kymflow 0.1.1

Linescan kymograph blood flow analysis.

KymFlow

KymFlow is a NiceGUI-based application for browsing kymograph TIFF files, editing metadata, and running Radon-based flow analysis.

The backend lives in src/kymflow_core and is completely GUI-agnostic, so scripts and notebooks can reuse the same API for analysis, metadata editing, or batch processing.

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Requirements

• Python 3.11+
• uv for dependency management (recommended)

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Quick Start

Install and Run GUI

1. Create a virtual environment:

   python -m venv kymflow-venv

2. Activate the virtual environment:

   # On macOS/Linux:
   source kymflow-venv/bin/activate
   
   # On Windows:
   kymflow-venv\Scripts\activate
   

3. Install KymFlow with GUI dependencies:

   pip install 'kymflow[gui]'
   

4. Run the GUI:

   python -m kymflow_gui.main
   

   The GUI will open in your default web browser at http://localhost:8080 (or the next available port).

Getting the Source

Clone the repository (or download the ZIP) from GitHub:

git clone https://github.com/mapmanager/kymflow.git
cd kymflow

All commands below assume you are in the project root.

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Installation (uv)

KymFlow uses a src/ layout and should be installed in editable mode. With uv this is a single command:

uv pip install -e ".[gui]"

This creates (or updates) .venv/, installs the package in editable mode, and pulls in the GUI + dev extras. If you add/remove dependencies in pyproject.toml, rerun the same command. Regular source edits do not require reinstalling.

Not using uv? Any standard tool can install the same extras via: pip install -e ".[gui]" or the equivalent in your environment.

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Running the GUI

Launch the NiceGUI app with:

uv run python -m kymflow_gui.main

This automatically uses the uv-managed environment and keeps editable imports intact. The GUI defaults to port 8080; tweak defaults in src/kymflow_gui/config.py if needed.

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Running Tests

uv pip install -e ".[test]"

uv run pytest tests/                    # Run all tests
uv run pytest tests/kymflow_core/      # Run only core tests
uv run pytest tests/kymflow_gui/       # Run only GUI tests (when you add them)

Run tests without data using

uv run pytest -m "not requires_data"

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Working with Jupyter Notebooks

Install the optional notebook extras (once):

uv pip install -e ".[notebook]"

Launch Jupyter Lab inside the repo (it will open in the notebooks/ folder by default):

uv run jupyter lab --notebook-dir notebooks

You can also use jupyter notebook if you prefer the classic interface. All dependencies run inside the same uv-managed environment.

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Project Layout

kymflow/
├─ src/
│  ├─ kymflow_core/       # backend (KymFile, metadata, analysis, repository)
│  └─ kymflow_gui/        # NiceGUI frontend (layout, components)
├─ tests/                 # unit/integration tests
├─ pyproject.toml
├─ README.md
└─ .venv/                 # uv-managed virtualenv

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Contributing

Issues and pull requests are welcome. Please include clear steps to reproduce bugs and run uv run pytest before submitting changes. More detailed guidelines will be added later.

Troubleshooting

To kill a stale nicegui. By default it should be running on port 8080.

sudo lsof -iTCP:8080 -sTCP:LISTEN

Then look for pid and kill <pid>

Development

To push a new version from local dev machine

edit version in pyproject.toml

version = "0.1.1"

Then

git commit -am "Bump version to 0.1.1"

git tag -a v0.1.1 -m "KymFlow 0.1.1"
git push origin main
git push origin v0.1.1

To append info to macOS app

Build your macOS app bundle and go to:

• GitHub → Releases → “Draft a new release”
• Select tag v0.1.1
• In the description, paste the 0.1.1 section from CHANGELOG.md.
• Attach the macOS .dmg / .zip / .app as an asset.
• Publish release.