Development

This guide will help you set up your development environment and contribute to the project.

Setting Up Development Environment

Clone the repository:

git clone https://github.com/argearriojas/singlecell-cookbook.git
cd singlecell-cookbook

Create the development environment:

Using venv:

python -m venv .venv
source .venv/bin/activate
pip install -e ".[dev]"

Using conda:

conda env create --file environment.yml
conda activate singlecell-cookbook

Code Style and Formatting

This project uses Ruff for code formatting and linting. The configuration is in ruff.toml, which specifies:

Line length of 88 characters
Double quotes for strings
4-space indentation
Other Python code style rules

Editor Setup

While you can use any editor, here are the minimal recommended settings for popular editors:

VSCode

Install the Ruff extension

Configure formatting:

{
    "[python]": {
        "editor.formatOnSave": true,
        "editor.defaultFormatter": "charliermarsh.ruff",
        "editor.codeActionsOnSave": {
            "source.fixAll": "explicit",
            "source.organizeImports": "explicit"
        }
    }
}

PyCharm

Install the Ruff plugin
Enable “Format on Save”
Set Ruff as the default formatter

Running Tests

To run the tests:

pytest tests/

Version Management

This project uses bump2version for version management. To bump the version:

For a patch release (bug fixes):
```
bump2version patch
```
For a minor release (new features, backwards compatible):
```
bump2version minor
```
For a major release (breaking changes):
```
bump2version major
```

This will: - Update version numbers in all configured files - Create a git commit with the version change - Create a git tag for the new version

Building Documentation

To build the documentation:

cd docs
make html

The built documentation will be in docs/build/html.