├── .github └── workflows │ ├── spellcheck.yml │ └── sphinx.yml ├── .gitignore ├── CITATION.cff ├── LICENSE ├── Makefile ├── README.md ├── content ├── conf.py ├── dependencies.md ├── environments.md ├── exercises.md ├── guide.md ├── img │ ├── dependency.png │ ├── docker_architecture.svg │ ├── docker_meme.jpg │ ├── kitchen │ │ ├── busy.png │ │ ├── libraries.png │ │ ├── linux.png │ │ ├── macos.png │ │ ├── recipe.png │ │ └── windows.png │ ├── python_environment.png │ ├── repro-pyramid.png │ ├── reproducibility_levels.png │ ├── reproducibility_nature.jpg │ ├── reproducible-research.jpg │ ├── reproducible_research_plus_lessons.png │ ├── reproducible_research_plus_lessons.svg │ ├── research_comic_phd.gif │ ├── snakemake.png │ ├── snakemake_dag.png │ ├── turing-way │ │ ├── 8-fair-principles.jpg │ │ └── reproducibility.jpg │ └── word-count │ │ ├── arrows.png │ │ ├── gutenberg.png │ │ ├── plot.png │ │ └── statistics.png ├── index.rst ├── intro.md ├── motivation.md ├── organizing-projects.md ├── 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