ephys-link 1.2.5__tar.gz → 1.2.8__tar.gz

{ephys_link-1.2.5 → ephys_link-1.2.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ephys-link
-Version: 1.2.5
+Version: 1.2.8
 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
@@ -31,6 +31,7 @@ Requires-Dist: platformdirs==4.2.0
 Requires-Dist: pyserial==3.5
 Requires-Dist: python-socketio==5.11.1
 Requires-Dist: pythonnet==3.0.3
+Requires-Dist: requests==2.31.0
 Requires-Dist: sensapex==1.400.0
 Requires-Dist: wheel==0.42.0
 Description-Content-Type: text/markdown
@@ -86,6 +87,12 @@ 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.
 
+## Launch from Pinpoint (Recommended)
+
+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. Follow the instructions in
+the [Pinpoint documentation](https://virtualbrainlab.org/pinpoint/tutorials/tutorial_ephys_link.html#configure-and-launch-ephys-link).
+
 ## Install as Standalone Executable
 
 1. Download the latest executable from

{ephys_link-1.2.5 → ephys_link-1.2.8}/README.md

@@ -49,6 +49,12 @@ 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.
 
+## Launch from Pinpoint (Recommended)
+
+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. Follow the instructions in
+the [Pinpoint documentation](https://virtualbrainlab.org/pinpoint/tutorials/tutorial_ephys_link.html#configure-and-launch-ephys-link).
+
 ## Install as Standalone Executable
 
 1. Download the latest executable from

{ephys_link-1.2.5 → ephys_link-1.2.8}/pyproject.toml

@@ -35,6 +35,7 @@ dependencies = [
     "pyserial==3.5",
     "python-socketio==5.11.1",
     "pythonnet==3.0.3",
+    "requests==2.31.0",
     "wheel==0.42.0",
     "sensapex==1.400.0",
 ]
@@ -91,6 +92,7 @@ dependencies = [
 ]
 [tool.hatch.envs.exe.scripts]
 build = "pyinstaller.exe ephys_link.spec -y"
+build_clean = "pyinstaller.exe ephys_link.spec -y --clean"
 
 [tool.coverage.run]
 source_pkgs = ["ephys_link", "tests"]

ephys_link-1.2.8/src/ephys_link/__about__.py

@@ -0,0 +1 @@
+__version__ = "1.2.8"

{ephys_link-1.2.5 → ephys_link-1.2.8}/src/ephys_link/__main__.py

@@ -1,4 +1,5 @@
 from argparse import ArgumentParser
+from sys import argv
 
 from ephys_link import common as com
 from ephys_link.__about__ import __version__ as version
@@ -9,11 +10,12 @@ from ephys_link.server import Server
 # Setup argument parser.
 parser = ArgumentParser(
     description="Electrophysiology Manipulator Link: a websocket interface for"
-    " manipulators in electrophysiology experiments",
+    " manipulators in electrophysiology experiments.",
     prog="python -m ephys-link",
 )
+parser.add_argument("-b", "--background", dest="background", action="store_true", help="Skip configuration window.")
 parser.add_argument(
-    "-b", "--background", dest="background", action="store_true", help="Launches in headless mode (no GUI)"
+    "-i", "--ignore-updates", dest="ignore_updates", action="store_true", help="Skip (ignore) checking for updates."
 )
 parser.add_argument(
     "-t",
@@ -21,23 +23,23 @@ parser.add_argument(
     type=str,
     dest="type",
     default="sensapex",
-    help='Manipulator type (i.e. "sensapex", "new_scale", or "new_scale_pathfinder").' ' 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("-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)",
+    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",
+    help="Port New Scale Pathfinder's server is on. Default: 8080.",
 )
 parser.add_argument(
     "-s",
@@ -46,14 +48,14 @@ parser.add_argument(
     default="no-e-stop",
     dest="serial",
     nargs="?",
-    help="Emergency stop serial port (i.e. COM3). Default: disables emergency stop",
+    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",
+    help="Print version and exit.",
 )
 
 
@@ -63,8 +65,8 @@ def main() -> None:
     # Parse arguments.
     args = parser.parse_args()
 
-    # Launch GUI if not background.
-    if not args.background:
+    # Launch GUI if there are no CLI arguments.
+    if len(argv) == 1:
         gui = GUI()
         gui.launch()
         return None
@@ -81,7 +83,7 @@ def main() -> None:
         e_stop.watch()
 
     # Launch with parsed arguments on main thread.
-    server.launch(args.type, args.port, args.pathfinder_port)
+    server.launch(args.type, args.port, args.pathfinder_port, args.ignore_updates)
 
 
 if __name__ == "__main__":

{ephys_link-1.2.5 → ephys_link-1.2.8}/src/ephys_link/common.py

@@ -12,6 +12,18 @@ from typing import TypedDict
 # Debugging flag
 DEBUG = False
 
+# Ephys Link ASCII
+ASCII = r"""
+  ______       _                 _      _       _
+ |  ____|     | |               | |    (_)     | |
+ | |__   _ __ | |__  _   _ ___  | |     _ _ __ | | __
+ |  __| | '_ \| '_ \| | | / __| | |    | | '_ \| |/ /
+ | |____| |_) | | | | |_| \__ \ | |____| | | | |   <
+ |______| .__/|_| |_|\__, |___/ |______|_|_| |_|_|\_\
+        | |           __/ |
+        |_|          |___/
+"""
+
 
 def dprint(message: str) -> None:
     """Print message if debug is enabled.

{ephys_link-1.2.5 → ephys_link-1.2.8}/src/ephys_link/server.py

@@ -11,17 +11,30 @@ every event, the server does the following:
 
 from __future__ import annotations
 
-import json
-import sys
+from json import loads
 from signal import SIGINT, SIGTERM, signal
+from sys import exit
 from typing import TYPE_CHECKING, Any
 
-import socketio
 from aiohttp import web
 from aiohttp.web_runner import GracefulExit
-
-from ephys_link import common as com
-from ephys_link.__about__ import __version__ as version
+from packaging import version
+from requests import get
+from requests.exceptions import ConnectionError
+from socketio import AsyncServer
+
+from ephys_link.__about__ import __version__
+from ephys_link.common import (
+    ASCII,
+    CanWriteInputDataFormat,
+    DriveToDepthInputDataFormat,
+    DriveToDepthOutputData,
+    GotoPositionInputDataFormat,
+    InsideBrainInputDataFormat,
+    PositionalOutputData,
+    StateOutputData,
+    dprint,
+)
 from ephys_link.platforms.new_scale_handler import NewScaleHandler
 from ephys_link.platforms.new_scale_pathfinder_handler import NewScalePathfinderHandler
 from ephys_link.platforms.sensapex_handler import SensapexHandler
@@ -34,7 +47,7 @@ if TYPE_CHECKING:
 class Server:
     def __init__(self):
         # Server and Socketio
-        self.sio = socketio.AsyncServer()
+        self.sio = AsyncServer()
         self.app = web.Application()
 
         # Is there a client connected?
@@ -117,7 +130,7 @@ class Server:
         :return: Version number as defined in :mod:`ephys_link.__about__`.
         :rtype: str
         """
-        return version
+        return __version__
 
     async def get_manipulators(self, _) -> str:
         """Get the list of discoverable manipulators.
@@ -127,7 +140,7 @@ class Server:
         :return: :class:`ephys_link.common.GetManipulatorsOutputData` as JSON formatted string.
         :rtype: str
         """
-        com.dprint("[EVENT]\t\t Get discoverable manipulators")
+        dprint("[EVENT]\t\t Get discoverable manipulators")
 
         return self.platform.get_manipulators().json()
 
@@ -141,7 +154,7 @@ class Server:
         :return: Error message on error, empty string otherwise.
         :rtype: str
         """
-        com.dprint(f"[EVENT]\t\t Register manipulator: {manipulator_id}")
+        dprint(f"[EVENT]\t\t Register manipulator: {manipulator_id}")
 
         return self.platform.register_manipulator(manipulator_id)
 
@@ -155,7 +168,7 @@ class Server:
         :return: Error message on error, empty string otherwise.
         :rtype: str
         """
-        com.dprint(f"[EVENT]\t\t Unregister manipulator: {manipulator_id}")
+        dprint(f"[EVENT]\t\t Unregister manipulator: {manipulator_id}")
 
         return self.platform.unregister_manipulator(manipulator_id)
 
@@ -169,7 +182,7 @@ class Server:
         :return: :class:`ephys_link.common.PositionalOutputData` as JSON formatted string.
         :rtype: str
         """
-        # com.dprint(f"[EVENT]\t\t Get position of manipulator" f" {manipulator_id}")
+        # dprint(f"[EVENT]\t\t Get position of manipulator" f" {manipulator_id}")
 
         return self.platform.get_pos(manipulator_id).json()
 
@@ -210,18 +223,18 @@ class Server:
         :rtype: str
         """
         try:
-            parsed_data: com.GotoPositionInputDataFormat = json.loads(data)
+            parsed_data: GotoPositionInputDataFormat = loads(data)
             manipulator_id = parsed_data["manipulator_id"]
             pos = parsed_data["pos"]
             speed = parsed_data["speed"]
         except KeyError:
             print(f"[ERROR]\t\t Invalid goto_pos data: {data}\n")
-            return com.PositionalOutputData([], "Invalid data format").json()
+            return PositionalOutputData([], "Invalid data format").json()
         except Exception as e:
             print(f"[ERROR]\t\t Error in goto_pos: {e}\n")
-            return com.PositionalOutputData([], "Error in goto_pos").json()
+            return PositionalOutputData([], "Error in goto_pos").json()
         else:
-            com.dprint(f"[EVENT]\t\t Move manipulator {manipulator_id} " f"to position {pos}")
+            dprint(f"[EVENT]\t\t Move manipulator {manipulator_id} " f"to position {pos}")
             goto_result = await self.platform.goto_pos(manipulator_id, pos, speed)
             return goto_result.json()
 
@@ -236,18 +249,18 @@ class Server:
         :rtype: str
         """
         try:
-            parsed_data: com.DriveToDepthInputDataFormat = json.loads(data)
+            parsed_data: DriveToDepthInputDataFormat = loads(data)
             manipulator_id = parsed_data["manipulator_id"]
             depth = parsed_data["depth"]
             speed = parsed_data["speed"]
         except KeyError:
             print(f"[ERROR]\t\t Invalid drive_to_depth data: {data}\n")
-            return com.DriveToDepthOutputData(-1, "Invalid data " "format").json()
+            return DriveToDepthOutputData(-1, "Invalid data " "format").json()
         except Exception as e:
             print(f"[ERROR]\t\t Error in drive_to_depth: {e}\n")
-            return com.DriveToDepthOutputData(-1, "Error in drive_to_depth").json()
+            return DriveToDepthOutputData(-1, "Error in drive_to_depth").json()
         else:
-            com.dprint(f"[EVENT]\t\t Drive manipulator {manipulator_id} to depth {depth}")
+            dprint(f"[EVENT]\t\t Drive manipulator {manipulator_id} to depth {depth}")
             drive_result = await self.platform.drive_to_depth(manipulator_id, depth, speed)
             return drive_result.json()
 
@@ -262,17 +275,17 @@ class Server:
         :rtype: str
         """
         try:
-            parsed_data: com.InsideBrainInputDataFormat = json.loads(data)
+            parsed_data: InsideBrainInputDataFormat = loads(data)
             manipulator_id = parsed_data["manipulator_id"]
             inside = parsed_data["inside"]
         except KeyError:
             print(f"[ERROR]\t\t Invalid set_inside_brain data: {data}\n")
-            return com.StateOutputData(False, "Invalid data format").json()
+            return StateOutputData(False, "Invalid data format").json()
         except Exception as e:
             print(f"[ERROR]\t\t Error in inside_brain: {e}\n")
-            return com.StateOutputData(False, "Error in set_inside_brain").json()
+            return StateOutputData(False, "Error in set_inside_brain").json()
         else:
-            com.dprint(f"[EVENT]\t\t Set manipulator {manipulator_id} inside brain to {inside}")
+            dprint(f"[EVENT]\t\t Set manipulator {manipulator_id} inside brain to {inside}")
             return self.platform.set_inside_brain(manipulator_id, inside).json()
 
     async def calibrate(self, _, manipulator_id: str) -> str:
@@ -285,7 +298,7 @@ class Server:
         :return: Error message on error, empty string otherwise.
         :rtype: str
         """
-        com.dprint(f"[EVENT]\t\t Calibrate manipulator" f" {manipulator_id}")
+        dprint(f"[EVENT]\t\t Calibrate manipulator" f" {manipulator_id}")
 
         return await self.platform.calibrate(manipulator_id, self.sio)
 
@@ -299,7 +312,7 @@ class Server:
         :return: Error message on error, empty string otherwise.
         :rtype: str
         """
-        com.dprint(f"[EVENT]\t\t Bypass calibration of manipulator" f" {manipulator_id}")
+        dprint(f"[EVENT]\t\t Bypass calibration of manipulator" f" {manipulator_id}")
 
         return self.platform.bypass_calibration(manipulator_id)
 
@@ -314,18 +327,18 @@ class Server:
         :rtype: str
         """
         try:
-            parsed_data: com.CanWriteInputDataFormat = json.loads(data)
+            parsed_data: CanWriteInputDataFormat = loads(data)
             manipulator_id = parsed_data["manipulator_id"]
             can_write = parsed_data["can_write"]
             hours = parsed_data["hours"]
         except KeyError:
             print(f"[ERROR]\t\t Invalid set_can_write data: {data}\n")
-            return com.StateOutputData(False, "Invalid data " "format").json()
+            return StateOutputData(False, "Invalid data " "format").json()
         except Exception as e:
             print(f"[ERROR]\t\t Error in inside_brain: {e}\n")
-            return com.StateOutputData(False, "Error in set_can_write").json()
+            return StateOutputData(False, "Error in set_can_write").json()
         else:
-            com.dprint(f"[EVENT]\t\t Set manipulator {manipulator_id} can_write state to {can_write}")
+            dprint(f"[EVENT]\t\t Set manipulator {manipulator_id} can_write state to {can_write}")
             return self.platform.set_can_write(manipulator_id, can_write, hours, self.sio).json()
 
     def stop(self, _) -> bool:
@@ -336,7 +349,7 @@ class Server:
         :return: True if successful, False otherwise.
         :rtype: bool
         """
-        com.dprint("[EVENT]\t\t Stop all manipulators")
+        dprint("[EVENT]\t\t Stop all manipulators")
 
         return self.platform.stop()
 
@@ -356,7 +369,13 @@ class Server:
         print(f"[UNKNOWN EVENT]:\t {data}")
         return "UNKNOWN_EVENT"
 
-    def launch(self, platform_type: str, server_port: int, pathfinder_port: int | None = None) -> None:
+    def launch(
+        self,
+        platform_type: str,
+        server_port: int,
+        pathfinder_port: int | None = None,
+        ignore_updates: bool = False,  # noqa: FBT002
+    ) -> None:
         """Launch the server.
 
         :param platform_type: Parsed argument for platform type.
@@ -365,6 +384,8 @@ class Server:
         :type server_port: int
         :param pathfinder_port: Port New Scale Pathfinder's server is on.
         :type pathfinder_port: int
+        :param ignore_updates: Flag to ignore checking for updates.
+        :type ignore_updates: bool
         :return: None
         """
 
@@ -379,16 +400,34 @@ class Server:
         elif platform_type == "new_scale_pathfinder":
             self.platform = NewScalePathfinderHandler(pathfinder_port)
         else:
-            sys.exit(f"[ERROR]\t\t Invalid manipulator type: {platform_type}")
-
-        # Preamble
-        print(f"=== Ephys Link v{version} ===")
+            exit(f"[ERROR]\t\t Invalid manipulator type: {platform_type}")
+
+        # Preamble.
+        print(ASCII)
+        print(f"v{__version__}")
+
+        # Check for newer version.
+        if not ignore_updates:
+            try:
+                version_request = get("https://api.github.com/repos/VirtualBrainLab/ephys-link/tags", timeout=10)
+                latest_version = version_request.json()[0]["name"]
+                if version.parse(latest_version) > version.parse(__version__):
+                    print(f"New version available: {latest_version}")
+                    print("Download at: https://github.com/VirtualBrainLab/ephys-link/releases/latest")
+            except ConnectionError:
+                pass
+
+        # Explain window.
+        print()
+        print("This is the Ephys Link server window.")
+        print("You may safely leave it running in the background.")
+        print("To stop the it, close this window or press CTRL + Pause/Break.")
+        print()
 
         # List available manipulators
         print("Available Manipulators:")
         print(self.platform.get_manipulators()["manipulators"])
-
-        print("\n(Shutdown server with CTRL+Pause/Break)\n")
+        print()
 
         # Mark that server is running
         self.is_running = True

ephys_link-1.2.5/src/ephys_link/__about__.py

@@ -1 +0,0 @@
-__version__ = "1.2.5"