Adds new docs with python and matlab snippets

RascalSoftware · Nov 11, 2024 · 53907b6 · 53907b6
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diff --git a/dev/.buildinfo b/dev/.buildinfo
@@ -0,0 +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: 5e478f088ee0a9eaa98bf0c40907626c
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/master/ADR.html → dev/ADR.html b/master/ADR.html → dev/ADR.html
diff --git a/master/DE.html → dev/DE.html b/master/DE.html → dev/DE.html
diff --git a/master/DREAM.html → dev/DREAM.html b/master/DREAM.html → dev/DREAM.html
diff --git a/master/_images/adaptiveSpPic.png → dev/_images/adaptiveSpPic.png b/master/_images/adaptiveSpPic.png → dev/_images/adaptiveSpPic.png
diff --git a/master/_images/banner.png → dev/_images/banner.png b/master/_images/banner.png → dev/_images/banner.png
diff --git a/master/_images/basicBackground.png → dev/_images/basicBackground.png b/master/_images/basicBackground.png → dev/_images/basicBackground.png
diff --git a/master/_images/bilayer.png → dev/_images/bilayer.png b/master/_images/bilayer.png → dev/_images/bilayer.png
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diff --git a/master/_images/contrastGroup.png → dev/_images/contrastGroup.png b/master/_images/contrastGroup.png → dev/_images/contrastGroup.png
diff --git a/master/_images/controlsBlock.png → dev/_images/controlsBlock.png b/master/_images/controlsBlock.png → dev/_images/controlsBlock.png
diff --git a/master/_images/controlsClass.png → dev/_images/controlsClass.png b/master/_images/controlsClass.png → dev/_images/controlsClass.png
diff --git a/master/_images/copyProject1.png → dev/_images/copyProject1.png b/master/_images/copyProject1.png → dev/_images/copyProject1.png
diff --git a/master/_images/copyProject2.png → dev/_images/copyProject2.png b/master/_images/copyProject2.png → dev/_images/copyProject2.png
diff --git a/master/_images/customTwoLayerFig.png → dev/_images/customTwoLayerFig.png b/master/_images/customTwoLayerFig.png → dev/_images/customTwoLayerFig.png
diff --git a/master/_images/dataAdded.png → dev/_images/dataAdded.png b/master/_images/dataAdded.png → dev/_images/dataAdded.png
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diff --git a/master/_images/deControls.png → dev/_images/deControls.png b/master/_images/deControls.png → dev/_images/deControls.png
diff --git a/master/_images/defaultData.png → dev/_images/defaultData.png b/master/_images/defaultData.png → dev/_images/defaultData.png
diff --git a/master/_images/dispControls.png → dev/_images/dispControls.png b/master/_images/dispControls.png → dev/_images/dispControls.png
diff --git a/master/_images/dispProblem1.png → dev/_images/dispProblem1.png b/master/_images/dispProblem1.png → dev/_images/dispProblem1.png
diff --git a/master/_images/dispProblem11.png → dev/_images/dispProblem11.png b/master/_images/dispProblem11.png → dev/_images/dispProblem11.png
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diff --git a/master/_images/dispProblem21.png → dev/_images/dispProblem21.png b/master/_images/dispProblem21.png → dev/_images/dispProblem21.png
diff --git a/master/_images/dispResults.png → dev/_images/dispResults.png b/master/_images/dispResults.png → dev/_images/dispResults.png
diff --git a/master/_images/dispResults1.png → dev/_images/dispResults1.png b/master/_images/dispResults1.png → dev/_images/dispResults1.png
diff --git a/master/_images/domainContrast.png → dev/_images/domainContrast.png b/master/_images/domainContrast.png → dev/_images/domainContrast.png
diff --git a/master/_images/domainContrastTable.png → dev/_images/domainContrastTable.png b/master/_images/domainContrastTable.png → dev/_images/domainContrastTable.png
diff --git a/master/_images/domainGraph.png → dev/_images/domainGraph.png b/master/_images/domainGraph.png → dev/_images/domainGraph.png
diff --git a/master/_images/domainLayersTable.png → dev/_images/domainLayersTable.png b/master/_images/domainLayersTable.png → dev/_images/domainLayersTable.png
diff --git a/master/_images/domainRatioTable.png → dev/_images/domainRatioTable.png b/master/_images/domainRatioTable.png → dev/_images/domainRatioTable.png
diff --git a/master/_images/dotsSLD.png → dev/_images/dotsSLD.png b/master/_images/dotsSLD.png → dev/_images/dotsSLD.png
diff --git a/master/_images/imaginarySL.png → dev/_images/imaginarySL.png b/master/_images/imaginarySL.png → dev/_images/imaginarySL.png
diff --git a/master/_images/layersGroup.png → dev/_images/layersGroup.png b/master/_images/layersGroup.png → dev/_images/layersGroup.png
diff --git a/master/_images/layersPic.png → dev/_images/layersPic.png b/master/_images/layersPic.png → dev/_images/layersPic.png
diff --git a/master/_images/lipidModel-1.png → dev/_images/lipidModel-1.png b/master/_images/lipidModel-1.png → dev/_images/lipidModel-1.png
diff --git a/master/_images/lipidModel-2.png → dev/_images/lipidModel-2.png b/master/_images/lipidModel-2.png → dev/_images/lipidModel-2.png
diff --git a/master/_images/lipidMonolayer.png → dev/_images/lipidMonolayer.png b/master/_images/lipidMonolayer.png → dev/_images/lipidMonolayer.png
diff --git a/master/_images/loadingBack.png → dev/_images/loadingBack.png b/master/_images/loadingBack.png → dev/_images/loadingBack.png
diff --git a/master/_images/model1.png → dev/_images/model1.png b/master/_images/model1.png → dev/_images/model1.png
diff --git a/master/_images/model2.png → dev/_images/model2.png b/master/_images/model2.png → dev/_images/model2.png
diff --git a/master/_images/parameterBlock.png → dev/_images/parameterBlock.png b/master/_images/parameterBlock.png → dev/_images/parameterBlock.png
diff --git a/master/_images/parameterGroup.png → dev/_images/parameterGroup.png b/master/_images/parameterGroup.png → dev/_images/parameterGroup.png
diff --git a/master/_images/parameterRemoveError.png → dev/_images/parameterRemoveError.png b/master/_images/parameterRemoveError.png → dev/_images/parameterRemoveError.png
diff --git a/master/_images/plot1.png → dev/_images/plot1.png b/master/_images/plot1.png → dev/_images/plot1.png
diff --git a/master/_images/plot2.png → dev/_images/plot2.png b/master/_images/plot2.png → dev/_images/plot2.png
diff --git a/master/_images/plots.png → dev/_images/plots.png b/master/_images/plots.png → dev/_images/plots.png
diff --git a/master/_images/projectClassMethods.png → dev/_images/projectClassMethods.png b/master/_images/projectClassMethods.png → dev/_images/projectClassMethods.png
diff --git a/master/_images/ratInput.png → dev/_images/ratInput.png b/master/_images/ratInput.png → dev/_images/ratInput.png
diff --git a/master/_images/ratRun.png → dev/_images/ratRun.png b/master/_images/ratRun.png → dev/_images/ratRun.png
diff --git a/master/_images/ratRun1.png → dev/_images/ratRun1.png b/master/_images/ratRun1.png → dev/_images/ratRun1.png
diff --git a/master/_images/ratRun2.png → dev/_images/ratRun2.png b/master/_images/ratRun2.png → dev/_images/ratRun2.png
diff --git a/master/_images/referenceChange.png → dev/_images/referenceChange.png b/master/_images/referenceChange.png → dev/_images/referenceChange.png
diff --git a/master/_images/reflectivitiesStruct.png → dev/_images/reflectivitiesStruct.png b/master/_images/reflectivitiesStruct.png → dev/_images/reflectivitiesStruct.png
diff --git a/master/_images/resampleContrast.png → dev/_images/resampleContrast.png b/master/_images/resampleContrast.png → dev/_images/resampleContrast.png
diff --git a/master/_images/resamplePic.png → dev/_images/resamplePic.png b/master/_images/resamplePic.png → dev/_images/resamplePic.png
diff --git a/master/_images/resolClass.png → dev/_images/resolClass.png b/master/_images/resolClass.png → dev/_images/resolClass.png
diff --git a/master/_images/resolClassModified.png → dev/_images/resolClassModified.png b/master/_images/resolClassModified.png → dev/_images/resolClassModified.png
diff --git a/master/_images/resultingParameterBlock1.png → dev/_images/resultingParameterBlock1.png b/master/_images/resultingParameterBlock1.png → dev/_images/resultingParameterBlock1.png
diff --git a/master/_images/resultingParameterBlock2.png → dev/_images/resultingParameterBlock2.png b/master/_images/resultingParameterBlock2.png → dev/_images/resultingParameterBlock2.png
diff --git a/master/_images/resultingParameterBlock3.png → dev/_images/resultingParameterBlock3.png b/master/_images/resultingParameterBlock3.png → dev/_images/resultingParameterBlock3.png
diff --git a/master/_images/resultingParameterBlock4.png → dev/_images/resultingParameterBlock4.png b/master/_images/resultingParameterBlock4.png → dev/_images/resultingParameterBlock4.png
diff --git a/master/_images/resultsStruct.png → dev/_images/resultsStruct.png b/master/_images/resultsStruct.png → dev/_images/resultsStruct.png
diff --git a/master/_images/simpleControls.png → dev/_images/simpleControls.png b/master/_images/simpleControls.png → dev/_images/simpleControls.png
diff --git a/master/_images/simpleLayer.png → dev/_images/simpleLayer.png b/master/_images/simpleLayer.png → dev/_images/simpleLayer.png
diff --git a/master/_images/simplexControls.png → dev/_images/simplexControls.png b/master/_images/simplexControls.png → dev/_images/simplexControls.png
diff --git a/master/_images/simplexControls1.png → dev/_images/simplexControls1.png b/master/_images/simplexControls1.png → dev/_images/simplexControls1.png
diff --git a/master/_images/simplexControls2.png → dev/_images/simplexControls2.png b/master/_images/simplexControls2.png → dev/_images/simplexControls2.png
diff --git a/master/_images/simplexFit.png → dev/_images/simplexFit.png b/master/_images/simplexFit.png → dev/_images/simplexFit.png
diff --git a/master/_images/simplexRun.png → dev/_images/simplexRun.png b/master/_images/simplexRun.png → dev/_images/simplexRun.png
diff --git a/master/_images/threeLayerGroup1.png → dev/_images/threeLayerGroup1.png b/master/_images/threeLayerGroup1.png → dev/_images/threeLayerGroup1.png
diff --git a/master/_images/threeLayerGroup2.png → dev/_images/threeLayerGroup2.png b/master/_images/threeLayerGroup2.png → dev/_images/threeLayerGroup2.png
diff --git a/master/_images/toolbox.png → dev/_images/toolbox.png b/master/_images/toolbox.png → dev/_images/toolbox.png
diff --git a/master/_images/twoLayerGroup.png → dev/_images/twoLayerGroup.png b/master/_images/twoLayerGroup.png → dev/_images/twoLayerGroup.png
diff --git a/master/_images/twoLayerRAT.png → dev/_images/twoLayerRAT.png b/master/_images/twoLayerRAT.png → dev/_images/twoLayerRAT.png
diff --git a/master/_sources/ADR.rst.txt → dev/_sources/ADR.rst.txt b/master/_sources/ADR.rst.txt → dev/_sources/ADR.rst.txt
diff --git a/master/_sources/DE.rst.txt → dev/_sources/DE.rst.txt b/master/_sources/DE.rst.txt → dev/_sources/DE.rst.txt
diff --git a/master/_sources/DREAM.rst.txt → dev/_sources/DREAM.rst.txt b/master/_sources/DREAM.rst.txt → dev/_sources/DREAM.rst.txt
diff --git a/master/_sources/advanced.rst.txt → dev/_sources/advanced.rst.txt b/master/_sources/advanced.rst.txt → dev/_sources/advanced.rst.txt
diff --git a/master/_sources/algorithms.rst.txt → dev/_sources/algorithms.rst.txt b/master/_sources/algorithms.rst.txt → dev/_sources/algorithms.rst.txt
diff --git a/master/_sources/api.rst.txt → dev/_sources/api.rst.txt b/master/_sources/api.rst.txt → dev/_sources/api.rst.txt
@@ -297,14 +297,14 @@ properly on terminal.
     :caption: Adding MATLAB custom file.
 
         %                       Row Name   Custom File Name  Language   Path
-        problem.addCustomFile('DSPC Model','customBilayer.m','matlab',pwd);
+        problem.addCustomFile('DSPC Model','customBilayer.m','matlab','pwd');
 
 .. code-block:: MATLAB
     :caption: Adding C++ custom file.
 
             % For C++, function name of the cpp file is supplied
             %                       Row Name        DLL/function Name  Language   Path
-            problem.addCustomFile('DSPC CPP Model','customBilayer','c++',pwd);
+            problem.addCustomFile('DSPC CPP Model','customBilayer','c++','pwd');
 
 
 

diff --git a/master/_sources/backgroundsClass.rst.txt → dev/_sources/backgroundsClass.rst.txt b/master/_sources/backgroundsClass.rst.txt → dev/_sources/backgroundsClass.rst.txt
diff --git a/dev/_sources/bayesPlot.rst.txt b/dev/_sources/bayesPlot.rst.txt
@@ -0,0 +1,7 @@
+.. _bayesPlot:
+
+
+Bayesian Plotting Functions.
+............................
+
+TODO
diff --git a/master/_sources/calcTypes.rst.txt → dev/_sources/calcTypes.rst.txt b/master/_sources/calcTypes.rst.txt → dev/_sources/calcTypes.rst.txt
diff --git a/master/_sources/chapter1.rst.txt → dev/_sources/chapter1.rst.txt b/master/_sources/chapter1.rst.txt → dev/_sources/chapter1.rst.txt
diff --git a/master/_sources/chapter2.rst.txt → dev/_sources/chapter2.rst.txt b/master/_sources/chapter2.rst.txt → dev/_sources/chapter2.rst.txt
diff --git a/master/_sources/contrastsClass.rst.txt → dev/_sources/contrastsClass.rst.txt b/master/_sources/contrastsClass.rst.txt → dev/_sources/contrastsClass.rst.txt
diff --git a/master/_sources/controlClass.rst.txt → dev/_sources/controlClass.rst.txt b/master/_sources/controlClass.rst.txt → dev/_sources/controlClass.rst.txt
diff --git a/master/_sources/controlsInfo.rst.txt → dev/_sources/controlsInfo.rst.txt b/master/_sources/controlsInfo.rst.txt → dev/_sources/controlsInfo.rst.txt
diff --git a/dev/_sources/conversionFuncs.rst.txt b/dev/_sources/conversionFuncs.rst.txt
@@ -0,0 +1,7 @@
+.. _conversionFuncs:
+
+
+Convert between RAT and RasCAL1
+...............................
+
+TODO
diff --git a/master/_sources/customFileClass.rst.txt → dev/_sources/customFileClass.rst.txt b/master/_sources/customFileClass.rst.txt → dev/_sources/customFileClass.rst.txt
@@ -22,14 +22,14 @@ properly on terminal.
     :caption: Adding MATLAB custom file.
 
         %                       Row Name   Custom File Name  Language   Path
-        problem.addCustomFile('DSPC Model','customBilayer.m','matlab',pwd);
+        problem.addCustomFile('DSPC Model','customBilayer.m','matlab','pwd');
 
 .. code-block:: MATLAB
     :caption: Adding C++ custom file.
 
             % For C++, function name of the cpp file is supplied
             %                       Row Name        DLL/function Name  Language   Path
-            problem.addCustomFile('DSPC CPP Model','customBilayer','c++',pwd);
+            problem.addCustomFile('DSPC CPP Model','customBilayer','c++','pwd');
 
 
 .. warning::

diff --git a/master/_sources/customLanguages.rst.txt → dev/_sources/customLanguages.rst.txt b/master/_sources/customLanguages.rst.txt → dev/_sources/customLanguages.rst.txt
diff --git a/master/_sources/customModels.rst.txt → dev/_sources/customModels.rst.txt b/master/_sources/customModels.rst.txt → dev/_sources/customModels.rst.txt
diff --git a/master/_sources/dataClass.rst.txt → dev/_sources/dataClass.rst.txt b/master/_sources/dataClass.rst.txt → dev/_sources/dataClass.rst.txt
diff --git a/master/_sources/devDocumentation.rst.txt → dev/_sources/devDocumentation.rst.txt b/master/_sources/devDocumentation.rst.txt → dev/_sources/devDocumentation.rst.txt
diff --git a/master/_sources/domainsCustomLayers.rst.txt → dev/_sources/domainsCustomLayers.rst.txt b/master/_sources/domainsCustomLayers.rst.txt → dev/_sources/domainsCustomLayers.rst.txt
diff --git a/master/_sources/domainsCustomXY.rst.txt → dev/_sources/domainsCustomXY.rst.txt b/master/_sources/domainsCustomXY.rst.txt → dev/_sources/domainsCustomXY.rst.txt
diff --git a/master/_sources/domainsStanlay.rst.txt → dev/_sources/domainsStanlay.rst.txt b/master/_sources/domainsStanlay.rst.txt → dev/_sources/domainsStanlay.rst.txt
diff --git a/master/_sources/entryFunctions.rst.txt → dev/_sources/entryFunctions.rst.txt b/master/_sources/entryFunctions.rst.txt → dev/_sources/entryFunctions.rst.txt
diff --git a/master/_sources/events.rst.txt → dev/_sources/events.rst.txt b/master/_sources/events.rst.txt → dev/_sources/events.rst.txt
diff --git a/master/_sources/imaginary.rst.txt → dev/_sources/imaginary.rst.txt b/master/_sources/imaginary.rst.txt → dev/_sources/imaginary.rst.txt
diff --git a/master/_sources/incoherent.rst.txt → dev/_sources/incoherent.rst.txt b/master/_sources/incoherent.rst.txt → dev/_sources/incoherent.rst.txt
@@ -13,5 +13,4 @@ domain that the 'domainClass' is used. As with 'normal reflectivity', we can han
    :maxdepth: 2
 
    domainsStanlay
-   domainsCustomLayers
-   domainsCustomXY
+   domainsCustomLayers
diff --git a/master/_sources/index.rst.txt → dev/_sources/index.rst.txt b/master/_sources/index.rst.txt → dev/_sources/index.rst.txt
diff --git a/master/_sources/install.rst.txt → dev/_sources/install.rst.txt b/master/_sources/install.rst.txt → dev/_sources/install.rst.txt
diff --git a/master/_sources/layersClass.rst.txt → dev/_sources/layersClass.rst.txt b/master/_sources/layersClass.rst.txt → dev/_sources/layersClass.rst.txt
diff --git a/dev/_sources/livePlot.rst.txt b/dev/_sources/livePlot.rst.txt
@@ -0,0 +1,7 @@
+.. _livePlot:
+
+
+Live Updating Plots
+...................
+
+TODO
diff --git a/master/_sources/magnetic.rst.txt → dev/_sources/magnetic.rst.txt b/master/_sources/magnetic.rst.txt → dev/_sources/magnetic.rst.txt
diff --git a/master/_sources/nestedSampling.rst.txt → dev/_sources/nestedSampling.rst.txt b/master/_sources/nestedSampling.rst.txt → dev/_sources/nestedSampling.rst.txt
diff --git a/master/_sources/oilWater.rst.txt → dev/_sources/oilWater.rst.txt b/master/_sources/oilWater.rst.txt → dev/_sources/oilWater.rst.txt
diff --git a/master/_sources/parallelisation.rst.txt → dev/_sources/parallelisation.rst.txt b/master/_sources/parallelisation.rst.txt → dev/_sources/parallelisation.rst.txt
diff --git a/master/_sources/parametersClass.rst.txt → dev/_sources/parametersClass.rst.txt b/master/_sources/parametersClass.rst.txt → dev/_sources/parametersClass.rst.txt
diff --git a/master/_sources/paramonte.rst.txt → dev/_sources/paramonte.rst.txt b/master/_sources/paramonte.rst.txt → dev/_sources/paramonte.rst.txt
diff --git a/master/_sources/projectClass.rst.txt → dev/_sources/projectClass.rst.txt b/master/_sources/projectClass.rst.txt → dev/_sources/projectClass.rst.txt
diff --git a/master/_sources/reference.rst.txt → dev/_sources/reference.rst.txt b/master/_sources/reference.rst.txt → dev/_sources/reference.rst.txt
diff --git a/master/_sources/resampling.rst.txt → dev/_sources/resampling.rst.txt b/master/_sources/resampling.rst.txt → dev/_sources/resampling.rst.txt
diff --git a/master/_sources/resolutionsClass.rst.txt → dev/_sources/resolutionsClass.rst.txt b/master/_sources/resolutionsClass.rst.txt → dev/_sources/resolutionsClass.rst.txt
diff --git a/master/_sources/savingAndClasses.rst.txt → dev/_sources/savingAndClasses.rst.txt b/master/_sources/savingAndClasses.rst.txt → dev/_sources/savingAndClasses.rst.txt
diff --git a/dev/_sources/simplePlot.rst.txt b/dev/_sources/simplePlot.rst.txt
@@ -0,0 +1,7 @@
+.. _simplePlotting:
+
+
+Basic Plotting Functions.
+.........................
+
+TODO
diff --git a/master/_sources/simplex.rst.txt → dev/_sources/simplex.rst.txt b/master/_sources/simplex.rst.txt → dev/_sources/simplex.rst.txt
diff --git a/master/_sources/support.rst.txt → dev/_sources/support.rst.txt b/master/_sources/support.rst.txt → dev/_sources/support.rst.txt
diff --git a/master/_sources/targetFunctions.rst.txt → dev/_sources/targetFunctions.rst.txt b/master/_sources/targetFunctions.rst.txt → dev/_sources/targetFunctions.rst.txt
diff --git a/master/_sources/tutorial.rst.txt → dev/_sources/tutorial.rst.txt b/master/_sources/tutorial.rst.txt → dev/_sources/tutorial.rst.txt
diff --git a/master/_sources/utilities.rst.txt → dev/_sources/utilities.rst.txt b/master/_sources/utilities.rst.txt → dev/_sources/utilities.rst.txt
@@ -9,9 +9,9 @@ These are mainly plotting functions:-
 
 
 .. toctree::
-   :maxdepth: 1
+   :maxdepth: 2
 
-   plotFuns
-   plotFunsBayes
+   simplePlot
+   bayesPlot
    livePlot
    conversionFuncs
diff --git a/master/_sources/utilityFunctions.rst.txt → dev/_sources/utilityFunctions.rst.txt b/master/_sources/utilityFunctions.rst.txt → dev/_sources/utilityFunctions.rst.txt
diff --git a/....1e8bd061cd6da7fc9cf755528e8ffc24.min.css → ....1e8bd061cd6da7fc9cf755528e8ffc24.min.css b/....1e8bd061cd6da7fc9cf755528e8ffc24.min.css → ....1e8bd061cd6da7fc9cf755528e8ffc24.min.css
diff --git a/master/_static/design-tabs.js → dev/_sphinx_design_static/design-tabs.js b/master/_static/design-tabs.js → dev/_sphinx_design_static/design-tabs.js
diff --git a/master/_static/alabaster.css → dev/_static/alabaster.css b/master/_static/alabaster.css → dev/_static/alabaster.css
diff --git a/master/_static/banner.png → dev/_static/banner.png b/master/_static/banner.png → dev/_static/banner.png
diff --git a/master/_static/basic.css → dev/_static/basic.css b/master/_static/basic.css → dev/_static/basic.css
diff --git a/master/_static/custom.css → dev/_static/custom.css b/master/_static/custom.css → dev/_static/custom.css
diff --git a/dev/_static/design-style.1e8bd061cd6da7fc9cf755528e8ffc24.min.css b/dev/_static/design-style.1e8bd061cd6da7fc9cf755528e8ffc24.min.css
diff --git a/dev/_static/design-tabs.js b/dev/_static/design-tabs.js
@@ -0,0 +1,27 @@
+var sd_labels_by_text = {};
+
+function ready() {
+  const li = document.getElementsByClassName("sd-tab-label");
+  for (const label of li) {
+    syncId = label.getAttribute("data-sync-id");
+    if (syncId) {
+      label.onclick = onLabelClick;
+      if (!sd_labels_by_text[syncId]) {
+        sd_labels_by_text[syncId] = [];
+      }
+      sd_labels_by_text[syncId].push(label);
+    }
+  }
+}
+
+function onLabelClick() {
+  // Activate other inputs with the same sync id.
+  syncId = this.getAttribute("data-sync-id");
+  for (label of sd_labels_by_text[syncId]) {
+    if (label === this) continue;
+    label.previousElementSibling.checked = true;
+  }
+  window.localStorage.setItem("sphinx-design-last-tab", syncId);
+}
+
+document.addEventListener("DOMContentLoaded", ready, false);
diff --git a/master/_static/doctools.js → dev/_static/doctools.js b/master/_static/doctools.js → dev/_static/doctools.js
diff --git a/master/_static/documentation_options.js → dev/_static/documentation_options.js b/master/_static/documentation_options.js → dev/_static/documentation_options.js
diff --git a/master/_static/file.png → dev/_static/file.png b/master/_static/file.png → dev/_static/file.png
diff --git a/master/_static/language_data.js → dev/_static/language_data.js b/master/_static/language_data.js → dev/_static/language_data.js
diff --git a/master/_static/logo.png → dev/_static/logo.png b/master/_static/logo.png → dev/_static/logo.png
diff --git a/master/_static/minus.png → dev/_static/minus.png b/master/_static/minus.png → dev/_static/minus.png
diff --git a/master/_static/plus.png → dev/_static/plus.png b/master/_static/plus.png → dev/_static/plus.png
diff --git a/master/_static/pygments.css → dev/_static/pygments.css b/master/_static/pygments.css → dev/_static/pygments.css
diff --git a/master/_static/searchtools.js → dev/_static/searchtools.js b/master/_static/searchtools.js → dev/_static/searchtools.js
diff --git a/master/_static/sphinx_highlight.js → dev/_static/sphinx_highlight.js b/master/_static/sphinx_highlight.js → dev/_static/sphinx_highlight.js
diff --git a/master/advanced.html → dev/advanced.html b/master/advanced.html → dev/advanced.html
diff --git a/master/algorithms.html → dev/algorithms.html b/master/algorithms.html → dev/algorithms.html
diff --git a/master/api.html → dev/api.html b/master/api.html → dev/api.html
@@ -402,15 +402,15 @@ <h3>Custom File Class<a class="headerlink" href="#custom-file-class" title="Perm
 <div class="literal-block-wrapper docutils container" id="id14">
 <div class="code-block-caption"><span class="caption-text">Adding MATLAB custom file.</span><a class="headerlink" href="#id14" title="Permalink to this code">¶</a></div>
 <div class="highlight-MATLAB notranslate"><div class="highlight"><pre><span></span><span class="w">    </span><span class="c">%                       Row Name   Custom File Name  Language   Path</span>
-<span class="w">    </span><span class="n">problem</span><span class="p">.</span><span class="n">addCustomFile</span><span class="p">(</span><span class="s">&#39;DSPC Model&#39;</span><span class="p">,</span><span class="s">&#39;customBilayer.m&#39;</span><span class="p">,</span><span class="s">&#39;matlab&#39;</span><span class="p">,</span><span class="nb">pwd</span><span class="p">);</span>
+<span class="w">    </span><span class="n">problem</span><span class="p">.</span><span class="n">addCustomFile</span><span class="p">(</span><span class="s">&#39;DSPC Model&#39;</span><span class="p">,</span><span class="s">&#39;customBilayer.m&#39;</span><span class="p">,</span><span class="s">&#39;matlab&#39;</span><span class="p">,</span><span class="s">&#39;pwd&#39;</span><span class="p">);</span>
 </pre></div>
 </div>
 </div>
 <div class="literal-block-wrapper docutils container" id="id15">
 <div class="code-block-caption"><span class="caption-text">Adding C++ custom file.</span><a class="headerlink" href="#id15" title="Permalink to this code">¶</a></div>
 <div class="highlight-MATLAB notranslate"><div class="highlight"><pre><span></span><span class="w">        </span><span class="c">% For C++, function name of the cpp file is supplied</span>
 <span class="w">        </span><span class="c">%                       Row Name        DLL/function Name  Language   Path</span>
-<span class="w">        </span><span class="n">problem</span><span class="p">.</span><span class="n">addCustomFile</span><span class="p">(</span><span class="s">&#39;DSPC CPP Model&#39;</span><span class="p">,</span><span class="s">&#39;customBilayer&#39;</span><span class="p">,</span><span class="s">&#39;c++&#39;</span><span class="p">,</span><span class="nb">pwd</span><span class="p">);</span>
+<span class="w">        </span><span class="n">problem</span><span class="p">.</span><span class="n">addCustomFile</span><span class="p">(</span><span class="s">&#39;DSPC CPP Model&#39;</span><span class="p">,</span><span class="s">&#39;customBilayer&#39;</span><span class="p">,</span><span class="s">&#39;c++&#39;</span><span class="p">,</span><span class="s">&#39;pwd&#39;</span><span class="p">);</span>
 </pre></div>
 </div>
 </div>

diff --git a/master/backgroundsClass.html → dev/backgroundsClass.html b/master/backgroundsClass.html → dev/backgroundsClass.html
diff --git a/dev/bayesPlot.html b/dev/bayesPlot.html
@@ -0,0 +1,113 @@
+
+<!DOCTYPE html>
+
+<html lang="en">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
+
+    <title>Bayesian Plotting Functions. &#8212; RAT 1.0.0-beta documentation</title>
+    <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
+    <link rel="stylesheet" type="text/css" href="_static/alabaster.css" />
+    <link rel="stylesheet" type="text/css" href="_static/design-style.1e8bd061cd6da7fc9cf755528e8ffc24.min.css" />
+    <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/design-tabs.js"></script>
+    <link rel="icon" href="_static/logo.png"/>
+    <link rel="index" title="Index" href="genindex.html" />
+    <link rel="search" title="Search" href="search.html" />
+    <link rel="next" title="Live Updating Plots" href="livePlot.html" />
+    <link rel="prev" title="Basic Plotting Functions." href="simplePlot.html" />
+
+  <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+
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+
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+  </head><body>
+  <div class="document">
+
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+<p class="logo">
+  <a href="index.html">
+    <img class="logo" src="_static/logo.png" alt="Logo" />
+
+  </a>
+</p>
+
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+
+
+<div id="searchbox" style="display: none" role="search">
+  <h3 id="searchlabel">Quick search</h3>
+    <div class="searchformwrapper">
+    <form class="search" action="search.html" method="get">
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
+      <input type="submit" value="Go" />
+    </form>
+    </div>
+</div>
+<script>document.getElementById('searchbox').style.display = "block"</script><h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="install.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="tutorial.html">Tutorial</a></li>
+<li class="toctree-l1"><a class="reference internal" href="algorithms.html">Algorithms</a></li>
+<li class="toctree-l1"><a class="reference internal" href="advanced.html">Advanced Topics</a></li>
+<li class="toctree-l1"><a class="reference internal" href="calcTypes.html">Different Calculation Types</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="utilities.html">Utility Functions</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="simplePlot.html">Basic Plotting Functions.</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Bayesian Plotting Functions.</a></li>
+<li class="toctree-l2"><a class="reference internal" href="livePlot.html">Live Updating Plots</a></li>
+<li class="toctree-l2"><a class="reference internal" href="conversionFuncs.html">Convert between RAT and RasCAL1</a></li>
+</ul>
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+        <div class="bodywrapper">
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+
+  <section id="bayesian-plotting-functions">
+<span id="bayesplot"></span><h1>Bayesian Plotting Functions.<a class="headerlink" href="#bayesian-plotting-functions" title="Permalink to this heading">¶</a></h1>
+<p>TODO</p>
+</section>
+
+
+          </div>
+
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+      </div>
+    <div class="clearer"></div>
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+      <a href="_sources/bayesPlot.rst.txt"
+          rel="nofollow">Page source</a>
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+</html>
diff --git a/master/calcTypes.html → dev/calcTypes.html b/master/calcTypes.html → dev/calcTypes.html
@@ -96,7 +96,6 @@ <h3 id="searchlabel">Quick search</h3>
 <li class="toctree-l1"><a class="reference internal" href="incoherent.html">Incoherent Summing (Domains)</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="domainsStanlay.html">Standard Layers Domains</a></li>
 <li class="toctree-l2"><a class="reference internal" href="domainsCustomLayers.html">Custom Models with Domains</a></li>
-<li class="toctree-l2"><a class="reference internal" href="domainsCustomXY.html">Custom XY Models with Domains</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="oilWater.html">Reflectivity from Oil/Water Samples</a></li>

diff --git a/master/chapter1.html → dev/chapter1.html b/master/chapter1.html → dev/chapter1.html
diff --git a/master/chapter2.html → dev/chapter2.html b/master/chapter2.html → dev/chapter2.html
diff --git a/master/contrastsClass.html → dev/contrastsClass.html b/master/contrastsClass.html → dev/contrastsClass.html
@@ -149,12 +149,6 @@ <h2>Reference<a class="headerlink" href="#reference" title="Permalink to this he
 </dl>
 </dd></dl>
 
-<dl class="mat staticmethod">
-<dt class="sig sig-object mat" id="API.projectClass.contrastsClass.setDefaultValues">
-<em class="property"><span class="pre">static</span> </em><span class="sig-name descname"><span class="pre">setDefaultValues</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="pre">contrast</span></em><span class="sig-paren">)</span><a class="headerlink" href="#API.projectClass.contrastsClass.setDefaultValues" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set non-empty default values when adding a contrast.</p>
-</dd></dl>
-
 <dl class="mat method">
 <dt class="sig sig-object mat" id="API.projectClass.contrastsClass.toStruct">
 <span class="sig-name descname"><span class="pre">toStruct</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="pre">allowedNames</span></em>, <em class="sig-param"><span class="pre">modelType</span></em>, <em class="sig-param"><span class="pre">dataTable</span></em><span class="sig-paren">)</span><a class="headerlink" href="#API.projectClass.contrastsClass.toStruct" title="Permalink to this definition">¶</a></dt>
@@ -193,12 +187,6 @@ <h2>Reference<a class="headerlink" href="#reference" title="Permalink to this he
 <p>contrastsClass.parseContrastInput(‘name’, ‘Contrast Name’)</p>
 </dd></dl>
 
-<dl class="mat staticmethod">
-<dt class="sig sig-object mat" id="API.projectClass.domainContrastsClass.setDefaultValues">
-<em class="property"><span class="pre">static</span> </em><span class="sig-name descname"><span class="pre">setDefaultValues</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="pre">contrast</span></em><span class="sig-paren">)</span><a class="headerlink" href="#API.projectClass.domainContrastsClass.setDefaultValues" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set non-empty default values when adding a contrast.</p>
-</dd></dl>
-
 <dl class="mat method">
 <dt class="sig sig-object mat" id="API.projectClass.domainContrastsClass.toStruct">
 <span class="sig-name descname"><span class="pre">toStruct</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="pre">allowedNames</span></em>, <em class="sig-param"><span class="pre">~</span></em>, <em class="sig-param"><span class="pre">~</span></em><span class="sig-paren">)</span><a class="headerlink" href="#API.projectClass.domainContrastsClass.toStruct" title="Permalink to this definition">¶</a></dt>

diff --git a/master/controlClass.html → dev/controlClass.html b/master/controlClass.html → dev/controlClass.html
diff --git a/master/controlsInfo.html → dev/controlsInfo.html b/master/controlsInfo.html → dev/controlsInfo.html