Feat: using uv

.github/workflows/ci.yml

@@ -15,19 +15,16 @@ jobs:
         python-version: [ '3.10' ]
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
+      - name: Install uv and set Python version
+        uses: astral-sh/setup-uv@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
-        run: |
-          python -m pip install -e .[linters] --no-cache-dir
-      - name: Run interrogate
-        run: interrogate parallax tests
+        run: uv sync --extra linters
       - name: Run Ruff Check
-        run: ruff check .
+        run: uv run ruff check .
       - name: Run Ruff Format Check
-        run: ruff format --check .
+        run: uv run ruff format --check .
 
   # Job 2: Build Documentation for PR to Main and Dev Branches
   build-docs:
@@ -37,21 +34,18 @@ jobs:
       - name: Checkout Repository
         uses: actions/checkout@v3
 
-      # Step 2: Set up Python
-      - name: Set up Python
-        uses: actions/setup-python@v4
+      # Step 2: Install uv and set Python version
+      - name: Install uv and set Python version
+        uses: astral-sh/setup-uv@v5
         with:
           python-version: '3.10'
 
-      # Step 3: Install dependencies (including Sphinx)
+      # Step 3: Install Dependencies
       - name: Install Dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -r docs/requirements.txt
+        run: uv sync --extra docs
 
       # Step 4: Build the documentation
       - name: Build Documentation
-        run: |
-          sphinx-build -b html docs/source docs/_build
+        run: uv run sphinx-build -b html docs/source docs/_build
         # Fail the workflow if documentation build fails
         continue-on-error: false

.github/workflows/pytest.yml

@@ -22,21 +22,13 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y libegl1 libxkbcommon-x11-0
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - name: Install uv and set Python version
+        uses: astral-sh/setup-uv@v5
         with:
           python-version: '3.10'
 
-      - name: Upgrade pip
-        run: python -m pip install --upgrade pip
-
       - name: Install package + test deps
-        run: |
-          pip install -e ".[test]"
-          # optional: linters too
-          pip install -e ".[linters]"
+        run: uv sync --extra test --extra linters
 
       - name: Run tests with coverage
-        run: |
-          pytest --cov=parallax --cov-report=term-missing
-        continue-on-error: true
+        run: uv run pytest --cov=parallax --cov-report=term-missing --cov-fail-under=30

.github/workflows/tag_and_publish.yml

@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - main
+  workflow_call:
 
 jobs:
   build-and-release:
@@ -14,16 +15,16 @@ jobs:
         with:
           fetch-depth: '0'  
 
-      - name: Set up Python
-        uses: actions/setup-python@v2  
+      - name: Install uv and set Python version
+        uses: astral-sh/setup-uv@v5
         with:
           python-version: '3.10'
 
       - name: Extract version from the package
         id: get_version
         shell: bash
         run: |
-          RELEASE_VERSION=$(python -c 'import parallax; print(parallax.__version__)')
+          RELEASE_VERSION=$(uv run python -c 'import parallax; print(parallax.__version__)')
           echo "RELEASE_VERSION=$RELEASE_VERSION" >> $GITHUB_ENV
           echo "Extracted RELEASE_VERSION: $RELEASE_VERSION"
 
@@ -47,18 +48,8 @@ jobs:
           draft: false
           prerelease: true
 
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install setuptools wheel twine build
-
-      - name: Install project
-        run: pip install -e . 
-
       - name: Build package
-        run: |
-          python -m build
-          twine check dist/*
+        run: uv build
 
       - name: Publish on PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
@@ -74,21 +65,18 @@ jobs:
       - name: Checkout Repository
         uses: actions/checkout@v3
 
-      # Step 2: Set up Python
-      - name: Set up Python
-        uses: actions/setup-python@v4
+      # Step 2: Install uv and set Python version
+      - name: Install uv and set Python version
+        uses: astral-sh/setup-uv@v5
         with:
           python-version: '3.10'
 
-      # Step 3: Install dependencies (including Sphinx)
+      # Step 3: Install Dependencies
       - name: Install Dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -r docs/requirements.txt
+        run: uv sync --extra docs
 
       # Step 4: Build the documentation
       - name: Build Documentation
-        run: |
-          sphinx-build -b html docs/source docs/_build
+        run: uv run sphinx-build -b html docs/source docs/_build
         # Fail the workflow if documentation build fails
         continue-on-error: false

.gitignore

@@ -34,4 +34,4 @@ debug
 .coverage
 
 # Environments
-venv/
+.venv/

README.md

@@ -7,36 +7,40 @@ setting up and performing acute *in vivo* electrophysiology experiments.
 
 **Documentation**: [parallax.readthedocs.io](https://parallax.readthedocs.io/en/latest/index.html).
 
-### Prerequisites
-- **Python==3.10** (Recommended to install via
-[Anaconda](https://www.anaconda.com/products/individual) or 
-[Miniconda](https://docs.conda.io/en/latest/miniconda.html))
-  -  Python 3.10 is required for the Spinnaker library.
-- [Spinnaker SDK 4.2](https://www.teledynevisionsolutions.com/products/spinnaker-sdk)
+## Prerequisites
+- **Python 3.10**: Required for compatibility with the Spinnaker library.
+- [Spinnaker SDK 4.2](https://www.teledynevisionsolutions.com/products/spinnaker-sdk) and Teledyne FLIR software for camera support.
+- We recommend using [`uv`](https://docs.astral.sh/uv/) for environment management.
 
 
-### Installation
-1. Create a virtual environment with **Python 3.10** and activate it:
-2. Install Parallax:
+## Installation
+#### 1. Install Parallax
+Option A, Install from PyPI:
 ```bash
-pip install parallax-app
+uv venv --python 3.10
+# On macOS/Linux: source .venv/bin/activate
+# On Windows: .venv\Scripts\activate
+uv pip install parallax-app
 ```
-
-To upgrade to the latest version, run:
+Option B, Install via local repository (Recommended):
 ```bash
-pip install parallax-app --upgrade
+git clone https://github.com/AllenNeuralDynamics/parallax.git
+cd parallax
+uv sync
 ```
 
-3. Install the camera interface [Spinnaker SDK 4.2](https://www.teledynevisionsolutions.com/products/spinnaker-sdk)
+#### 2. Install Spinnaker
+Install the camera interface [Spinnaker SDK 4.2](https://www.teledynevisionsolutions.com/products/spinnaker-sdk)
 ```bash
 # Install from the **wheel file** that comes with the Spinnaker SDK ver.4.2.
 # Replace **<WHEEL_PATH>** with the *full path* to your `.whl`:
-pip install "<WHEEL_PATH>"
+uv pip install "<WHEEL_PATH>"
+# Example) uv pip install spinnaker_python-4.2.0.88-cp310-cp310-win_amd64.whl
 ```
 
-### Running Parallax
+## Running Parallax
 ```bash
-python -m parallax
+uv run parallax
 ```
 
 ### Optional: Enable SuperPoint + SuperGlue Reticle Detection
@@ -47,16 +51,21 @@ The SuperGluePretrainedNetwork is not included in this repository and is distrib
 Please review their [license](https://github.com/magicleap/SuperGluePretrainedNetwork) before use.
 
 Manual Setup Instructions
-1. Clone the repository if it hasn't been done already.
+Clone the repository if it hasn't been done already.
 ```bash
 git clone https://github.com/AllenNeuralDynamics/parallax.git
+cd parallax
+```
+1. Install the required `sfm` dependency from GitHub:
+```bash
+uv pip install git+https://github.com/AllenNeuralDynamics/sfm.git@main
 ```
 
 2. Clone the repository into the external/ folder in your Parallax project root:
 ```bash
-pip install git+https://github.com/AllenNeuralDynamics/sfm.git@main
 git clone https://github.com/magicleap/SuperGluePretrainedNetwork.git external/SuperGluePretrainedNetwork
 ```
+
 3. Verify your folder structure looks like this:
 ```bash
 parallax/
@@ -70,28 +79,36 @@ parallax/
 ```
 
 ### For developers:
-1. Clone the repository:
+The following are tools used to ensure code quality in this project.
+- Install dependencies:
 ```bash
-git clone https://github.com/AllenNeuralDynamics/parallax.git
+uv sync --all-extras
 ```
-2. Install the package along with dev dependencies:
+
+- Unit Testing
 ```bash
-pip install -e .[dev]
+uv run pytest tests
 ```
 
-### Documentation
-1. To install the dependencies:
+- Linting
+```bash
+uv run ruff check
+```
+
+- Type Check
 ```bash
-pip install -e .[docs]
+uv run mypy parallax
 ```
-2. Then to create the documentation html files, run:
+
+### Documentation
+Create the documentation html files, run:
 ```bash
-sphinx-build -b html docs/ docs/_build
+uv run sphinx-build -b html docs/source docs/_build
 ```
 
 ### Support and Contribution
 If you encounter any problems or would like to contribute to the project, 
-please submit an [Issue](https://github.com/AllenNeuralDynamics/parallax/issues) 
+please submit an [Issue](https://github.com/AllenNeuralDynamics/parallax/issues)
 on GitHub.
 
 ### License

parallax/__init__.py

@@ -4,7 +4,7 @@
 
 import os
 
-__version__ = "1.16.1"
+__version__ = "1.17.0"
 
 # allow multiple OpenMP instances
 os.environ["KMP_DUPLICATE_LIB_OK"] = "True"

parallax/__main__.py

@@ -17,8 +17,8 @@
 from parallax.model import Model
 from parallax.session.session_manager import SessionManager
 
-# Main function to run the Parallax application
-if __name__ == "__main__":
+
+def main():
     # Print the ASCII art
     print(f"Parallax version {__version__}")
     print(PARALLAX_ASCII)
@@ -47,7 +47,11 @@
     app.exec()
 
     # Clean up on exit
-    atexit.register(main_window.update_config_from_ui)
     atexit.register(model.save_config)
     atexit.register(model.save_session)
     atexit.register(model.clean)
+
+
+# Execute when run directly as a module
+if __name__ == "__main__":
+    main()

parallax/main_window.py

@@ -262,6 +262,7 @@ def closeEvent(self, event):
         Args:
             event (QCloseEvent): The close event triggered when the widget is closed.
         """
+        self.update_config_from_ui()
         self.model.close_clac_instance()
         self.model.close_reticle_metadata_instance()
         self.model.close_stage_ipconfig_instance()