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CONTRIBUTING.md

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Contribute

Seeking support and report an issue

For cuisto-related issues, you can open an issue here explaining your issue. Please provide as much relevant information as you can, such as platform, Python version, cuisto version, data sample and code snippets to help reproduce the issues.

You can also use the Issues to ask questions. We'll try to get back to you as soon as possible.

For QuPath and/or ABBA-related issues and questions, you can find support over at the image.sc forum.

Contribute

You can contribute a fix or a new feature to this project with the following steps:

  1. Create a conda environment with Python 3.12
conda create -n cuisto-dev python=3.12
  1. Fork the project on GitHub.
  2. Clone the project
git clone https://github.com/<your-github-username>/cuisto
  1. Activate the environement and install the package in editable mode, with the development dependencies
conda activate cuisto-dev
pip install -e .[doc,dev]
  1. Make a new git branch where you will apply the changes
git checkout -b your-branch-name
  1. Make your changes and test them. You can add tests in the tests folder and run them with pytest. Once done, git add, git commit and git push the changes.
  2. Make a Pull Request from your branch to the cuisto repository.

Styleguides

Python code

Python code should be PEP8 compliant. We use ruff with a line length of 88 to format the code.

Docstrings are formatted with the numpy convention.

Groovy code

We use camelCase for file and variable names. The scripts should contain a docstring with the filename and a short description of what it does. See an existing example.

Documentation

The documentation is written in Markdown, using mkdocs and mkdocs-material.

See the existing pages to know how to format things, including :

  • `code` for code snippets, /file/paths and scriptName.groovy. The latter should contain a backlink to the actual file in the Github repository.