Organize TOC

api/configure.md

@@ -3,4 +3,7 @@ uid: configure
 title: Configuration Operators
 ---
 
-Device configuration operators belong in a top-level chain of operators between [`CreateContext`](xref:OpenEphys.Onix1.CreateContext) and [`StartAcquisition`](xref:OpenEphys.Onix1.StartAcquisition) to configure devices contained by ONIX hardware hubs.
+Aggregate configuration operators belong in a top-level chain of operators between
+[`CreateContext`](xref:OpenEphys.Onix1.CreateContext) and [`StartAcquisition`](xref:OpenEphys.Onix1.StartAcquisition) to
+configure ONIX hardware hubs. These are known as aggregate configuration operators because they configure an aggregation
+of devices (also referred to as a hub) on a given headstage, miniscope, breakout board, etc..

api/constants.md

@@ -0,0 +1,6 @@
+---
+uid: constants
+title: Constants
+---
+
+These constants are used throughout the <xref:OpenEphys.Onix1> Bonsai package to assign names to numbered values.

api/data-elements.md

@@ -0,0 +1,6 @@
+---
+uid: data-elements
+title: Data Elements
+---
+
+Data elements are produced by <xref:OpenEphys.Onix1> Bonsai operators.

api/device-configure.md

@@ -3,7 +3,7 @@ uid: device-configure
 title: Device Configuration Operators
 ---
 
-> [!IMPORTANT]
+> [!TIP]
 >  Device configuration operators are not recommended for using off-the-shelf Open Ephys hardware. Use aggregate [configuration operators](xref:configure) instead. Aggregate [configuration operators](xref:configure) confer the following benefits:
 > - The `address` and `name` properties of aggregate configuration operators undergo automatic configuration which reduces the risk of erroneous configuration.
 > - The workflow is less cluttered with configuration operators as one aggregate configuration operator corresponds to multiple device operators. This improves workflow legibility and expedites the workflow scripting process.

api/overview.md

@@ -0,0 +1,9 @@
+---
+uid: OpenEphys.Onix1
+title: OpenEphys.Onix1
+---
+
+`OpenEphys.Onix1` is a Bonsai package containing interfaces for data acquisition and control of ONIX hardware. This section
+of the docs is dedicated to facilitate construction of workflows using the OpenEphys.Onix1 package.
+
+In Bonsai, press <kbd>F1</kbd> while an OpenEphys.Onix1 node is selected in the workflow editor to quickly open this reference.

docfx.json

@@ -3,9 +3,7 @@
     {
       "src": [
         {
-          "files": [
-            "src/**.csproj"
-          ]
+          "files": ["src/**.csproj"]
         }
       ],
       "dest": "api",
@@ -19,35 +17,20 @@
         "index.md": "landing"
       }
     },
-    "content": [
-      "articles/**.{md,yml}",
-      "api/**.{md,yml}",
-      "toc.yml",
-      "index.md"
-    ],
-    "resource": [
-          "logo.svg",
-          "favicon.png",
-          "images/**",
-          "workflows/**"
+    "content": [ 
+      {
+        "files": ["articles/**.{md,yml}", "api/**.{md,yml}", "toc.yml", "index.md"],
+        "exclude": ["api/overview.md"]
+      }
     ],
+    "resource": ["logo.svg", "favicon.png", "images/**", "workflows/**"],
     "output": "_site",
     "overwrite": [
       {
-        "files": [
-        ],
-        "exclude": [
-          "obj/**",
-          "_site/**"
-        ]
+        "files": ["api/overview.md"]
       }
     ],
-    "template": [
-      "default",
-      "modern",
-      "template",
-      "docfx-tools/template"
-    ],
+    "template": ["default", "modern", "template", "docfx-tools/template"],
     "globalMetadata": {
       "_enableNewTab": true,
       "_enableSearch": true,
@@ -77,4 +60,4 @@
   "rules": {
     "InvalidBookmark": "suggestion"
   }
-}
+}

template/ManagedReference.html.primary.tmpl

@@ -8,4 +8,14 @@
 
 {{#isEnum}}
   {{>partials/enum}}
-{{/isEnum}}
+{{/isEnum}}
+
+{{#isNamespace}}
+  <div>
+    <h1 data-uid="{{{uid}}}" class="text-break">
+      {{{title}}}
+      <a class="header-action link-secondary" title="View source" href="https://github.com/open-ephys/bonsai-onix1/tree/main/OpenEphys.Onix1"><i class="bi bi-code-slash"></i></a>
+    </h1>
+  </div>
+  {{{conceptual}}}
+{{/isNamespace}}

template/partials/class.tmpl.partial

@@ -1,11 +1,8 @@
 {{#oe.operator.configureDevice}}
-  <div class="CAUTION alert alert-danger">
-    <h5>Caution</h5>
+  <div class="Important alert alert-info">
+    <h5>TIP</h5>
     <p>
-      This is a device configuration operator. Device configuration operators are not recommended for interfacing with off-the-shelf ONIX hardware. Use <a class="xref" href="configure.html">aggregate configuration operators</a> to do that instead.
-    </p>
-    <p>
-      To understand the benefits of <a class="xref" href="configure.html">aggregate configuration operators</a>, refer to the <a class="xref" href="device-configure.html">device configuration operators</a> page.
+      This is a device configuration operator. <a class="xref" href="configure.html">Aggregate configuration operators</a> are recommended in lieu of <a class="xref" href="device-configure.html">device configuration operators</a> for interfacing with Open Ephys Onix hardware.
     </p>
   </div>
 {{/oe.operator.configureDevice}}

template/toc.extension.js

@@ -8,84 +8,98 @@ exports.preTransform = function (model) {
   if (model.items[0].name === 'OpenEphys.Onix1'){
     if (model.items[0].items){
       itemsItemsLength = model.items[0].items.length;
-      let items = [{
-        'name': 'Core Operators',
-        'href' : 'core.html',
-        'topicHref': 'core.html',
-        'topicUid': 'core',
-        'items': []}, {
-        'name': 'Configuration Operators',
-        'href' : 'configure.html',
-        'topicHref': 'configure.html',
-        'topicUid': 'configure',
-        'items': []}, {
-        'name': 'Data I/O Operators',
-        'href' : 'dataio.html',
-        'topicHref': 'dataio.html',
-        'topicUid': 'dataio',
-        'items': []}, {
-        'name': 'Other',
-        'items': [
+      let items = [
+        {
+          'name': 'Core Operators',
+          'href' : 'core.html',
+          'topicHref': 'core.html',
+          'topicUid': 'core',
+          'items': []
+        }, 
+        {
+          'name': 'Configuration Operators',
+          'href' : 'configure.html',
+          'topicHref': 'configure.html',
+          'topicUid': 'configure',
+          'items': []
+        }, 
+        {
+          'name': 'Data I/O Operators',
+          'href' : 'dataio.html',
+          'topicHref': 'dataio.html',
+          'topicUid': 'dataio',
+          'items': []
+        }, 
+        {
+          'name': 'Data Elements',
+          'href' : 'data-elements.html',
+          'topicHref': 'data-elements.html',
+          'topicUid': 'data-elements',
+          'items': []
+        }, 
+        {
+          'name': 'Other',
+          'topicUid': 'other',
+          'items': 
+          [
+            {
+              'name': 'Device Configuration Operators',
+              'href' : 'device-configure.html',
+              'topicHref': 'device-configure.html',
+              'topicUid': 'device-configure',
+              'items': []
+            },
+            {
+              'name': 'Constants',
+              'href' : 'constants.html',
+              'topicHref': 'constants.html',
+              'topicUid': 'constants',
+              'items': []
+            }
+          ]
+        }
+      ];
+      for (let i = 0; i < itemsItemsLength; i++) 
+      {
+        globalYml = '~/api/' + model.items[0].items[i].topicUid + '.yml';
+        globalModel = model.__global._shared[globalYml];
+        if (globalModel?.type === 'class' || globalModel?.type === 'struct')
+        {
+          if (model.items[0].items[i].name.includes('CreateContext') || model.items[0].items[i].name.includes('StartAcquisition'))
           {
-            'name': 'Device Configuration Operators',
-            'href' : 'device-configure.html',
-            'topicHref': 'device-configure.html',
-            'topicUid': 'device-configure',
-            'items': [],
+            items[0].items.push(model.items[0].items[i]);
           }
-        ]
-      }];
-      for (let i = 0; i < itemsItemsLength; i++) {
-        globalYml = '~/api/' + model.items[0].items[i].topicUid + '.yml';
-        if (model.items[0].items[i].name.includes('Frame') || 
-            model.items[0].items[i].name.includes('DeviceFactory') ||
-            model.items[0].items[i].name.includes('ContextTask') ||
-            model.items[0].items[i].name.includes('DeviceNameConverter') ||
-            model.items[0].items[i].name.includes('ConfigureDS90UB9x') ||
-            model.items[0].items[i].name.includes('ConfigureFmcLinkController') ||
-            model.items[0].items[i].name.includes('DeviceContext') ||
-            model.items[0].items[i].name.includes('NeuropixelsV2QuadShankElectrode') ||
-            model.items[0].items[i].name.includes('NeuropixelsV2QuadShankProbeConfiguration') ||
-            model.items[0].items[i].name.includes('NeuropixelsV1eAdc')){
-          model.items[0].items[i].hide = true;
-        }
-        else if (model.__global._shared[globalYml] && model.__global._shared[globalYml].type === 'enum') {
-          model.items[0].items[i].hide = true;
-        }
-        else {
-          if (model.__global._shared[globalYml] && model.__global._shared[globalYml].type === 'class'){
-            const inheritanceLength = model.__global._shared[globalYml].inheritance.length;
-            device = false;
-            hub = false;
-            for (let j = 0; j < inheritanceLength; j++){
-              if (model.__global._shared[globalYml].inheritance[j].uid === 'OpenEphys.Onix1.SingleDeviceFactory'){
-                device = true;
-              }
-              else if (model.__global._shared[globalYml].inheritance[j].uid === 'OpenEphys.Onix1.MultiDeviceFactory'){
-                hub = true;
-              }
-            }
-            if (model.items[0].items[i].name.includes('CreateContext') || model.items[0].items[i].name.includes('StartAcquisition')){
-              items[0].items.push(model.items[0].items[i]);
-            }
-            else if (device){
-              items[3].items[0].items.push(model.items[0].items[i]);
-            }
-            else if (hub){
-              items[1].items.push(model.items[0].items[i]);
-            }
-            else {
-              items[2].items.push(model.items[0].items[i]);
-            }
+          else if (globalModel?.inheritance.some(inherited => inherited.uid === 'OpenEphys.Onix1.MultiDeviceFactory'))
+          {
+            items[1].items.push(model.items[0].items[i]);
           }
+          else if (globalModel?.inheritance.some(inherited => inherited.uid === 'OpenEphys.Onix1.SingleDeviceFactory'))
+          {
+            items[4].items[0].items.push(model.items[0].items[i]);
+          }
+          else if ((globalModel.syntax?.content[0].value.includes('ElementCategory.Source') || 
+          globalModel.syntax?.content[0].value.includes('ElementCategory.Sink') ||
+          globalModel?.inheritance.some(inherited => inherited.uid.includes('Bonsai.Source')) ||
+          globalModel?.inheritance.some(inherited => inherited.uid.includes('Bonsai.Sink'))) &&
+          !globalModel.syntax?.content[0].value.includes('abstract'))
+          {
+            items[2].items.push(model.items[0].items[i]);
+          }
+          else if (model.items[0].items[i].name.includes('ContextTask') || 
+          model.items[0].items[i].name.includes('OutputClockParameters') ||
+          globalModel?.inheritance.some(inherited => inherited.uid === 'OpenEphys.Onix1.DataFrame' || inherited.uid === 'OpenEphys.Onix1.BufferedDataFrame'))
+          {
+            items[3].items.push(model.items[0].items[i]);
+          }
+        }
+        else if (globalModel && globalModel.type === 'enum') 
+        {
+          items[4].items[1].items.push(model.items[0].items[i]);
         }
       }
       model.items[0].items = items;
     }
   }
-  // if (model.items[1].name === 'OpenEphys.Onix1.Design'){
-  //   model.items.splice(1, 1);
-  // }
   return model;
 }