ephys-link 2.0.0__py3-none-any.whl → 2.0.0b2__py3-none-any.whl

ephys_link/{utils → util}/console.py

@@ -1,127 +1,133 @@
-"""Console class for printing messages to the console.
-
-Configure the console to print error and debug messages.
-
-Usage:
-    Create a Console object and call the appropriate method to print messages.
-"""
-
-from logging import DEBUG, ERROR, INFO, basicConfig, getLogger
-from typing import final
-
-from rich.logging import RichHandler
-from rich.traceback import install
-
-
-@final
-class Console:
-    def __init__(self, *, enable_debug: bool) -> None:
-        """Initialize console properties.
-
-        Args:
-            enable_debug: Enable debug mode.
-        """
-        # Repeat message fields.
-        self._last_message = (0, "", "")
-        self._repeat_counter = 0
-
-        # Config logger.
-        basicConfig(
-            format="%(message)s",
-            datefmt="[%I:%M:%S %p]",
-            handlers=[RichHandler(rich_tracebacks=True, markup=True)],
-        )
-        self._log = getLogger("rich")
-        self._log.setLevel(DEBUG if enable_debug else INFO)
-
-        # Install Rich traceback.
-        _ = install()
-
-    def debug_print(self, label: str, msg: str) -> None:
-        """Print a debug message to the console.
-
-        Args:
-            label: Label for the debug message.
-            msg: Debug message to print.
-        """
-        self._repeatable_log(DEBUG, f"[b green]{label}", f"[green]{msg}")
-
-    def info_print(self, label: str, msg: str) -> None:
-        """Print info to console.
-
-        Args:
-            label: Label for the message.
-            msg: Message to print.
-        """
-        self._repeatable_log(INFO, f"[b blue]{label}", msg)
-
-    def error_print(self, label: str, msg: str) -> None:
-        """Print an error message to the console.
-
-        Args:
-            label: Label for the error message.
-            msg: Error message to print.
-        """
-        self._repeatable_log(ERROR, f"[b red]{label}", f"[red]{msg}")
-
-    def critical_print(self, msg: str) -> None:
-        """Print a critical message to the console.
-
-        Args:
-            msg: Critical message to print.
-        """
-        self._log.critical(f"[b i red]{msg}")
-
-    @staticmethod
-    def pretty_exception(exception: Exception) -> str:
-        """Pretty print an exception.
-
-        Args:
-            exception: Exception to pretty print.
-
-        Returns:
-            Pretty printed exception.
-        """
-        return f"{type(exception).__name__}: {exception}"
-
-    def exception_error_print(self, label: str, exception: Exception) -> None:
-        """Print an error message with exception details to the console.
-
-        Args:
-            label: Label for the error message.
-            exception: Exception to print.
-        """
-        self._log.exception(f"[b magenta]{label}:[/] [magenta]{Console.pretty_exception(exception)}")
-
-    # Helper methods.
-    def _repeatable_log(self, log_type: int, label: str, message: str) -> None:
-        """Add a row to the output table.
-
-        Args:
-            log_type: Type of log.
-            label: Label for the message.
-            message: Message.
-        """
-
-        # Compute if this is a repeated message.
-        message_set = (log_type, label, message)
-        if message_set == self._last_message:
-            # Handle repeat.
-            self._repeat_counter += 1
-
-            # Add an ellipsis row for first repeat.
-            if self._repeat_counter == 1:
-                self._log.log(log_type, "...")
-        else:
-            # Handle novel message.
-            if self._repeat_counter > 0:
-                # Complete previous repeat.
-                self._log.log(
-                    self._last_message[0],
-                    f"{self._last_message[1]}:[/] {self._last_message[2]}[/] x {self._repeat_counter}",
-                )
-                self._repeat_counter = 0
-
-            # Log new message.
-            self._log.log(log_type, f"{label}:[/] {message}")
-            self._last_message = message_set
+# ruff: noqa: T201
+"""Console class for printing messages to the console.
+
+Configure the console to print error and debug messages.
+
+Usage: Create a Console object and call the appropriate method to print messages.
+"""
+
+from logging import DEBUG, ERROR, INFO, basicConfig, getLogger
+
+from rich.logging import RichHandler
+from rich.traceback import install
+
+
+class Console:
+    def __init__(self, *, enable_debug: bool) -> None:
+        """Initialize console properties.
+
+        :param enable_debug: Enable debug mode.
+        :type enable_debug: bool
+        """
+        # Repeat message fields.
+        self._last_message = (0, "", "")
+        self._repeat_counter = 0
+
+        # Config logger.
+        basicConfig(
+            level=DEBUG if enable_debug else INFO,
+            format="%(message)s",
+            datefmt="[%I:%M:%S %p]",
+            handlers=[RichHandler(rich_tracebacks=True)],
+        )
+        self._log = getLogger("rich")
+
+        # Install Rich traceback.
+        install()
+
+    def debug_print(self, label: str, msg: str) -> None:
+        """Print a debug message to the console.
+
+        :param label: Label for the debug message.
+        :type label: str
+        :param msg: Debug message to print.
+        :type msg: str
+        """
+        self._repeatable_log(DEBUG, f"[b green]{label}", f"[green]{msg}")
+
+    def info_print(self, label: str, msg: str) -> None:
+        """Print info to console.
+
+        :param label: Label for the message.
+        :type label: str
+        :param msg: Message to print.
+        :type msg: str
+        """
+        self._repeatable_log(INFO, f"[b blue]{label}", msg)
+
+    def error_print(self, label: str, msg: str) -> None:
+        """Print an error message to the console.
+
+        :param label: Label for the error message.
+        :type label: str
+        :param msg: Error message to print.
+        :type msg: str
+        """
+        self._repeatable_log(ERROR, f"[b red]{label}", f"[red]{msg}")
+
+    def critical_print(self, msg: str) -> None:
+        """Print a critical message to the console.
+
+        :param msg: Critical message to print.
+        :type msg: str
+        """
+        self._log.critical(f"[b i red]{msg}", extra={"markup": True})
+
+    @staticmethod
+    def pretty_exception(exception: Exception) -> str:
+        """Pretty print an exception.
+
+        :param exception: Exception to pretty print.
+        :type exception: Exception
+        :return: Pretty printed exception.
+        :rtype: str
+        """
+        return f"{type(exception).__name__}: {exception}"
+
+    def exception_error_print(self, label: str, exception: Exception) -> None:
+        """Print an error message with exception details to the console.
+
+        :param label: Label for the error message.
+        :type label: str
+        :param exception: Exception to print.
+        :type exception: Exception
+        """
+        self._log.exception(
+            f"[b magenta]{label}:[/] [magenta]{Console.pretty_exception(exception)}", extra={"markup": True}
+        )
+
+    # Helper methods.
+    def _repeatable_log(self, log_type: int, label: str, message: str) -> None:
+        """Add a row to the output table.
+
+        :param log_type: Type of log.
+        :type log_type: int
+        :param label: Label for the message.
+        :type label: str
+        :param message: Message.
+        :type message: str
+        """
+
+        # Compute if this is a repeated message.
+        message_set = (log_type, label, message)
+        if message_set == self._last_message:
+            # Handle repeat.
+            self._repeat_counter += 1
+
+            # Add an ellipsis row for first repeat.
+            if self._repeat_counter == 1:
+                self._log.log(log_type, "...")
+        else:
+            # Handle novel message.
+            if self._repeat_counter > 0:
+                # Complete previous repeat.
+                self._log.log(
+                    self._last_message[0],
+                    f"{self._last_message[1]}:[/] {self._last_message[2]}[/] x {self._repeat_counter}",
+                    extra={"markup": True},
+                )
+                self._repeat_counter = 0
+
+            # Log new message.
+            self._log.log(log_type, f"{label}:[/] {message}", extra={"markup": True})
+            self._last_message = message_set

ephys_link-2.0.0b2.dist-info/METADATA

@@ -0,0 +1,167 @@
+Metadata-Version: 2.3
+Name: ephys-link
+Version: 2.0.0b2
+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
+Project-URL: Source, https://github.com/VirtualBrainLab/ephys-link
+Author-email: Kenneth Yang <kjy5@uw.edu>
+Maintainer-email: Kenneth Yang <kjy5@uw.edu>
+License-Expression: GPL-3.0-only
+License-File: LICENSE
+Keywords: electrophysiology,ephys,manipulator,neuroscience,neurotech,new-scale,sensapex,socket-io,virtualbrainlab
+Classifier: Intended Audience :: End Users/Desktop
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: <3.13,>=3.10
+Requires-Dist: aiohttp==3.9.5
+Requires-Dist: colorama==0.4.6
+Requires-Dist: platformdirs==4.2.2
+Requires-Dist: pyserial==3.5
+Requires-Dist: python-socketio[asyncio-client]==5.11.3
+Requires-Dist: pythonnet==3.0.3
+Requires-Dist: requests==2.32.3
+Requires-Dist: rich==13.7.1
+Requires-Dist: sensapex==1.400.1
+Requires-Dist: vbl-aquarium==0.0.19
+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)
+[![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)
+[![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)
+
+<!-- [![Build](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/build.yml/badge.svg)](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/build.yml) -->
+
+<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">
+
+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.
+
+**Supported Manipulators:**
+
+| Manufacturer | Model                                                                   |
+|--------------|-------------------------------------------------------------------------|
+| Sensapex     | <ul> <li>uMp-4</li> <li>uMp-3</li> </ul>                                |
+| New Scale    | <ul> <li>Pathfinder MPM Control v2.8+</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.
+
+For more information regarding the server's implementation and how the code is organized, see
+the [package's development documentation](https://virtualbrainlab.org/ephys_link/development.html).
+
+For detailed descriptions of the server's API, see
+the [API reference](https://virtualbrainlab.org/api_reference_ephys_link.html).
+
+# 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 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.
+
+**NOTE:** Ephys Link is an HTTP server without cross-origin support. The server
+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
+   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".
+
+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: `8081`
+
+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 as a Python package
+
+```bash
+pip install ephys-link
+```
+
+Import the modules you need and launch the server.
+
+```python
+from ephys_link.server import Server
+
+server = Server()
+server.launch("sensapex", args.proxy_address, 8081)
+```
+
+## 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
+
+   ```bash
+   hatch shell
+   ```
+
+This will create a virtual environment, install Python 12 (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/).
+
+# Documentation and More Information
+
+Complete documentation including API usage and development installation can be
+found on the [Virtual Brain Lab Documentation page][docs] for Ephys Link.
+
+# Citing
+
+If this project is used as part of a research project you should cite
+the [Pinpoint repository][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.
+
+[Pinpoint]: https://github.com/VirtualBrainLab/Pinpoint
+
+[StopSignal]: https://github.com/VirtualBrainLab/StopSignal
+
+[docs]: https://virtualbrainlab.org/ephys_link/installation_and_use.html

ephys_link-2.0.0b2.dist-info/RECORD

@@ -0,0 +1,25 @@
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{ephys_link-2.0.0.dist-info → ephys_link-2.0.0b2.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.27.0
+Generator: hatchling 1.25.0
 Root-Is-Purelib: true
 Tag: py3-none-any