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Installation

This page covers the full installation of UELer. Follow the steps below to set up a working environment.

Requirements

  • Python ≥ 3.10
  • micromamba (recommended) or conda/mamba
  • Git

Step 1 — Set Up the Environment

The easiest way to create a compatible environment is using the provided environment.yml file.

# Download the environment file from the repository
# Then create the environment:
micromamba env create --name ark-analysis-ueler --file environment.yml

conda env create --name ark-analysis-ueler --file environment.yml

This installs all required packages, including ark-analysis, ipywidgets, jupyter-scatter, dask, and other dependencies.

Step 2 — Clone the Repository

Navigate to the directory where you want to install UELer and clone the repository:

git clone https://github.com/HartmannLab/UELer.git
cd UELer

Step 3 — Activate the Environment

micromamba activate ark-analysis-ueler

Step 4 — Install UELer

Install the package in editable mode so that you can update it with git pull without reinstalling:

pip install -e .

Updating UELer

To update to the latest version, navigate to your UELer directory and pull the latest changes:

cd <path-to-UELer-folder>
git pull

No reinstall is needed when using editable mode.

Updating Your Environment

If you are upgrading from v0.1.7-alpha or earlier, you need to install additional packages:

micromamba activate ark-analysis-ueler
micromamba install dask
micromamba install dask-image

Installing for Development

If you plan to contribute to UELer or run the test suite, install the dev extras:

pip install -e ".[dev]"

This adds pytest and pytest-cov to your environment.

To run the test suite:

python -m unittest discover tests

Installing MkDocs (for documentation contributors)

To build and preview the documentation locally:

pip install mkdocs-material
mkdocs serve

The documentation site is then available at http://127.0.0.1:8000.

Troubleshooting

Widget not rendering in VS Code

If the interactive scatter plots are not shown in VS Code, UELer automatically falls back to a static Matplotlib figure. See the FAQ for details.

ModuleNotFoundError on import

Make sure you have activated the correct environment and that pip install -e . completed without errors.