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Update the README
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Marius1311 committed Oct 16, 2024
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# Analysis template repository

This contains the raw structure I usually use when doing single-cell/spatial data analysis. This template is based on ideas from Philipp Weiler, I took heavy inspiration and copied parts from [his template repository](https://github.com/WeilerP/sc_analysis_template).
This contains the raw structure I usually use when doing single-cell/spatial data analysis. This template is based on ideas from Philipp Weiler's [template repository](https://github.com/WeilerP/sc_analysis_template) as well as the [scverse cookiecutter template](https://github.com/scverse/cookiecutter-scverse).

## Set up

1. Rename `src/fancypackage/`.
2. Update `pyproject.toml` to include the correct information
2. Update `pyproject.toml` to include the following information:
- Project name
- Project description
- Project-specific Python requirements
- Project author
- Project maintainers
- Project URLs
3. Update `src/fancypackage/core/_constants.py` to include any paths relevant to your analysis and that should be accessible from any script or Jupyter notebook
3. Update `src/fancypackage/ul/constants.py` to include any paths relevant to your analysis and that should be accessible from any script or Jupyter notebook
4. Update this README to include the relevant information about your project.

## Installation

```bash
pip install -e ".[dev]"
pip install -e ".[dev,test]"
pre-commit install
```

## Things to keep in mind

Whenever you use a new single-cell tool, add it to `known_bio` in `pyproject.toml` s.t. `isort` can work correctly.

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