Automatically generate a round's clade list, save it, and submit a PR

bsweger commented 2 weeks ago

Background

When #25 is complete, this hub will have a function that generates a list of clades to be forecast for each modeling round.

The next step is to provided an automated way to schedule a run of this function prior to each round, and write the resulting .json file of clades to variant-nowcast-hub/auxiliary-data/modeled-clades/YYYY-MM-DD.json, where YYYY-MM-DD is the reference date of the upcoming round.

(note: we decided to save each reference date's clades in a separate file, rather than appending to a single, large file).

Definition of done

[x] schedule the invocation of the update_clades_list function
[x] write the output to the directory above
[x] submit the update as PR to this repo, so it can be reviewed and merged by hub admins

elray1 commented 2 weeks ago

since we now have a separate file for each week, with the reference date in the file name, do we need this to be json? or could it literally just be a text file with e.g. comma-separated names of clades?

bsweger commented 1 week ago

since we now have a separate file for each week, with the reference date in the file name, do we need this to be json? or could it literally just be a text file with e.g. comma-separated names of clades?

It can be whatever we want it to be!

elray1 commented 1 week ago

i really struggle with pointless decisions like this, but i guess maybe making it json makes it easy to parse with standard tools

bsweger commented 2 days ago

@elray1 @nickreich I have a GitHub workflow setup in this branch and will submit the PR for it once we have this one merged in: https://github.com/reichlab/variant-nowcast-hub/pull/27

reichlab / variant-nowcast-hub

Automatically generate a round's clade list, save it, and submit a PR #26