ephys-link 2.0.0b10__tar.gz → 2.0.1__tar.gz

{ephys_link-2.0.0b10 → ephys_link-2.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ephys-link
-Version: 2.0.0b10
+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-2.0.0b10 → 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-2.0.0b10 → 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-2.0.0b10 → 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]
@@ -59,10 +56,11 @@ path = "src/ephys_link/__about__.py"
 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-2.0.0b10 → 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-2.0.0b10 → 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-2.0.0b10/src/ephys_link/__about__.py

@@ -1 +0,0 @@
-__version__ = "2.0.0b10"