ephys-link 2.0.0b9__tar.gz → 2.0.1__tar.gz

{ephys_link-2.0.0b9 → ephys_link-2.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ephys-link
-Version: 2.0.0b9
+Version: 2.0.1
 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
@@ -17,34 +17,31 @@ 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 :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
 Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
-Requires-Python: <3.14,>=3.10
-Requires-Dist: aiohttp==3.11.11
+Requires-Python: >=3.13
+Requires-Dist: aiohttp==3.11.16
 Requires-Dist: colorama==0.4.6
 Requires-Dist: keyboard==0.13.5
 Requires-Dist: packaging==24.2
-Requires-Dist: platformdirs==4.3.6
+Requires-Dist: platformdirs==4.3.7
 Requires-Dist: pyserial==3.5
 Requires-Dist: python-socketio[asyncio-client]==5.12.1
 Requires-Dist: requests==2.32.3
-Requires-Dist: rich==13.9.4
+Requires-Dist: rich==14.0.0
 Requires-Dist: sensapex==1.400.3
-Requires-Dist: vbl-aquarium==1.0.0b3
+Requires-Dist: vbl-aquarium==1.0.0
 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)
-[![Deploy Documentation](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/deploy-docs.yml/badge.svg)](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/deploy-docs.yml)
-[![Pydantic v2](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/pydantic/pydantic/main/docs/badge/v2.json)](https://pydantic.dev)
 [![Hatch project](https://img.shields.io/badge/%F0%9F%A5%9A-Hatch-4051b5.svg)](https://github.com/pypa/hatch)
+[![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv)
 [![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)
+[![Pydantic v2](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/pydantic/pydantic/main/docs/badge/v2.json)](https://pydantic.dev)
 [![Checked with pyright](https://microsoft.github.io/pyright/img/pyright_badge.svg)](https://microsoft.github.io/pyright/)
 
 <!-- [![Build](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/build.yml/badge.svg)](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/build.yml) -->
@@ -59,22 +56,23 @@ to communicate with manipulators used in electrophysiology experiments.
 
 # Installation
 
-## Launch from Pinpoint (Recommended)
+## 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).
+manipulators are connected to, you can launch the server from within Pinpoint. See the documentation
+on [connecting from Pinpoint](../usage/using_ephys_link.md#connecting-to-pinpoint).
+
+## Install as a Standalone Executable
 
-## Install as Standalone Executable
+Download the latest standalone executable or zip from
+the [releases page](https://github.com/VirtualBrainLab/ephys-link/releases/latest).
 
-1. Download the latest standalone executable or zip from
-   the [releases page](https://github.com/VirtualBrainLab/ephys-link/releases/latest).
-2. Double-click the executable file to start.
+Then see the [usage documentation](../usage/starting_ephys_link.md) for how to run the server.
 
 # 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.
+Complete documentation including how to add manipulators and API usage can be
+found on [Ephys Link's Documentation Website][docs].
 
 # Citing
 
@@ -88,4 +86,4 @@ through the issues tab.
 
 [Pinpoint]: https://github.com/VirtualBrainLab/Pinpoint
 
-[docs]: https://virtualbrainlab.github.io/ephys-link/
+[docs]: https://ephys-link.virtualbrainlab.org

{ephys_link-2.0.0b9 → ephys_link-2.0.1}/README.md

@@ -1,10 +1,10 @@
 # Electrophysiology Manipulator Link
 
 [![PyPI version](https://badge.fury.io/py/ephys-link.svg)](https://badge.fury.io/py/ephys-link)
-[![Deploy Documentation](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/deploy-docs.yml/badge.svg)](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/deploy-docs.yml)
-[![Pydantic v2](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/pydantic/pydantic/main/docs/badge/v2.json)](https://pydantic.dev)
 [![Hatch project](https://img.shields.io/badge/%F0%9F%A5%9A-Hatch-4051b5.svg)](https://github.com/pypa/hatch)
+[![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv)
 [![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)
+[![Pydantic v2](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/pydantic/pydantic/main/docs/badge/v2.json)](https://pydantic.dev)
 [![Checked with pyright](https://microsoft.github.io/pyright/img/pyright_badge.svg)](https://microsoft.github.io/pyright/)
 
 <!-- [![Build](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/build.yml/badge.svg)](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/build.yml) -->
@@ -19,22 +19,23 @@ to communicate with manipulators used in electrophysiology experiments.
 
 # Installation
 
-## Launch from Pinpoint (Recommended)
+## 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).
+manipulators are connected to, you can launch the server from within Pinpoint. See the documentation
+on [connecting from Pinpoint](../usage/using_ephys_link.md#connecting-to-pinpoint).
+
+## Install as a Standalone Executable
 
-## Install as Standalone Executable
+Download the latest standalone executable or zip from
+the [releases page](https://github.com/VirtualBrainLab/ephys-link/releases/latest).
 
-1. Download the latest standalone executable or zip from
-   the [releases page](https://github.com/VirtualBrainLab/ephys-link/releases/latest).
-2. Double-click the executable file to start.
+Then see the [usage documentation](../usage/starting_ephys_link.md) for how to run the server.
 
 # 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.
+Complete documentation including how to add manipulators and API usage can be
+found on [Ephys Link's Documentation Website][docs].
 
 # Citing
 
@@ -48,4 +49,4 @@ through the issues tab.
 
 [Pinpoint]: https://github.com/VirtualBrainLab/Pinpoint
 
-[docs]: https://virtualbrainlab.github.io/ephys-link/
+[docs]: https://ephys-link.virtualbrainlab.org

{ephys_link-2.0.0b9 → ephys_link-2.0.1}/ephys_link.spec

@@ -1,22 +1,27 @@
 # -*- mode: python ; coding: utf-8 -*-
 
-from ephys_link.__about__ import __version__ as version
-
 from argparse import ArgumentParser
 
+from PyInstaller.utils.hooks import collect_submodules
+
+from ephys_link.__about__ import __version__ as version
+
 parser = ArgumentParser()
 parser.add_argument("-d", "--dir", action="store_true", help="Outputs a directory")
 options = parser.parse_args()
 
 FILE_NAME = f"EphysLink-v{version}"
 
+# Collect binding modules.
+bindings = [binding for binding in collect_submodules("ephys_link.bindings") if binding != "ephys_link.bindings"]
+
 # noinspection PyUnresolvedReferences
 a = Analysis(
     ['src\\ephys_link\\__main__.py'],
     pathex=[],
     binaries=[('src\\ephys_link\\resources', 'ephys_link\\resources')],
     datas=[],
-    hiddenimports=['engineio.async_drivers.aiohttp'],
+    hiddenimports=['engineio.async_drivers.aiohttp'] + bindings,
     hookspath=[],
     hooksconfig={},
     runtime_hooks=[],

{ephys_link-2.0.0b9 → ephys_link-2.0.1}/mkdocs.yml

@@ -1,9 +1,9 @@
 # yaml-language-server: $schema=https://squidfunk.github.io/mkdocs-material/schema.json
 
 site_name: Ephys Link
-site_url: https://virtualbrainlab.github.io/ephys-link
+site_url: https://ephys-link.virtualbrainlab.org
 repo_url: https://github.com/VirtualBrainLab/ephys-link
-repo_name: virtualbrainlab/ephys-link
+repo_name: VirtualBrainLab/ephys-link
 copyright: Copyright © 2024 Virtual Brain Lab
 extra:
   social:
@@ -86,9 +86,9 @@ plugins:
             docstring_style: google
             show_symbol_type_heading: true
             show_symbol_type_toc: true
-          import:
+          inventories:
             - https://docs.python.org/3/objects.inv
-            - https://virtualbrainlab.github.io/vbl-aquarium/objects.inv
+            - https://aquarium.virtualbrainlab.org/objects.inv
 nav:
   - Home:
       - About: index.md

{ephys_link-2.0.0b9 → ephys_link-2.0.1}/pyproject.toml

@@ -7,16 +7,13 @@ 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 = ">=3.10, <3.14"
+requires-python = ">=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 :: 3.10",
-    "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
     "Programming Language :: Python :: Implementation :: CPython",
     "Programming Language :: Python :: Implementation :: PyPy",
@@ -29,17 +26,17 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Medical Science Apps.",
 ]
 dependencies = [
-    "aiohttp==3.11.11",
+    "aiohttp==3.11.16",
     "colorama==0.4.6",
     "keyboard==0.13.5",
     "packaging==24.2",
-    "platformdirs==4.3.6",
+    "platformdirs==4.3.7",
     "pyserial==3.5",
     "python-socketio[asyncio_client]==5.12.1",
     "requests==2.32.3",
     "sensapex==1.400.3",
-    "rich==13.9.4",
-    "vbl-aquarium==1.0.0b3"
+    "rich==14.0.0",
+    "vbl-aquarium==1.0.0"
 ]
 
 [project.urls]
@@ -56,13 +53,14 @@ el = "ephys_link.__main__:main"
 path = "src/ephys_link/__about__.py"
 
 [tool.hatch.build.targets.sdist]
-exclude = ["/.github", "/.idea"]
+exclude = ["/.github", "/.idea", "/docs"]
 
 [tool.hatch.envs.default]
-python = "3.13.1"
+installer = "uv"
+python = "3.13"
 dependencies = [
-    "pyinstaller==6.11.1",
-    "basedpyright==1.23.1",
+    "pyinstaller==6.12.0",
+    "basedpyright==1.28.5",
 ]
 [tool.hatch.envs.default.scripts]
 exe = "pyinstaller.exe ephys_link.spec -y -- -d && pyinstaller.exe ephys_link.spec -y"
@@ -71,14 +69,15 @@ check = "basedpyright"
 check-watched = "basedpyright --watch"
 
 [tool.hatch.envs.docs]
-python = "3.13.1"
+installer = "uv"
+python = "3.13"
 skip-install = true
 dependencies = [
-    "mkdocs-material==9.5.49",
-    "mkdocstrings-python==1.13.0",
+    "mkdocs-material==9.6.11",
+    "mkdocstrings-python==1.16.10",
     "mkdocs-gen-files==0.5.0",
-    "mkdocs-literate-nav==0.6.1",
-    "mkdocs-section-index==0.3.9"
+    "mkdocs-literate-nav==0.6.2",
+    "mkdocs-section-index==0.3.10"
 ]
 [tool.hatch.envs.docs.scripts]
 serve = "mkdocs serve"

ephys_link-2.0.1/src/ephys_link/__about__.py

@@ -0,0 +1 @@
+__version__ = "2.0.1"

{ephys_link-2.0.0b9 → ephys_link-2.0.1}/src/ephys_link/bindings/mpm_binding.py

@@ -127,7 +127,7 @@ class MPMBinding(BaseBinding):
         manipulator_data: dict[str, float] = await self._manipulator_data(manipulator_id)
 
         # Apply PosteriorAngle to Polar to get the correct angle.
-        adjusted_polar: int = manipulator_data["Polar"] - (await self._query_data())["PosteriorAngle"]
+        adjusted_polar: int = manipulator_data["Polar"] - (await self._query_data())["PosteriorAngle"]  # pyright: ignore [reportAny]
 
         return Vector3(
             x=adjusted_polar if adjusted_polar > 0 else 360 + adjusted_polar,
@@ -299,7 +299,7 @@ class MPMBinding(BaseBinding):
             return self.cache
 
     async def _manipulator_data(self, manipulator_id: str) -> dict[str, Any]:  # pyright: ignore [reportExplicitAny]
-        probe_data: list[dict[str, Any]] = (await self._query_data())["ProbeArray"]  # pyright: ignore [reportExplicitAny]
+        probe_data: list[dict[str, Any]] = (await self._query_data())["ProbeArray"]  # pyright: ignore [reportExplicitAny, reportAny]
         for probe in probe_data:
             if probe["Id"] == manipulator_id:
                 return probe

{ephys_link-2.0.0b9 → ephys_link-2.0.1}/src/ephys_link/bindings/ump_4_binding.py

@@ -100,7 +100,7 @@ class Ump4Binding(BaseBinding):
             raise RuntimeError(error_message)
 
         # Handle empty end position.
-        if not movement.last_pos:  # pyright: ignore [reportUnknownMemberType]
+        if movement.last_pos is None or len(movement.last_pos) == 0:  # pyright: ignore [reportUnknownMemberType, reportUnknownArgumentType]
             error_message = f"Manipulator {manipulator_id} did not reach target position"
             raise RuntimeError(error_message)
 

ephys_link-2.0.0b9/docs/development/adding_a_manipulator.md

@@ -1,77 +0,0 @@
-# Adding a Manipulator
-
-By the end of this section, you will be able to add a manipulator platform to Ephys Link and control it using the server
-API. This is a software development guide and assumes you have experience with Python. It is encouraged to
-read [how the system works first](../home/how_it_works.md) before proceeding.
-
-## Set Up for Development
-
-1. Fork the [Ephys Link repository](https://github.com/VirtualBrainLab/ephys-link).
-2. Follow the instructions for [installing Ephys Link for development](index.md#installing-for-development) to get all
-   the necessary dependencies and tools set up. In this case, you'll want to clone your fork.
-3. (Optional) Familiarize yourself with the [repo's organization](code_organization.md).
-
-## Create a Manipulator Binding
-
-Manipulators are added to Ephys Link through bindings. A binding is a Python class that extends the abstract base class
-[`BaseBinding`][ephys_link.utils.base_binding] and defines the methods Ephys Link expects from a platform.
-
-Create a new Python module in `src/ephys_link/bindings` for your manipulator. Make a class that extends
-[`BaseBinding`][ephys_link.utils.base_binding]. Most IDEs will automatically import the necessary classes and tell you
-the methods you need to implement. See the reference for [`BaseBinding`][ephys_link.utils.base_binding] for detailed
-descriptions of the expected behavior.
-
-As described in the [system overview](../home/how_it_works.md), Ephys Link converts all manipulator movement into a
-common "unified space" which is
-the [left-hand cartesian coordinate system](https://www.scratchapixel.com/lessons/mathematics-physics-for-computer-graphics/geometry/coordinate-systems.html).
-The two methods [
-`platform_space_to_unified_space`](../../reference/ephys_link/utils/base_binding/#ephys_link.utils.base_binding.BaseBinding.platform_space_to_unified_space)
-and [
-`unified_space_to_platform_space`](../../reference/ephys_link/utils/base_binding/#ephys_link.utils.base_binding.BaseBinding.unified_space_to_platform_space)
-are used to convert between your manipulator's coordinate system and the unified space.
-
-!!! tip
-
-    See
-    the [Sensapex uMp-4](https://github.com/VirtualBrainLab/ephys-link/blob/main/src/ephys_link/bindings/ump_4_bindings.py)
-    binding for an example where the platform has a Python API (Sensapex's SDK) and
-    the [New Scale Pathfinder MPM](https://github.com/VirtualBrainLab/ephys-link/blob/main/src/ephys_link/bindings/mpm_bindings.py)
-    binding, for example, where the platform uses a REST API for an external provider.
-
-### Binding Names
-
-The two naming methods [
-`get_display_name`](../../reference/ephys_link/utils/base_binding/#ephys_link.utils.base_binding.BaseBinding.get_display_name)
-and [
-`get_cli_name`](../../reference/ephys_link/utils/base_binding/#ephys_link.utils.base_binding.BaseBinding.get_cli_name)
-are used to identify the binding in the user interface. As described by their documentation, `get_display_name` should
-return a human-readable name for the binding, while `get_cli_name` should return the name used to launch the binding
-from the command line (what is passed to the `-t` flag). For example, Sensapex uMp-4 manipulator's `get_cli_name`
-returns `ump-4` because the CLI launch command is `ephys_link.exe -b -t ump-4`.
-
-### Custom Additional Arguments
-
-Sometimes you may want to pass extra data to your binding on initialization. For example, New Scale Pathfinder MPM
-bindings need to know what the HTTP server port is. To add custom arguments, define them as arguments on the `__init__`
-method of your binding then pass in the appropriate data when the binding is instantiated in the [
-`_get_binding_instance`](https://github.com/VirtualBrainLab/ephys-link/blob/f79c1ec68ec1805e1a4e231e1934127893f7bd20/src/ephys_link/back_end/platform_handler.py#L58)
-method of the [`PlatformHandler`][ephys_link.back_end.platform_handler].
-Use [New Scale Pathfinder MPM's binding][ephys_link.bindings.mpm_binding] as an example of how to do this.
-
-## Test Your Binding
-
-Once you've implemented your binding, you can test it by running Ephys Link using your binding
-`ephys_link -b -t <cli_name>`. You can interact with it using the [Socket.IO API](socketio_api.md) or Pinpoint.
-
-## Code standards
-
-We use automatic static analyzers to check code quality. See
-the [corresponding section in the code organization documentation](code_organization.md#static-analysis) for more
-information.
-
-## Submit Your Changes
-
-When satisfied with your changes, submit a pull request to the main repository. We will review your changes and
-merge them if they meet our standards!
-
-Feel free to [reach out](../home/contact.md) to us if you have any questions or need help with your binding!

ephys_link-2.0.0b9/docs/development/code_organization.md

@@ -1,41 +0,0 @@
-# Code Organization
-
-This section gives an overview of Ephys Link's internal architecture. It is intended for
-maintainers of Ephys Link.
-
-## File Structure
-
-Ephys Link starts from the `__main__.py` file. It imports each component of the application and calls the launch
-sequence.
-
-### Where to find things
-
-- `back_end`: the Socket.IO server and the manipulator API.
-- `front_end`: configuration GUI and CLI definition.
-- `bindings`: manipulator binding implementations.
-- `utils`: common utilities and helper functions (including
-  [the base binding abstract base class][ephys_link.utils.base_binding]).
-
-## Control Flow
-
-As described in ["How It Works"](../home/how_it_works.md), Ephys Link is primarily a server that responds to events. The
-server exposes the events and passes them to the chosen manipulator binding. Everything is asynchronous and uses callbacks
-to return responses to the clients when ready.
-
-[`PlatformHandler`][ephys_link.back_end.platform_handler] is responsible for converting between the server API and the
-manipulator binding API. Because of this module, you don't have to worry about the details of the server API when
-writing a manipulator binding.
-
-## Static Analysis
-
-The project is strictly type-checked using [`hatch fmt` (ruff)](https://hatch.pypa.io/1.9/config/static-analysis/)
-and [basedpyright](https://docs.basedpyright.com/latest/). All PRs are checked against these tools.
-
-While they are invaluable in enforcing good code, they can be annoying when working with libraries that inherently
-return `Any` (like HTTP requests) or are not strictly statically typed. In those situations, we have added inline
-comments to ignore specific checks. We try to only use this in scenarios where missing typing information comes from
-external sources, and it is not possible to make local type hints. Do not use file-wide ignores under any circumstances.
-We also do not make stubs since they would be challenging to maintain.
-
-We encourage using the type checker as a tool to help strengthen your code and only apply inline comments to ignore
-specific instances where external libraries cause errors. 

ephys_link-2.0.0b9/docs/development/index.md

@@ -1,27 +0,0 @@
-# Developing with Ephys Link
-
-Ephys Link is free and open-source software. All of our code is available
-on [GitHub](https://github.com/VirtualBrainLab/ephys-link), and we welcome contributions from the community!
-
-This section describes:
-
-- [The Socket.IO server's API](socketio_api.md) and how to communicate with Ephys Link from a client application
-- How to [add a new manipulator](adding_a_manipulator.md) to Ephys Link
-- General [code organization](code_organization.md) for Ephys Link
-- Auto-generated [source code reference](../reference/SUMMARY.md) intended for developers who are maintaining Ephys Link
-
-## Installing 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 13 (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/).