populationgenomics / automated-interpretation-pipeline

Rare Disease variant prioritisation MVP

MIT License

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Linter changes, fixes scheduled index job #348

Closed MattWellie closed 3 months ago

MattWellie commented 3 months ago

Fixes

The report hunter process (collect all previous AIP reports into an HTML index page) doesn't work, and hasn't worked in ages
It requires a docker image with specific libraries installed, and values in config that weren't previously satisfied in the chrono-triggered runs

Proposed Changes

Runs the whole process in the AIP image (built on top of the driver image as a base, so all dependencies satisfied)
No expectation that a cohorts section of the config file exists (no need for this check)
All functional changes here are contained in .github/workflows/index_page_builder.yaml (only run twice a week, not 3 times. Run in the AIP docker image) and report_hunter.py (remove part of the config check), everything else is linting

Additional

Following suggestion here, alters the pre-commit hooks, and generates a ton of changes due to the addition of isort

MattWellie commented 3 months ago

This to me is a Linting PR + deploy docker update and I think the PR title should reflect that

Yeah this was rough timing - it was an isolated workflow fix, then you mentioned isort on Slack. I didn't think it would change quite so many files... Title is now pretty misleading, so i'll sort that out