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[FEATURE] | Ratify a CI implementation #19

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G-kodes opened this issue Nov 16, 2021 · 2 comments
Open

[FEATURE] | Ratify a CI implementation #19

G-kodes opened this issue Nov 16, 2021 · 2 comments
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enhancement New feature or request

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@G-kodes
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G-kodes commented Nov 16, 2021

Is your feature request related to a problem? Please describe.
This project is currently maintained and developed by @G-kodes. Good ven the scope and capacity for word, a CI implementation would help greatly in managing code development and issue debugging. It would also help a lot for reproducibility for research purposes.

Describe the solution you'd like
Use Genome-In-A-Bottle to create a CI implementation for GitHub Actions.
.

@G-kodes G-kodes added the enhancement New feature or request label Nov 16, 2021
@G-kodes G-kodes self-assigned this Nov 16, 2021
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G-kodes commented Nov 18, 2021

An initial CI pipeline has been enabled. Unfortunately of the three possible tests, only 1 works.

  • Lint (--lint)
  • Build DAG (--dry-run)
  • Run generated unit tests (run from inside .tests folder)

I have noted the un-mentioned issue regarding the Unit Tests that prevents users who use relative paths in their Snakefile at snakemake/snakemake-github-action#18.

The issue around the lint profile is currently under some discussion with multiple issues around their linters. The most promising and related issue is snakemake/snakemake#881.

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G-kodes commented Jan 11, 2022

The PEP validation problem was caused was caused by an indentation issue.

pepkit/eido#33 (comment)

G-kodes added a commit that referenced this issue Jan 11, 2022
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