Improves documentation and few bug fixes

ISISNeutronMuon · May 14, 2020 · 8b85115 · 8b85115
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diff --git a/docs/_images/align_sample.png b/docs/_images/align_sample.png
diff --git a/docs/_images/aligned_sample.png b/docs/_images/aligned_sample.png
diff --git a/docs/_images/area_tool.png b/docs/_images/area_tool.png
diff --git a/docs/_images/graphics_grid.png b/docs/_images/graphics_grid.png
diff --git a/docs/_images/graphics_help.png b/docs/_images/graphics_help.png
diff --git a/docs/_images/graphics_plane.png b/docs/_images/graphics_plane.png
diff --git a/docs/_images/graphics_plane_custom.png b/docs/_images/graphics_plane_custom.png
diff --git a/docs/_images/graphics_point_mgr.png b/docs/_images/graphics_point_mgr.png
diff --git a/docs/_images/graphics_select_area.png b/docs/_images/graphics_select_area.png
diff --git a/docs/_images/graphics_select_line.png b/docs/_images/graphics_select_line.png
diff --git a/docs/_images/insert_fiducial.png b/docs/_images/insert_fiducial.png
diff --git a/docs/_images/insert_measurement.png b/docs/_images/insert_measurement.png
diff --git a/docs/_images/insert_sample.png b/docs/_images/insert_sample.png
diff --git a/docs/_images/insert_vector.png b/docs/_images/insert_vector.png
diff --git a/docs/_images/line_tool.png b/docs/_images/line_tool.png
diff --git a/docs/_images/open_existing.png b/docs/_images/open_existing.png
diff --git a/docs/_images/plane_alignment.png b/docs/_images/plane_alignment.png
diff --git a/docs/_images/point_from_graphics.png b/docs/_images/point_from_graphics.png
diff --git a/docs/_images/preferences.png b/docs/_images/preferences.png
diff --git a/docs/_images/question.png b/docs/_images/question.png
diff --git a/docs/_images/refresh.png b/docs/_images/refresh.png
diff --git a/docs/_images/run_sim.png b/docs/_images/run_sim.png
diff --git a/docs/_images/script.png b/docs/_images/script.png
diff --git a/docs/_images/start.png b/docs/_images/start.png
diff --git a/docs/_images/steps.jpg b/docs/_images/steps.jpg
diff --git a/docs/_images/transform_sample.png b/docs/_images/transform_sample.png
diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: '',
-    VERSION: '1.0.0-beta',
+    VERSION: '1.0.0-rc',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',

diff --git a/docs/add_fiducials.html b/docs/add_fiducials.html
@@ -4,7 +4,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Insert Fiducial Points &#8212; SScanSS 2 1.0.0-beta documentation</title>
+    <title>Insert Fiducial Points &#8212; SScanSS 2 1.0.0-rc documentation</title>
     <link rel="stylesheet" href="_static/bootstrap-sphinx.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="_static/style.css" type="text/css" />
@@ -15,6 +15,8 @@
     <link rel="shortcut icon" href="_static/favicon.ico"/>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
+    <link rel="next" title="Insert Measurement Points" href="add_measurements.html" />
+    <link rel="prev" title="Transform Sample" href="transform_sample.html" />
 <meta charset='utf-8'>
 <meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
 <meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
@@ -37,7 +39,7 @@
         </button>
         <a class="navbar-brand" href="index.html">
           SScanSS 2</a>
-        <span class="navbar-text navbar-version pull-left"><b>1.0.0-beta</b></span>
+        <span class="navbar-text navbar-version pull-left"><b>1.0.0-rc</b></span>
       </div>
 
         <div class="collapse navbar-collapse nav-collapse">
@@ -56,7 +58,13 @@
      href="index.html">Site <b class="caret"></b></a>
   <ul class="dropdown-menu globaltoc"
       role="menu"
-      aria-labelledby="dLabelGlobalToc"></ul>
+      aria-labelledby="dLabelGlobalToc"><ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="api.html">Developer guide</a></li>
+<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="guides.html">User guide</a></li>
+</ul>
+</ul>
 </li>
 
                 <li class="dropdown">

diff --git a/docs/add_measurements.html b/docs/add_measurements.html
diff --git a/docs/add_sample.html b/docs/add_sample.html
@@ -4,7 +4,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Insert Sample &#8212; SScanSS 2 1.0.0-beta documentation</title>
+    <title>Insert Sample &#8212; SScanSS 2 1.0.0-rc documentation</title>
     <link rel="stylesheet" href="_static/bootstrap-sphinx.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="_static/style.css" type="text/css" />
@@ -15,6 +15,8 @@
     <link rel="shortcut icon" href="_static/favicon.ico"/>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
+    <link rel="next" title="Transform Sample" href="transform_sample.html" />
+    <link rel="prev" title="Scene Management" href="scene.html" />
 <meta charset='utf-8'>
 <meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
 <meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
@@ -37,7 +39,7 @@
         </button>
         <a class="navbar-brand" href="index.html">
           SScanSS 2</a>
-        <span class="navbar-text navbar-version pull-left"><b>1.0.0-beta</b></span>
+        <span class="navbar-text navbar-version pull-left"><b>1.0.0-rc</b></span>
       </div>
 
         <div class="collapse navbar-collapse nav-collapse">
@@ -56,7 +58,13 @@
      href="index.html">Site <b class="caret"></b></a>
   <ul class="dropdown-menu globaltoc"
       role="menu"
-      aria-labelledby="dLabelGlobalToc"></ul>
+      aria-labelledby="dLabelGlobalToc"><ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="api.html">Developer guide</a></li>
+<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="guides.html">User guide</a></li>
+</ul>
+</ul>
 </li>
 
                 <li class="dropdown">

diff --git a/docs/add_vectors.html b/docs/add_vectors.html
@@ -4,7 +4,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Insert Measurement Vectors &#8212; SScanSS 2 1.0.0-beta documentation</title>
+    <title>Insert Measurement Vectors &#8212; SScanSS 2 1.0.0-rc documentation</title>
     <link rel="stylesheet" href="_static/bootstrap-sphinx.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="_static/style.css" type="text/css" />
@@ -15,6 +15,8 @@
     <link rel="shortcut icon" href="_static/favicon.ico"/>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
+    <link rel="next" title="Instrument Configuration" href="configure_instrument.html" />
+    <link rel="prev" title="Insert Measurement Points" href="add_measurements.html" />
 <meta charset='utf-8'>
 <meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
 <meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
@@ -37,7 +39,7 @@
         </button>
         <a class="navbar-brand" href="index.html">
           SScanSS 2</a>
-        <span class="navbar-text navbar-version pull-left"><b>1.0.0-beta</b></span>
+        <span class="navbar-text navbar-version pull-left"><b>1.0.0-rc</b></span>
       </div>
 
         <div class="collapse navbar-collapse nav-collapse">
@@ -56,7 +58,13 @@
      href="index.html">Site <b class="caret"></b></a>
   <ul class="dropdown-menu globaltoc"
       role="menu"
-      aria-labelledby="dLabelGlobalToc"></ul>
+      aria-labelledby="dLabelGlobalToc"><ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="api.html">Developer guide</a></li>
+<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="guides.html">User guide</a></li>
+</ul>
+</ul>
 </li>
 
                 <li class="dropdown">

diff --git a/docs/align_sample.html b/docs/align_sample.html
@@ -4,7 +4,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Align Sample on Instrument &#8212; SScanSS 2 1.0.0-beta documentation</title>
+    <title>Align Sample on Instrument &#8212; SScanSS 2 1.0.0-rc documentation</title>
     <link rel="stylesheet" href="_static/bootstrap-sphinx.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="_static/style.css" type="text/css" />
@@ -15,6 +15,8 @@
     <link rel="shortcut icon" href="_static/favicon.ico"/>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
+    <link rel="next" title="Simulating Experiments" href="simulation.html" />
+    <link rel="prev" title="Instrument Configuration" href="configure_instrument.html" />
 <meta charset='utf-8'>
 <meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
 <meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
@@ -37,7 +39,7 @@
         </button>
         <a class="navbar-brand" href="index.html">
           SScanSS 2</a>
-        <span class="navbar-text navbar-version pull-left"><b>1.0.0-beta</b></span>
+        <span class="navbar-text navbar-version pull-left"><b>1.0.0-rc</b></span>
       </div>
 
         <div class="collapse navbar-collapse nav-collapse">
@@ -56,7 +58,13 @@
      href="index.html">Site <b class="caret"></b></a>
   <ul class="dropdown-menu globaltoc"
       role="menu"
-      aria-labelledby="dLabelGlobalToc"></ul>
+      aria-labelledby="dLabelGlobalToc"><ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="api.html">Developer guide</a></li>
+<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="guides.html">User guide</a></li>
+</ul>
+</ul>
 </li>
 
                 <li class="dropdown">

diff --git a/docs/api.html b/docs/api.html
@@ -4,7 +4,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Developer guide &#8212; SScanSS 2 1.0.0-beta documentation</title>
+    <title>Developer guide &#8212; SScanSS 2 1.0.0-rc documentation</title>
     <link rel="stylesheet" href="_static/bootstrap-sphinx.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="_static/style.css" type="text/css" />
@@ -15,6 +15,8 @@
     <link rel="shortcut icon" href="_static/favicon.ico"/>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
+    <link rel="next" title="Instrument Description File (IDF)" href="idf.html" />
+    <link rel="prev" title="Introduction" href="introduction.html" />
 <meta charset='utf-8'>
 <meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
 <meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
@@ -37,7 +39,7 @@
         </button>
         <a class="navbar-brand" href="index.html">
           SScanSS 2</a>
-        <span class="navbar-text navbar-version pull-left"><b>1.0.0-beta</b></span>
+        <span class="navbar-text navbar-version pull-left"><b>1.0.0-rc</b></span>
       </div>
 
         <div class="collapse navbar-collapse nav-collapse">
@@ -56,7 +58,13 @@
      href="index.html">Site <b class="caret"></b></a>
   <ul class="dropdown-menu globaltoc"
       role="menu"
-      aria-labelledby="dLabelGlobalToc"></ul>
+      aria-labelledby="dLabelGlobalToc"><ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Developer guide</a></li>
+<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
+<li class="toctree-l1"><a class="reference internal" href="guides.html">User guide</a></li>
+</ul>
+</ul>
 </li>
 
                 <li class="dropdown">

diff --git a/docs/configure_instrument.html b/docs/configure_instrument.html
@@ -4,7 +4,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Instrument Configuration &#8212; SScanSS 2 1.0.0-beta documentation</title>
+    <title>Instrument Configuration &#8212; SScanSS 2 1.0.0-rc documentation</title>
     <link rel="stylesheet" href="_static/bootstrap-sphinx.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="_static/style.css" type="text/css" />
@@ -15,6 +15,8 @@
     <link rel="shortcut icon" href="_static/favicon.ico"/>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
+    <link rel="next" title="Align Sample on Instrument" href="align_sample.html" />
+    <link rel="prev" title="Insert Measurement Vectors" href="add_vectors.html" />
 <meta charset='utf-8'>
 <meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
 <meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
@@ -37,7 +39,7 @@
         </button>
         <a class="navbar-brand" href="index.html">
           SScanSS 2</a>
-        <span class="navbar-text navbar-version pull-left"><b>1.0.0-beta</b></span>
+        <span class="navbar-text navbar-version pull-left"><b>1.0.0-rc</b></span>
       </div>
 
         <div class="collapse navbar-collapse nav-collapse">
@@ -56,7 +58,13 @@
      href="index.html">Site <b class="caret"></b></a>
   <ul class="dropdown-menu globaltoc"
       role="menu"
-      aria-labelledby="dLabelGlobalToc"></ul>
+      aria-labelledby="dLabelGlobalToc"><ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="api.html">Developer guide</a></li>
+<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="guides.html">User guide</a></li>
+</ul>
+</ul>
 </li>
 
                 <li class="dropdown">