ephys-link 1.0.0rc1__tar.gz → 1.0.6a0__tar.gz

ephys_link-1.0.6a0/.gitignore

@@ -0,0 +1,295 @@
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ephys_link-1.0.6a0/PKG-INFO

@@ -0,0 +1,158 @@
+Metadata-Version: 2.1
+Name: ephys-link
+Version: 1.0.6a0
+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 :: OS Independent
+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,>=3.8
+Requires-Dist: aiohttp==3.9.1
+Requires-Dist: pyserial==3.5
+Requires-Dist: python-socketio==5.10.0
+Requires-Dist: pythonnet==3.0.3
+Requires-Dist: sensapex==1.400.0
+Requires-Dist: wheel==0.42.0
+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)
+
+ <img width="100%" src="https://github.com/VirtualBrainLab/ephys-link/assets/82800265/c89e433c-2ce0-4f27-aa9d-66f89c59c979" 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.
+
+Currently, Ephys Link only supports Sensapex uMp-4 and uMp-3 Micromanipulators and New Scale 3-axis
+manipulators. However, this platform is designed to be extensible to other
+manipulators and more may be added in the future.
+
+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. [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++ Build Tools](https://visualstudio.microsoft.com/visual-cpp-build-tools/) (MSVC v143+) to
+       be installed.
+2. An **x86 Windows PC is required** to run the server.
+3. 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
+   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.
+
+> ### Using a Python virtual environment is encouraged.
+>
+> Create a virtual environment by running `python -m venv ephys_link`
+>
+> Activate the environment by running `.\ephys_link\scripts\activate`
+>
+> A virtual environment helps to isolate installed packages from other packages on your computer and ensures a clean
+> installation of Ephys Link
+
+**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.
+
+## Install for use
+
+Run the following command to install the server:
+
+```bash
+pip install ephys-link
+```
+
+Update the server like any other Python package:
+
+```bash
+pip install --upgrade ephys-link
+```
+
+## Install for development
+
+1. Clone the repository.
+2. Run the following command in the root directory of the repository to install the package along with development
+   tools:
+
+   ```bash
+   pip install -e .[dev]
+   ```
+
+# Usage
+
+Run the following commands in a terminal to start the server for the desired manipulator platform:
+
+| 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` |
+
+There are a couple additional aliases for the Ephys Link executable: `ephys_link` and `el`.
+
+By default, the server will broadcast with its local IP address on port 8081.
+**Copy this information into Pinpoint to connect**.
+
+For example, if the server is running on the same computer that Pinpoint is, use
+
+- Server: `localhost`
+- Port: `8081`
+
+# 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-1.0.0rc1 → ephys_link-1.0.6a0}/README.md

@@ -3,7 +3,8 @@
 [![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)
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![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)
 
  <img width="100%" src="https://github.com/VirtualBrainLab/ephys-link/assets/82800265/c89e433c-2ce0-4f27-aa9d-66f89c59c979" alt="Manipulator and probe in pinpoint moving in sync">
 
@@ -13,7 +14,7 @@ Socket.IO-compliant application (such
 as [Pinpoint](https://github.com/VirtualBrainLab/Pinpoint))
 to communicate with manipulators used in electrophysiology experiments.
 
-Currently, Ephys Link only supports Sensapex uMp-4 Micromanipulators and New Scale 3-axis
+Currently, Ephys Link only supports Sensapex uMp-4 and uMp-3 Micromanipulators and New Scale 3-axis
 manipulators. However, this platform is designed to be extensible to other
 manipulators and more may be added in the future.
 
@@ -84,8 +85,8 @@ Run the following commands in a terminal to start the server for the desired man
 
 | Manipulator Platform                 | Command                              |
 |--------------------------------------|--------------------------------------|
-| Sensapex UMP-4                       | `ephys-link`                         |
-| Sensapex UMP-3                       | `ephys-link -t ump3`                 |
+| 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` |
 

ephys_link-1.0.6a0/pyproject.toml

@@ -0,0 +1,104 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "ephys-link"
+dynamic = ["version"]
+description = "A Python Socket.IO server that allows any Socket.IO-compliant application to communicate with manipulators used in electrophysiology experiments."
+readme = "README.md"
+requires-python = ">=3.8, <3.13"
+license = "GPL-3.0-only"
+keywords = ["socket-io", "manipulator", "electrophysiology", "ephys", "sensapex", "neuroscience", "neurotech", "virtualbrainlab", "new-scale"]
+authors = [{ name = "Kenneth Yang", email = "kjy5@uw.edu" }]
+maintainers = [{ name = "Kenneth Yang", email = "kjy5@uw.edu" }]
+classifiers = [
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Programming Language :: Python :: Implementation :: PyPy",
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Operating System :: OS Independent",
+    "Intended Audience :: End Users/Desktop",
+    "Intended Audience :: Healthcare Industry",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Medical Science Apps.",
+]
+dependencies = [
+    "aiohttp==3.9.1",
+    "pyserial==3.5",
+    "python-socketio==5.10.0",
+    "pythonnet==3.0.3",
+    "wheel==0.42.0",
+    "sensapex==1.400.0",
+]
+
+[project.urls]
+Documentation = "https://virtualbrainlab.org/ephys_link/installation_and_use.html"
+Issues = "https://github.com/VirtualBrainLab/ephys-link/issues"
+Source = "https://github.com/VirtualBrainLab/ephys-link"
+
+[project.scripts]
+ephys-link = "ephys_link.__main__:main"
+ephys_link = "ephys_link.__main__:main"
+el = "ephys_link.__main__:main"
+
+[tool.hatch.version]
+path = "src/ephys_link/__about__.py"
+
+[tool.hatch.build.targets.sdist]
+exclude = ["/.github", "/.idea"]
+
+[tool.hatch.envs.default]
+dependencies = [
+    "coverage[toml]>=6.5",
+    "pytest",
+]
+[tool.hatch.envs.default.scripts]
+test = "pytest {args:tests}"
+test-cov = "coverage run -m pytest {args:tests}"
+cov-report = [
+    "- coverage combine",
+    "coverage report",
+]
+cov = [
+    "test-cov",
+    "cov-report",
+]
+
+[[tool.hatch.envs.all.matrix]]
+python = ["3.8", "3.9", "3.10", "3.11", "3.12"]
+
+[tool.hatch.envs.types]
+dependencies = [
+    "mypy>=1.0.0",
+]
+[tool.hatch.envs.types.scripts]
+check = "mypy --install-types --non-interactive {args:src/ephys_link tests}"
+
+[tool.coverage.run]
+source_pkgs = ["ephys_link", "tests"]
+branch = true
+parallel = true
+omit = [
+    "src/ephys_link/__about__.py",
+]
+
+[tool.coverage.paths]
+ephys_link = ["src/ephys_link", "*/ephys-link/src/ephys_link"]
+tests = ["tests", "*/ephys-link/tests"]
+
+[tool.coverage.report]
+exclude_lines = [
+    "no cov",
+    "if __name__ == .__main__.:",
+    "if TYPE_CHECKING:",
+]
+
+[tool.ruff.lint]
+extend-ignore = ["T201", "PLW0603", "BLE001", "FBT001", "ARG002", "S310"]

ephys_link-1.0.6a0/src/ephys_link/__about__.py

@@ -0,0 +1 @@
+__version__ = "1.0.6a0"

{ephys-link-1.0.0rc1 → ephys_link-1.0.6a0}/src/ephys_link/__main__.py

@@ -69,12 +69,9 @@ parser.add_argument(
     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"
+    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",
@@ -113,7 +110,7 @@ def main() -> None:
 
     # Parse arguments
     args = parser.parse_args()
-    com.set_debug(args.debug)
+    com.DEBUG = args.debug
 
     # Setup serial port
     if args.serial != "no-e-stop":

{ephys-link-1.0.0rc1 → ephys_link-1.0.6a0}/src/ephys_link/common.py

@@ -4,23 +4,14 @@ Contains globally used helper functions and typed dictionaries (to be used as
 callback parameters)
 """
 
+from __future__ import annotations
+
 from typing import TypedDict
 
 # Debugging flag
 DEBUG = False
 
 
-def set_debug(debug: bool) -> None:
-    """Set debug flag
-
-    :param debug: True to enable debug mode, False to disable
-    :type debug: bool
-    :return: None
-    """
-    global DEBUG
-    DEBUG = debug
-
-
 def dprint(message: str) -> None:
     """Print message if debug is enabled
 
@@ -81,11 +72,9 @@ class GetManipulatorsOutputData(dict):
         :code:`{"manipulators": ["1", "2"], "error": ""}`
     """
 
-    def __init__(
-        self, manipulators: list, num_axes: int, dimensions: list, error: str
-    ) -> None:
+    def __init__(self, manipulators: list, num_axes: int, dimensions: list, error: str) -> None:
         """Constructor"""
-        super(GetManipulatorsOutputData, self).__init__(
+        super().__init__(
             manipulators=manipulators,
             num_axes=num_axes,
             dimensions=dimensions,
@@ -107,7 +96,7 @@ class PositionalOutputData(dict):
 
     def __init__(self, position: list, error: str) -> None:
         """Constructor"""
-        super(PositionalOutputData, self).__init__(position=position, error=error)
+        super().__init__(position=position, error=error)
 
 
 class AngularOutputData(dict):
@@ -121,7 +110,21 @@ class AngularOutputData(dict):
 
     def __init__(self, angles: list, error: str) -> None:
         """Constructor"""
-        super(AngularOutputData, self).__init__(angles=angles, error=error)
+        super().__init__(angles=angles, error=error)
+
+
+class ShankCountOutputData(dict):
+    """Output format for (num_shanks, error)
+
+    :param shank_count: Number of shanks on the probe
+    :type shank_count: int
+    :param error: Error message
+    :type error: str
+    """
+
+    def __init__(self, shank_count: int, error: str) -> None:
+        """Constructor"""
+        super().__init__(shank_count=shank_count, error=error)
 
 
 class DriveToDepthOutputData(dict):
@@ -137,7 +140,7 @@ class DriveToDepthOutputData(dict):
 
     def __init__(self, depth: float, error: str) -> None:
         """Create drive to depth output data dictionary"""
-        super(DriveToDepthOutputData, self).__init__(depth=depth, error=error)
+        super().__init__(depth=depth, error=error)
 
 
 class StateOutputData(dict):
@@ -153,4 +156,4 @@ class StateOutputData(dict):
 
     def __init__(self, state: bool, error: str) -> None:
         """Create state output data dictionary"""
-        super(StateOutputData, self).__init__(state=state, error=error)
+        super().__init__(state=state, error=error)