Socket.IO API docs (#423)

* Grammarly and shorted README

* Start API

* Get position

* up to set depth

* Socket.io API

* Grammarly

Author: kjy5

README.md

@@ -12,42 +12,13 @@
 The [Electrophysiology Manipulator Link](https://github.com/VirtualBrainLab/ephys-link)
 (or Ephys Link for short) is a Python [Socket.IO](https://socket.io/docs/v4/#what-socketio-is) server that allows any
 Socket.IO-compliant application (such
-as [Pinpoint](https://github.com/VirtualBrainLab/Pinpoint))
+as [Pinpoint][Pinpoint])
 to communicate with manipulators used in electrophysiology experiments.
 
 <img width="100%" src="https://github.com/VirtualBrainLab/ephys-link/assets/82800265/0c7c60b1-0926-4697-a461-221554f82de1" alt="Manipulator and probe in pinpoint moving in sync">
 
-**Supported Manipulators:**
-
-| Manufacturer | Model                                                   |
-|--------------|---------------------------------------------------------|
-| Sensapex     | <ul> <li>uMp-4</li> <li>uMp-3 (Coming Soon!)</li> </ul> |
-| New Scale    | <ul> <li>Pathfinder MPM Control v2.8+</li> </ul>        |
-| Scientifica  | <ul> <li>InVivoStar (Coming Soon!)</li> </ul>           |
-| LabMaker     | <ul> <li>(Coming Soon!)</li> </ul>                      |
-
-Ephys Link is an open and extensible platform. It is designed to easily support integration with other manipulators.
-
-For more information regarding the server's implementation and how the code is organized, see
-the [package's development documentation](https://virtualbrainlab.org/ephys_link/development.html).
-
-For detailed descriptions of the server's API, see
-the [API reference](https://virtualbrainlab.org/api_reference_ephys_link.html).
-
 # Installation
 
-## Prerequisites
-
-1. An **x86 Windows PC is required** to run the server.
-2. For Sensapex devices, the controller unit must be connected via an ethernet
-   cable and powered. A USB-to-ethernet adapter is acceptable. For New Scale manipulators,
-   the controller unit must be connected via USB and be powered by a 6V power
-   supply.
-3. To use the emergency stop feature, ensure an Arduino with
-   the [StopSignal](https://github.com/VirtualBrainLab/StopSignal) sketch is
-   connected to the computer. Follow the instructions on that repo for how to
-   set up the Arduino.
-
 ## Launch from Pinpoint (Recommended)
 
 Pinpoint comes bundled with the correct version of Ephys Link. If you are using Pinpoint on the same computer your
@@ -56,52 +27,9 @@ the [Pinpoint documentation](https://virtualbrainlab.org/pinpoint/tutorials/tuto
 
 ## Install as Standalone Executable
 
-1. Download the latest executable from
+1. Download the latest standalone executable or zip from
    the [releases page](https://github.com/VirtualBrainLab/ephys-link/releases/latest).
-2. Double-click the executable file to launch the configuration window.
-    1. Take note of the IP address and port. **Copy this information into Pinpoint to connect**.
-3. Select the desired configuration and click "Launch Server".
-
-The configuration window will close and the server will launch. Your configurations will be saved for future use.
-
-To connect to the server from Pinpoint, provide the IP address and port. For example, if the server is running on the
-same computer that Pinpoint is, use
-
-- Server: `localhost`
-- Port: `8081`
-
-If the server is running on a different (local) computer, use the IP address of that computer as shown in the startup
-window instead of `localhost`.
-
-## Install as a Python package
-
-```bash
-pip install ephys-link
-```
-
-Import main and run (this will launch the setup GUI).
-
-```python
-from ephys_link.__main__ import main
-
-main()
-```
-
-## Install for Development
-
-1. Clone the repository.
-2. Install [Hatch](https://hatch.pypa.io/latest/install/)
-3. In a terminal, navigate to the repository's root directory and run
-
-   ```bash
-   hatch shell
-   ```
-
-This will create a virtual environment, install Python 12 (if not found), and install the package in editable mode.
-
-If you encounter any dependency issues (particularly with `aiohttp`), try installing the latest Microsoft Visual C++
-(MSVC v143+ x86/64) and the Windows SDK (10/11)
-via [Visual Studio Build Tools Installer](https://visualstudio.microsoft.com/visual-cpp-build-tools/).
+2. Double-click the executable file to start.
 
 # Documentation and More Information
 
@@ -111,7 +39,7 @@ found on the [Virtual Brain Lab Documentation page][docs] for Ephys Link.
 # Citing
 
 If this project is used as part of a research project you should cite
-the [Pinpoint repository][Pinpoint]. Please email
+the [Pinpoint repository](https://github.com/VirtualBrainLab/Pinpoint). Please email
 Dan ([[email protected]](mailto:[email protected])) if you have questions.
 
 Please reach out to Kenneth ([[email protected]](mailto:[email protected])) for questions
@@ -120,6 +48,4 @@ through the issues tab.
 
 [Pinpoint]: https://github.com/VirtualBrainLab/Pinpoint
 
-[StopSignal]: https://github.com/VirtualBrainLab/StopSignal
-
-[docs]: https://virtualbrainlab.org/ephys_link/installation_and_use.html
+[docs]: https://virtualbrainlab.github.io/ephys-link/

docs/development/adding_a_manipulator.md

@@ -36,7 +36,7 @@ are used to convert between your manipulator's coordinate system and the unified
     the [Sensapex uMp-4](https://github.com/VirtualBrainLab/ephys-link/blob/main/src/ephys_link/bindings/ump_4_bindings.py)
     binding for an example where the platform has a Python API (Sensapex's SDK) and
     the [New Scale Pathfinder MPM](https://github.com/VirtualBrainLab/ephys-link/blob/main/src/ephys_link/bindings/mpm_bindings.py)
-    binding for an example where the platform uses a REST API to an external provider.
+    binding, for example, where the platform uses a REST API for an external provider.
 
 ### Binding Names
 
@@ -52,11 +52,11 @@ returns `ump-4` because the CLI launch command is `ephys_link.exe -b -t ump-4`.
 ### Custom Additional Arguments
 
 Sometimes you may want to pass extra data to your binding on initialization. For example, New Scale Pathfinder MPM
-bindings needs to know what the HTTP server port is. To add custom arguments, define them as arguments on the `__init__`
+bindings need to know what the HTTP server port is. To add custom arguments, define them as arguments on the `__init__`
 method of your binding then pass in the appropriate data when the binding is instantiated in the [
 `_get_binding_instance`](https://github.com/VirtualBrainLab/ephys-link/blob/f79c1ec68ec1805e1a4e231e1934127893f7bd20/src/ephys_link/back_end/platform_handler.py#L58)
 method of the [`PlatformHandler`][ephys_link.back_end.platform_handler].
-Use [New Scale Pathfinder MPM's binding][ephys_link.bindings.mpm_binding] as an example for how to do this.
+Use [New Scale Pathfinder MPM's binding][ephys_link.bindings.mpm_binding] as an example of how to do this.
 
 ## Test Your Binding
 
@@ -71,7 +71,7 @@ information.
 
 ## Submit Your Changes
 
-When you're satisfied with your changes, submit a pull request to the main repository. We will review your changes and
+When satisfied with your changes, submit a pull request to the main repository. We will review your changes and
 merge them if they meet our standards!
 
 Feel free to [reach out](../home/contact.md) to us if you have any questions or need help with your binding!

docs/development/code_organization.md

@@ -19,7 +19,7 @@ sequence.
 ## Control Flow
 
 As described in ["How It Works"](../home/how_it_works.md), Ephys Link is primarily a server that responds to events. The
-server exposes the events and pass them to the chosen manipulator binding. Everything is asynchronous and uses callbacks
+server exposes the events and passes them to the chosen manipulator binding. Everything is asynchronous and uses callbacks
 to return responses to the clients when ready.
 
 [`PlatformHandler`][ephys_link.back_end.platform_handler] is responsible for converting between the server API and the
@@ -28,12 +28,12 @@ writing a manipulator binding.
 
 ## Static Analysis
 
-The project is strictly type checked using [`hatch fmt` (ruff)](https://hatch.pypa.io/1.9/config/static-analysis/)
+The project is strictly type-checked using [`hatch fmt` (ruff)](https://hatch.pypa.io/1.9/config/static-analysis/)
 and [basedpyright](https://docs.basedpyright.com/latest/). All PRs are checked against these tools.
 
-While they are very helpful in enforcing good code, they can be annoying when working with libraries that inherently
-return `Any` (like HTTP requests) or are not strictly statically typed. In those situations we have added inline
-comments to ignore specific checks. We try to only use this in scenarios where missing typing information came from
+While they are invaluable in enforcing good code, they can be annoying when working with libraries that inherently
+return `Any` (like HTTP requests) or are not strictly statically typed. In those situations, we have added inline
+comments to ignore specific checks. We try to only use this in scenarios where missing typing information comes from
 external sources, and it is not possible to make local type hints. Do not use file-wide ignores under any circumstances.
 We also do not make stubs since they would be challenging to maintain.
 

docs/development/index.md

@@ -8,7 +8,7 @@ This section describes:
 - [The Socket.IO server's API](socketio_api.md) and how to communicate with Ephys Link from a client application
 - How to [add a new manipulator](adding_a_manipulator.md) to Ephys Link
 - General [code organization](code_organization.md) for Ephys Link
-- Auto generated [source code reference](../reference/SUMMARY.md) intended for developers who are maintaining Ephys Link
+- Auto-generated [source code reference](../reference/SUMMARY.md) intended for developers who are maintaining Ephys Link
 
 ## Installing for Development
 
@@ -24,4 +24,4 @@ This will create a virtual environment, install Python 13 (if not found), and in
 
 If you encounter any dependency issues (particularly with `aiohttp`), try installing the latest Microsoft Visual C++
 (MSVC v143+ x86/64) and the Windows SDK (10/11)
-via [Visual Studio Build Tools Installer](https://visualstudio.microsoft.com/visual-cpp-build-tools/).
+via [Visual Studio Build Tools Installer](https://visualstudio.microsoft.com/visual-cpp-build-tools/).