406 add back emergency stop button (#425)

kjy5 · web-flow · commit 432015422201 · 2025-01-10T06:28:08.000Z
* Use keyboard emergency stop

* Use a keyboard shortcut that will work anywhere

* Run type checker

* Update documentation

* Update links

* Added mdformat again

* Removed because it does too much

* Fixed link

* Install Python in Ci

* Run type check in non-installed env
diff --git a/.github/workflows/autoformat-and-lint.yml b/.github/workflows/autoformat-and-lint.yml
@@ -22,6 +22,12 @@ jobs:
           ref: ${{ github.head_ref }}
           token: ${{ secrets.WORKFLOW_COMMIT }}
 
+      - name: 🐍 Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+          cache: "pip"
+         
       - name: 📦 Install Hatch
         uses: pypa/hatch@install
 
@@ -37,6 +43,6 @@ jobs:
 
       - name: 🧶 Lint
         run: hatch fmt --check
-      
-#      - name: 🔍 Type Check
-#        run: hatch -e types run check
+
+      - name: 🔍 Type Check
+        run: hatch run check
diff --git a/docs/development/socketio_api.md b/docs/development/socketio_api.md
@@ -1,14 +1,13 @@
 # Socket.IO API
 
-This section documents the 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)!
+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
+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
@@ -19,7 +18,7 @@ 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.
+[Socket.IO acknowledgments](https://socket.io/docs/v4/#acknowledgements).
 
 ### Get Ephys Link Version
 
diff --git a/docs/home/installation.md b/docs/home/installation.md
@@ -7,16 +7,13 @@
    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.
+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/connecting_to_pinpoint.md).
+on [connecting from Pinpoint](../usage/using_ephys_link.md#connecting-to-pinpoint).
 
 ## Install as a Standalone Executable
 
diff --git a/docs/index.md b/docs/index.md
@@ -32,7 +32,7 @@ to communicate with manipulators used in electrophysiology experiments.
 
     Learn how to use Ephys Link to control your manipulators.
 
-    [:octicons-arrow-right-24: Usage](usage/index.md)
+    [:octicons-arrow-right-24: Usage](usage/starting_ephys_link.md)
 
 -   __:fontawesome-regular-square-plus: Add a Manipulator Platform__
 
diff --git a/docs/usage/connecting_to_pinpoint.md b/docs/usage/connecting_to_pinpoint.md
diff --git a/docs/usage/starting_ephys_link.md b/docs/usage/starting_ephys_link.md
@@ -5,8 +5,8 @@ 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](connecting_to_pinpoint.md) and using Ephys Link
-    for [experiment automation](experiment_automation.md).
+    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).
diff --git a/docs/usage/using_ephys_link.md b/docs/usage/using_ephys_link.md
@@ -0,0 +1,31 @@
+# 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!
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -102,8 +102,7 @@ nav:
           - home/citing.md
   - Usage:
       - usage/starting_ephys_link.md
-      - usage/connecting_to_pinpoint.md
-      - usage/experiment_automation.md
+      - usage/using_ephys_link.md
   - Development:
       - development/index.md
       - development/socketio_api.md
diff --git a/pyproject.toml b/pyproject.toml
@@ -31,6 +31,7 @@ classifiers = [
 dependencies = [
     "aiohttp==3.11.11",
     "colorama==0.4.6",
+    "keyboard==0.13.5",
     "packaging==24.2",
     "platformdirs==4.3.6",
     "pyserial==3.5",
@@ -61,7 +62,7 @@ exclude = ["/.github", "/.idea"]
 python = "3.13.1"
 dependencies = [
     "pyinstaller==6.11.1",
-    "basedpyright==1.23.1"
+    "basedpyright==1.23.1",
 ]
 [tool.hatch.envs.default.scripts]
 exe = "pyinstaller.exe ephys_link.spec -y -- -d && pyinstaller.exe ephys_link.spec -y"
diff --git a/src/ephys_link/__main__.py b/src/ephys_link/__main__.py
@@ -8,8 +8,11 @@
     ```
 """
 
+from asyncio import run
 from sys import argv
 
+from keyboard import add_hotkey
+
 from ephys_link.back_end.platform_handler import PlatformHandler
 from ephys_link.back_end.server import Server
 from ephys_link.front_end.cli import CLI
@@ -37,7 +40,8 @@ def main() -> None:
     # 4. Instantiate the Platform Handler with the appropriate platform bindings.
     platform_handler = PlatformHandler(options, console)
 
-    # 5. Instantiate the Emergency Stop service.
+    # 5. Add hotkeys for emergency stop.
+    _ = add_hotkey("ctrl+alt+shift+q", lambda: run(platform_handler.emergency_stop()))
 
     # 6. Start the server.
     Server(options, platform_handler, console).launch()
diff --git a/src/ephys_link/back_end/platform_handler.py b/src/ephys_link/back_end/platform_handler.py
@@ -308,3 +308,8 @@ async def stop_all(self) -> str:
             return self._console.pretty_exception(e)
         else:
             return ""
+
+    async def emergency_stop(self) -> None:
+        """Stops all manipulators with a message."""
+        self._console.critical_print("Emergency Stopping All Manipulators...")
+        _ = await self.stop_all()
diff --git a/src/ephys_link/bindings/mpm_binding.py b/src/ephys_link/bindings/mpm_binding.py
@@ -83,7 +83,7 @@ def __init__(self, port: int = 8080) -> None:
         self._movement_stopped = False
 
         # Data cache.
-        self.cache = {}
+        self.cache: dict[str, Any] = {}  # pyright: ignore [reportExplicitAny]
         self.cache_time = 0
 
     @staticmethod
@@ -286,7 +286,7 @@ async def _query_data(self) -> dict[str, Any]:  # pyright: ignore [reportExplici
             # Update cache if it's expired.
             if get_running_loop().time() - self.cache_time > self.CACHE_LIFETIME:
                 # noinspection PyTypeChecker
-                self.cache = (await get_running_loop().run_in_executor(None, get, self._url)).json()  # pyright: ignore [reportAny]
+                self.cache = (await get_running_loop().run_in_executor(None, get, self._url)).json()
                 self.cache_time = get_running_loop().time()
         except ConnectionError as connectionError:
             error_message = f"Unable to connect to MPM HTTP server: {connectionError}"
