Standardize pathogen-repo-ci use across pathogen repos

[joverlee521]

Ideas here came out of discussion with @tsibley in our 1:1 regarding #62 (comment). This would supersede #63 + #62.

Proposal

With the standardization of pathogen repos following the pathogen-repo-guide, we can now enforce the standardized use of the pathogen-repo-ci workflow.

In order to use the centralized pathogen-repo-ci, a pathogen repo will need to meet two requirements.

1. follow a strict repo organization (currently required to have a phylogenetic subdirectory)

2. use a standard mechanism for specifying the CI build, e.g. use a standard CI config that can be specified with

   nextstrain build phylogenetic --configfiles build-configs/ci/config.yaml
   

This would simplify each pathogen repo's CI workflow to:

name: CI

on:
  - push
  - pull_request

jobs:
  ci:
    uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@master

Then the docker-base/conda-base CIs can be simplified to just matrix of pathogen repos instead of needing to pass in additional build args.

Concrete steps

• Pin existing uses of pathogen-repo-ci #93
• Update pathogen-repo-ci to "generic"/"smart" workflow #89
• Update pathogen repos to conform to smart pathogen-repo-ci #94
• CI: Update test-pathogen-repo-ci docker-base#223
• CI: Update test-pathogen-repo-ci conda-base#85
• CI: Update pathogen-repo-ci augur#1549

[victorlin]

I'm a bit out of the loop here. What's the difference between mpox's CI (which uses pathogen-repo-build) and avian-flu's CI (which uses pathogen-repo-ci)? Can avian-flu use pathogen-repo-build? Or is mpox's use of pathogen-repo-build considered temporary and will be replaced during the 3rd task here?

[joverlee521]

Or is mpox's use of pathogen-repo-build considered temporary and will be replaced during the 3rd task here?

Yup, the use of the pathogen-repo-build in CI is considered a temporary change (if ~6 months is considered temporary 😅). The plan would be to switch all pathogen GitHub Action CI workflows back to pathogen-repo-ci.

[genehack]

Related/precursor work: #89