Run pathogen CI on multiple subdirs

[victorlin]

conda-base/.github/workflows/ci.yaml

Line 138 in 02cf82e

# XXX TODO: Test on multiple platforms (os, maybe arch) via the matrix too

Expanding the above TODO into a GitHub issue.

Currently, pathogen CI only runs on linux-64 – test-pathogen-repo-ci uses nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@v0 which runs the build on ubuntu-latest.

This means osx-64 (and soon osx-arm64) is not tested on pathogen repo CI.

Tasks

1. Use osx-arm64 packages on Apple silicon cli#379
2. pathogen-repo-ci: Add input for GH Action runner .github#103
3. In this repo's ci.yaml, specify a list of runners as input to jobs.test-pathogen-repo-ci

[victorlin]

Trying this out with 5dfbe2f + manual CI run.

[victorlin]

The above test involved changes across 3 repos:

1. 5dfbe2f
2. nextstrain/.github@baf4c03...edaf923
3. nextstrain/cli@53a96c5

but it was successful!

The biggest potential blocker to getting these pushed through is that there's no immediate way to use a newer version of pathogen-repo-ci.yaml. Currently it's pinned to v0 and can't be updated to anything newer because the pathogen workflows are not compatible (#78, nextstrain/.github#84). We could get around this by referencing an unmerged commit like I've done in 5dfbe2f but it's not ideal.

[joverlee521]

We could add a separate job that uses a newer version of pathogen-repo-ci.yaml and test on the "modern" pathogen repos. GH search for repos using pathogen-repo-ci.yaml@master shows this currently includes mpox, seasonal-cov, and zika. We can add more pathogens as we continue to work on nextstrain/.github#94

[victorlin]

^ that would directly address #78!

[joverlee521]

With #85 merged, we can update the latest pathogen-repo-ci workflow to add a new input for specifying GH Action runners. Tracking in nextstrain/.github#103.