Merge branch 'main' into issue-121-socket

To merge-in the submodule pointer which fixes broken refs

Author: cjsha

.gitmodules

@@ -1,6 +1,6 @@
 [submodule "docfx-tools"]
 	path = docfx-tools
 	url = https://github.com/bonsai-rx/docfx-tools
-[submodule "src/onix-bonsai-onix1"]
-	path = src/onix-bonsai-onix1
-	url = https://github.com/open-ephys/onix-bonsai-onix1.git
+[submodule "src/bonsai-onix1"]
+	path = src/bonsai-onix1
+	url = https://github.com/open-ephys/bonsai-onix1.git

README.md

@@ -3,7 +3,7 @@
 
 # Onix1 Bonsai Docs
 
-Documentation for the [Onix1 Bonsai package](https://github.com/open-ephys/onix-bonsai-onix1).
+Documentation for the [Onix1 Bonsai package](https://github.com/open-ephys/bonsai-onix1).
 
 These docs are built using [docfx](https://dotnet.github.io/docfx/index.html).
 

articles/getting-started/install-configure-bonsai.md

@@ -38,9 +38,10 @@ The Bonsai package manager can be accessed from Bonsai's landing window or its w
 
 The following packages are required to run the workflows in this documentation are:
 
+* `OpenEphys.Onix1.Design`: An extension of the `OpenEphys.Onix1` library that includes graphical user interfaces (GUIs). Installing OpenEphys.Onix1.Design automatically installs `OpenEphys.Onix1` as a dependency.
 * `Bonsai.StarterPack`: the "standard library" for Bonsai that contains tools that are used in almost every workflow.
-* `OpenEphys.Commutator`: Bonsai package for controlling Open Ephys commutators.
-* `OpenEphys.Onix1.Design`: An extension of the `OpenEphys.Onix1` library that includes graphical user interfaces (GUIs).
+* `OpenEphys.Commutator`: for controlling Open Ephys commutators.
+* `OpenEphys.Sockets.Bonsai`: for establishing TCP Sockets (to stream data to the Open Ephys GUI, for example).
 
 > [!TIP]
 > Additional packages will allow you to extend the functionality of ONIX hardware beyond the scope
@@ -49,43 +50,16 @@ The following packages are required to run the workflows in this documentation a
 > estimation](https://bonsai-rx.org/sleap/), [HARP behavioral devices](https://harp-tech.org/), and
 > much more.
 
-#### OpenEphys.Onix1.Design
-
-To install the `OpenEphys.Onix1.Design` package, open the package manager and:
+To install packages, open the package manager and:
 
 1.  Click the `Browse` tab.
-1.  Set `Package source` to `All` or `NuGet`.
-1.  Search `OpenEphys.Onix1.Design`.
+1.  Set `Package source` to `All`.
+1.  Search for the exact package name listed above, e.g. `OpenEphys.Onix1.Design`.
 1.  Click `Install`.
-1.  Click `I Accept` when the license agreement window appears.
+1.  If a license agreement window appears, click `I Accept`.
 
 ![Bonsai OpenEphys.Onix1.Design Install Screenshot](../../images/bonsai-install-OpenEphys.Onix1.Design.webp){width=650px}
 
-> [!NOTE]
-> Installing OpenEphys.Onix1.Design automatically installs `OpenEphys.Onix1` because it's a dependency.
-
-#### Bonsai.StarterPack
-
-To install the `Bonsai.StarterPack` package, open the package manager and:
-
-1.  Click the `Browse` tab.
-1.  Set `Package source` to `Bonsai Packages`.
-1.  Search for `Bonsai.StarterPack`.
-1.  Click `Install`.
-
-![Bonsai Bonsai.StarterPack Install Screenshot](../../images/bonsai-install-Bonsai.StarterPack.webp){width=650px}
-
-#### OpenEphys.Commutator
-
-To install the `OpenEphys.Commutator` package, open the package manager and:
-
-1.  Click the `Browse` tab.
-1.  Set `Package source` to `All` or `NuGet`.
-1.  Search for `OpenEphys.Commutator`.
-1.  Click `Install`.
-
-![Bonsai OpenEphys.Commutator Install Screenshot](../../images/bonsai-install-OpenEphys.Commutator.webp){width=650px}
-
 ### Update Packages
 
 It is good practice to periodically check for package updates. To do this, open the package manager and:

articles/hardware/hs64/load-data.md

@@ -3,7 +3,8 @@ uid: hs64_load-data
 title: Load Data
 ---
 
-The following python script can be used to load and plot the data produced by the Headstage 64 [example workflow](xref:hs64_workflow).
+The following python script can be used to load and plot the data produced by the Headstage 64
+[example workflow](xref:hs64_workflow).
 
 [!code-python[](../../../workflows/hardware/hs64/load-hs64.py)]
 

articles/hardware/np1e/load-data.md

@@ -3,15 +3,15 @@ uid: np1e_load-data
 title: Load Data
 ---
 
-The following python script can be used to load and plot the data produced by the NeuropixelsV1e Headstage [example workflow](xref:np1e).
+The following python script can be used to load and plot the data produced by the NeuropixelsV1e
+Headstage [example workflow](xref:np1e).
 
 [!code-python[](../../../workflows/hardware/np1e/load-np1e.py)]
 
 > [!NOTE]
-> To plot probeinterface data, [save the probe configuration file](xref:np1e_gui#save-probeinterface-file) into the same directory of your data.
-
-> [!NOTE]
-> This script will attempt to load entire files into arrays. For long recordings, data will need to
-> be split into more manageable chunks by:
-> - Modifying this script to partially load files
-> - Modifying the workflow to cyclically create new files after a certain duration
+> - To plot probeinterface data, [save the probe configuration file](xref:np1e_gui#save-probeinterface-file) 
+>   into the same directory of your data.
+> - This script will attempt to load entire files into arrays. For long recordings, data will need to
+>   be split into more manageable chunks by:
+>   - Modifying this script to partially load files
+>   - Modifying the workflow to cyclically create new files after a certain duration

articles/hardware/np2e/load-data.md

@@ -3,15 +3,18 @@ uid: np2e_load-data
 title: Load Data
 ---
 
-The following python script can be used to load and plot the data produced by the NeuropixelsV1e Headstage [example workflow](xref:np2e).
+The following python script can be used to load and plot the data produced by the NeuropixelsV2e
+Headstage [example workflow](xref:np2e).
 
 [!code-python[](../../../workflows/hardware/np2e/load-np2e.py)]
 
 > [!NOTE]
-> To plot probeinterface data, [save the probe configuration file](xref:np2e_gui#save-probeinterface-file) into the same directory of your data.
-
-> [!NOTE]
-> This script will attempt to load entire files into arrays. For long recordings, data will need to
-> be split into more manageable chunks by:
-> - Modifying this script to partially load files
-> - Modifying the workflow to cyclically create new files after a certain duration
+> - To plot probeinterface data, [save the probe configuration file](xref:np2e_gui#save-probeinterface-file) 
+>   into the same directory of your data.
+> - By default, this script only populates plots for the Neuropixels 2.0 probe A and leaves plots
+>   for Neuropixels 2.0 probe B empty. If you are recording from both probes and want to plot probe
+>   B ephys and probe data, uncomment the relevant lines in the script.
+> - This script will attempt to load entire files into arrays. For long recordings, data will need to
+>   be split into more manageable chunks by:
+>   - Modifying this script to partially load files
+>   - Modifying the workflow to cyclically create new files after a certain duration

articles/hardware/rhs2116/load-data.md

@@ -3,7 +3,8 @@ uid: rhs2116_load-data
 title: Load Data
 ---
 
-The following python script can be used to load and plot the data produced by the Headstage Rhs2116 [example workflow](xref:rhs2116).
+The following python script can be used to load and plot the data produced by the Headstage Rhs2116
+[example workflow](xref:rhs2116).
 
 [!code-python[](../../../workflows/hardware/rhs2116/load-rhs2116.py)]
 

build.ps1

@@ -1,5 +1,5 @@
 # Build project
-$libPath = ".\src\onix-bonsai-onix1\"
+$libPath = ".\src\bonsai-onix1\"
 dotnet build $libPath --configuration Release
 
 # Export workflow vectors

docfx-utils.ps1

@@ -11,7 +11,7 @@ param
 # this is called removeartifacts instead of clean because clean might be already mean something in powershell?
 function removeartifacts
 {
-    $deletePaths = ".\workflows\**\*.svg", ".\workflows\hardware\**\*.svg", ".\workflows\**\*.bonsai.layout", ".\workflows\hardware\**\*.bonsai.layout", ".\api\*.yml", ".\api\.manifest", ".\_site\", ".\_raw\", ".\_view\", ".\src\onix-bonsai-onix1\artifacts\"
+    $deletePaths = ".\workflows\**\*.svg", ".\workflows\hardware\**\*.svg", ".\workflows\**\*.bonsai.layout", ".\workflows\hardware\**\*.bonsai.layout", ".\api\*.yml", ".\api\.manifest", ".\_site\", ".\_raw\", ".\_view\", ".\src\bonsai-onix1\artifacts\"
     foreach($deletePath in $deletePaths){if (Test-Path $deletePath){Remove-Item $deletePath -Recurse}}
     Write-Output ""
 }
@@ -22,7 +22,7 @@ function lychee($lycheePath)
 {
     Write-Output "`nRunning lychee..."
     Write-Output "------------------------------------------`n"
-    Invoke-Expression "& `"$lycheePath`" --no-progress --base _site --exclude ^https://github\.com.*merge.* --exclude ^https://github\.com.*apiSpec.* --exclude ^https://github\.com/open-ephys/onix1-bonsai-docs/blob/.* '_site/**/*.html' --max-retries 0 --max-concurrency 32 --cache --max-cache-age 1d"
+    Invoke-Expression "& `"$lycheePath`" --no-progress --base _site --exclude ^https://github\.com.*merge.* --exclude ^https://github\.com.*apiSpec.* --exclude ^https://github\.com/open-ephys/bonsai-onix1-docs/blob/.* '_site/**/*.html' --max-retries 0 --max-concurrency 32 --cache --max-cache-age 1d"
     Write-Output "`n"
 }