Update labels to fix duplicate errors

source/User-Manual/Exploring-the-user-interface.rst

@@ -40,7 +40,7 @@ Processors handle four types of data:
 
 * **Text events:** messages generated by the user or other processors, or sent via the network. Some processors have specific behaviors that are triggered by text events.
 
-In addition, it's important to keep in mind that every continuous signal, event, and spike must be associated with a single *data stream*, or a collection of channels that are sampled synchronously. Any time you merge together data from different Sources, channels from each source will belong to different data streams. In addition, some Source processors (such as :ref:`neuropixelspxi`) generate multiple data streams. In most cases, data from separate streams will be processed independently, because samples from different streams are not guaranteed to be aligned. See the :ref:`whatsnew` page for more information about modifying parameters for individual streams.
+In addition, it's important to keep in mind that every continuous signal, event, and spike must be associated with a single *data stream*, or a collection of channels that are sampled synchronously. Any time you merge together data from different Sources, channels from each source will belong to different data streams. In addition, some Source processors (such as :ref:`neuropixelspxi`) generate multiple data streams. In most cases, data from separate streams will be processed independently, because samples from different streams are not guaranteed to be aligned. See the :ref:`whatsnewinv06x` page for more information about modifying parameters for individual streams.
 
 
 3. Message Center
@@ -129,7 +129,7 @@ View
 Help
 -----
 
-* **Online documentation...**: Open the GUI's documentation site in a browser window (requires access to the interent).
+* **Online documentation...**: Open the GUI's documentation site in a browser window (requires access to the internet).
 
 
 Debug console
@@ -155,14 +155,13 @@ Windows
 Debug console is automatically displayed on Windows when you run the :code:`open-ephys` application.
 
 
-
 Log files
 ###############
 
-Every action taken by the user is logged to a file, along with additional information that can be useful for spotting issues when things go wrong. If the GUI exits sucessfully, the latest log file will be overwritten the next time the GUI is launched. If the GUI crashes, then the name of the latest log file will be appended with a unique date string.
+Every action taken by the user is logged to a file, along with additional information that can be useful for spotting issues when things go wrong. If the GUI exits successfully, the latest log file will be overwritten the next time the GUI is launched. If the GUI crashes, then the name of the latest log file will be appended with a unique date string.
 
 Linux
--------
+------
 
 Log files are written to :code:`/home/<username>/open-ephys/configs-api8`
 

source/User-Manual/Hardware-requirements.rst

@@ -19,6 +19,8 @@ More than 1000 `Open Ephys acquisition boards <https://open-ephys.org/acq-board>
 
 The following hardware is recommended for experiments that use the acquisition board:
 
+.. _computer-specs-open-ephys:
+
 Computer specs
 #####################
 
@@ -58,6 +60,8 @@ Neuropixels are quickly become a new standard for electrophysiology, given their
 
 The following hardware is recommended for experiments with Neuropixels:
 
+.. _computer-specs-neuropixels:
+
 Computer specs
 ################
 
@@ -79,6 +83,8 @@ Other hardware
 
 The following summarizes the additional hardware you'll need to buy to run Neuropixels experiments. OneBoxes, PXI basestations, headstages, and probes can be ordered from `neuropixels.org <https://neuropixels.org>`__. Other PXI components are available from NI.
 
+.. _onebox-hardware-requirements:
+
 OneBox
 -------
 

source/User-Manual/Installing-the-GUI.rst

@@ -21,6 +21,8 @@ Via installer (recommended)
 
 4. The GUI will be installed in :code:`C:\\Program Files\\Open Ephys\\open-ephys.exe`.
 
+.. _windows-via-zip:
+
 Via .zip file
 --------------
 
@@ -73,6 +75,8 @@ The GUI is available at the gentoo science overlay.
 .. note:: Brave users can also install the main branch version (:code:`emerge --ask --verbose =sci-biology/open-ephys-gui-9999`) or the development branch version (:code:`emerge --ask --verbose =sci-biology/open-ephys-gui-99999999`). Since installation is slotted, you can keep all versions installed simultaneously, in case you want to try them without removing the stable version.
 
 
+.. _linux-via-zip:
+
 Via .zip file (all distros)
 ----------------------------
 
@@ -103,7 +107,9 @@ Via DMG (recommended)
 
 4. Double-click on the **open-ephys** app bundle to launch the GUI.
 
-.. note:: Depending on your security settings, you may see a message announcing that "'open-ephys' cannot be opened because the developer cannot be verified." If so, go to System Prefererences > Security and Privacy > General and click "Open Anyway" to allow the GUI to launch.
+.. note:: Depending on your security settings, you may see a message announcing that "'open-ephys' cannot be opened because the developer cannot be verified." If so, go to System Preferences > Security and Privacy > General and click "Open Anyway" to allow the GUI to launch.
+
+.. _macos-via-zip:
 
 Via .zip file
 --------------

source/User-Manual/Plugins/Ephys-Socket.rst

@@ -9,7 +9,7 @@ Ephys Socket
 .. image:: ../../_static/images/plugins/ephyssocket/ephyssocket-01.png
   :alt: Annotated Ephys Socket Editor
 
-.. csv-table:: Receives formatted data from a TCP socket that implements a particular :ref:`header format <Header Format for Custom Data Streams>`. A common use case is to receive data streamed from :ref:`Bonsai <In Bonsai>`. This is intended to be a quick way to stream ephys data from a third-party application and visualize in the Open Ephys GUI. Below is a way to setup streaming between Bonsai and the Open Ephys GUI, which can be extended to other software and/or hardware that carry the same header format.
+.. csv-table:: Receives formatted data from a TCP socket that implements a particular :ref:`header-format`. A common use case is to receive data streamed from :ref:`in-bonsai`. This is intended to be a quick way to stream ephys data from a third-party application and visualize in the Open Ephys GUI. Below is a way to setup streaming between Bonsai and the Open Ephys GUI, which can be extended to other software and/or hardware that carry the same header format.
    :widths: 18, 80
 
    "*Plugin Type*", "Source"
@@ -28,6 +28,8 @@ The Plugin Installer also allows you to upgrade to the latest version of this pl
 Plugin Configuration
 ######################
 
+.. _in-bonsai:
+
 In Bonsai
 -----------
 
@@ -96,11 +98,12 @@ In the Open Ephys GUI
 
 .. warning:: This plugin does not guarantee that samples will not be lost in transit, so it's essential to save your data stream on the Bonsai end. There are at least two ways data loss can occur: 1) When a data stream is first connected, there is no guarantee that the data will be saved, since data is not acquired immediately after connecting the socket. 2) If too much data is being sent and the Open Ephys GUI cannot process the data quickly enough, some packets may be lost due to the TCP buffer filling up. If you suspect samples are being dropped (e.g., if the LFP Viewer is not updating at the expected speed), sending a lower bandwidth might fix the problem.
 
+.. _header-format:
 
 Header Format for Custom Data Streams
 ######################################
 
-While the :code:`SendMatOverSocket` node (found in **OpenEphys.Sockets.Bonsai**, see :ref:`In Bonsai` for details) is a common use case for sending `OpenCV.Net.Mat` data over the TCP socket, it is not the only way to stream data. As long as whatever is used to stream data (e.g., a Python script that sends data over the TCP socket) correctly prepends a header to the data stream, Ephys Socket can correctly interpret the data.
+While the :code:`SendMatOverSocket` node (found in **OpenEphys.Sockets.Bonsai**, see :ref:`in-bonsai` for details) is a common use case for sending `OpenCV.Net.Mat` data over the TCP socket, it is not the only way to stream data. As long as whatever is used to stream data (e.g., a Python script that sends data over the TCP socket) correctly prepends a header to the data stream, Ephys Socket can correctly interpret the data.
 
 An example Python script is included in the `Resources <https://github.com/open-ephys-plugins/ephys-socket/tree/main/Resources>`__ folder of the plugin repository, which implements the format described here. Each variable is 4 bytes long (with the exception of the Bit Depth, which is 2 bytes long), and must be sent in the order listed below. The total header length is 22 bytes.
 

source/User-Manual/Plugins/Neuropixels-PXI.rst

@@ -81,7 +81,7 @@ This plugin can stream data from the following Neuropixels probe types:
    "Neuropixels 2.0 (quad base)", "1536 wideband", "**≥0.7.x**", "`BS169, BSC191`_"
    "Neuropixels Opto", "384 AP, 384 LFP", "≥0.4.x", "Special basestation required"
 
-.. important:: Regardless of which probe type you're using, we recommend updating to the most recent Neuropixels PXI plugin and basestation firmware (`BS169, BSC191`_). This firmware is required for plugin version **0.7.x** and higher, as well as the latest version of SpikeGLX. See :ref:`Updating basestation firmware` section for information on how to modify your firmware.
+.. important:: Regardless of which probe type you're using, we recommend updating to the most recent Neuropixels PXI plugin and basestation firmware (`BS169, BSC191`_). This firmware is required for plugin version **0.7.x** and higher, as well as the latest version of SpikeGLX. See :ref:`updating-basestation-firmware` section for information on how to modify your firmware.
 
 .. warning:: In version 0.6.x of this plugin, commercial Neuropixels 2.0 (multishank) probes did not have the correct scaling applied to account for the lower bit depth of the ADC compared to the beta probes (12 vs. 14 bits). To correct this, any data acquired with from these probes with this plugin should be multiplied by 4. This issue is fixed in version 0.7.x.
 
@@ -96,7 +96,7 @@ Connecting to the PXI system
 
 Before using this plugin, make sure you've followed all of the steps in the `Neuropixels User Manual <https://www.neuropixels.org/support>`__ to set up and configure your hardware. Prior to using your Neuropixels PXI basestation, you must install the Enclustra drivers (available for `Windows 7/8 <https://github.com/open-ephys-plugins/neuropixels-pxi/raw/main/Resources/Enclustra_Win7%268.zip>`__ and `Windows 10 <https://github.com/open-ephys-plugins/neuropixels-pxi/raw/main/Resources/Enclustra_Win10.zip>`__). See section 4.2.2 of the User Manual for installation instructions.
 
-Once your PXI system is up and running, you can drag and drop the "Neuropix-PXI" module from the Processor List onto the Editor Viewport. The GUI will automatically connect to any available basestations in your PXI chassis with probes connected. If no basestations are found, the plugin can be run in simulation mode. If no probes are found, the plugin editor will display information about each basestation, and can be used to perform a firmware update (see :ref:`Updating basestation firmware` below).
+Once your PXI system is up and running, you can drag and drop the "Neuropix-PXI" module from the Processor List onto the Editor Viewport. The GUI will automatically connect to any available basestations in your PXI chassis with probes connected. If no basestations are found, the plugin can be run in simulation mode. If no probes are found, the plugin editor will display information about each basestation, and can be used to perform a firmware update (see :ref:`updating-basestation-firmware` below).
 
 The editor will automatically create a probe selection interface for each basestation that's available. Each basestation can communicate with up to 4 probes (for Neuropixels 1.0, NHP, and Ultra) or 8 probes (for 2.0). When the probes are initially detected, they show up as orange circles. Once they are initialized, connected probes become green. After the probes turn green, the plugin is ready to begin data acquisition.
 
@@ -323,12 +323,14 @@ If you have a headstage test module, you can run a suite of tests to ensure the
 
 .. note:: The headstage tests have been re-enabled as of plugin version 0.5.x. However, we have also found that the headstage tests are rarely needed to accurately diagnose a problem with data transmission. If you are unsure whether your headstage is functional, swapping it out with a different headstage is usually more informative than running the headstage tests.
 
+.. _updating-basestation-firmware:
+
 Updating basestation firmware
 ######################################
 
 Version **0.7.x** of the Neuropixels PXI plugin requires a basestation firmware update. The latest firmware (BS169, BSC189) can be downloaded `here <https://github.com/open-ephys-plugins/neuropixels-pxi/blob/main/Resources/imec-firmware-for-plugin-0.7.x.zip>`__.
 
-The currently installed firmware version will appear in the info section of the Neuropixels settings interface (upper right text block). If your basesation firmware version is "2.0169" and your basestation connect board firmware version is "3.2191", you already have the latest firmware installed.
+The currently installed firmware version will appear in the info section of the Neuropixels settings interface (upper right text block). If your basestation firmware version is "2.0169" and your basestation connect board firmware version is "3.2191", you already have the latest firmware installed.
 
 If you need to update your firmware, first click the "UPDATE FIRMWARE" button to open the firmware update interface:
 

source/User-Manual/Plugins/OneBox.rst

@@ -2,6 +2,8 @@
 .. role:: raw-html-m2r(raw)
    :format: html
 
+.. _onebox-plugin:
+
 ################
 OneBox
 ################
@@ -47,7 +49,7 @@ Compatible probes
 This plugin can stream data from any of the following Neuropixels probes:
 
 .. csv-table::
-   :widths: 70, 40, 40, 50
+   :widths: 70, 40
 
    "**Probe**", "**Channels**"
    "Neuropixels 1.0", "384 AP, 384 LFP"

source/User-Manual/Plugins/Rhythm-Plugins.rst

@@ -2,6 +2,8 @@
 .. role:: raw-html-m2r(raw)
    :format: html
 
+:orphan:
+
 #################
 Rhythm Plugins
 #################

source/conf.py

@@ -231,4 +231,7 @@
 linkcheck_anchors = False
 
 extensions.append("sphinx_tabs.tabs")
-extensions.append("sphinx.ext.autosectionlabel")
+
+suppress_warnings = [
+  'duplicate_declaration.cpp'
+  ]