286 launch gui (#287)

* Extract serial to e stop class

* Simplified main

* Privatized fields, reworking gui script

* Moved signal to server, launched GUI

* Add all manipulator options

* Save settings

* Version bump

* Update README for gui and exe

* Updated README, working on exe

* Use single EXE with versioned name

* Add icon to EXE

* Update launch language

* Fixed optional annotation

* Add build action to test building

* Use windows host for build

* Add build cache

* Add build badge

Author: kjy5

.github/workflows/build.yml

@@ -0,0 +1,34 @@
+name: Build
+
+on:
+  pull_request:
+  merge_group:
+
+jobs:
+  build:
+    name: Build
+    runs-on: windows-latest
+
+    steps:
+      - name: 🛎 Checkout
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.head_ref }}
+
+      - name: 🐍 Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.12'
+          cache: 'pip'
+
+      - name: 📦 Install Hatch
+        run: pip install hatch
+      
+      - name: 🗃️ Cache Build Artifacts
+        uses: actions/cache@v4
+        with:
+          path: build
+          key: ${{ runner.os }}-build
+
+      - name: 🔨 Build
+        run: hatch -e exe run build

README.md

@@ -1,6 +1,7 @@
 # Electrophysiology Manipulator Link
 
 [![PyPI version](https://badge.fury.io/py/ephys-link.svg)](https://badge.fury.io/py/ephys-link)
+[![Build](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/build.yml/badge.svg)](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/build.yml)
 [![CodeQL](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/codeql-analysis.yml/badge.svg)](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/codeql-analysis.yml)
 [![Dependency Review](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/dependency-review.yml/badge.svg)](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/dependency-review.yml)
 [![Hatch project](https://img.shields.io/badge/%F0%9F%A5%9A-Hatch-4051b5.svg)](https://github.com/pypa/hatch)
@@ -33,17 +34,12 @@ the [API reference](https://virtualbrainlab.org/api_reference_ephys_link.html).
 
 ## Prerequisites
 
-1. [Python ≥ 3.8, < 3.13](https://www.python.org/downloads/release/python-3116/)
-    1. Python 3.12+ requires the latest version
-       of Microsoft Visual C++ (MSVC v143+ x86/64) and the Windows SDK (10/11) to
-       be installed. They can be acquired through
-       the [Visual Studio Build Tools Installer](https://visualstudio.microsoft.com/visual-cpp-build-tools/).
-2. An **x86 Windows PC is required** to run the server.
-3. For Sensapex devices, the controller unit must be connected via an ethernet
+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.
-4. To use the emergency stop feature, ensure an Arduino with
+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.
@@ -52,59 +48,70 @@ the [API reference](https://virtualbrainlab.org/api_reference_ephys_link.html).
 is currently designed to interface with local/desktop instances of Pinpoint. It
 will not work with the web browser versions of Pinpoint at this time.
 
-<div style="padding: 15px; border: 1px solid transparent; border-color: transparent; margin-bottom: 20px; border-radius: 4px; color: #31708f; background-color: #d9edf7; border-color: #bce8f1;">
-<h3>Using a Python virtual environment is encouraged.</h3>
-<p>Create a virtual environment by running <code>python -m venv ephys_link</code></p>
-<p>Activate the environment by running <code>.\ephys_link\scripts\activate</code></p>
-<p>A virtual environment helps to isolate installed packages from other packages on your computer and ensures a clean installation of Ephys Link</p>
-</div>
+## Install as Standalone Executable
 
-## Install for use
+1. Download the latest executable 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".
 
-Run the following command to install the server:
+The configuration window will close and the server will launch. Your configurations will be saved for future use.
 
-```bash
-pip install ephys-link
-```
+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
 
-Update the server like any other Python package:
+- Server: `localhost`
+- Port: `8081`
 
-```bash
-pip install --upgrade ephys-link
-```
+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 for development
+## 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
+3. Install 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/).
+4. In a terminal, navigate to the repository's root directory and run
 
    ```bash
-   hatch shell
+      hatch shell
    ```
 
-This will create a virtual environment and install the package in editable mode.
+This will create a virtual environment, install Python 12 (if not found), and install the package in editable mode.
+
+## Install as a Python package
 
-# Usage
+```bash
+pip install ephys-link
+```
+
+Import the modules you need and launch the server.
 
-Run the following commands in a terminal to start the server for the desired manipulator platform:
+```python
+from ephys_link.server import Server
 
-| Manipulator Platform                 | Command                              |
-|--------------------------------------|--------------------------------------|
-| Sensapex uMp-4                       | `ephys-link`                         |
-| Sensapex uMp-3                       | `ephys-link -t ump3`                 |
-| New Scale                            | `ephys-link -t new_scale`            |
-| New Scale via Pathfinder HTTP server | `ephys-link -t new_scale_pathfinder` |
+server = Server()
+server.launch("sensapex", 8081)
+```
 
-There are a couple additional aliases for the Ephys Link executable: `ephys_link` and `el`.
+# CLI Usage
 
-By default, the server will broadcast with its local IP address on port 8081.
-**Copy this information into Pinpoint to connect**.
+Ephys Link can be launched from the command line directly. This is useful for computers or servers without graphical
+user interfaces.
 
-For example, if the server is running on the same computer that Pinpoint is, use
+Run the following commands in a terminal to start the server for the desired manipulator platform without the startup
+window:
 
-- Server: `localhost`
-- Port: `8081`
+| Manipulator Platform                 | Command                                     |
+|--------------------------------------|---------------------------------------------|
+| Sensapex uMp-4                       | `ephys-link.exe -b`                         |
+| Sensapex uMp-3                       | `ephys-link.exe -b -t ump3`                 |
+| New Scale                            | `ephys-link.exe -b -t new_scale`            |
+| New Scale via Pathfinder HTTP server | `ephys-link.exe -b -t new_scale_pathfinder` |
+
+More options can be viewed by running `ephys-link.exe -h`.
 
 # Documentation and More Information
 

assets/icon.ico

@@ -1,5 +1,6 @@
 # -*- mode: python ; coding: utf-8 -*-
 
+from ephys_link.__about__ import __version__ as version
 
 a = Analysis(
     ['src\\ephys_link\\__main__.py'],
@@ -18,26 +19,21 @@ pyz = PYZ(a.pure)
 exe = EXE(
     pyz,
     a.scripts,
+    a.binaries,
+    a.datas,
     [],
-    exclude_binaries=True,
-    name='ephys_link',
+    name=f"ephys_link-v{version}-Windows-x86_64",
     debug=False,
     bootloader_ignore_signals=False,
     strip=False,
     upx=True,
+    upx_exclude=[],
+    runtime_tmpdir=None,
     console=True,
     disable_windowed_traceback=False,
     argv_emulation=False,
     target_arch=None,
     codesign_identity=None,
     entitlements_file=None,
-)
-coll = COLLECT(
-    exe,
-    a.binaries,
-    a.datas,
-    strip=False,
-    upx=True,
-    upx_exclude=[],
-    name='ephys_link',
+    icon='assets\\icon.ico',
 )

ephys_link.spec

@@ -31,6 +31,7 @@ classifiers = [
 ]
 dependencies = [
     "aiohttp==3.9.1",
+    "platformdirs==4.1.0",
     "pyserial==3.5",
     "python-socketio==5.11.0",
     "pythonnet==3.0.3",

pyproject.toml

@@ -1 +1 @@
-__version__ = "1.1.1"
+__version__ = "1.2.0"

src/ephys_link/__about__.py

@@ -1,71 +1,20 @@
-import argparse
-import signal
-import time
-from threading import Event, Thread
-
-import serial
-import serial.tools.list_ports as ports
+from argparse import ArgumentParser
 
 from ephys_link import common as com
 from ephys_link.__about__ import __version__ as version
+from ephys_link.emergency_stop import EmergencyStop
+from ephys_link.gui import GUI
 from ephys_link.server import Server
 
-# Setup Arduino serial port (emergency stop)
-poll_rate = 0.05
-kill_serial_event = Event()
-poll_serial_thread: Thread
-
-# Create Server
-server = Server()
-
-
-def poll_serial(kill_event: Event, serial_port: str) -> None:
-    """Continuously poll serial port for data
-
-    :param kill_event: Event to stop polling
-    :type kill_event: Event
-    :param serial_port: The serial port to poll
-    :type serial_port: str
-    :return: None
-    """
-    target_port = serial_port
-    if serial_port is None:
-        # Search for serial ports
-        for port, desc, _ in ports.comports():
-            if "Arduino" in desc or "USB Serial Device" in desc:
-                target_port = port
-                break
-    elif serial_port == "no-e-stop":
-        # Stop polling if no-e-stop is specified
-        return None
-
-    ser = serial.Serial(target_port, 9600, timeout=poll_rate)
-    while not kill_event.is_set():
-        if ser.in_waiting > 0:
-            ser.readline()
-            # Cause a break
-            com.dprint("[EMERGENCY STOP]\t\t Stopping all manipulators")
-            server.platform.stop()
-            ser.reset_input_buffer()
-        time.sleep(poll_rate)
-    print("Close poll")
-    ser.close()
-
-
-def close_serial(_, __) -> None:
-    """Close the serial connection"""
-    print("[INFO]\t\t Closing serial")
-    kill_serial_event.set()
-    poll_serial_thread.join()
-
-
-# Setup argument parser
-parser = argparse.ArgumentParser(
+# Setup argument parser.
+parser = ArgumentParser(
     description="Electrophysiology Manipulator Link: a websocket interface for"
     " manipulators in electrophysiology experiments",
     prog="python -m ephys-link",
 )
-# parser.add_argument("-g", "--gui", dest="gui", action="store_true", help="Launches GUI")
+parser.add_argument(
+    "-b", "--background", dest="background", action="store_true", help="Launches in headless mode (no GUI)"
+)
 parser.add_argument(
     "-t",
     "--type",
@@ -111,34 +60,28 @@ def close_serial(_, __) -> None:
 def main() -> None:
     """Main function"""
 
-    # Parse arguments
+    # Parse arguments.
     args = parser.parse_args()
-    com.DEBUG = args.debug
 
-    # Setup serial port
-    if args.serial != "no-e-stop":
-        # Register serial exit
-        signal.signal(signal.SIGTERM, close_serial)
-        signal.signal(signal.SIGINT, close_serial)
+    # Launch GUI if not background.
+    if not args.background:
+        gui = GUI()
+        gui.launch()
+        return None
+
+    # Otherwise, create Server from CLI.
+    server = Server()
 
-        # Start emergency stop system if serial is provided
-        global poll_serial_thread
-        poll_serial_thread = Thread(
-            target=poll_serial,
-            args=(
-                kill_serial_event,
-                args.serial,
-            ),
-            daemon=True,
-        )
-        poll_serial_thread.start()
+    # Continue with CLI if not.
+    com.DEBUG = args.debug
 
-    # Register server exit
-    signal.signal(signal.SIGTERM, server.close_server)
-    signal.signal(signal.SIGINT, server.close_server)
+    # Setup serial port.
+    if args.serial != "no-e-stop":
+        e_stop = EmergencyStop(server, args.serial)
+        e_stop.watch()
 
-    # Launch with parsed arguments on main thread
-    server.launch_server(args.type, args.port, args.pathfinder_port)
+    # Launch with parsed arguments on main thread.
+    server.launch(args.type, args.port, args.pathfinder_port)
 
 
 if __name__ == "__main__":