Docs 0.9 (#1038)

* Add obvious impropers to OPLS-AA. * Clear messages and update status bar when regenerating configuration. * Correctly set empty combo box if no pointer set. * Rename function, add getter, mark overrides. * Actually update values. * Return the correct value. * Remove unused includes. * Update shortcodes. * Create legacy examples section. * Update shortcodes and overhaul current examples. * Update team. * Update cli options. * Remove simulationblock page. * Remove refs to heartbeat and state files. * Update SCARF info. * Sort targets vs control keywords. * Fix examples main page, update warn shortcode. * Fix module link. * Fix entity. * Add gui-node shortcode. * Remove static img dir. * Copy images on web build, use only svg in shortcodes. * Update module link. * Update silica example. * Reinstate deleted web-only content in img/, copy in GUI svgs in CI. * Bump Hugo to v0.98. * Update module mixin. * Generalise optional gui-button shortcode icons. * Generalise gui-tab shortcode. * Update suggested example times. * Fix keyword argument types, fix typos, add dangle-focussed calculate module docs and update keyword descriptions in source files. * Update benzene example. * Update DM contributors. * Update run information. * Update calculation modules. * Update roadmap.
disorderedmaterials · May 24, 2022 · e200a59 · e200a59
1 parent b8b80a1
commit e200a59
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diff --git a/.azure-pipelines/templates/build-web.yml b/.azure-pipelines/templates/build-web.yml
@@ -3,7 +3,7 @@ parameters:
     default: false
     type: boolean
   - name: hugo_version
-    default: '0.79.0'
+    default: '0.98.0'
   - name: web_dir_root
     default: 'github.com/disorderedmaterials/dissolve/edit/develop/web'
   - name: last_hash_url
@@ -20,6 +20,10 @@ steps:
       wget https://github.com/gohugoio/hugo/releases/download/v${{ parameters.hugo_version }}/hugo_extended_${{ parameters.hugo_version }}_Linux-64bit.deb -O '$(Pipeline.Workspace)/hugo.deb'
       sudo dpkg -i $(Pipeline.Workspace)/hugo*.deb
     displayName: 'Download & Install Hugo (Extended Version)'
+  - bash: |
+      set -ex
+      cp -v src/gui/icons/*.svg web/static/img
+    displayName: 'Copy Icons'
   - bash: |
       set -ex
       cd web

diff --git a/src/modules/calculate_angle/angle.cpp b/src/modules/calculate_angle/angle.cpp
@@ -142,17 +142,17 @@ CalculateAngleModule::CalculateAngleModule() : Module("CalculateAngle"), analyse
     keywords_.addTarget<ConfigurationKeyword>("Configuration", "Set target configuration for the module", targetConfiguration_);
 
     // Control
-    keywords_.add<Vec3DoubleKeyword>("Control", "RangeAB", "Range (min, max, binwidth) of A-B distance axis", rangeAB_,
+    keywords_.add<Vec3DoubleKeyword>("Control", "RangeAB", "Range (min, max, binwidth) of A-B distance binning", rangeAB_,
                                      Vec3<double>(0.0, 0.0, 1.0e-5), std::nullopt, Vec3Labels::MinMaxBinwidthlabels);
-    keywords_.add<Vec3DoubleKeyword>("Control", "RangeBC", "Range (min, max, binwidth) of B-C distance axis", rangeBC_,
+    keywords_.add<Vec3DoubleKeyword>("Control", "RangeBC", "Range (min, max, binwidth) of B-C distance binning", rangeBC_,
                                      Vec3<double>(0.0, 0.0, 1.0e-5), std::nullopt, Vec3Labels::MinMaxBinwidthlabels);
-    keywords_.add<Vec3DoubleKeyword>("Control", "AngleRange", "Range (min, max, binwidth) of angle axis", angleRange_,
+    keywords_.add<Vec3DoubleKeyword>("Control", "AngleRange", "Range (min, max, binwidth) of angle binning", angleRange_,
                                      Vec3<double>(0.0, 0.0, 1.0e-5), std::nullopt, Vec3Labels::MinMaxBinwidthlabels);
-    keywords_.add<SpeciesSiteVectorKeyword>("Control", "SiteA", "Add site(s) which represent 'A' in the interaction A-B-C",
+    keywords_.add<SpeciesSiteVectorKeyword>("Control", "SiteA", "Specify site(s) which represent 'A' in the interaction A-B-C",
                                             selectA_->speciesSites(), selectA_->axesRequired());
-    keywords_.add<SpeciesSiteVectorKeyword>("Control", "SiteB", "Add site(s) which represent 'B' in the interaction A-B-C",
+    keywords_.add<SpeciesSiteVectorKeyword>("Control", "SiteB", "Specify site(s) which represent 'B' in the interaction A-B-C",
                                             selectB_->speciesSites(), selectB_->axesRequired());
-    keywords_.add<SpeciesSiteVectorKeyword>("Control", "SiteC", "Add site(s) which represent 'C' in the interaction A-B-C",
+    keywords_.add<SpeciesSiteVectorKeyword>("Control", "SiteC", "Specify site(s) which represent 'C' in the interaction A-B-C",
                                             selectC_->speciesSites(), selectC_->axesRequired());
     keywords_.add<BoolKeyword>("Control", "ExcludeSameMoleculeAB",
                                "Whether to exclude correlations between A and B sites on the same molecule",

diff --git a/src/modules/calculate_axisangle/axisangle.cpp b/src/modules/calculate_axisangle/axisangle.cpp
@@ -102,15 +102,18 @@ CalculateAxisAngleModule::CalculateAxisAngleModule() : Module("CalculateAxisAngl
     keywords_.addTarget<ConfigurationKeyword>("Configuration", "Set target configuration for the module", targetConfiguration_);
 
     // Control
-    keywords_.add<Vec3DoubleKeyword>("Control", "DistanceRange", "Range (min, max, binwidth) of distance axis", distanceRange_,
+    keywords_.add<Vec3DoubleKeyword>("Control", "DistanceRange", "Range (min, max, binwidth) of distance binning",
+                                     distanceRange_, Vec3<double>(0.0, 0.0, 1.0e-5), std::nullopt,
+                                     Vec3Labels::MinMaxBinwidthlabels);
+    keywords_.add<Vec3DoubleKeyword>("Control", "AngleRange", "Range (min, max, binwidth) of angle binning", angleRange_,
                                      Vec3<double>(0.0, 0.0, 1.0e-5), std::nullopt, Vec3Labels::MinMaxBinwidthlabels);
-    keywords_.add<Vec3DoubleKeyword>("Control", "AngleRange", "Range (min, max, binwidth) of angle axis", angleRange_,
-                                     Vec3<double>(0.0, 0.0, 1.0e-5), std::nullopt, Vec3Labels::MinMaxBinwidthlabels);
-    keywords_.add<SpeciesSiteVectorKeyword>("Control", "SiteA", "Add site(s) which represent 'A' in the interaction A-B...C",
+    keywords_.add<SpeciesSiteVectorKeyword>("Control", "SiteA",
+                                            "Specify site(s) which represent 'A' in the interaction A-B...C",
                                             selectA_->speciesSites(), selectA_->axesRequired());
     keywords_.add<EnumOptionsKeyword<OrientedSite::SiteAxis>>("Control", "AxisA", "Axis to use from site A",
                                                               calculateAxisAngle_->axis(0), OrientedSite::siteAxis());
-    keywords_.add<SpeciesSiteVectorKeyword>("Control", "SiteB", "Add site(s) which represent 'B' in the interaction A-B...C",
+    keywords_.add<SpeciesSiteVectorKeyword>("Control", "SiteB",
+                                            "Specify site(s) which represent 'B' in the interaction A-B...C",
                                             selectB_->speciesSites(), selectB_->axesRequired());
     keywords_.add<EnumOptionsKeyword<OrientedSite::SiteAxis>>("Control", "AxisB", "Axis to use from site B",
                                                               calculateAxisAngle_->axis(1), OrientedSite::siteAxis());

diff --git a/src/modules/calculate_dangle/dangle.cpp b/src/modules/calculate_dangle/dangle.cpp
@@ -103,9 +103,10 @@ CalculateDAngleModule::CalculateDAngleModule() : Module("CalculateDAngle"), anal
     keywords_.addTarget<ConfigurationKeyword>("Configuration", "Set target configuration for the module", targetConfiguration_);
 
     // Control
-    keywords_.add<Vec3DoubleKeyword>("Control", "DistanceRange", "Range (min, max, binwidth) of distance axis", distanceRange_,
-                                     Vec3<double>(0.0, 0.0, 1.0e-5), std::nullopt, Vec3Labels::MinMaxBinwidthlabels);
-    keywords_.add<Vec3DoubleKeyword>("Control", "AngleRange", "Range (min, max, binwidth) of angle axis", angleRange_,
+    keywords_.add<Vec3DoubleKeyword>("Control", "DistanceRange", "Range (min, max, binwidth) of distance binning",
+                                     distanceRange_, Vec3<double>(0.0, 0.0, 1.0e-5), std::nullopt,
+                                     Vec3Labels::MinMaxBinwidthlabels);
+    keywords_.add<Vec3DoubleKeyword>("Control", "AngleRange", "Range (min, max, binwidth) of angle binning", angleRange_,
                                      Vec3<double>(0.0, 0.0, 1.0e-5), std::nullopt, Vec3Labels::MinMaxBinwidthlabels);
     keywords_.add<SpeciesSiteVectorKeyword>("Control", "SiteA", "Add site(s) which represent 'A' in the interaction A-B...C",
                                             selectA_->speciesSites(), selectA_->axesRequired());

diff --git a/web/.gitignore b/web/.gitignore
@@ -1,4 +1,6 @@
 # Git ignore file for dissolve-web/
 public/*
 resources/*
+static/img/*.svg
+static/img/*.png
 hugo
diff --git a/web/assets/scss/_content.scss b/web/assets/scss/_content.scss
@@ -1,4 +1,7 @@
-// Navbar
+/*
+ * Navbar
+ */
+
 .td-navbar .navbar-brand {
     svg {
         margin: 5px 10px;
@@ -10,7 +13,10 @@
   background-color: #17132a;
 }
 
-// Labels
+/*
+ * Labels
+ */
+
 .label {
     border-radius: 5px;
     display: inline-block;
@@ -50,8 +56,140 @@
     padding: 1px 10px 1px 10px;
 }
 
-// Left-aligned button
-.btn.left { 
+/*
+ * GUI Element Indicators
+ */
+
+// Tab
+.gui-tab {
+   border-radius: 2px;
+   border: 1px solid #aebfcd;
+   background-color: #eeefed;
+   padding: 1px 10px 1px 30px;
+   font-size: 85%;
+   margin: 5px 0 5px 0;
+   position: relative;
+   line-height: 1.0;
+}
+
+.gui-tab::before {
+  content: '';
+  width: 15px;
+  height: 15px;
+  left: 7px;
+  top: 1px;
+  position: absolute;
+  background-repeat: no-repeat;
+  background-size: 18px;
+}
+
+.gui-tab::after {
+  content: '';
+}
+
+// Button
+.gui-button {
+   display: inline-block;
+   border-radius: 5px;
+   border: 1px solid #aebfcd;
+   background-color: #edefed;
+   padding: 3px 25px 1px 25px;
+   font-size: 85%;
+   font-weight: bold;
+   position: relative;
+   margin: 2px 0 2px 0;
+   line-height: 1.0;
+}
+
+.gui-button::before {
+  content: ' ';
+  width: 15px;
+  height: 15px;
+  left: 7px;
+  top: 0px;
+  position: absolute;
+  background-repeat: no-repeat;
+  background-size: 17px;
+}
+
+.gui-button::after {
+  content: '';
+}
+
+// Module
+.gui-module {
+   padding: 0px 0px 0px 1.2em;
+   position: relative;
+}
+
+.gui-module::before {
+  content: '';
+  width: 1.1em;
+  height: 1.1em;
+  left: 0px;
+  top: 0px;
+  position: absolute;
+  background-repeat: no-repeat;
+  background-size: 1.1em;
+}
+
+.gui-module::after {
+  content: '';
+}
+
+@mixin gui-module($module) {
+  .gui-module.gui-module-#{$module}::before{
+       background-image: url(/img/modules_#{$module}.svg);
+  }
+}
+@mixin generate-gui-module(){
+   @each $module in $modules{
+     @include gui-module($module);
+   }
+}
+$modules: ("accumulate", "analyse", "atomshake", "benchmark", "bragg", "calculateangle", "calculateavgmol", "calculateaxisangle", "calculatecn", "calculatedangle", "calculaterdf", "calculatesdf", "calibrate", "checkspecies", "checks", "datatest", "energy", "epsr", "exportcoordinates", "exportpairpotentials", "exporttrajectory", "forces", "geometryoptimisation", "importtrajectory", "intrashake", "md", "molshake", "neutronsq", "rdf", "sq", "xraysq");
+@include generate-gui-module();
+
+// Node
+.gui-node {
+   padding: 0px 0px 0px 1.2em;
+   position: relative;
+}
+
+.gui-node::before {
+  content: '';
+  width: 1.1em;
+  height: 1.1em;
+  left: 0px;
+  top: 0px;
+  position: absolute;
+  background-repeat: no-repeat;
+  background-size: 1.1em;
+}
+
+.gui-node::after {
+  content: '';
+}
+
+@mixin gui-node($node) {
+  .gui-node.gui-node-#{$node}::before{
+       background-image: url(/img/nodes_#{$node}.svg);
+  }
+}
+@mixin generate-gui-node(){
+   @each $node in $nodes{
+     @include gui-node($node);
+   }
+}
+$nodes: ("add", "aliases", "box", "calculateangle", "calculateaxisangle", "calculatebase", "calculatedistance", "calculatevector", "collect1d", "collect2d", "collect3d", "context", "coordinatesets", "cylindricalregion", "dynamicsite", "fit1d", "generalregion", "integrate1d", "node", "nodereference", "nodes", "operatebase", "operatedivide", "operateexpression", "operategridnormalise", "operatemultiply", "operatenormalise", "operatenumberdensitynormalise", "operatesitepopulationnormalise", "operatesphericalshellnormalise", "parameters", "pickbase", "pick", "pickproximity", "pickregion", "process1d", "process2d", "process3d", "regionbase", "remove", "select", "sequence", "sum1d", "transmute");
+@include generate-gui-node();
+
+/*
+ * Buttons
+ */
+
+// Left-aligned navigation button
+.btn.left {
     border-radius: 5px;
     width: inherit;
     margin: 5px auto 5px 0;
@@ -60,7 +198,7 @@
     padding: auto;
 }
 
-// Right-aligned button
+// Right-aligned navigation button
 .btn.right {
     border-radius: 5px;
     width: inherit;
@@ -87,7 +225,7 @@ blockquote {
   padding-top: 15px;
   padding-bottom: 1px;
   padding-right: 10px;
-  border-left: 8px solid #ddd ;
+  border-left: 8px solid #ddd;
   line-height: 1.6;
   position: relative;
   background: #f9f9f9;
@@ -124,23 +262,23 @@ blockquote.tip {
   border-left: 8px solid #78C0A8;
 }
 blockquote.tip::before {
-  background-image: url(/img/blocktip.svg);
+  background-image: url(/img/block_tip.svg);
 }
 
 // Warning
 blockquote.warn {
   border-left: 8px solid #fb9a49;
 }
 blockquote.warn::before {
-  background-image: url(/img/blockwarn.svg);
+  background-image: url(/img/block_warn.svg);
 }
 
 // Question
 blockquote.question {
   border-left: 8px solid #329819;
 }
 blockquote.question::before {
-  background-image: url(/img/blockquestion.svg);
+  background-image: url(/img/block_question.svg);
 }
 
 // Action (Quote-style)
@@ -152,25 +290,22 @@ blockquote.actionquote {
 blockquote.action {
   width: 85%;
   margin-bottom: 10px;
-  line-height: 1.0;
   border-left: 8px solid #478cc6;
 }
 blockquote.iconaction {
   width: 85%;
   margin-bottom: 10px;
-  line-height: 1.0;
   border-left: 8px solid #6947c6;
 }
 blockquote.step {
   width: 85%;
   margin-bottom: 10px;
-  line-height: 1.0;
   border-left: 16px solid #aebfcd;
 }
 blockquote.step::before {
   left: 5px;
   top: 10px;
-  background-image: url(/img/action-general.svg);
+  background-image: url(/img/action_general.svg);
 }
 
 // Action (Dissolve)
@@ -179,21 +314,21 @@ blockquote.action-menu {
   border-left: 8px solid #478cc6;
 }
 blockquote.action-dissolve::before {
-  background-image: url(/img/action-dissolve.png);
+  background-image: url(/img/action_dissolve.svg);
 }
 
 // Action (Tabs)
 blockquote.action-tabs::before {
   left: 8px;
   top: 8px;
-  background-image: url(/img/action-tabs.svg);
+  background-image: url(/img/action_tabs.svg);
 }
 
 // Action (Groups)
 blockquote.action-groups::before {
   left: 8px;
   top: 8px;
-  background-image: url(/img/action-groups.svg);
+  background-image: url(/img/action_groups.svg);
 }
 
 // Action (Menu)
@@ -202,14 +337,14 @@ blockquote.action-menu {
 }
 blockquote.action-menu::before {
   left: 8px;
-  background-image: url(/img/action-menu.svg);
+  background-image: url(/img/action_menu.svg);
 }
 
 // Action (Mouse)
 blockquote.action-mouse::before {
   left: 10px;
   top: 8px;
-  background-image: url(/img/action-mouse.svg);
+  background-image: url(/img/action_mouse.svg);
 }
 
 // Action (Key)
@@ -219,19 +354,19 @@ blockquote.action-key {
 blockquote.action-key::before {
   left: 10px;
   top: 8px;
-  background-image: url(/img/action-key.svg);
+  background-image: url(/img/action_key.svg);
 }
 
 // Action (Edit)
 blockquote.action-edit::before {
-  background-image: url(/img/action-edit.svg);
+  background-image: url(/img/action_edit.svg);
 }
 
 // Action (Settings)
 blockquote.action-settings {
 }
 blockquote.action-settings::before {
-  background-image: url(/img/action-settings.svg);
+  background-image: url(/img/action_settings.svg);
 }
 
 // Tables