8000 Apply best practices by hoferand · Pull Request #76 · epigen/unsupervised_analysis · GitHub
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Apply best practices#76

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sreichl merged 5 commits intomainfrom
hoferand/best-practices
Mar 13, 2026
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Apply best practices#76
sreichl merged 5 commits intomainfrom
hoferand/best-practices

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@hoferand hoferand commented Mar 10, 2026 •
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For local formatting the following commands can be used:

Markdown/YAML:

npx prettier . --write

Snakemake:

snakefmt .

Python:

black .

R:

Rscript -e 'install.packages("styler", repos = "https://cloud.r-project.org")' # Only necessary once
Rscript -e 'styler::style_dir(".")'

hoferand
hoferand commented Mar 10, 2026
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hoferand commented Mar 13, 2026

I enabled all kinds of analyzes in the config file that I found, and it still works (on my machine 😅) => ready for review and merge

jfi: I also played with codex to automatically configure the workflow with prompts like i only need PCA, can you disable the rest? only edit the config file and it worked pretty well 🔥

@hoferand hoferand marked this pull request as ready for review March 13, 2026 10:42
@sreichl sreichl merged commit 1cdaefd into main Mar 13, 2026
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sreichl commented Mar 13, 2026

merged assuming complete testing and only linting related changes

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