Add regex filter

.config/dotnet-tools.json

@@ -7,6 +7,12 @@
       "commands": [
         "docfx"
       ]
+    },
+    "doclinkchecker": {
+      "version": "1.19.0",
+      "commands": [
+        "DocLinkChecker"
+      ]
     }
   }
 }

.github/workflows/DocLinkChecker.config

@@ -0,0 +1,29 @@
+{
+  "DocumentationFiles": {
+    "src": ".",
+    "Files": [
+      "**/*.md",
+      "*.md"
+    ],
+    "Exclude": [
+      "_site/*",
+      ".bonsai/*",
+      "src/*"
+    ]
+  },
+  "ResourceFolderNames": [
+  ],
+  "DocLinkChecker": {
+    "RelativeLinkStrategy": "All",
+    "CheckForOrphanedResources": true,
+    "CleanupOrphanedResources": false,
+    "ValidatePipeTableFormatting": true,
+    "ValidateExternalLinks": true,
+    "ConcurrencyLevel": 5,
+    "MaxHttpRedirects": 20,
+    "ExternalLinkDurationWarning": 3000,
+    "WhitelistUrls": [
+      "http://localhost"
+    ]
+  }
+}

.github/workflows/build.yml

@@ -2,10 +2,10 @@
 name: Build docs
 
 on:
-  workflow_dispatch:
   push:
-    branches:
-      main
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
 
 jobs:
   build:
@@ -15,12 +15,19 @@ jobs:
         uses: actions/[email protected]
         with:
           submodules: true
-    
+
       - name: Setup .NET Core SDK
         uses: actions/[email protected]
         with:
           dotnet-version: 8.x
 
+      - name: Install DocLinkChecker
+        run: dotnet tool install DocLinkChecker
+
+      # Check for missing / broken links in the *.md files prior to building the website
+      - name: Check Documentation Links
+        run: dotnet DocLinkChecker -v -f .github/workflows/DocLinkChecker.config
+
       - name: Setup DocFX
         run: dotnet tool restore
 
@@ -29,17 +36,56 @@ jobs:
         run: .\Setup.ps1
 
       - name: Build Documentation
-        run: .\build.ps1
-
+        run: .\build.ps1 --logLevel Warning --warningsAsErrors
+
+      - name: Upload Artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: _site
+          path: _site
+          if-no-files-found: error
+
+  check:
+    name: Check Links
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Download Artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: _site
+          path: _site
+
+      # This checks for missing / broken links in the *.html files after building the website.
+      # We need to run this step here to check that all auto-generated API pages have valid links too.
+      - name: Check HTML Links After Building
+        uses: lycheeverse/[email protected]
+        with:
+          args: --verbose --no-progress --base _site --exclude ^https://github\.com.*merge.* --exclude ^https://github\.com.*apiSpec.* '_site/**/*.html'
+          fail: true
+
+  deploy:
+    name: Deploy docs to gh-pages
+    runs-on: ubuntu-latest
+    needs: [ build, check ]
+    if: github.event_name == 'push'
+    steps:
+      - name: Download Artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: _site
+          path: _site
+
       - name: Checkout gh-pages
         uses: actions/[email protected]
         with:
           ref: gh-pages
           path: gh-pages
 
       - name: Publish to github pages
-        uses: peaceiris/actions-gh-pages@v3.9.3
+        uses: peaceiris/actions-gh-pages@v4.0.0
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: _site
           force_orphan: true
+

apidoc/OpenEphys.Onix.ConfigureBreakoutBoard.md

@@ -1,5 +1,5 @@
 ---
-uid: OpenEphys.Onix.ConfigureBreakoutBoard
+uid: OpenEphys.Onix1.ConfigureBreakoutBoard
 ---
 
 [!INCLUDE [Hub Template](hub_template.md)]

apidoc/OpenEphys.Onix.ConfigureHeadstage64.md

@@ -1,5 +1,5 @@
 ---
-uid: OpenEphys.Onix.ConfigureHeadstage64
+uid: OpenEphys.Onix1.ConfigureHeadstage64
 ---
 
 [!INCLUDE [Hub Template](hub_template.md)]

apidoc/OpenEphys.Onix.ConfigureNeuropixelsV1eHeadstage.md

@@ -1,5 +1,5 @@
 ---
-uid: OpenEphys.Onix.ConfigureNeuropixelsV1eHeadstage
+uid: OpenEphys.Onix1.ConfigureNeuropixelsV1eHeadstage
 ---
 
 [!INCLUDE [Hub Template](hub_template.md)]

apidoc/OpenEphys.Onix.ConfigureNeuropixelsV2eBetaHeadstage.md

@@ -1,5 +1,5 @@
 ---
-uid: OpenEphys.Onix.ConfigureNeuropixelsV2eBetaHeadstage
+uid: OpenEphys.Onix1.ConfigureNeuropixelsV2eBetaHeadstage
 ---
 
 [!INCLUDE [Hub Template](hub_template.md)]

apidoc/OpenEphys.Onix.ConfigureNeuropixelsV2eHeadstage.md

@@ -1,5 +1,5 @@
 ---
-uid: OpenEphys.Onix.ConfigureNeuropixelsV2eHeadstage
+uid: OpenEphys.Onix1.ConfigureNeuropixelsV2eHeadstage
 ---
 
 [!INCLUDE [Hub Template](hub_template.md)]

articles/getting-started/initialize_oni_context.md

@@ -3,22 +3,22 @@ uid: InitializeOniContext
 title: Initialize the ONI Context
 ---
 
-The [`CreateContext`](xref:OpenEphys.Onix.CreateContext) operator initializes the acquisition context, and it should be the first node you add to your workflow as it provides access to the hardware device table for all other configuration operators. There are several different ways to find this node and add it to the workflow:
+The [`CreateContext`](xref:OpenEphys.Onix1.CreateContext) operator initializes the acquisition context, and it should be the first node you add to your workflow as it provides access to the hardware device table for all other configuration operators. There are several different ways to find this node and add it to the workflow:
 
 1. From the Bonsai editor, navigate to the toolbox on the left side of the screen and expand the **Source** section. Next, expand the **OpenEphys.Onix** section, and find the `CreateContext` line. The node can then be added by either double-clicking it, or dragging and dropping the node into the workflow.
 
-    ![Search for CreateContext node manually](~/images/bonsai-editor-place-create-context-manually.png){width=700px}
+    ![Search for CreateContext node manually](../../images/bonsai-editor-place-create-context-manually.png){width=700px}
 
 2. Click on the textbox at the top of the toolbox on the left, or from Ctrl + E to focus on the textbox, and type `CreateContext` to search for the node. Same as (1), the node can be placed by double-clicking or dragging and dropping; additionally, if the `CreateContext` string is highlighted Enter can be pressed to place the node immediately.
 
-    ![Search for CreateContext node from textbox](~/images/bonsai-editor-place-create-context-search.png){width=700px}
+    ![Search for CreateContext node from textbox](../../images/bonsai-editor-place-create-context-search.png){width=700px}
 
-3. Hover over the image of the [`CreateContext`](xref:OpenEphys.Onix.CreateContext) workflow below, and click on the clipboard icon in the top-right corner of the workflow image to copy the workflow to the clipboard. Navigate back to Bonsai, and paste the copied workflow into the active editor. Pasting can be done via Ctrl + V, or right-clicking in the editor and choosing **Paste**.
+3. Hover over the image of the [`CreateContext`](xref:OpenEphys.Onix1.CreateContext) workflow below, and click on the clipboard icon in the top-right corner of the workflow image to copy the workflow to the clipboard. Navigate back to Bonsai, and paste the copied workflow into the active editor. Pasting can be done via Ctrl + V, or right-clicking in the editor and choosing **Paste**.
 
 ## CreateContext Workflow
 
-This is a nominally functional workflow that provides access to the ONI context, from which all nodes can then be linked to and configured, while also demonstrating how a Breakout Board can be configured before finishing the configuration chain by placing a [`StartAcquisition`](xref:OpenEphys.Onix.StartAcquisition) node:
+This is a nominally functional workflow that provides access to the ONI context, from which all nodes can then be linked to and configured, while also demonstrating how a Breakout Board can be configured before finishing the configuration chain by placing a [`StartAcquisition`](xref:OpenEphys.Onix1.StartAcquisition) node:
 
 :::workflow 
-![CreateContext](~/workflows/operators/ConfigureBreakoutBoard.bonsai)
+![CreateContext](../../workflows/operators/ConfigureBreakoutBoard.bonsai)
 :::

articles/getting-started/next_steps.md

@@ -5,6 +5,6 @@ title: Next Steps
 
 Continue browsing <xref:GettingStarted> and check out specific nodes on the left to see how to configure each node, as well as some ways to visualize data. Each page will have a fully functional workflow that can be copied into Bonsai to provide an easy starting point for generating data.
 
-For more technical information on each node, head to the <xref:OpenEphys.Onix> to see a more developer-focused view of each node.
+For more technical information on each node, head to the <xref:OpenEphys.Onix1> to see a more developer-focused view of each node.
 
 More complex and in-depth tutorials for placing multiple nodes and moving towards generating data in an experimental setting can be found in the <xref:TutorialsLandingPage>.

articles/getting-started/node_types.md

@@ -7,8 +7,8 @@ In Bonsai, all objects are called "nodes", and have a specific function associat
 
 | Node Type | Description | Example ONIX nodes |
 | --------- | ----------- | ------------------ |
-| Source    | Generate event streams from devices or files | [`CreateContext`](xref:OpenEphys.Onix.CreateContext), [`Bno055Data`](xref:OpenEphys.Onix.Bno055Data), [`NeuropixelsV1eData`](xref:OpenEphys.Onix.NeuropixelsV1eData) |
-| Sink      | Save data or trigger external outputs | [`ConfigureHeadstage64`](xref:OpenEphys.Onix.ConfigureHeadstage64), [`ConfigureNeuropixelsV1eHeadstage`](xref:OpenEphys.Onix.ConfigureNeuropixelsV1eHeadstage) |
-| Combinator | Manage control flow or synchronize parallel inputs | [`StartAcquisition`](xref:OpenEphys.Onix.StartAcquisition) |
+| Source    | Generate event streams from devices or files | [`CreateContext`](xref:OpenEphys.Onix1.CreateContext), [`Bno055Data`](xref:OpenEphys.Onix1.Bno055Data), [`NeuropixelsV1eData`](xref:OpenEphys.Onix1.NeuropixelsV1eData) |
+| Sink      | Save data or trigger external outputs | [`ConfigureHeadstage64`](xref:OpenEphys.Onix1.ConfigureHeadstage64), [`ConfigureNeuropixelsV1eHeadstage`](xref:OpenEphys.Onix1.ConfigureNeuropixelsV1eHeadstage) |
+| Combinator | Manage control flow or synchronize parallel inputs | [`StartAcquisition`](xref:OpenEphys.Onix1.StartAcquisition) |
 
 Nodes are placed in the Bonsai editor and can be saved into a "workflow", which is a grouping of nodes and saved settings. This workflow can then be run to perform some task, depending on what nodes are placed.

articles/getting-started/tips_and_tricks.md

@@ -11,7 +11,7 @@ The order of nodes is also important for which actions can be taken. In the tabl
 
 | Goal | Clicks / Keystrokes | Description |
 | ---- | ------------------- | ----------- |
-| Link two nodes | Click and hold the first node, drag the cursor to the second node, and release | While dragging the cursor, it will temporarily change to a red symbol until there is a valid target (e.g., the second node), where it will change to an up arrow | 
+| Link two nodes | Click and hold the first node, drag the cursor to the second node, and release | While dragging the cursor, it will temporarily change to a red symbol until there is a valid target (e.g., the second node), where it will change to an up arrow |
 | Link two nodes | Right-click the first node, and select **Create Connection**. Select the second node | While moving the cursor, it will change to an up arrow. A valid node target will change color when hovering over it |
 | Link two nodes on placement | Click on a node in the editor to select it, then place a node using either method (1) or (2) above | If a node is currently selected in the editor when a new node is added, whether it is added by clicking and dragging, double-clicking, or pressing **Enter**, the newly placed node will be connected to the first node automatically |
 | Unlink two nodes | Click the first node to select it, hold **Shift**, click and hold the first node, drag to the second node, and release | While dragging the cursor, it will temporarily change to a red symbol until there is a valid target (e.g., the second node), where it will change to an up arrow |
@@ -20,7 +20,7 @@ The order of nodes is also important for which actions can be taken. In the tabl
 | Change order of nodes in a row | Hold **Ctrl**, click and hold the first node, drag to the right to the second node, and release | This action does not require that the node be selected prior to performing the action. This can change the order of any two nodes that are a part of the same row; it is not constrained to adjacent nodes. Note that if the new placement of the nodes is not valid (such as giving a `Source` node an input), it will knock the node of the current row and remove any connections |
 
 > [!Note]
-> In the context of `OpenEphys.Onix`, almost all workflows should have the top row containing a [`CreateContext`](xref:OpenEphys.Onix.CreateContext) node connected to an arbitrary number of `Configure*` nodes, finished with a [`StartAcquisition`](xref:OpenEphys.Onix.StartAcquisition) node. Subsequent rows can contain the corresponding `*Data` nodes configured above, and any processing / visualizing nodes needed.
+> In the context of `OpenEphys.Onix1`, almost all workflows should have the top row containing a [`CreateContext`](xref:OpenEphys.Onix1.CreateContext) node connected to an arbitrary number of `Configure*` nodes, finished with a [`StartAcquisition`](xref:OpenEphys.Onix1.StartAcquisition) node. Subsequent rows can contain the corresponding `*Data` nodes configured above, and any processing / visualizing nodes needed.
 
 <br>
 
@@ -29,6 +29,6 @@ The order of nodes is also important for which actions can be taken. In the tabl
 Some nodes, specifically many of the `Configure*` nodes, can have a GUI attached to the node that allows for easy manipulation of **Configuration** properties in a graphical environment. These GUIs can be accessed by double-clicking on a node; if there is a GUI assigned to it, then it will be opened up in a new window. Please note that not all nodes have GUIs, but if you think that a node would benefit from having this functionality added please reach out to us.
 
 > [!Note]
-> GUIs are not part of the base `OpenEphys.Onix` library. To take advantage of this added functionality, you must install the accompanying `OpenEphys.Onix.Design` library using the Bonsai package manager.
+> GUIs are not part of the base `OpenEphys.Onix1` library. To take advantage of this added functionality, you must install the accompanying `OpenEphys.Onix1.Design` library using the Bonsai package manager.
 
-A number of Bonsai nodes also come shipped with GUIs, but similar to `OpenEphys.Onix`, the corresponding `*.Design` library must be installed before it can be leveraged.
+A number of Bonsai nodes also come shipped with GUIs, but similar to `OpenEphys.Onix1`, the corresponding `*.Design` library must be installed before it can be leveraged.

articles/hubs/breakoutboard.md

@@ -4,7 +4,7 @@ title: BreakoutBoard
 isGuide: true
 isHeadstage: true
 headstage: BreakoutBoard
-devices: [ { id: MemoryMonitor, file: device-memorymonitor }, { id: Heartbeat, file: device-heartbeat }, { id: DigitalIO, file: device-digitalio } , { id: AnalogIO, file: device-analogio } ]
+devices: [ { id: MemoryMonitor, file: ~/articles/devices/memorymonitor }, { id: Heartbeat, file: ~/articles/devices/heartbeat }, { id: DigitalIO, file: ~/articles/devices/breakoutdigitalio } , { id: AnalogIO, file: ~/articles/devices/breakoutanalogio } ]
 workflow: true
 workflow_file: ~/workflows/hubs/BreakoutBoard.bonsai
 ---

articles/hubs/headstage64.md

@@ -4,7 +4,7 @@ title: Headstage64
 isGuide: true
 isHeadstage: true
 headstage: Headstage64
-devices: [ { id: TS4231, file: device-ts4231 }, { id: RHD2164, file: device-rhd2164 }, { id: BNO055, file: device-bno055 } ]
+devices: [ { id: TS4231, file: ~/articles/devices/ts4231 }, { id: RHD2164, file: ~/articles/devices/rhd2164 }, { id: BNO055, file: ~/articles/devices/bno055 } ]
 workflow: true
 workflow_file: ~/workflows/hubs/Headstage64.bonsai
 ---

articles/hubs/neuropixelsv1e.md

@@ -4,7 +4,7 @@ title: NeuropixelsV1eHeadstage
 isGuide: true
 isHeadstage: true
 headstage: NeuropixelsV1e
-devices: [ { id: NeuropixelsV1e, file: device-neuropixelsv1e }, { id: BNO055, file: device-bno055_neuropixelsv1e } ]
+devices: [ { id: NeuropixelsV1e, file: ~/articles/devices/neuropixelsv1e }, { id: BNO055, file: ~/articles/devices/bno055_neuropixelsv1e } ]
 workflow: true
 workflow_file: ~/workflows/hubs/NeuropixelsV1e.bonsai
 ---

articles/hubs/neuropixelsv2e.md

@@ -4,7 +4,7 @@ title: NeuropixelsV2eHeadstage
 isGuide: true
 isHeadstage: true
 headstage: NeuropixelsV2e
-devices: [ { id: NeuropixelsV2e, file: device-neuropixelsv2e }, { id: BNO055, file: device-bno055_neuropixelsv2e } ]
+devices: [ { id: NeuropixelsV2e, file: ~/articles/devices/neuropixelsv2e }, { id: BNO055, file: ~/articles/devices/bno055_neuropixelsv2e } ]
 workflow: true
 workflow_file: ~/workflows/hubs/NeuropixelsV2e.bonsai
 ---

articles/hubs/neuropixelsv2ebeta.md

@@ -4,7 +4,7 @@ title: NeuropixelsV2eBetaHeadstage
 isGuide: true
 isHeadstage: true
 headstage: NeuropixelsV2eBeta
-devices: [ { id: NeuropixelsV2eBeta, file: device-neuropixelsv2ebeta }, { id: BNO055, file: device-bno055_neuropixelsv2e } ]
+devices: [ { id: NeuropixelsV2eBeta, file: ~/articles/devices/neuropixelsv2ebeta }, { id: BNO055, file: ~/articles/devices/bno055_neuropixelsv2e } ]
 workflow: true
 workflow_file: ~/workflows/hubs/NeuropixelsV2eBeta.bonsai
 ---

build.ps1

@@ -3,6 +3,6 @@ $libPath = ".\src\onix-bonsai-onix1\"
 dotnet build $libPath --configuration Release
 
 # Export workflow vectors
-$libPath = Join-Path $libPath "artifacts\bin\OpenEphys.Onix\release"
+$libPath = Join-Path $libPath "artifacts\bin\OpenEphys.Onix1\release"
 .\docfx-tools\modules\Export-Image.ps1 -bootstrapperPath .\.bonsai\Bonsai.exe $libPath
 dotnet docfx @args

filter.yml

@@ -12,11 +12,7 @@ apiRules:
       uidRegex: OpenEphys.Onix.DeviceContext
 - exclude:
       uidRegex: ^.*DeviceFactory
-- exclude:
-      uidRegex: ^.*DataFrame
-- exclude:
-      type: Enum      
 - exclude:
       uidRegex: OpenEphys.Onix.ConfigureFmcLinkController
 - exclude:
-      uidRegex: OpenEphys.Onix.ConfigureDS90UB9x
+      uidRegex: OpenEphys.Onix.ConfigureDS90UB9x

index.md

@@ -24,9 +24,9 @@ Other major advantages include:
 
 <div class="quick-links">
 
-| <xref:GettingStarted> | <xref:OpenEphys.Onix> | <xref:TutorialsLandingPage> |
-|:--------------:|:-------------------:|:---------:|:---:|
-| [![User Guide](images/macbook.svg){width=200}](xref:GettingStarted) | [![Operator Guide](images/books.svg){width=200}](xref:OpenEphys.Onix) | [![Tutorials](images/running.svg){width=200}](xref:TutorialsLandingPage) |
-| [New to Bonsai or <br>OpenEphys.Onix? Start here!](xref:GettingStarted) | [Operator references here](xref:OpenEphys.Onix) | [Check out our tutorials <br>for useful workflows](xref:TutorialsLandingPage) |
+| <xref:GettingStarted> | <xref:OpenEphys.Onix1> | <xref:TutorialsLandingPage> |
+|:--------------:|:-------------------:|:---------:|
+| [![User Guide](images/macbook.svg){width=200}](xref:GettingStarted) | [![Operator Guide](images/books.svg){width=200}](xref:OpenEphys.Onix1) | [![Tutorials](images/running.svg){width=200}](xref:TutorialsLandingPage) |
+| [New to Bonsai or <br>OpenEphys.Onix? Start here!](xref:GettingStarted) | [Operator references here](xref:OpenEphys.Onix1) | [Check out our tutorials <br>for useful workflows](xref:TutorialsLandingPage) |
 
 </div>

template/conceptual.html.primary.tmpl

@@ -31,8 +31,8 @@
 {{>partials/device.visualize_text}}
 {{/visualize_text}}
 
-<p>Refer to <a class="xref" href="getting_started-visualizing_data.html">Visualizing Data</a> for more information on visualizers and how to download them.</p>
-<p>Note that data will not be shown until a workflow is running. Check out <a class="xref" href="getting_started-running_a_workflow.html">Running a Workflow</a> to see how to run a workflow.</p>
+<p>Refer to <a class="xref" href="~/articles/getting-started/visualizing_data.html">Visualizing Data</a> for more information on visualizers and how to download them.</p>
+<p>Note that data will not be shown until a workflow is running. Check out <a class="xref" href="~/articles/getting-started/running_a_workflow.html">Running a Workflow</a> to see how to run a workflow.</p>
 
 {{/visualize}}
 {{/isGuide}}