kymflow 0.1.0

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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 3.9+
• uv for dependency management (recommended)

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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,test]" 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 that require proprietary TIFF data auto-skip when the sample data is unavailable.

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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>