https://github.com/martibosch/cookiecutter-data-snake

Reproducible data science template using Python, snakemake, mamba and more :snake:
https://github.com/martibosch/cookiecutter-data-snake

cookiecutter data-science open-science python reproducible-science

Last synced: 4 days ago
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Reproducible data science template using Python, snakemake, mamba and more :snake:

• Host: GitHub
• URL: https://github.com/martibosch/cookiecutter-data-snake
• Owner: martibosch
• License: gpl-3.0
• Created: 2022-07-21T12:20:04.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2024-06-10T23:10:00.000Z (7 months ago)
• Last Synced: 2024-06-11T16:30:23.236Z (7 months ago)
• Topics: cookiecutter, data-science, open-science, python, reproducible-science
• Language: Python
• Homepage:
• Size: 226 KB
• Stars: 2
• Watchers: 3
• Forks: 1
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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# Cookiecutter Data Snake

A reproducible data science template using a bunch of snakes :snake:, i.e., Python, snakemake, mamba, and more.

![skeptical snake](https://raw.githubusercontent.com/martibosch/cookiecutter-data-snake/main/data-snake.png "skeptical snake")

This cookiecutter is based on [`cookiecutter-data-science`](http://drivendata.github.io/cookiecutter-data-science/), with the following main differences:

- [snakemake](https://snakemake.github.io) to orchestrate the data analysis workflow instead of [GNU Make](https://www.gnu.org/software/make) ([recommended in `cookiecutter-data-science`](https://drivendata.github.io/cookiecutter-data-science/)). The advantages of snakemake are its more Pythonic syntax as well as the availability of a dedicated code formatter, i.e., [snakefmt](https://github.com/snakemake/snakefmt) (see pre-commit item below).

- [mamba](https://github.com/mamba-org/mamba) as a package manager, which provides a CLI that is almost identical to [conda](https://conda.io) but _(much) faster_.

- [pre-commit](https://pre-commit.com) to manage multi-language pre-commit hooks, including: [ruff](https://github.com/astral-sh/ruff) to format and lint Python files (`.py`), [nbstripout](https://github.com/kynan/nbstripout) and [nbQA](https://nbqa.readthedocs.io) to format and lint Jupyter Notebooks (`.ipynb`); [snakefmt](https://github.com/snakemake/snakefmt) to format Snakefiles and more.

## Requirements to use the cookiecutter template:

- Python 3.8+

- [cookiecutter](http://cookiecutter.readthedocs.org), which can be installed with pip, conda or mamba (see [the official installation instructions](https://cookiecutter.readthedocs.org/en/latest/installation.html)).

- [mamba](https://github.com/mamba-org/mamba), which can be installed using conda or [mambaforge](https://github.com/conda-forge/miniforge#mambaforge) (see [the official installation instructions](https://github.com/mamba-org/mamba#installation))

## To start a new project, run:

```bash

$ cookiecutter gh:martibosch/cookiecutter-data-snake

```

fill the required parameters and then follow the instructions in the generated `README.md` file.

## Acknowledgments

- Project based on [Henk Griffioen's version](https://github.com/hgrif/cookiecutter-ds-python) of the [cookiecutter data science project template](https://drivendata.github.io/cookiecutter-data-science). #cookiecutterdatascience