Move hardware tutorial under user guide (#58)

* Move hardware tutorial under user guide - This change implements breakout tutorial only - This provides scaffolding for other hardware tutorials Co-authored-by: bparks13 <bap@open-ephys.org> Co-authored-by: jonnew <jpn@open-ephys.org>
open-ephys · Sep 25, 2024 · 5e1dca5 · 5e1dca5
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diff --git a/README.md b/README.md
@@ -75,7 +75,7 @@ git submodule update --recursive --remote
 The following three commands are run remotely by remote GitHub Actions serve upon pushing to a branch. The branch will not be able to merge to main unless all three commands complete successfully without any errors. Confirm that they can complete successfully without errors locally before committing and pushing. Otherwise, the branch becomes cluttered with potentially several attempts to pass the link-check process. Run: 
 
 ``` console
-.\build.ps1 --logLevel Warning --warningsAsErrors
+.\build.ps1 --logLevel Suggestion --warningsAsErrors
 dotnet DocLinkChecker -v -f .github/workflows/DocLinkChecker.config
 ```
 

diff --git a/articles/devices/bno055-neuropixelsv1e.md b/articles/devices/bno055-neuropixelsv1e.md
diff --git a/articles/devices/bno055-neuropixelsv2e.md b/articles/devices/bno055-neuropixelsv2e.md
diff --git a/articles/devices/bno055.md b/articles/devices/bno055.md
diff --git a/articles/devices/breakoutanalogio.md b/articles/devices/breakoutanalogio.md
diff --git a/articles/devices/breakoutdigitalio.md b/articles/devices/breakoutdigitalio.md
diff --git a/articles/devices/electricalstimulator.md b/articles/devices/electricalstimulator.md
diff --git a/articles/devices/heartbeat.md b/articles/devices/heartbeat.md
diff --git a/articles/devices/memorymonitor.md b/articles/devices/memorymonitor.md
diff --git a/articles/devices/neuropixelsv1e.md b/articles/devices/neuropixelsv1e.md
diff --git a/articles/devices/neuropixelsv2e.md b/articles/devices/neuropixelsv2e.md
diff --git a/articles/devices/neuropixelsv2ebeta.md b/articles/devices/neuropixelsv2ebeta.md
diff --git a/articles/devices/opticalstimulator.md b/articles/devices/opticalstimulator.md
diff --git a/articles/devices/rhd2164.md b/articles/devices/rhd2164.md
diff --git a/articles/devices/ts4231.md b/articles/devices/ts4231.md
diff --git a/articles/getting-started/bonsai-usage.md b/articles/getting-started/bonsai-usage.md
@@ -1,5 +1,5 @@
 ---
-uid: BonsaiUsage
+uid: bonsai-usage
 title: Bonsai Usage
 ---
 

diff --git a/articles/getting-started/getting-started.md b/articles/getting-started/getting-started.md
diff --git a/articles/getting-started/index.md b/articles/getting-started/index.md
@@ -0,0 +1,15 @@
+---
+uid: getting-started
+title: Getting Started
+---
+
+Welcome to the user guide! The next few pages are dedicated to users who are unfamiliar with ONIX
+and Bonsai, and will teach them what ONIX is, how to download and install Bonsai, open a new file,
+place operators (and understand what an operator is), reorder a workflow, run a workflow, and
+finally visualize data.
+
+For those who are already familiar with Bonsai and are looking for a particular device or headstage
+to learn more about the hardware and how to utilize it, the table of contents on the left contains
+entries for each available device and headstage. Choose a page to learn more about the hardware and
+view a fully complete workflow that can be copied directly into Bonsai to aid in quickly setting up
+and collecting data from a system.
diff --git a/articles/getting-started/initialize-oni-context.md b/articles/getting-started/initialize-oni-context.md
@@ -1,5 +1,5 @@
 ---
-uid: InitializeOniContext
+uid: initialize-onicontext
 title: Initialize the ONI Context
 ---
 

diff --git a/articles/getting-started/install-configure-bonsai.md b/articles/getting-started/install-configure-bonsai.md
@@ -1,5 +1,5 @@
 ---
-uid: BonsaiInstallationAndConfiguration
+uid: install-configure-bonsai
 title: Bonsai Installation and Configuration
 ---
 
@@ -29,6 +29,30 @@ The following packages required to run the workflows in this documentation are:
 > [!TIP]
 > Additional packages will allow you to extend the functionality of ONIX hardware beyond the scope of this documentation. There are packages that allow ONIX be combined with [visual psychophysics](https://bonsai-rx.org/docs/tutorials/vision-psychophysics.html), [markerless pose estimation](https://bonsai-rx.org/sleap/), [HARP behavioral devices](https://harp-tech.org/), and much more.
 
+### OpenEphys.Onix1
+
+To install the `OpenEphys.Onix1` package [open the package manager](#open-bonsai-package-manager) and:
+
+1.  Click the `Browse` tab.
+1.  Set `Package source` to `All` or `NuGet`.
+1.  Search `OpenEphys.Onix1`.
+1.  Click `Install`.
+1.  Click `I Accept` when the license agreement window appears.
+
+![Bonsai OpenEphys.Onix1 Install Screenshot](../../images/bonsai-install-OpenEphys.Onix1.webp){width=650px}
+
+### OpenEphys.Onix1.Design
+
+To install the `OpenEphys.Onix1.Design` package [open the package manager](#open-bonsai-package-manager) and:
+
+1.  Click the `Browse` tab.
+1.  Set `Package source` to `All` or `NuGet`.
+1.  Search `OpenEphys.Onix1.Design`.
+1.  Click `Install`.
+1.  Click `I Accept` when the license agreement window appears.
+
+![Bonsai OpenEphys.Onix1.Design Install Screenshot](../../images/bonsai-install-OpenEphys.Onix1.Design.webp){width=650px}
+
 ### Bonsai.StarterPack
 
 To install the `Bonsai.StarterPack` package [open the package manager](#open-bonsai-package-manager) and:
@@ -51,18 +75,6 @@ To install the `OpenEphys.Commutator` package [open the package manager](#open-b
 
 ![Bonsai OpenEphys.Commutator Install Screenshot](../../images/bonsai-install-OpenEphys.Commutator.webp){width=650px}
 
-### OpenEphys.Onix1.Design
-
-To install the `OpenEphys.Onix1.Design` package [open the package manager](#open-bonsai-package-manager) and:
-
-1.  Click the `Browse` tab.
-1.  Set `Package source` to `All` or `NuGet`.
-1.  Search `OpenEphys.Onix1.Design`.
-1.  Click `Install`.
-1.  Click `I Accept` when the license agreement window appears.
-
-![Bonsai OpenEphys.Onix1.Design Install Screenshot](../../images/bonsai-install-OpenEphys.Onix1.Design.webp){width=650px}
-
 ## Update Packages in Bonsai
 
 It is good practice to periodically check for package updates. To do this, [open the package manager](#open-bonsai-package-manager) and:
@@ -90,4 +102,4 @@ Sometimes it is helpful to uninstall packages. [Open the package manager](#open-
 
 ## Next Steps
 
-Now that Bonsai has been installed and configured, it is time to start constructing a workflow to capture data from your ONIX system. The following sections give a high-level understanding of how Bonsai is organized, and some of the ONIX-specific concepts that will be useful for learning how to work with the operators. If you are familiar with Bonsai, you might want to skip to the <xref:headstages-index> section.
+Now that Bonsai has been installed and configured, it is time to start constructing a workflow to capture data from your ONIX system. The following sections give a high-level understanding of how Bonsai is organized, and some of the ONIX-specific concepts that will be useful for learning how to work with the operators. If you are familiar with Bonsai, you might want to skip to the <xref:tutorials> section.
diff --git a/articles/getting-started/next-steps.md b/articles/getting-started/next-steps.md
@@ -1,10 +1,10 @@
 ---
-uid: NextSteps
+uid: next-steps
 title: Next Steps
 ---
 
-Continue browsing <xref:GettingStarted> and check out specific operators on the left to see how to configure each operator, 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.
+Continue browsing <xref:getting-started> and check out specific operators on the left to see how to configure each operator, 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 operator, head to the <xref:OpenEphys.Onix1> to see a more developer-focused view of each operator.
 
-More complex and in-depth tutorials for placing multiple operators and moving towards generating data in an experimental setting can be found in the <xref:TutorialsLandingPage>.
+More complex and in-depth tutorials for placing multiple operators and moving towards generating data in an experimental setting can be found in the <xref:tutorials>.
diff --git a/articles/getting-started/node-types.md → articles/getting-started/operator-types.md b/articles/getting-started/node-types.md → articles/getting-started/operator-types.md
@@ -1,5 +1,5 @@
 ---
-uid: OperatorTypes
+uid: operator-types
 title: Operator Types
 ---
 

diff --git a/articles/getting-started/property-categories.md b/articles/getting-started/property-categories.md
@@ -1,10 +1,12 @@
 ---
-uid: PropertyCategories
+uid: property-categories
 title: Property Categories
 ---
 
 There are specific categories of properties that define when an operator's properties can be modified. 
 
 `Configuration` properties only have effect when a workflow is started and are used to initialize the hardware state. If they are changed while a workflow is running they will have no effect.
 
-`Acquisition` properties can be manipulated when the workflow is running and will have an immediate effect on hardware. For instance stimulus waveform parameters can be modified in real-time and sent to the device multiple times while the workflow is running to shape stimulation patterns.
+`Acquisition` properties can be manipulated when the workflow is running and will have an immediate effect on hardware. For instance stimulus waveform parameters can be modified in real-time and sent to the device multiple times while the workflow is running to shape stimulation patterns.
+
+`Devices` properties refer to the individual devices available within a particular aggregate operator. Aggregate operators include <xref:OpenEphys.Onix1.ConfigureHeadstage64>, <xref:OpenEphys.Onix1.ConfigureBreakoutBoard>, and more. Explore other available options under the [aggregate configuration operators](xref:configure) page.
diff --git a/articles/getting-started/start-workflow.md b/articles/getting-started/start-workflow.md
@@ -1,6 +1,6 @@
 ---
-uid: StartAWorkflow
-title: Start a Workflow
+uid: start-workflow
+title: Start Workflow
 ---
 
 Once all operators have been placed and linked correctly, and all **Configuration** properties have been set, it is now possible to run a workflow. Note that some aspects of Bonsai are only available in specific contexts; for instance, the GUIs mentioned above can only be opened when a workflow is not running. Once a workflow is running, these GUIs are not accessible, but visualizers for certain operators can be opened to view the streaming data.

diff --git a/articles/getting-started/tips-tricks.md b/articles/getting-started/tips-tricks.md
@@ -1,13 +1,13 @@
 ---
-uid: TipsAndTricks
+uid: tips-and-tricks
 title: Tips and Tricks
 ---
 
 ## Bonsai Operator Actions
 
 When running a workflow in Bonsai, operators are evaluated from left to right, and top to bottom. In a workflow, each node represents an operator defining an sequence of values. Nodes can be connected to other nodes, from left to right. Each connection indicates that the downstream operator on the right subscribes, or "listens", to the notifications of the upstream operator on the left. The table below provides some useful information to effectively use the workflow editor. It provides information on how to add connections between operators, remove connections, reordering operators horizontally and vertically, as well as some shortcuts to aid in placing operators more efficiently.
 
-Aside from determining the order of exceution, the order of operators within a workflow determines which editing actions can be taken. In the table below, the "first" operator is always the one that is on the left side, or on the bottom for multiple rows of operators. If the first operator clicked is on the right side, or on the top, these actions will not work.
+Aside from determining the order of execution, the order of operators within a workflow determines which editing actions can be taken. In the table below, the "first" operator is always the one that is on the left side, or on the bottom for multiple rows of operators. If the first operator clicked is on the right side, or on the top, these actions will not work.
 
 | Goal | Clicks / Keystrokes | Description |
 | ---- | ------------------- | ----------- |

diff --git a/articles/getting-started/visualizing-data.md → articles/getting-started/visualize-data.md b/articles/getting-started/visualizing-data.md → articles/getting-started/visualize-data.md
@@ -1,6 +1,6 @@
 ---
-uid: VisualizingData
-title: Visualizing Data
+uid: visualize-data
+title: Visualize Data
 ---
 
 To visualize data from any `*Data` operator, typically the variable that needs to be visualized must first be output from the operator. To do this, right-click on any `*Data` operator and select the first option; this will be something similar to `Output (OpenEphys.Onix1.*DataFrame)`. From the drop-down list, select the corresponding data variable to be visualized. Doing so will create a new operator in the workflow.