Up front... This was originally just a PR to update documentation/remove anything that's completely useless
Then I discovered that there really wasn't a reason to exclude all the linting rules I've been skipping (I just copy-pasted some config from prod-pipes). I got stuck in re-enabling the rules, and tweaking the code/type hints to pass all the new tests. It all got a bit out of hand.
updates documentation, removes duds, deletes a couple of scripts which were just for the CPG (we now use this in the main pipeline)
throws all the code inside a src directory, as a test case for the changes I'm proposing here
re-enables ~120 linting rules, and the corresponding changes required to pass them.
this is not a complete fix, but I'm planning to adopt the phenotype matching changes, and should probably build that on top of this, instead of reconciling those changes later
Up front... This was originally just a PR to update documentation/remove anything that's completely useless
Then I discovered that there really wasn't a reason to exclude all the linting rules I've been skipping (I just copy-pasted some config from prod-pipes). I got stuck in re-enabling the rules, and tweaking the code/type hints to pass all the new tests. It all got a bit out of hand.
Fixes
Proposed Changes
srcdirectory, as a test case for the changes I'm proposing hereChecklist