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# Analysis template repository | ||
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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). | ||
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## Set up | ||
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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. | ||
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## Installation | ||
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```bash | ||
pip install -e ".[dev]" | ||
pip install -e ".[dev,test]" | ||
pre-commit install | ||
``` | ||
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## Things to keep in mind | ||
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Whenever you use a new single-cell tool, add it to `known_bio` in `pyproject.toml` s.t. `isort` can work correctly. |