ephys-link 1.1.1__tar.gz → 1.2.0__tar.gz

{ephys_link-1.1.1 → ephys_link-1.2.0}/.gitignore

@@ -32,7 +32,6 @@ MANIFEST
 #  Usually these files are written by a python script from a template
 #  before PyInstaller builds the exe, so as to inject date/other infos into it.
 *.manifest
-*.spec
 
 # Installer logs
 pip-log.txt

{ephys_link-1.1.1 → ephys_link-1.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ephys-link
-Version: 1.1.1
+Version: 1.2.0
 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
@@ -27,6 +27,7 @@ Classifier: Programming Language :: Python :: Implementation :: PyPy
 Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Requires-Python: <3.13,>=3.8
 Requires-Dist: aiohttp==3.9.1
+Requires-Dist: platformdirs==4.1.0
 Requires-Dist: pyserial==3.5
 Requires-Dist: python-socketio==5.11.0
 Requires-Dist: pythonnet==3.0.3
@@ -37,6 +38,7 @@ Description-Content-Type: text/markdown
 # 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)
@@ -52,10 +54,10 @@ to communicate with manipulators used in electrophysiology experiments.
 
 **Supported Manipulators:**
 
-| Manufacturer | Model                                                             |
-|--------------|-------------------------------------------------------------------|
-| Sensapex     | <ul> <li>uMp-4</li> <li>uMp-3</li> </ul>                          |
-| New Scale    | <ul> <li>Pathfinder MPM Control</li> <li>M3-USB-3:1-EP</li> </ul> |
+| Manufacturer | Model                                                                     |
+|--------------|---------------------------------------------------------------------------|
+| Sensapex     | <ul> <li>uMp-4</li> <li>uMp-3</li> </ul>                                  |
+| New Scale    | <ul> <li>Pathfinder MPM Control v2.8.8+</li> <li>M3-USB-3:1-EP</li> </ul> |
 
 Ephys Link is an open and extensible platform. It is designed to easily support integration with other manipulators.
 
@@ -69,17 +71,12 @@ 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.
@@ -88,59 +85,79 @@ 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
    ```
 
-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.
 
-# Usage
+## Install as a Python package
 
-Run the following commands in a terminal to start the server for the desired manipulator platform:
+```bash
+pip install ephys-link
+```
 
-| 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` |
+Import the modules you need and launch the server.
 
-There are a couple additional aliases for the Ephys Link executable: `ephys_link` and `el`.
+```python
+from ephys_link.server import Server
 
-By default, the server will broadcast with its local IP address on port 8081.
-**Copy this information into Pinpoint to connect**.
+server = Server()
+server.launch("sensapex", 8081)
+```
 
-For example, if the server is running on the same computer that Pinpoint is, use
+# CLI Usage
 
-- Server: `localhost`
-- Port: `8081`
+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
+ephys_link-vX.X.X-Windows-x86_64.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.
+
+Run the following commands in a terminal to start the server for the desired manipulator platform without the startup
+window (replace `ephys_link.exe` with the actual name of the executable you downloaded):
+
+| Manipulator Platform                     | Command                                     |
+|------------------------------------------|---------------------------------------------|
+| Sensapex uMp-4                           | `ephys_link.exe -b`                         |
+| Sensapex uMp-3                           | `ephys_link.exe -b -t ump3`                 |
+| New Scale Pathfinder MPM Control v2.8.8+ | `ephys_link.exe -b -t new_scale_pathfinder` |
+| New Scale M3-USB-3:1-EP                  | `ephys_link.exe -b -t new_scale`            |
+
+More options can be viewed by running `ephys_link.exe -h`.
 
 # Documentation and More Information
 

{ephys_link-1.1.1 → ephys_link-1.2.0}/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)
@@ -16,10 +17,10 @@ to communicate with manipulators used in electrophysiology experiments.
 
 **Supported Manipulators:**
 
-| Manufacturer | Model                                                             |
-|--------------|-------------------------------------------------------------------|
-| Sensapex     | <ul> <li>uMp-4</li> <li>uMp-3</li> </ul>                          |
-| New Scale    | <ul> <li>Pathfinder MPM Control</li> <li>M3-USB-3:1-EP</li> </ul> |
+| Manufacturer | Model                                                                     |
+|--------------|---------------------------------------------------------------------------|
+| Sensapex     | <ul> <li>uMp-4</li> <li>uMp-3</li> </ul>                                  |
+| New Scale    | <ul> <li>Pathfinder MPM Control v2.8.8+</li> <li>M3-USB-3:1-EP</li> </ul> |
 
 Ephys Link is an open and extensible platform. It is designed to easily support integration with other manipulators.
 
@@ -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 +48,79 @@ 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
    ```
 
-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.
 
-# Usage
+## Install as a Python package
 
-Run the following commands in a terminal to start the server for the desired manipulator platform:
+```bash
+pip install ephys-link
+```
 
-| 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` |
+Import the modules you need and launch the server.
 
-There are a couple additional aliases for the Ephys Link executable: `ephys_link` and `el`.
+```python
+from ephys_link.server import Server
 
-By default, the server will broadcast with its local IP address on port 8081.
-**Copy this information into Pinpoint to connect**.
+server = Server()
+server.launch("sensapex", 8081)
+```
 
-For example, if the server is running on the same computer that Pinpoint is, use
+# CLI Usage
 
-- Server: `localhost`
-- Port: `8081`
+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
+ephys_link-vX.X.X-Windows-x86_64.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.
+
+Run the following commands in a terminal to start the server for the desired manipulator platform without the startup
+window (replace `ephys_link.exe` with the actual name of the executable you downloaded):
+
+| Manipulator Platform                     | Command                                     |
+|------------------------------------------|---------------------------------------------|
+| Sensapex uMp-4                           | `ephys_link.exe -b`                         |
+| Sensapex uMp-3                           | `ephys_link.exe -b -t ump3`                 |
+| New Scale Pathfinder MPM Control v2.8.8+ | `ephys_link.exe -b -t new_scale_pathfinder` |
+| New Scale M3-USB-3:1-EP                  | `ephys_link.exe -b -t new_scale`            |
+
+More options can be viewed by running `ephys_link.exe -h`.
 
 # Documentation and More Information
 

ephys_link-1.2.0/ephys_link.spec

@@ -0,0 +1,39 @@
+# -*- mode: python ; coding: utf-8 -*-
+
+from ephys_link.__about__ import __version__ as version
+
+a = Analysis(
+    ['src\\ephys_link\\__main__.py'],
+    pathex=[],
+    binaries=[('src\\ephys_link\\resources', 'ephys_link\\resources')],
+    datas=[],
+    hiddenimports=['engineio.async_drivers.aiohttp', 'engineio.async_aiohttp'],
+    hookspath=[],
+    hooksconfig={},
+    runtime_hooks=[],
+    excludes=[],
+    noarchive=False,
+)
+pyz = PYZ(a.pure)
+
+exe = EXE(
+    pyz,
+    a.scripts,
+    a.binaries,
+    a.datas,
+    [],
+    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,
+    icon='assets\\icon.ico',
+)

{ephys_link-1.1.1 → ephys_link-1.2.0}/pyproject.toml

@@ -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",
@@ -82,6 +83,14 @@ dependencies = [
 [tool.hatch.envs.types.scripts]
 check = "mypy --install-types --non-interactive {args:src/ephys_link tests}"
 
+[tool.hatch.envs.exe]
+python = "3.12"
+dependencies = [
+    "pyinstaller==6.3.0",
+]
+[tool.hatch.envs.exe.scripts]
+build = "pyinstaller.exe ephys_link.spec -y"
+
 [tool.coverage.run]
 source_pkgs = ["ephys_link", "tests"]
 branch = true

ephys_link-1.2.0/src/ephys_link/__about__.py

@@ -0,0 +1 @@
+__version__ = "1.2.0"

ephys_link-1.2.0/src/ephys_link/__main__.py

@@ -0,0 +1,88 @@
+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 argument parser.
+parser = ArgumentParser(
+    description="Electrophysiology Manipulator Link: a websocket interface for"
+    " manipulators in electrophysiology experiments",
+    prog="python -m ephys-link",
+)
+parser.add_argument(
+    "-b", "--background", dest="background", action="store_true", help="Launches in headless mode (no GUI)"
+)
+parser.add_argument(
+    "-t",
+    "--type",
+    type=str,
+    dest="type",
+    default="sensapex",
+    help='Manipulator type (i.e. "sensapex", "new_scale", or "new_scale_pathfinder").' ' Default: "sensapex"',
+)
+parser.add_argument("-d", "--debug", dest="debug", action="store_true", help="Enable debug mode")
+parser.add_argument(
+    "-p",
+    "--port",
+    type=int,
+    default=8081,
+    dest="port",
+    help="Port to serve on. Default: 8081 (avoids conflict with other HTTP servers)",
+)
+parser.add_argument(
+    "--pathfinder_port",
+    type=int,
+    default=8080,
+    dest="pathfinder_port",
+    help="Port New Scale Pathfinder's server is on. Default: 8080",
+)
+parser.add_argument(
+    "-s",
+    "--serial",
+    type=str,
+    default="no-e-stop",
+    dest="serial",
+    nargs="?",
+    help="Emergency stop serial port (i.e. COM3). Default: disables emergency stop",
+)
+parser.add_argument(
+    "-v",
+    "--version",
+    action="version",
+    version=f"Electrophysiology Manipulator Link v{version}",
+    help="Print version and exit",
+)
+
+
+def main() -> None:
+    """Main function"""
+
+    # Parse arguments.
+    args = parser.parse_args()
+
+    # Launch GUI if not background.
+    if not args.background:
+        gui = GUI()
+        gui.launch()
+        return None
+
+    # Otherwise, create Server from CLI.
+    server = Server()
+
+    # Continue with CLI if not.
+    com.DEBUG = args.debug
+
+    # 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(args.type, args.port, args.pathfinder_port)
+
+
+if __name__ == "__main__":
+    main()

ephys_link-1.2.0/src/ephys_link/emergency_stop.py

@@ -0,0 +1,67 @@
+from signal import SIGINT, SIGTERM, signal
+from threading import Event, Thread
+from time import sleep
+
+from serial import Serial
+from serial.tools import list_ports
+
+from ephys_link.common import dprint
+from ephys_link.server import Server
+
+
+class EmergencyStop:
+    """Serial system for emergency stop"""
+
+    def __init__(self, server: Server, serial_port: str) -> None:
+        """Setup serial port for emergency stop
+
+        :param server: The Ephys Link server instance
+        :type server: Server
+        :param serial_port: The serial port to poll
+        :type serial_port: str
+        :return: None
+        """
+        self._server = server
+        self._serial_port = serial_port
+        self._poll_rate = 0.05
+        self._kill_serial_event = Event()
+        self._poll_serial_thread = Thread(target=self._poll_serial, daemon=True)
+
+        # Register signals
+        signal(SIGTERM, self._close_serial)
+        signal(SIGINT, self._close_serial)
+
+    def watch(self) -> None:
+        """Start polling serial port for emergency stop"""
+        self._poll_serial_thread.start()
+
+    def _poll_serial(self) -> None:
+        """Continuously poll serial port for data
+
+        Close port on kill event
+        """
+        target_port = self._serial_port
+        if self._serial_port is None:
+            # Search for serial ports
+            for port, desc, _ in list_ports.comports():
+                if "Arduino" in desc or "USB Serial Device" in desc:
+                    target_port = port
+                    break
+
+        serial = Serial(target_port, 9600, timeout=self._poll_rate)
+        while not self._kill_serial_event.is_set():
+            if serial.in_waiting > 0:
+                serial.readline()
+                # Cause a break
+                dprint("[EMERGENCY STOP]\t\t Stopping all manipulators")
+                self._server.platform.stop()
+                serial.reset_input_buffer()
+            sleep(self._poll_rate)
+        print("Close poll")
+        serial.close()
+
+    def _close_serial(self, _, __) -> None:
+        """Close the serial connection"""
+        print("[INFO]\t\t Closing serial")
+        self._kill_serial_event.set()
+        self._poll_serial_thread.join()

ephys_link-1.2.0/src/ephys_link/gui.py

@@ -0,0 +1,163 @@
+from json import dumps, load
+from os import makedirs
+from os.path import exists
+from socket import gethostbyname, gethostname
+from tkinter import CENTER, RIGHT, BooleanVar, E, IntVar, StringVar, Tk, ttk
+
+from platformdirs import user_config_dir
+
+import ephys_link.common as com
+from ephys_link.__about__ import __version__ as version
+from ephys_link.emergency_stop import EmergencyStop
+from ephys_link.server import Server
+
+SETTINGS_DIR = f"{user_config_dir()}\\VBL\\Ephys Link"
+SETTINGS_FILENAME = "settings.json"
+
+
+class GUI:
+    """GUI definition for Ephys Link"""
+
+    def __init__(self) -> None:
+        """Setup and construction of the Tk GUI"""
+
+        self._root = Tk()
+
+        # Create default settings dictionary
+        settings = {"type": "sensapex", "debug": False, "port": 8081, "pathfinder_port": 8080, "serial": "no-e-stop"}
+
+        # Read settings.
+        if exists(f"{SETTINGS_DIR}\\{SETTINGS_FILENAME}"):
+            with open(f"{SETTINGS_DIR}\\{SETTINGS_FILENAME}") as settings_file:
+                settings = load(settings_file)
+
+        self._type = StringVar(value=settings["type"])
+        self._debug = BooleanVar(value=settings["debug"])
+        self._port = IntVar(value=settings["port"])
+        self._pathfinder_port = IntVar(value=settings["pathfinder_port"])
+        self._serial = StringVar(value=settings["serial"])
+
+    def launch(self) -> None:
+        """Build and launch GUI"""
+
+        # Build and run GUI.
+        self._build_gui()
+        self._root.mainloop()
+
+    def _build_gui(self):
+        """Build GUI"""
+
+        self._root.title(f"Ephys Link v{version}")
+
+        mainframe = ttk.Frame(self._root, padding=3)
+        mainframe.grid(column=0, row=0, sticky="news")
+        self._root.columnconfigure(0, weight=1)
+        self._root.rowconfigure(0, weight=1)
+        mainframe.columnconfigure(0, weight=1)
+        mainframe.rowconfigure(0, weight=1)
+
+        # Server serving settings.
+
+        server_serving_settings = ttk.LabelFrame(mainframe, text="Serving Settings", padding=3)
+        server_serving_settings.grid(column=0, row=0, sticky="news")
+
+        # IP.
+        ttk.Label(server_serving_settings, text="IP:", anchor=E, justify=RIGHT).grid(column=0, row=0, sticky="we")
+        ttk.Label(server_serving_settings, text=gethostbyname(gethostname())).grid(column=1, row=0, sticky="we")
+
+        # Port.
+        ttk.Label(server_serving_settings, text="Port:", anchor=E, justify=RIGHT).grid(column=0, row=1, sticky="we")
+        ttk.Entry(server_serving_settings, textvariable=self._port, width=5, justify=CENTER).grid(
+            column=1, row=1, sticky="we"
+        )
+
+        # ---
+
+        # Platform type.
+        platform_type_settings = ttk.LabelFrame(mainframe, text="Platform Type", padding=3)
+        platform_type_settings.grid(column=0, row=1, sticky="news")
+
+        ttk.Radiobutton(
+            platform_type_settings,
+            text="Sensapex uMp-4",
+            variable=self._type,
+            value="sensapex",
+        ).grid(column=0, row=0, sticky="we")
+        ttk.Radiobutton(
+            platform_type_settings,
+            text="Sensapex uMp-3",
+            variable=self._type,
+            value="ump3",
+        ).grid(column=0, row=1, sticky="we")
+        ttk.Radiobutton(
+            platform_type_settings,
+            text="Pathfinder MPM Control v2.8.8+",
+            variable=self._type,
+            value="new_scale_pathfinder",
+        ).grid(column=0, row=2, sticky="we")
+        ttk.Radiobutton(
+            platform_type_settings,
+            text="New Scale M3-USB-3:1-EP",
+            variable=self._type,
+            value="new_scale",
+        ).grid(column=0, row=3, sticky="we")
+
+        # ---
+
+        # New Scale Settings.
+        new_scale_settings = ttk.LabelFrame(mainframe, text="Pathfinder Settings", padding=3)
+        new_scale_settings.grid(column=0, row=2, sticky="news")
+
+        # Port
+        ttk.Label(new_scale_settings, text="HTTP Server Port:", anchor=E, justify=RIGHT).grid(
+            column=0, row=1, sticky="we"
+        )
+        ttk.Entry(new_scale_settings, textvariable=self._pathfinder_port, width=5, justify=CENTER).grid(
+            column=1, row=1, sticky="we"
+        )
+
+        # ---
+
+        # Emergency Stop serial port.
+        e_stop_settings = ttk.LabelFrame(mainframe, text="Emergency Stop Settings", padding=3)
+        e_stop_settings.grid(column=0, row=3, sticky="news")
+
+        # Serial Port
+        ttk.Label(e_stop_settings, text="Serial Port:", anchor=E, justify=RIGHT).grid(column=0, row=1, sticky="we")
+        ttk.Entry(e_stop_settings, textvariable=self._serial, justify=CENTER).grid(column=1, row=1, sticky="we")
+
+        # Server launch button.
+        ttk.Button(
+            mainframe,
+            text="Launch Server",
+            command=self._launch_server,
+        ).grid(column=0, row=4, columnspan=2, sticky="we")
+
+    def _launch_server(self) -> None:
+        """Launch server based on GUI settings"""
+
+        # Close GUI.
+        self._root.destroy()
+
+        # Save settings.
+        settings = {
+            "type": self._type.get(),
+            "debug": self._debug.get(),
+            "port": self._port.get(),
+            "pathfinder_port": self._pathfinder_port.get(),
+            "serial": self._serial.get(),
+        }
+        makedirs(SETTINGS_DIR, exist_ok=True)
+        with open(f"{SETTINGS_DIR}\\{SETTINGS_FILENAME}", "w+") as f:
+            f.write(dumps(settings))
+
+        # Launch server.
+        server = Server()
+
+        com.DEBUG = self._debug.get()
+
+        if self._serial.get() != "no-e-stop":
+            e_stop = EmergencyStop(server, self._serial.get())
+            e_stop.watch()
+
+        server.launch(self._type.get(), self._port.get(), self._pathfinder_port.get())

{ephys_link-1.1.1 → ephys_link-1.2.0}/src/ephys_link/server.py

@@ -9,8 +9,11 @@ every event, the server does the following:
 4. Relay the response from :mod:`ephys_link.sensapex_handler` to the callback function
 """
 
+from __future__ import annotations
+
 import json
 import sys
+from signal import SIGINT, SIGTERM, signal
 from typing import TYPE_CHECKING, Any
 
 import socketio
@@ -40,10 +43,14 @@ class Server:
         # Is the server running?
         self.is_running = False
 
-        # Current platform handler (defaults to Sensapex)
+        # Current platform handler (defaults to Sensapex).
         self.platform: PlatformHandler = SensapexHandler()
 
-        # Attach server to the web app
+        # Register server exit handlers.
+        signal(SIGTERM, self.close_server)
+        signal(SIGINT, self.close_server)
+
+        # Attach server to the web app.
         self.sio.attach(self.app)
 
         # Declare events
@@ -349,7 +356,7 @@ class Server:
         print(f"[UNKNOWN EVENT]:\t {data}")
         return "UNKNOWN_EVENT"
 
-    def launch_server(self, platform_type: str, server_port: int, pathfinder_port: int) -> None:
+    def launch(self, platform_type: str, server_port: int, pathfinder_port: int | None = None) -> None:
         """Launch the server.
 
         :param platform_type: Parsed argument for platform type.

ephys_link-1.1.1/src/ephys_link/__about__.py

@@ -1 +0,0 @@
-__version__ = "1.1.1"

ephys_link-1.1.1/src/ephys_link/__main__.py

@@ -1,145 +0,0 @@
-import argparse
-import signal
-import time
-from threading import Event, Thread
-
-import serial
-import serial.tools.list_ports as ports
-
-from ephys_link import common as com
-from ephys_link.__about__ import __version__ as version
-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(
-    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(
-    "-t",
-    "--type",
-    type=str,
-    dest="type",
-    default="sensapex",
-    help='Manipulator type (i.e. "sensapex", "new_scale", or "new_scale_pathfinder").' ' Default: "sensapex"',
-)
-parser.add_argument("-d", "--debug", dest="debug", action="store_true", help="Enable debug mode")
-parser.add_argument(
-    "-p",
-    "--port",
-    type=int,
-    default=8081,
-    dest="port",
-    help="Port to serve on. Default: 8081 (avoids conflict with other HTTP servers)",
-)
-parser.add_argument(
-    "--pathfinder_port",
-    type=int,
-    default=8080,
-    dest="pathfinder_port",
-    help="Port New Scale Pathfinder's server is on. Default: 8080",
-)
-parser.add_argument(
-    "-s",
-    "--serial",
-    type=str,
-    default="no-e-stop",
-    dest="serial",
-    nargs="?",
-    help="Emergency stop serial port (i.e. COM3). Default: disables emergency stop",
-)
-parser.add_argument(
-    "-v",
-    "--version",
-    action="version",
-    version=f"Electrophysiology Manipulator Link v{version}",
-    help="Print version and exit",
-)
-
-
-def main() -> None:
-    """Main function"""
-
-    # 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)
-
-        # 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()
-
-    # Register server exit
-    signal.signal(signal.SIGTERM, server.close_server)
-    signal.signal(signal.SIGINT, server.close_server)
-
-    # Launch with parsed arguments on main thread
-    server.launch_server(args.type, args.port, args.pathfinder_port)
-
-
-if __name__ == "__main__":
-    main()

ephys_link-1.1.1/src/ephys_link/gui.py

@@ -1,167 +0,0 @@
-import socket
-from argparse import Namespace
-from threading import Event, Thread
-from tkinter import CENTER, RIGHT, E, IntVar, StringVar, Tk, ttk
-
-# GUI Variables
-is_running = False
-server_port: IntVar
-platform_type: StringVar
-new_scale_port: IntVar
-e_stop_serial_port: StringVar
-server_launch_button_text: StringVar
-
-
-class GUI:
-    """GUI definition for Ephys Link
-
-    :param root: Root object of the Tk GUI
-    :type root: Tk
-    """
-
-    def __init__(
-        self,
-        root: Tk,
-        launch_func: callable,
-        manipulator_stop_func: callable,
-        poll_serial_func: callable,
-        parsed_args: Namespace,
-    ) -> None:
-        """Setup and construction of the Tk GUI"""
-
-        # Fields
-        self._root = root
-        self._launch_func = launch_func
-        self._manipulator_stop_func = manipulator_stop_func
-        self._poll_serial_func = poll_serial_func
-        self._kill_serial_event = Event()
-        self._parsed_args = parsed_args
-
-        # Update GUI variables with defaults
-        global server_port, platform_type, new_scale_port, e_stop_serial_port
-        global server_launch_button_text
-        server_port = IntVar(value=self._parsed_args.port)
-        platform_type = StringVar(value=self._parsed_args.type)
-        new_scale_port = IntVar(value=self._parsed_args.new_scale_port)
-        e_stop_serial_port = StringVar(value=self._parsed_args.serial)
-        server_launch_button_text = StringVar(value="Start Server")
-
-        # Build GUI
-        self.build_gui()
-
-    def build_gui(self):
-        """Build GUI"""
-
-        self._root.title("Ephys Link")
-
-        mainframe = ttk.Frame(self._root, padding=3)
-        mainframe.grid(column=0, row=0, sticky="news")
-        self._root.columnconfigure(0, weight=1)
-        self._root.rowconfigure(0, weight=1)
-        mainframe.columnconfigure(0, weight=1)
-        mainframe.rowconfigure(0, weight=1)
-
-        # Server serving settings
-
-        server_serving_settings = ttk.LabelFrame(mainframe, text="Serving settings", padding=3)
-        server_serving_settings.grid(column=0, row=0, sticky="news")
-
-        # IP
-        ttk.Label(server_serving_settings, text="IP:", anchor=E, justify=RIGHT).grid(column=0, row=0, sticky="we")
-        ttk.Label(server_serving_settings, text=socket.gethostbyname(socket.gethostname())).grid(
-            column=1, row=0, sticky="we"
-        )
-
-        # Port
-        ttk.Label(server_serving_settings, text="Port:", anchor=E, justify=RIGHT).grid(column=0, row=1, sticky="we")
-        ttk.Entry(server_serving_settings, textvariable=server_port, width=5, justify=CENTER).grid(
-            column=1, row=1, sticky="we"
-        )
-
-        # ---
-
-        # Platform type
-        platform_type_settings = ttk.LabelFrame(mainframe, text="Platform Type", padding=3)
-        platform_type_settings.grid(column=0, row=1, sticky="news")
-
-        ttk.Radiobutton(
-            platform_type_settings,
-            text="Sensapex uMp",
-            variable=platform_type,
-            value="sensapex",
-        ).grid(column=0, row=0, sticky="we")
-        ttk.Radiobutton(
-            platform_type_settings,
-            text="New Scale",
-            variable=platform_type,
-            value="new_scale",
-        ).grid(column=0, row=1, sticky="we")
-
-        # ---
-
-        # New Scale Settings
-        new_scale_settings = ttk.LabelFrame(mainframe, text="New Scale settings", padding=3)
-        new_scale_settings.grid(column=0, row=2, sticky="news")
-
-        # Port
-        ttk.Label(new_scale_settings, text="HTTP Server Port:", anchor=E, justify=RIGHT).grid(
-            column=0, row=1, sticky="we"
-        )
-        ttk.Entry(new_scale_settings, textvariable=new_scale_port, width=5, justify=CENTER).grid(
-            column=1, row=1, sticky="we"
-        )
-
-        # ---
-
-        # Emergency Stop serial port
-        e_stop_settings = ttk.LabelFrame(mainframe, text="Emergency Stop Settings", padding=3)
-        e_stop_settings.grid(column=0, row=3, sticky="news")
-
-        # Serial Port
-        ttk.Label(e_stop_settings, text="Serial Port:", anchor=E, justify=RIGHT).grid(column=0, row=1, sticky="we")
-        ttk.Entry(e_stop_settings, textvariable=e_stop_serial_port, justify=CENTER).grid(column=1, row=1, sticky="we")
-
-        # Server start/stop button
-        ttk.Button(
-            mainframe,
-            textvariable=server_launch_button_text,
-            command=lambda: self.start_stop_server(not is_running),
-        ).grid(column=0, row=4, columnspan=2, sticky="we")
-
-    def start_stop_server(self, start: bool) -> None:
-        """Start/stop server and update button text
-
-        :param start: Whether to start or stop the server
-        :type start: bool
-        :return None
-        """
-        global is_running
-        is_running = not is_running
-        if start:
-            # Launch serial
-            Thread(
-                target=self._poll_serial_func,
-                args=(
-                    self._kill_serial_event,
-                    e_stop_serial_port.get(),
-                ),
-                daemon=True,
-            ).start()
-            # Launch server
-            Thread(
-                target=self._launch_func,
-                args=(platform_type.get(), server_port.get(), new_scale_port.get()),
-                daemon=True,
-            ).start()
-
-            # Update UI
-            server_launch_button_text.set("Close Server")
-        else:
-            # Stop serial
-            self._kill_serial_event.set()
-
-            # Stop manipulators
-            self._manipulator_stop_func(0)
-
-            # Close
-            self._root.destroy()