Add docs for internal Nextstrain team #45
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This will hold docs for setting up Nextstrain pathogen repos that is meant for the internal team. External users can consult for their own use, but it will not be written with them in mind!
| ### `pathogen-repo-ci` Requirements | ||
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| > [!IMPORTANT] | ||
| > If your pathogen repo does not meet these requirements, please update the | ||
| > repo to conform to them to maintain uniformity of Nextstrain pathogen repos. | ||
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| 1. The pathogen repo must have a top level `nextstrain-pathogen.yaml` file. | ||
| 2. To run the CI step for a workflow (ingest, nextclade, or phylogenetic), the | ||
| directory must contain a `build-configs/ci/config.yaml` config file. | ||
| 3. At least one of the CI steps must be run or else the CI workflow will exit with an error. |
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I waffled on whether this should be here or point to docs in the .github repo. I just put it here so it's all in one place, but feel free to push back.
| branches: | ||
| - main | ||
| pull_request: | ||
| workflow_dispatch: |
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I'd encourage adding a basic schedule: on here too. It's really nice to come back to a repo after a while of inactivity and know if CI has broken due to the passage of time before you do some work and expect CI to pass.
non-blocking
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I'd encourage adding a basic schedule: on here too. It's really nice to come back to a repo after a while of inactivity and know if CI has broken due to the passage of time before you do some work and expect CI to pass.
True! What would be a reasonable schedule here? Once a week?
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I'd say once a day? CI hours are "free" and in this case should ideally only take a few minutes each to run (I'd hope!).
Schedule would ideally be staggered so we don't get a "thundering herd" of pathogen repo CI jobs every day, but we can't stagger with a static template and maybe GitHub already staggers things enough for us (intentionally or unintentionally).
# Routinely check that we continue to work in the face of external changes.
schedule:
# Every day at 18:37 UTC / 10:37 Seattle (winter) / 11:37 Seattle (summer)
- cron: "37 18 * * *"There was a problem hiding this comment.
Added in b183592
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| jobs: | ||
| ci: | ||
| uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@master |
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Presumably once we tag v1 (when? I'd have thought by now?) we'll suggest that here?
non-blocking
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Tagging the repo is on my TODO list; I was waiting for the "smart" pathogen-repo-ci to land, which just happened yesterday (and it looks like you've got at least one further outstanding change).
As suggested by @tsibley in review <#45 (comment)>
Description of proposed changes
I didn't want to take the time to set up of full Read the Docs project since I'm not even sure that's needed.
Just using Markdown files to document:
Related issue(s)
Resolves #10
Checklist