Merge branch 'VirtualBrainLab:main' into parallax

hannalee2 · web-flow · commit 65abf17e3280 · 2025-05-01T10:10:06.000-07:00
diff --git a/.github/workflows/code-quality.yml b/.github/workflows/code-quality.yml
@@ -47,7 +47,7 @@ jobs:
           token: ${{ secrets.WORKFLOW_COMMIT }}
 
       - name: 🔭 Install UV
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v6
         with:
           enable-cache: true
           cache-dependency-glob: "**/pyproject.toml"
diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml
@@ -30,7 +30,7 @@ jobs:
           ref: ${{ github.head_ref }}
 
       - name: 🔭 Install UV
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v6
         with:
           enable-cache: true
           cache-dependency-glob: "**/pyproject.toml"
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -26,7 +26,7 @@ jobs:
           ref: ${{ github.head_ref }}
 
       - name: 🔭 Install UV
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v6
         with:
           enable-cache: true
           cache-dependency-glob: "**/pyproject.toml"
@@ -58,7 +58,7 @@ jobs:
           ref: ${{ github.head_ref }}
 
       - name: 🔭 Install UV
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v6
         with:
           enable-cache: true
           cache-dependency-glob: "**/pyproject.toml"
diff --git a/.idea/ephys-link.iml b/.idea/ephys-link.iml
diff --git a/.idea/misc.xml b/.idea/misc.xml
diff --git a/README.md b/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) -->
@@ -19,17 +19,18 @@ 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
 
diff --git a/docs/development/adding_a_manipulator.md b/docs/development/adding_a_manipulator.md
@@ -6,7 +6,10 @@ 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).
+1. Fork the [Ephys Link repository](https://github.com/VirtualBrainLab/ephys-link). If you're new to contributing, we
+   recommend
+   reading [this guide](https://docs.github.com/en/get-started/exploring-projects-on-github/contributing-to-a-project)
+   by GitHub.
 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).
diff --git a/docs/development/index.md b/docs/development/index.md
@@ -26,4 +26,25 @@ 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/).
+via [Visual Studio Build Tools Installer](https://visualstudio.microsoft.com/visual-cpp-build-tools/).
+
+## Contributing Code
+
+We recommend first time contributors to
+read [this guide](https://docs.github.com/en/get-started/exploring-projects-on-github/contributing-to-a-project) by
+GitHub to understand how to contribute changes.
+
+## Deploying New Releases
+
+!!! note
+
+    Only VBL members can make official releases.
+
+There is a [GitHub action](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/release.yml) configured to
+build and publish Ephys Link as a standalone EXE and as a PyPI package. The trigger is to make and push a new tag.
+
+```bash
+git switch main
+git tag v2.0.0
+git push origin --tags
+```
diff --git a/docs/home/installation.md b/docs/home/installation.md
@@ -3,40 +3,39 @@
 ## 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,
+2. For Sensapex devices, the controller unit must be powered and connected via an Ethernet
+   cable to the computer running Ephys Link. 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 a keyboard is attached.
 
-## Pinpoint (Recommended Method)
+## 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. See the documentation
 on [connecting from Pinpoint](../usage/using_ephys_link.md#connecting-to-pinpoint).
 
 ## Install as a Standalone Executable
 
-Download the latest standalone executable or zip from the [releases page](https://github.com/VirtualBrainLab/ephys-link/releases/latest).
+Download the latest standalone executable or zip from
+the [releases page](https://github.com/VirtualBrainLab/ephys-link/releases/latest).
 
 Then see the [usage documentation](../usage/starting_ephys_link.md) for how to run the server.
 
-## Install as a Python package
+## Install as a Python Package (Not Recommended)
 
-Ephys Link uses the latest stable version of Python. It requires a minimum of Python 3.10.
+Ephys Link is a Python package released on PyPI and can be included in projects as such.
 
-```bash
-pip install ephys-link
-```
-
-or with [pipx](https://pipx.pypa.io/stable/) (recommended)
+**This is not the recommended method of using Ephys Link.** This is only for advanced
+use cases where Ephys Link is used as a library in another project. Ephys Link will exclusively support the latest
+version of Python its dependencies support.
 
 ```bash
-pipx install ephys-link
+pip install ephys-link
 ```
 
 Then see the [usage documentation](../usage/starting_ephys_link.md) for how to run the server.
 
 ## Install for Development
 
-See [development documentation](../development/index.md#installing-for-development) for more information.
+See [development documentation](../development/index.md#installing-for-development) for more information.
diff --git a/docs/index.md b/docs/index.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/)
 
 The [Electrophysiology Manipulator Link](https://github.com/VirtualBrainLab/ephys-link)
diff --git a/pyproject.toml b/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",
@@ -29,16 +26,16 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Medical Science Apps.",
 ]
 dependencies = [
-    "aiohttp==3.11.12",
+    "aiohttp==3.11.18",
     "colorama==0.4.6",
     "keyboard==0.13.5",
-    "packaging==24.2",
-    "platformdirs==4.3.6",
+    "packaging==25.0",
+    "platformdirs==4.3.7",
     "pyserial==3.5",
-    "python-socketio[asyncio_client]==5.12.1",
+    "python-socketio[asyncio_client]==5.13.0",
     "requests==2.32.3",
-    "sensapex==1.400.3",
-    "rich==13.9.4",
+    "sensapex==1.400.4",
+    "rich==14.0.0",
     "vbl-aquarium==1.0.0"
 ]
 
@@ -62,8 +59,8 @@ exclude = ["/.github", "/.idea", "/docs"]
 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"
@@ -76,11 +73,11 @@ installer = "uv"
 python = "3.13"
 skip-install = true
 dependencies = [
-    "mkdocs-material==9.6.5",
-    "mkdocstrings-python==1.16.1",
+    "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"
diff --git a/src/ephys_link/__about__.py b/src/ephys_link/__about__.py
@@ -1 +1 @@
-__version__ = "2.0.0"
+__version__ = "2.1.0b1"
diff --git a/src/ephys_link/back_end/platform_handler.py b/src/ephys_link/back_end/platform_handler.py
@@ -71,10 +71,22 @@ def _get_binding_instance(self, options: EphysLinkOptions) -> BaseBinding:
         Returns:
             Bindings for the specified platform type.
         """
+
+        # What the user supplied.
+        selected_type = options.type
+
         for binding_type in get_bindings():
             binding_cli_name = binding_type.get_cli_name()
 
-            if binding_cli_name == options.type:
+            # Notify deprecation of "ump-4" and "ump-3" CLI options and fix.
+            if selected_type in ("ump-4", "ump-3"):
+                self._console.error_print(
+                    "DEPRECATION",
+                    f"CLI option '{selected_type}' is deprecated and will be removed in v3.0.0. Use 'ump' instead.",
+                )
+                selected_type = "ump"
+
+            if binding_cli_name == selected_type:
                 # Pass in HTTP port for Pathfinder MPM.
                 if binding_cli_name == "pathfinder-mpm":
                     return MPMBinding(options.mpm_port)
diff --git a/src/ephys_link/bindings/fake_binding.py b/src/ephys_link/bindings/fake_binding.py
@@ -57,8 +57,9 @@ async def get_angles(self, manipulator_id: str) -> Vector3:
     async def get_shank_count(self, manipulator_id: str) -> int:
         return 1
 
+    @staticmethod
     @override
-    def get_movement_tolerance(self) -> float:
+    def get_movement_tolerance() -> float:
         return 0.001
 
     @override
diff --git a/src/ephys_link/bindings/mpm_binding.py b/src/ephys_link/bindings/mpm_binding.py
diff --git a/src/ephys_link/bindings/ump_4_binding.py b/src/ephys_link/bindings/ump_4_binding.py
diff --git a/src/ephys_link/bindings/ump_binding.py b/src/ephys_link/bindings/ump_binding.py
diff --git a/src/ephys_link/utils/base_binding.py b/src/ephys_link/utils/base_binding.py
