Merge pull request #63 from flika-org/dev

Merging Dev into Master

Author: kyleellefsen

.github/workflows/publish-to-pypi.yml

@@ -1,5 +1,8 @@
 name: Publish to PyPi
-on: push
+on:
+  push:
+    branches:
+      - master
 jobs:
   publish: 
     name: publish
@@ -12,7 +15,7 @@ jobs:
       - name: Set up Python 
         uses: actions/setup-python@v4
         with:
-          python-version: "3.11"
+          python-version: "3.12"
       - name: Build package
         run: |
           python -m pip install -U pip build

.github/workflows/run-tests.yml

@@ -0,0 +1,65 @@
+name: Run Tests
+
+on:
+  # Only run on a branch that doesn't exist
+  push:
+    branches: [ "branch-that-does-not-exist" ]
+  pull_request:
+    branches: [ "branch-that-does-not-exist" ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.13"]
+
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    
+    - name: Install system dependencies for PySide6
+      run: |
+        sudo apt-get update
+        # Install Qt dependencies based on Qt X11 requirements documentation
+        # https://doc.qt.io/qt-6/linux-requirements.html
+        sudo apt-get install -y \
+          libegl1 \
+          libfontconfig1 \
+          libxcb1 \
+          libx11-6 \
+          libx11-xcb1 \
+          libxcb-glx0 \
+          libxcb-icccm4 \
+          libxcb-image0 \
+          libxcb-keysyms1 \
+          libxcb-randr0 \
+          libxcb-render0 \
+          libxcb-render-util0 \
+          libxcb-shape0 \
+          libxcb-shm0 \
+          libxcb-sync1 \
+          libxcb-util1 \
+          libxcb-xfixes0 \
+          libxcb-xkb1 \
+          libxkbcommon0 \
+          libxkbcommon-x11-0 \
+          libdbus-1-3
+    
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install .[dev]
+    
+    - name: Run tests
+      run: |
+        pytest flika --cov=flika
+    
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        fail_ci_if_error: false 

AUTHORS.rst

@@ -1,5 +1,5 @@
 The MIT License (MIT)
-Copyright (c) 2015-2017 Kyle Ellefsen
+Copyright (c) 2015-2025 Kyle Ellefsen
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
 

CHANGELOG.rst

@@ -1,3 +1,4 @@
 recursive-include flika *.ui *.png *.ico
 include README.md
-include flika.desktop
+include flika.desktop
+recursive-include examples *.py

LICENSE

@@ -0,0 +1,58 @@
+# flika
+
+![flika screencapture](flika/docs/_static/img/flika_screencapture.gif)
+
+**flika** is an interactive image processing program for biologists written in Python.
+
+## Website
+[flika-org.github.io](http://flika-org.github.io/)
+
+## Documentation
+[flika-org.github.io/contents.html](http://flika-org.github.io/contents.html)
+
+## Install
+[flika-org.github.io/getting-started.html#installation](http://flika-org.github.io/getting-started.html#installation)
+
+## Development
+
+This is how Kyle installs Flika for development on a mac.
+
+```fish
+brew install [email protected]
+python3.13 -m venv ~/venvs/flika; source ~/venvs/flika/bin/activate.fish; python -m pip install --upgrade pip;
+cd ~/git
+git clone https://github.com/flika-org/flika.git
+cd ~/git/flika
+python -m pip install -e .
+ipython
+In [1]: import flika
+In [2]: flika.start_flika()
+```
+
+For tests:
+```fish
+pip install -e .[dev]
+pytest flika --cov=flika
+```
+
+Cleanup :
+```fish
+deactivate
+rm -r ~/venvs/flika
+```
+
+
+## Contributors
+
+- [Kyle Ellefsen](https://github.com/KyleEllefsen)
+- [Brett Settle](https://github.com/BrettJSettle)
+- [George Dickinson](https://github.com/gddickinson)
+- [Kevin Tarhan](https://github.com/KevinTarhan)
+
+
+## Development
+
+- Ruff is used for linting/formatting
+- VSCode/Cursor is the usually IDE
+- Python 3.13 is the (current) development version
+- PySide6 is used for the GUI

MANIFEST.in

@@ -0,0 +1,56 @@
+# Flika Examples
+
+This directory contains example scripts demonstrating various features and use cases of Flika, an interactive image processing program for biologists.
+
+## Running Examples
+
+### Prerequisites
+
+These examples assume you have Flika installed in your Python environment. If you haven't already installed Flika, follow these steps:
+
+```bash
+# Clone the repository (if you haven't already)
+git clone https://github.com/flika-org/flika.git
+cd flika
+
+# Create and activate a virtual environment (recommended)
+python -m venv ~/venvs/flika
+source ~/venvs/flika/bin/activate
+
+# Install flika in development mode
+pip install -e .
+```
+
+### Running an Example
+
+Each example can be run directly with Python:
+
+```bash
+python examples/generate_random_video.py
+```
+
+All examples launch an IPython interactive terminal by default, allowing you to interact with the flika objects after the initial script runs.
+
+## Utils Directory
+
+The `utils/` subdirectory contains shared code and utilities used across multiple examples:
+
+- `ipython_helper.py`: Helpers for running scripts in IPython
+- Common initialization code
+- Shared helper functions
+
+### Using the IPython Helper
+
+All examples use the `run_in_ipython` helper to create an interactive IPython environment. You can use this in your own examples:
+
+```python
+from utils import run_in_ipython
+
+def my_flika_demo():
+    import flika
+    flika.start_flika()
+    # Your flika code here
+
+if __name__ == "__main__":
+    run_in_ipython(my_flika_demo)
+```

README.md

@@ -0,0 +1,32 @@
+"""
+Random Image Stack Example
+
+This example demonstrates how to generate a random image stack using flika
+and perform basic operations on it.
+"""
+
+from utils import run_in_ipython
+
+
+def random_image_demo():
+    """Generate a random image stack and display information about it."""
+    import flika
+    import flika.global_vars as g  # noqa: F401
+
+    # Start flika
+    print("Starting flika...")
+    flika.start_flika()
+
+    # Generate a random image stack
+    print("Generating random image stack...")
+    window = flika.process.stacks.generate_random_image(nFrames=100, width=128)
+
+    # Display information about the generated image stack
+    print(f"Created window: {window.name}")
+    print(f"Image dimensions: {window.image.shape}")
+    print(f"Data type: {window.image.dtype}")
+
+
+if __name__ == "__main__":
+    # Run the demo in IPython
+    run_in_ipython(random_image_demo)