build/.doctrees/C++APIReference/ExecutableModelFactory.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/GillespieIntegrator.doctree b/docs/docs-build/.doctrees/C++APIReference/GillespieIntegrator.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/Integrator.doctree b/docs/docs-build/.doctrees/C++APIReference/Integrator.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/IntegratorFactory.doctree b/docs/docs-build/.doctrees/C++APIReference/IntegratorFactory.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/NLEQ1Solver.doctree b/docs/docs-build/.doctrees/C++APIReference/NLEQ1Solver.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/NLEQ2Solver.doctree b/docs/docs-build/.doctrees/C++APIReference/NLEQ2Solver.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/RK45Integrator.doctree b/docs/docs-build/.doctrees/C++APIReference/RK45Integrator.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/RK4Integrator.doctree b/docs/docs-build/.doctrees/C++APIReference/RK4Integrator.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/RoadRunnerMap.doctree b/docs/docs-build/.doctrees/C++APIReference/RoadRunnerMap.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/SBMLValidator.doctree b/docs/docs-build/.doctrees/C++APIReference/SBMLValidator.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/Solver.doctree b/docs/docs-build/.doctrees/C++APIReference/Solver.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/SolverFactory.doctree b/docs/docs-build/.doctrees/C++APIReference/SolverFactory.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/SteadyStateSolver.doctree b/docs/docs-build/.doctrees/C++APIReference/SteadyStateSolver.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/Variant.doctree b/docs/docs-build/.doctrees/C++APIReference/Variant.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/index.doctree b/docs/docs-build/.doctrees/C++APIReference/index.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/ASTNodeCodeGen.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/ASTNodeCodeGen.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/ASTNodeFactory.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/ASTNodeFactory.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/AssignmentRuleEvaluator.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/AssignmentRuleEvaluator.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/CodeGen.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/CodeGen.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/CodeGenBase.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/CodeGenBase.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/EvalConversionFactorCodeGen.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/EvalConversionFactorCodeGen.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/EvalInitialConditionsCodeGen.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/EvalInitialConditionsCodeGen.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/EvalRateRuleRatesCodeGen.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/EvalRateRuleRatesCodeGen.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/EvalReactionRatesCodeGen.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/EvalReactionRatesCodeGen.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/EvalVolatileStoichCodeGen.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/EvalVolatileStoichCodeGen.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/EventAssignCodeGen.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/EventAssignCodeGen.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/EventCodeGenBase.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/EventCodeGenBase.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/EventQueue.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/EventQueue.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/EventTriggerCodeGen.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/EventTriggerCodeGen.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/FunctionResolver.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/FunctionResolver.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/KineticLawParameterResolver.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/KineticLawParameterResolver.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/LLVMCompiler.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/LLVMCompiler.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/LLVMException.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/LLVMException.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/LLVMExecutableModel.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/LLVMExecutableModel.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/LLVMModelData.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/LLVMModelData.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/LLVMModelDataSymbols.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/LLVMModelDataSymbols.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/LLVMModelGenerator.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/LLVMModelGenerator.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/LLVMModelSymbols.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/LLVMModelSymbols.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/LoadSymbolResolverBase.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/LoadSymbolResolverBase.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/ModelDataIRBuilder.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/ModelDataIRBuilder.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/ModelDataSymbolResolver.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/ModelDataSymbolResolver.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/ModelGeneratorContext.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/ModelGeneratorContext.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/ModelInitialValueSymbolResolver.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/ModelInitialValueSymbolResolver.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/ModelResources.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/ModelResources.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/Random.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/Random.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/SBMLInitialValueSymbolResolver.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/SBMLInitialValueSymbolResolver.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/SetInitialValueCodeGenBase.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/SetInitialValueCodeGenBase.doctree
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diff --git a/docs/docs-build/.doctrees/C++APIReference/llvm/SymbolForest.doctree b/docs/docs-build/.doctrees/C++APIReference/llvm/SymbolForest.doctree
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diff --git a/docs/docs-build/.doctrees/C++APIReference/rrFileName.doctree b/docs/docs-build/.doctrees/C++APIReference/rrFileName.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/rrIniFile.doctree b/docs/docs-build/.doctrees/C++APIReference/rrIniFile.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/rrIniKey.doctree b/docs/docs-build/.doctrees/C++APIReference/rrIniKey.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/rrIniSection.doctree b/docs/docs-build/.doctrees/C++APIReference/rrIniSection.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/rrLogger.doctree b/docs/docs-build/.doctrees/C++APIReference/rrLogger.doctree
diff --git a/docs/docs-build/.doctrees/C++APIReference/rrNLEQ1Interface.doctree b/docs/docs-build/.doctrees/C++APIReference/rrNLEQ1Interface.doctree
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diff --git a/docs/docs-build/.doctrees/C++APIReference/rrRoadRunnerData.doctree b/docs/docs-build/.doctrees/C++APIReference/rrRoadRunnerData.doctree
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diff --git a/docs/docs-build/.doctrees/rrplugins/rrplugins_chisquare_plugin.doctree b/docs/docs-build/.doctrees/rrplugins/rrplugins_chisquare_plugin.doctree
diff --git a/docs/docs-build/.doctrees/rrplugins/rrplugins_monte_carlo_plugin.doctree b/docs/docs-build/.doctrees/rrplugins/rrplugins_monte_carlo_plugin.doctree
diff --git a/docs/docs-build/.doctrees/rrplugins/rrplugins_testmodel_plugin.doctree b/docs/docs-build/.doctrees/rrplugins/rrplugins_testmodel_plugin.doctree
diff --git a/docs/docs-build/.doctrees/selecting_values.doctree b/docs/docs-build/.doctrees/selecting_values.doctree
diff --git a/docs/docs-build/.doctrees/sensitivities/sensitivities_index.doctree b/docs/docs-build/.doctrees/sensitivities/sensitivities_index.doctree
diff --git a/docs/docs-build/.doctrees/simulation_and_integration.doctree b/docs/docs-build/.doctrees/simulation_and_integration.doctree
diff --git a/docs/docs-build/.doctrees/stability.doctree b/docs/docs-build/.doctrees/stability.doctree
diff --git a/docs/docs-build/.doctrees/steady_state.doctree b/docs/docs-build/.doctrees/steady_state.doctree
diff --git a/docs/docs-build/.doctrees/stochastic.doctree b/docs/docs-build/.doctrees/stochastic.doctree
diff --git a/docs/docs-build/.doctrees/stoichiometric.doctree b/docs/docs-build/.doctrees/stoichiometric.doctree
diff --git a/docs/docs-build/.doctrees/tutorial/changing_initial_conditions.doctree b/docs/docs-build/.doctrees/tutorial/changing_initial_conditions.doctree
diff --git a/docs/docs-build/.doctrees/tutorial/changing_parameters.doctree b/docs/docs-build/.doctrees/tutorial/changing_parameters.doctree
diff --git a/docs/docs-build/.doctrees/tutorial/import_roadrunner.doctree b/docs/docs-build/.doctrees/tutorial/import_roadrunner.doctree
diff --git a/docs/docs-build/.doctrees/tutorial/jit_engines.doctree b/docs/docs-build/.doctrees/tutorial/jit_engines.doctree
diff --git a/docs/docs-build/.doctrees/tutorial/loading_models.doctree b/docs/docs-build/.doctrees/tutorial/loading_models.doctree
diff --git a/docs/docs-build/.doctrees/tutorial/plotting_data.doctree b/docs/docs-build/.doctrees/tutorial/plotting_data.doctree
diff --git a/docs/docs-build/.doctrees/tutorial/running_simulations.doctree b/docs/docs-build/.doctrees/tutorial/running_simulations.doctree
diff --git a/docs/docs-build/.doctrees/tutorial/selecting_output.doctree b/docs/docs-build/.doctrees/tutorial/selecting_output.doctree
diff --git a/docs/docs-build/.doctrees/tutorial/solvers.doctree b/docs/docs-build/.doctrees/tutorial/solvers.doctree
diff --git a/docs/docs-build/.doctrees/tutorial/tutorial.doctree b/docs/docs-build/.doctrees/tutorial/tutorial.doctree
diff --git a/docs/docs-build/.doctrees/tutorial/what_is_rr.doctree b/docs/docs-build/.doctrees/tutorial/what_is_rr.doctree
diff --git a/docs/docs-build/.doctrees/tutorial/what_is_sbml.doctree b/docs/docs-build/.doctrees/tutorial/what_is_sbml.doctree
diff --git a/docs/docs-build/.doctrees/utility_functions.doctree b/docs/docs-build/.doctrees/utility_functions.doctree
diff --git a/docs/docs-build/C++APIReference/CVODEIntegrator.html b/docs/docs-build/C++APIReference/CVODEIntegrator.html
@@ -295,29 +295,6 @@ <h1>CVODEIntegrator<a class="headerlink" href="#cvodeintegrator" title="Permalin
 </p>
 </dd></dl>
 
-<dl class="cpp function">
-<dt class="sig sig-object cpp" id="_CPPv4N2rr15CVODEIntegrator25setConcentrationToleranceE7Setting">
-<span id="_CPPv3N2rr15CVODEIntegrator25setConcentrationToleranceE7Setting"></span><span id="_CPPv2N2rr15CVODEIntegrator25setConcentrationToleranceE7Setting"></span><span id="rr::CVODEIntegrator::setConcentrationTolerance__Setting"></span><span class="target" id="classrr_1_1CVODEIntegrator_1a386a755bab0c72a5d93a7e09ba95fafe"></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">setConcentrationTolerance</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">value</span></span><span class="sig-paren">)</span><span class="w"> </span><span class="k"><span class="pre">override</span></span><a class="headerlink" href="#_CPPv4N2rr15CVODEIntegrator25setConcentrationToleranceE7Setting" title="Permalink to this definition"></a><br /></dt>
-<dd><p>Sets tolerance based on concentration of species. </p>
-<p>
-First converts the concentration tolerances to amount tolerances by multiplying the compartment volume of species. Whichever is smaller will be stored as absolute_tolerance and used in the integration process. <dl class="simple">
-<dt><strong>Author</strong></dt><dd><p>FY</p>
-</dd>
-</dl>
-</p>
-</dd></dl>
-
-<dl class="cpp function">
-<dt class="sig sig-object cpp" id="_CPPv4N2rr15CVODEIntegrator25getConcentrationToleranceEv">
-<span id="_CPPv3N2rr15CVODEIntegrator25getConcentrationToleranceEv"></span><span id="_CPPv2N2rr15CVODEIntegrator25getConcentrationToleranceEv"></span><span id="rr::CVODEIntegrator::getConcentrationTolerance"></span><span class="target" id="classrr_1_1CVODEIntegrator_1a7f68228148cf04688881f636a34deb48"></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">getConcentrationTolerance</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="#_CPPv4N2rr15CVODEIntegrator25getConcentrationToleranceEv" title="Permalink to this definition"></a><br /></dt>
-<dd><p>Gets tolerance based on concentration of species. </p>
-<p><dl class="simple">
-<dt><strong>Author</strong></dt><dd><p>FY </p>
-</dd>
-</dl>
-</p>
-</dd></dl>
-
 <dl class="cpp function">
 <dt class="sig sig-object cpp" id="_CPPv4N2rr15CVODEIntegrator13resetSettingsEv">
 <span id="_CPPv3N2rr15CVODEIntegrator13resetSettingsEv"></span><span id="_CPPv2N2rr15CVODEIntegrator13resetSettingsEv"></span><span id="rr::CVODEIntegrator::resetSettings"></span><span class="target" id="classrr_1_1CVODEIntegrator_1ac18581f5c000940449032e166ef48e79"></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">resetSettings</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="#_CPPv4N2rr15CVODEIntegrator13resetSettingsEv" title="Permalink to this definition"></a><br /></dt>
@@ -459,6 +436,13 @@ <h1>CVODEIntegrator<a class="headerlink" href="#cvodeintegrator" title="Permalin
 <dd><p>getter for the internal CVode memory buffer </p>
 </dd></dl>
 
+<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>
+<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>
+
 <dl class="cpp function">
 <dt class="sig sig-object cpp" id="_CPPv4N2rr15CVODEIntegrator10IntegratorEP15ExecutableModel">
 <span id="_CPPv3N2rr15CVODEIntegrator10IntegratorEP15ExecutableModel"></span><span id="_CPPv2N2rr15CVODEIntegrator10IntegratorEP15ExecutableModel"></span><span id="rr::CVODEIntegrator::Integrator__ExecutableModelP"></span><span class="target" id="classrr_1_1CVODEIntegrator_1a8a79e9633a25767a1683a0334fd1d917"></span><span class="k"><span class="pre">explicit</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">Integrator</span></span></span><span class="sig-paren">(</span><a class="reference internal" href="rrExecutableModel.html#_CPPv4N2rr15ExecutableModelE" title="rr::ExecutableModel"><span class="n"><span class="pre">ExecutableModel</span></span></a><span class="w"> </span><span class="p"><span class="pre">*</span></span><span class="n sig-param"><span class="pre">model</span></span><span class="sig-paren">)</span><a class="headerlink" href="#_CPPv4N2rr15CVODEIntegrator10IntegratorEP15ExecutableModel" title="Permalink to this definition"></a><br /></dt>

diff --git a/docs/docs-build/C++APIReference/Dictionary.html b/docs/docs-build/C++APIReference/Dictionary.html
@@ -142,7 +142,7 @@ <h1>Dictionary<a class="headerlink" href="#dictionary" title="Permalink to this
 <span id="_CPPv3N2rr10DictionaryE"></span><span id="_CPPv2N2rr10DictionaryE"></span><span id="rr::Dictionary"></span><span class="target" id="classrr_1_1Dictionary"></span><span class="k"><span class="pre">class</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">Dictionary</span></span></span><a class="headerlink" href="#_CPPv4N2rr10DictionaryE" title="Permalink to this definition"></a><br /></dt>
 <dd><p>This class is frozen, no new features A dictionary interface that objects can implement. </p>
 <p>These are automatically mapped to python dictionaries. </p>
-<p>Subclassed by rr::BasicDictionary, <a class="reference internal" href="rrNLEQ1Interface.html#classrr_1_1NLEQ1Interface"><span class="std std-ref">rr::NLEQ1Interface</span></a>, <a class="reference internal" href="rrNLEQ2Interface.html#classrr_1_1NLEQ2Interface"><span class="std std-ref">rr::NLEQ2Interface</span></a></p>
+<p>Subclassed by rr::BasicDictionary</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">
@@ -186,7 +186,7 @@ <h1>Dictionary<a class="headerlink" href="#dictionary" title="Permalink to this
 
 <dl class="cpp function">
 <dt class="sig sig-object cpp" id="_CPPv4NK2rr10Dictionary7getKeysEv">
-<span id="_CPPv3NK2rr10Dictionary7getKeysEv"></span><span id="_CPPv2NK2rr10Dictionary7getKeysEv"></span><span id="rr::Dictionary::getKeysC"></span><span class="target" id="classrr_1_1Dictionary_1a378b4142bc6b038465b375d36350b51e"></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="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="p"><span class="pre">&gt;</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">getKeys</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="p"><span class="pre">=</span></span><span class="w"> </span><span class="m"><span class="pre">0</span></span><a class="headerlink" href="#_CPPv4NK2rr10Dictionary7getKeysEv" title="Permalink to this definition"></a><br /></dt>
+<span id="_CPPv3NK2rr10Dictionary7getKeysEv"></span><span id="_CPPv2NK2rr10Dictionary7getKeysEv"></span><span id="rr::Dictionary::getKeysC"></span><span class="target" id="classrr_1_1Dictionary_1ae8e4240deda5ee2dc7d472476bd92b47"></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="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="p"><span class="pre">&gt;</span></span><span class="w"> </span><span class="sig-name descname"><span class="n"><span class="pre">getKeys</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="p"><span class="pre">=</span></span><span class="w"> </span><span class="m"><span class="pre">0</span></span><a class="headerlink" href="#_CPPv4NK2rr10Dictionary7getKeysEv" title="Permalink to this definition"></a><br /></dt>
 <dd><p>list of keys in this object. </p>
 </dd></dl>