ephys-link 2.0.0b9__tar.gz → 2.0.0b10__tar.gz

{ephys_link-2.0.0b9 → ephys_link-2.0.0b10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ephys-link
-Version: 2.0.0b9
+Version: 2.0.0b10
 Summary: A Python Socket.IO server that allows any Socket.IO-compliant application to communicate with manipulators used in electrophysiology experiments.
 Project-URL: Documentation, https://virtualbrainlab.org/ephys_link/installation_and_use.html
 Project-URL: Issues, https://github.com/VirtualBrainLab/ephys-link/issues

{ephys_link-2.0.0b9 → ephys_link-2.0.0b10}/ephys_link.spec

@@ -1,22 +1,27 @@
 # -*- mode: python ; coding: utf-8 -*-
 
-from ephys_link.__about__ import __version__ as version
-
 from argparse import ArgumentParser
 
+from PyInstaller.utils.hooks import collect_submodules
+
+from ephys_link.__about__ import __version__ as version
+
 parser = ArgumentParser()
 parser.add_argument("-d", "--dir", action="store_true", help="Outputs a directory")
 options = parser.parse_args()
 
 FILE_NAME = f"EphysLink-v{version}"
 
+# Collect binding modules.
+bindings = [binding for binding in collect_submodules("ephys_link.bindings") if binding != "ephys_link.bindings"]
+
 # noinspection PyUnresolvedReferences
 a = Analysis(
     ['src\\ephys_link\\__main__.py'],
     pathex=[],
     binaries=[('src\\ephys_link\\resources', 'ephys_link\\resources')],
     datas=[],
-    hiddenimports=['engineio.async_drivers.aiohttp'],
+    hiddenimports=['engineio.async_drivers.aiohttp'] + bindings,
     hookspath=[],
     hooksconfig={},
     runtime_hooks=[],

{ephys_link-2.0.0b9 → ephys_link-2.0.0b10}/pyproject.toml

@@ -56,7 +56,7 @@ el = "ephys_link.__main__:main"
 path = "src/ephys_link/__about__.py"
 
 [tool.hatch.build.targets.sdist]
-exclude = ["/.github", "/.idea"]
+exclude = ["/.github", "/.idea", "/docs"]
 
 [tool.hatch.envs.default]
 python = "3.13.1"

ephys_link-2.0.0b10/src/ephys_link/__about__.py

@@ -0,0 +1 @@
+__version__ = "2.0.0b10"

ephys_link-2.0.0b9/docs/development/adding_a_manipulator.md

@@ -1,77 +0,0 @@
-# Adding a Manipulator
-
-By the end of this section, you will be able to add a manipulator platform to Ephys Link and control it using the server
-API. This is a software development guide and assumes you have experience with Python. It is encouraged to
-read [how the system works first](../home/how_it_works.md) before proceeding.
-
-## Set Up for Development
-
-1. Fork the [Ephys Link repository](https://github.com/VirtualBrainLab/ephys-link).
-2. Follow the instructions for [installing Ephys Link for development](index.md#installing-for-development) to get all
-   the necessary dependencies and tools set up. In this case, you'll want to clone your fork.
-3. (Optional) Familiarize yourself with the [repo's organization](code_organization.md).
-
-## Create a Manipulator Binding
-
-Manipulators are added to Ephys Link through bindings. A binding is a Python class that extends the abstract base class
-[`BaseBinding`][ephys_link.utils.base_binding] and defines the methods Ephys Link expects from a platform.
-
-Create a new Python module in `src/ephys_link/bindings` for your manipulator. Make a class that extends
-[`BaseBinding`][ephys_link.utils.base_binding]. Most IDEs will automatically import the necessary classes and tell you
-the methods you need to implement. See the reference for [`BaseBinding`][ephys_link.utils.base_binding] for detailed
-descriptions of the expected behavior.
-
-As described in the [system overview](../home/how_it_works.md), Ephys Link converts all manipulator movement into a
-common "unified space" which is
-the [left-hand cartesian coordinate system](https://www.scratchapixel.com/lessons/mathematics-physics-for-computer-graphics/geometry/coordinate-systems.html).
-The two methods [
-`platform_space_to_unified_space`](../../reference/ephys_link/utils/base_binding/#ephys_link.utils.base_binding.BaseBinding.platform_space_to_unified_space)
-and [
-`unified_space_to_platform_space`](../../reference/ephys_link/utils/base_binding/#ephys_link.utils.base_binding.BaseBinding.unified_space_to_platform_space)
-are used to convert between your manipulator's coordinate system and the unified space.
-
-!!! tip
-
-    See
-    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 example, where the platform uses a REST API for an external provider.
-
-### Binding Names
-
-The two naming methods [
-`get_display_name`](../../reference/ephys_link/utils/base_binding/#ephys_link.utils.base_binding.BaseBinding.get_display_name)
-and [
-`get_cli_name`](../../reference/ephys_link/utils/base_binding/#ephys_link.utils.base_binding.BaseBinding.get_cli_name)
-are used to identify the binding in the user interface. As described by their documentation, `get_display_name` should
-return a human-readable name for the binding, while `get_cli_name` should return the name used to launch the binding
-from the command line (what is passed to the `-t` flag). For example, Sensapex uMp-4 manipulator's `get_cli_name`
-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 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 of how to do this.
-
-## Test Your Binding
-
-Once you've implemented your binding, you can test it by running Ephys Link using your binding
-`ephys_link -b -t <cli_name>`. You can interact with it using the [Socket.IO API](socketio_api.md) or Pinpoint.
-
-## Code standards
-
-We use automatic static analyzers to check code quality. See
-the [corresponding section in the code organization documentation](code_organization.md#static-analysis) for more
-information.
-
-## Submit Your Changes
-
-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!

ephys_link-2.0.0b9/docs/development/code_organization.md

@@ -1,41 +0,0 @@
-# Code Organization
-
-This section gives an overview of Ephys Link's internal architecture. It is intended for
-maintainers of Ephys Link.
-
-## File Structure
-
-Ephys Link starts from the `__main__.py` file. It imports each component of the application and calls the launch
-sequence.
-
-### Where to find things
-
-- `back_end`: the Socket.IO server and the manipulator API.
-- `front_end`: configuration GUI and CLI definition.
-- `bindings`: manipulator binding implementations.
-- `utils`: common utilities and helper functions (including
-  [the base binding abstract base class][ephys_link.utils.base_binding]).
-
-## 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 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
-manipulator binding API. Because of this module, you don't have to worry about the details of the server API when
-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/)
-and [basedpyright](https://docs.basedpyright.com/latest/). All PRs are checked against these tools.
-
-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.
-
-We encourage using the type checker as a tool to help strengthen your code and only apply inline comments to ignore
-specific instances where external libraries cause errors. 

ephys_link-2.0.0b9/docs/development/index.md

@@ -1,27 +0,0 @@
-# Developing with Ephys Link
-
-Ephys Link is free and open-source software. All of our code is available
-on [GitHub](https://github.com/VirtualBrainLab/ephys-link), and we welcome contributions from the community!
-
-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
-
-## Installing 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 13 (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/).

ephys_link-2.0.0b9/docs/development/socketio_api.md

@@ -1,418 +0,0 @@
-# Socket.IO API
-
-This section documents the [Socket.IO](https://socket.io/) API. The document is intended for developers building client
-applications communicating with the server. If you are looking for information on how to set up and run the server, see
-the [installation guide](../home/installation.md)!
-
-## Data Types
-
-All messages on Socket.IO are passed as strings. Complex data structures are JSON encoded, converted to strings, and
-then sent. These structures have their JSON schemas documented
-on [VBL Aquarium](https://github.com/VirtualBrainLab/vbl-aquarium/tree/main/models/schemas/ephys_link).
-
-This documentation will reference the Pydantic versions of these models as they are extensively documented. For most
-functions, their functions and responses are documented by these models. Follow the links to the VBL Aquarium
-documentation for a model to learn more. These models have a `.to_json_string()` method that will convert the model
-object to a string that can be sent over Socket.IO.
-
-## Events
-
-Client applications should send messages to these events to interact with the server. The server will respond using
-[Socket.IO acknowledgments](https://socket.io/docs/v4/#acknowledgements).
-
-### Get Ephys Link Version
-
-| Event         | Input | Response |
-|---------------|-------|----------|
-| `get_version` | None  | `string` |
-
-[Semantically Versioned](https://semver.org/) number.
-
-__Examples:__
-
-Input: None
-
-Response:
-
-- `"2.0.0"`
-- `"2.0.0b2`
-
-### Get Pinpoint ID
-
-| Event             | Input | Response |
-|-------------------|-------|----------|
-| `get_pinpoint_id` | None  | `string` |
-
-Proxy connection ID (first 8 characters of a UUID v4).
-
-__Example:__
-
-Input: None
-
-Response: `"81f8de08"`
-
-### Get Platform Info
-
-| Event               | Input | Return                                                        |
-|---------------------|-------|---------------------------------------------------------------|
-| `get_platform_info` | None  | [`PlatformInfo`][vbl_aquarium.models.ephys_link.PlatformInfo] |
-
-__Example:__
-
-Input: N/A
-
-Response:
-
-```json
-{
-  "Name": "Sensapex uMp-4",
-  "CliName": "ump-4",
-  "AxesCount": 4,
-  "Dimensions": {
-    "x": 20.0,
-    "y": 20.0,
-    "z": 20.0,
-    "w": 20.0
-  }
-}
-```
-
-### List Available Manipulators
-
-| Event              | Input | Return                                                                             |
-|--------------------|-------|------------------------------------------------------------------------------------|
-| `get_manipulators` | None  | [`GetManipulatorResponse`][vbl_aquarium.models.ephys_link.GetManipulatorsResponse] |
-
-__Examples:__
-
-Input: N/A
-
-Response:
-
-- Normal:
-
-```json
-{
-  "Manipulators": [
-    "1",
-    "2",
-    "3"
-  ],
-  "Error": ""
-}
-```
-
-- Error:
-
-```json
-{
-  "Manipulators": [],
-  "Error": "No manipulators found"
-}
-```
-
-### Get Manipulator Position
-
-| Event          | Input                     | Return                                                                    |
-|----------------|---------------------------|---------------------------------------------------------------------------|
-| `get_position` | Manipulator ID (`string`) | [`PositionalResponse`][vbl_aquarium.models.ephys_link.PositionalResponse] |
-
-__Examples:__
-
-Input:
-
-- `"1"`
-- `"A"`
-
-Response:
-
-- Normal:
-
-```json
-{
-  "Position": {
-    "x": 12.45,
-    "y": 7.89,
-    "z": 0.81,
-    "w": 8.12
-  },
-  "Error": ""
-}
-```
-
-- Error:
-
-```json
-{
-  "Position": {
-    "x": 0.0,
-    "y": 0.0,
-    "z": 0.0,
-    "w": 0.0
-  },
-  "Error": "Unable to Read Manipulator Position"
-}
-```
-
-### Get Manipulator Angles
-
-| Event        | Input                     | Return                                                              |
-|--------------|---------------------------|---------------------------------------------------------------------|
-| `get_angles` | Manipulator ID (`string`) | [`AngularResponse`][vbl_aquarium.models.ephys_link.AngularResponse] |
-
-__Examples:__
-
-Input:
-
-- `"1"`
-- `"A"`
-
-Response:
-
-- Normal:
-
-```json
-    {
-  "Angles": {
-    "x": 45.0,
-    "y": 0.0,
-    "z": 90.0
-  },
-  "Error": ""
-}
-```
-
-- Error:
-
-```json
-  {
-  "Angles": {
-    "x": 0.0,
-    "y": 0.0,
-    "z": 0.0
-  },
-  "Error": "Unable to Read Manipulator Angles"
-}
-
-```
-
-### Get Probe Shank Count
-
-| Event             | Input                     | Return                                                                    |
-|-------------------|---------------------------|---------------------------------------------------------------------------|
-| `get_shank_count` | Manipulator ID (`string`) | [`ShankCountResponse`][vbl_aquarium.models.ephys_link.ShankCountResponse] |
-
-__Examples:__
-
-Input:
-
-- `"1"`
-- `"A"`
-
-Response:
-
-- Normal:
-
-```json
-{
-  "ShankCount": 3,
-  "Error": ""
-}
-```
-
-- Error:
-
-```json
-{
-  "ShankCount": 1,
-  "Error": "Unable to Read Probe Shank Count"
-}
-```
-
-### Set Manipulator Position
-
-| Event          | Input                                                                     | Return                                                                    |
-|----------------|---------------------------------------------------------------------------|---------------------------------------------------------------------------|
-| `set_position` | [`SetPositionRequest`][vbl_aquarium.models.ephys_link.SetPositionRequest] | [`PositionalResponse`][vbl_aquarium.models.ephys_link.PositionalResponse] |
-
-__Examples:__
-
-Input:
-
-```json
-{
-  "ManipulatorId": "1",
-  "Position": {
-    "x": 1.5,
-    "y": 2.0,
-    "z": 0.0,
-    "w": 0.84
-  },
-  "Speed": 0.05
-}
-```
-
-Response:
-
-- Normal:
-
-```json
-{
-  "Position": {
-    "x": 1.5,
-    "y": 2.0,
-    "z": 0.0,
-    "w": 0.84
-  },
-  "Error": ""
-}
-```
-
-- Manipulator is set to be inside the brain (position setting is disallowed):
-
-```json
-{
-  "Position": {
-    "x": 0.0,
-    "y": 0.0,
-    "z": 0.0,
-    "w": 0.0
-  },
-  "Error": "Can not move manipulator while inside the brain. Set the depth (\"set_depth\") instead."
-}
-```
-
-- The manipulator did not make it to the final destination. This is not necessarily unintentional. This response is
-  produced
-  if a movement is stopped.
-
-```json
-{
-  "Position": {
-    "x": 0.0,
-    "y": 0.0,
-    "z": 0.0,
-    "w": 0.0
-  },
-  "Error": "Manipulator 1 did not reach target position on axis x. Requests: 1.5, got: 0.82."
-}
-```
-
-### Set Manipulator Depth
-
-| Event       | Input                                                               | Return                                                                |
-|-------------|---------------------------------------------------------------------|-----------------------------------------------------------------------|
-| `set_depth` | [`SetDepthRequest`][vbl_aquarium.models.ephys_link.SetDepthRequest] | [`SetDepthResponse`][vbl_aquarium.models.ephys_link.SetDepthResponse] |
-
-__Examples:__
-
-Input:
-
-```json
-{
-  "ManipulatorId": "1",
-  "Depth": 1.7,
-  "Speed": 0.005
-}
-```
-
-Response:
-
-- Normal:
-
-```json
-{
-  "Depth": 1.7,
-  "Error": ""
-}
-```
-
-- The manipulator did not make it to the final destination. This is not necessarily unintentional. This response is
-  produced
-  if a drive is stopped.
-
-```json
-{
-  "Depth": 0,
-  "Error": "Manipulator 1 did not reach target depth. Requested: 1.7, got: 0.6."
-}
-```
-
-### Set Manipulator to be Inside the Brain
-
-| Event              | Input                                                                           | Return                                                                        |
-|--------------------|---------------------------------------------------------------------------------|-------------------------------------------------------------------------------|
-| `set_inside_brain` | [`SetInsideBrainRequest`][vbl_aquarium.models.ephys_link.SetInsideBrainRequest] | [`BooleanStateResponse`][vbl_aquarium.models.ephys_link.BooleanStateResponse] |
-
-__Examples:__
-
-Input:
-
-```json
-{
-  "ManipulatorId": "1",
-  "Inside": true
-}
-```
-
-Response:
-
-- Normal:
-
-```json
-{
-  "State": true,
-  "Error": ""
-}
-```
-
-- Error
-
-```json
-{
-  "State": false,
-  "Error": "Unable to complete operation."
-}
-```
-
-### Stop a Manipulator's movement
-
-| Event  | Input                     | Return                   |
-|--------|---------------------------|--------------------------|
-| `stop` | Manipulator ID (`string`) | Error Message (`string`) |
-
-__Examples:__
-
-Input:
-
-- "1"
-- "A"
-
-Response:
-
-- Normal: `""`
-- Error: `"Unable to stop manipulator."`
-
-### Stop All Manipulators
-
-| Event      | Input | Return                   |
-|------------|-------|--------------------------|
-| `stop_all` | None  | Error Message (`string`) |
-
-__Examples:__
-
-Input: None
-
-Response:
-
-- Normal: `""`
-- Error: `"Unable to stop manipulator."`
-
-### Unknown Event (Error)
-
-Response: `{"error", "Unknown event."}`
-
-## Notes
-
-- In the examples, the error response messages are generic examples. The actual error strings you see will be driven by
-  what exceptions are raised by the binding.

ephys_link-2.0.0b9/docs/home/citing.md

@@ -1,9 +0,0 @@
-# Citing
-
-If this project is used as part of a research project you should cite
-the [Pinpoint repository](https://github.com/VirtualBrainLab/Pinpoint). Please email
-Dan ([dbirman@uw.edu](mailto:dbirman@uw.edu)) if you have questions.
-
-Please reach out to Kenneth ([kjy5@uw.edu](mailto:kjy5@uw.edu)) for questions
-about the Electrophysiology Manipulator Link server. Bugs may be reported
-through the issues tab.

ephys_link-2.0.0b9/docs/home/contact.md

@@ -1,10 +0,0 @@
-# Contact
-
-Kenneth J. Yang is the primary developer and maintainer of Ephys Link. You can each him by his email: [kjy5@uw.edu](mailto:kjy5@uw.edu).
-
-Daniel Birman is the co-developer of Ephys Link. His information on the VBL [about page](https://virtualbrainlab.org/about/overview.html).
-
-As an open-source project, we welcome [bug reports](https://github.com/VirtualBrainLab/ephys-link/issues)
-and [discussions](https://github.com/VirtualBrainLab/ephys-link/discussions) on
-our [GitHub page](https://github.com/VirtualBrainLab/ephys-link)!
-

ephys_link-2.0.0b9/docs/home/how_it_works.md

@@ -1,76 +0,0 @@
-# How It Works
-
-This section provides an overview of how Ephys Link works. It is intended for users who want to understand the
-software's architecture and how it interacts with other systems.
-
-## Why Ephys Link?
-
-There exist many manipulator platforms in neuroscience research, each with its unique API and software. This diversity
-makes it difficult for tool developers to support multiple platforms. Ephys Link aims to solve this problem by providing
-a unified API for interacting with manipulators. This allows developers to write code that works with any manipulator
-supported by Ephys Link.
-
-## Ephys Link Architecture
-
-```mermaid
-flowchart LR
-    n1["Client Application"]
-    n3["Manipulator 1"]
-    n4["Manipulator 2"]
-    subgraph s1["Ephys Link"]
-        n6["Rectangle"]
-        n2["Server"]
-    end
-    n6["Bindings"] ---|" Manipulator 1 API "| n3
-    n1 ---|" Send Request "| n2
-    n2 ---|" Callback Response "| n1
-    n6 ---|" Manipulator 2 API "| n4
-    n3 --- n6
-    n4 --- n6
-    n2 ---|" Parse Request "| n6
-    n6 ---|" Send Response "| n2
-```
-
-This diagram shows the high-level architecture of Ephys Link. Ephys Link acts as an intermediary between a client
-applications and manipulators.
-
-Within Ephys Link, there is a server component that handles external communication and there are the bindings for each
-proprietary manipulator platform API. The server passes requests from client applications to the appropriate manipulator
-bindings which convert the requests to the appropriate manipulator API calls.
-
-## Example Message Flow
-
-Consider the following example of a request to move a manipulator to a specific position:
-
-```mermaid
-sequenceDiagram
-    participant C as Client Application
-    box Ephys Link
-        participant S as Server
-        participant B as Bindings
-    end
-    participant M as Manipulator Platform
-    C ->> S: Move manipulator to position (x, y, z)
-    S ->> B: set_position(x, y, z)
-    B ->> M: move(a, b, c, d)
-    loop Update Position
-        C -->> S: Get the current position
-        S -->> B: get_position()
-        B -->> M: position()
-        M -->> B: Now at (a, b, c, d)
-        B -->> S: Now at (x, y, z)
-        S -->> C: Now at (x, y, z)
-    end
-    M ->> B: Completed move, at (a, b, c, d)
-    B ->> S: Completed move, at (x, y, z)
-    S ->> C: Completed move, at (x, y, z)
-```
-
-Some things to notice:
-
-- The client application only ever speaks in (x, y, z) coordinates, never in the native manipulator platform's
-  coordinate system. The binding handles the conversion.
-- While one command is being fulfilled, the client application can still query the manipulator's current position.
-  Later, the manipulator can report when it is done and complete the movement request.
-- The manipulator often has a different API than Ephys Link (`move` vs `set_position`), but the binding handles the
-  translation.

ephys_link-2.0.0b9/docs/home/installation.md

@@ -1,40 +0,0 @@
-# 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 a keyboard is attached.
-
-## Pinpoint (Recommended Method)
-
-Pinpoint comes bundled with the correct version of Ephys Link. If you are using Pinpoint on the same computer your
-manipulators are connected to, you can launch the server from within Pinpoint. See the documentation
-on [connecting from Pinpoint](../usage/using_ephys_link.md#connecting-to-pinpoint).
-
-## Install as a Standalone Executable
-
-Download the latest standalone executable or zip from the [releases page](https://github.com/VirtualBrainLab/ephys-link/releases/latest).
-
-Then see the [usage documentation](../usage/starting_ephys_link.md) for how to run the server.
-
-## Install as a Python package
-
-```bash
-pip install ephys-link
-```
-
-or with [pipx](https://pipx.pypa.io/stable/) (recommended)
-
-```bash
-pipx install ephys-link
-```
-
-Then see the [usage documentation](../usage/starting_ephys_link.md) for how to run the server.
-
-## Install for Development
-
-See [development documentation](../development/index.md#installing-for-development) for more information.

ephys_link-2.0.0b9/docs/home/supported_manipulators.md

@@ -1,12 +0,0 @@
-# Supported Manipulators
-
-This is a current list of planned and supported manipulators in Ephys Link. If you use a manipulator that is not listed
-here, we suggest reaching out to your manipulator's manufacturer to request support for Ephys Link. Direct them to
-contact [Kenneth Yang and Daniel Birman](https://virtualbrainlab.org/about/overview.html)!
-
-| 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-2.0.0b9/docs/index.md

@@ -1,52 +0,0 @@
-# Electrophysiology Manipulator Link
-
-[![PyPI version](https://badge.fury.io/py/ephys-link.svg)](https://badge.fury.io/py/ephys-link)
-[![Deploy Documentation](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/deploy-docs.yml/badge.svg)](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/deploy-docs.yml)
-[![Pydantic v2](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/pydantic/pydantic/main/docs/badge/v2.json)](https://pydantic.dev)
-[![Hatch project](https://img.shields.io/badge/%F0%9F%A5%9A-Hatch-4051b5.svg)](https://github.com/pypa/hatch)
-[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
-[![Checked with pyright](https://microsoft.github.io/pyright/img/pyright_badge.svg)](https://microsoft.github.io/pyright/)
-
-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))
-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">
-
-<div class="grid cards" markdown>
-
--   __:fontawesome-solid-download: Get Started__
-
-    ---
-
-    Install Ephys Link and get started in seconds.
-
-
-    [:octicons-arrow-right-24: Install](home/installation.md)
-
--   __:fontawesome-solid-computer: Usage__
-
-    ---
-
-    Learn how to use Ephys Link to control your manipulators.
-
-    [:octicons-arrow-right-24: Usage](usage/starting_ephys_link.md)
-
--   __:fontawesome-regular-square-plus: Add a Manipulator Platform__
-
-    ---
-
-    Add a new manipulator platform to Ephys Link to enable control.
-
-    [:octicons-arrow-right-24: Develop](development/adding_a_manipulator.md)
-
--   __:fontawesome-solid-book-open: Learn About Pinpoint__
-
-    ---
-
-    Pinpoint is an experiment planning and automation tool that uses Ephys Link.
-
-    [:octicons-arrow-right-24: Learn More](https://virtualbrainlab.org/pinpoint/installation_and_use.html)
-</div>

ephys_link-2.0.0b9/docs/stylesheets/extra.css

@@ -1,5 +0,0 @@
-:root {
-    --md-primary-fg-color: #0FBBBB;
-    --md-primary-fg-color--light: #0FBBBB;
-    --md-primary-fg-color--dark: #0FBBBB;
-}

ephys_link-2.0.0b9/docs/stylesheets/mkdocstrings.css

@@ -1,42 +0,0 @@
-/* Fancier color for operators such as * and |. */
-.doc-signature .o {
-    color: var(--md-code-hl-special-color);
-}
-
-/* Fancier color for constants such as None, True, and False. */
-.doc-signature .kc {
-    color: var(--md-code-hl-constant-color);
-}
-
-/* Fancier color for built-in types (only useful when cross-references are used). */
-.doc-signature .n > a[href^="https://docs.python.org/"][href*="/functions.html#"],
-.doc-signature .n > a[href^="https://docs.python.org/"][href*="/stdtypes.html#"] {
-    color: var(--md-code-hl-constant-color);
-}
-/* Indentation. */
-div.doc-contents:not(.first) {
-    padding-left: 25px;
-    border-left: .05rem solid var(--md-typeset-table-color);
-}
-
-/* Mark external links as such. */
-a.external::after,
-a.autorefs-external::after {
-    /* https://primer.style/octicons/arrow-up-right-24 */
-    mask-image: url('data:image/svg+xml,<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M18.25 15.5a.75.75 0 00.75-.75v-9a.75.75 0 00-.75-.75h-9a.75.75 0 000 1.5h7.19L6.22 16.72a.75.75 0 101.06 1.06L17.5 7.56v7.19c0 .414.336.75.75.75z"></path></svg>');
-    -webkit-mask-image: url('data:image/svg+xml,<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M18.25 15.5a.75.75 0 00.75-.75v-9a.75.75 0 00-.75-.75h-9a.75.75 0 000 1.5h7.19L6.22 16.72a.75.75 0 101.06 1.06L17.5 7.56v7.19c0 .414.336.75.75.75z"></path></svg>');
-    content: ' ';
-
-    display: inline-block;
-    vertical-align: middle;
-    position: relative;
-
-    height: 1em;
-    width: 1em;
-    background-color: currentColor;
-}
-
-a.external:hover::after,
-a.autorefs-external:hover::after {
-    background-color: var(--md-accent-fg-color);
-}

ephys_link-2.0.0b9/docs/usage/experiment_automation.md

@@ -1,10 +0,0 @@
-# Experiment Automation
-
-Pinpoint and Ephys Link can work together to automate manual procedures in electrophysiology experiments. Follow the
-[instructions on Pinpoint's documentation](https://virtualbrainlab.org//pinpoint/tutorials/tutorial_ephys_copilot.html)
-to use automation in your next experiment!
-
-!!! note
-
-    Automation is still in early development. We recommend [contacting](https://virtualbrainlab.org/about/overview.html)
-    Dan Birman and Kenneth Yang if you would like to try it out!

ephys_link-2.0.0b9/docs/usage/starting_ephys_link.md

@@ -1,62 +0,0 @@
-# Starting Ephys Link
-
-Ephys Link is a server that runs in the background.
-
-!!! info
-
-    Most people should use Ephys Link through Pinpoint. See documentation
-    on [connecting from Pinpoint](using_ephys_link.md#connecting-to-pinpoint) and using Ephys Link
-    for [experiment automation](using_ephys_link.md#experiment-automation).
-
-If you are building a client application that will talk to Ephys Link, see
-the [Socket.IO API reference](../development/socketio_api.md).
-
-There are different ways of launching Ephys Link depending on its installation.
-
-## Standalone Executable (GUI)
-
-1. 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**.
-2. 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: `3000`
-
-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`.
-
-## Standalone Executable (CLI)
-
-Ephys Link can be launched from the command line directly without the
-configuration window. This is useful for computers
-or servers without graphical user interfaces.
-
-With the standalone executable downloaded, invoking the executable from the
-command line:
-
-```bash
-EphysLink-vX.X.X.exe -b
-```
-
-Use the actual name of the executable you downloaded. The `-b` or `--background` flag will launch the server without the
-configuration window and read configuration from CLI arguments.
-
-Here are some examples of how to start Ephys Link with a specific platform (replace `EphysLink.exe` with the actual name
-of the executable you downloaded):
-
-| Manipulator Platform                   | Command                              |
-|----------------------------------------|--------------------------------------|
-| Sensapex uMp-4 (default)               | `EphysLink.exe -b`                   |
-| New Scale Pathfinder MPM Control v2.8+ | `EphysLink.exe -b -t pathfinder-mpm` |
-
-More options can be viewed by running `EphysLink.exe -h`.
-
-## Python Package
-
-Ephys Link can be invoked from the command line with the same arguments as the standalone executable using the
-`ephys-link` binary (or `el` for short).

ephys_link-2.0.0b9/docs/usage/using_ephys_link.md

@@ -1,31 +0,0 @@
-# Using Ephys Link
-
-Ephys Link is designed to interact with other software. Any [Socket.IO](https://socket.io/) client application can talk
-to Ephys Link and access connected manipulators. [Pinpoint](https://github.com/VirtualBrainLab/Pinpoint) is a first-party application that does just that!
-
-!!! info "Stop All Movement"
-
-    As you start using Ephys Link with other software you may want to stop all manipulators in case of an emergency.
-    <br/><br/>
-    Press the keyboard shortcut <kbd>ctrl</kbd> + <kbd>shift</kbd> + <kbd>alt</kbd> + <kbd>q</kbd> to "quit" all
-    movement.
-
-## Connecting to Pinpoint
-
-[Pinpoint](https://github.com/VirtualBrainLab/Pinpoint) is a tool for planning electrophysiology recordings and other
-_in vivo_ insertions, as well as tracking the position of probes in real-time inside the brain.
-
-Ephys Link was developed alongside Pinpoint to facilitate tracking and positioning of manipulators. Follow the
-[instructions on Pinpoint's documentation](https://virtualbrainlab.org//pinpoint/tutorials/tutorial_ephys_link.html) to
-use Ephys Link inside Pinpoint!
-
-## Experiment Automation
-
-Pinpoint and Ephys Link can work together to automate manual procedures in electrophysiology experiments. Follow the
-[instructions on Pinpoint's documentation](https://virtualbrainlab.org//pinpoint/tutorials/tutorial_ephys_copilot.html)
-to use automation in your next experiment!
-
-!!! note
-
-    Automation is still in early development. We recommend [contacting](https://virtualbrainlab.org/about/overview.html)
-    Dan Birman and Kenneth Yang if you would like to try it out!

ephys_link-2.0.0b9/src/ephys_link/__about__.py

@@ -1 +0,0 @@
-__version__ = "2.0.0b9"