Add GH Action workflow to update downstream repos#73
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joverlee521 wants to merge 6 commits intomainfrom
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Add GH Action workflow to update downstream repos#73joverlee521 wants to merge 6 commits intomainfrom
joverlee521 wants to merge 6 commits intomainfrom
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victorlin
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We should only be keeping a single copy of the vendored repo in each downstream repo, so deduplicate the matrix by repo. In cases where there are multiple copies, we are prioritizing the `nextstrain/shared` remote since that is the newer version. This is prompted by the error in the workflow when avian-flu had two paths to update. <#73 (comment)>
victorlin
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Apr 15, 2026
Searches the Nextstrain GitHub org to find repos that have the `.gitrepo` file with the nextstrain/shared remote to create a matrix of repos to potentially update. Installs and uses `git subrepo` to pull in the latest changes with the `--force` flag to avoid merge conflicts to due rebasing in the downstream repo. If there are changes pulled down, then `git subrepo` will create a single commit. If there is a single commit, then push up the changes to a branch and create or update the PR in the downstream repo. Nothing happens if there were no changes and workflow exits with error if it encounters more than one commit.
I was unable to get the search/code API to work with the 'OR' syntax so just added a separate query for nextstrain/ingest and concatenated the two arrays. Deduplicated the final array to guard against potential overlap.
We should only be keeping a single copy of the vendored repo in each downstream repo, so deduplicate the matrix by repo. In cases where there are multiple copies, we are prioritizing the `nextstrain/shared` remote since that is the newer version. This is prompted by the error in the workflow when avian-flu had two paths to update. <#73 (comment)>
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Prevent the workflow from overwriting additional work on the remote branch. This allows us to add manual updates directly to the PRs without having to worry about them being overwritten by the next update run. Prompted by feedback from @victorlin in review <#73 (comment)>
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Do not allow `git subrepo` to overwrite local changes in automatic updates. This will increase failures in the automatic updates but will flag merge conflicts with local changes in downstream repos for manual fixes. Prompted by feedback from @jameshadfield and @victorlin in review <#73 (comment)>
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GH API calls return 30 items by default¹ so use `--paginate` + `--slurp` to return all pages and get all items.² ¹ <https://docs.github.com/en/rest/using-the-rest-api/using-pagination-in-the-rest-api?apiVersion=2026-03-10> ² <https://cli.github.com/manual/gh_api>
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Prevent the workflow from overwriting additional work on the remote branch. This allows us to add manual updates directly to the PRs without having to worry about them being overwritten by the next update run. Prompted by feedback from @victorlin in review <#73 (comment)>
joverlee521
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Do not allow `git subrepo` to overwrite local changes in automatic updates. This will increase failures in the automatic updates but will flag merge conflicts with local changes in downstream repos for manual fixes. Prompted by feedback from @jameshadfield and @victorlin in review <#73 (comment)>
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Do not allow `git subrepo` to overwrite local changes in automatic updates. This will increase failures in the automatic updates but will flag merge conflicts with local changes in downstream repos for manual fixes. Note this requires us to fetch all git history for the downstream repos since `git subrepo pull` now needs to validate the parent commit. Prompted by feedback from @jameshadfield and @victorlin in review <#73 (comment)>
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Do not allow `git subrepo` to overwrite local changes in automatic updates. This will increase failures in the automatic updates but will flag merge conflicts with local changes in downstream repos for manual fixes. Note this requires us to fetch all git history for the downstream repos since `git subrepo pull` now needs to validate the parent commit. Prompted by feedback from @jameshadfield and @victorlin in review <#73 (comment)>
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Try to fetch remote branch and add subrepo changes to prevent automatic updates from overwriting manual updates. This also allows us to skip unnecessary pushes to the PR if the remote branch is already up-to-date.
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victorlin
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If there's no other feedback, I'll merge this Monday. The merge of this PR should automatically trigger a workflow run to update downstream repos. Since this is a new change, the existing PRs in downstream repos should get updated. Then I'll go through those PRs to fix and merge them, which should finally allow us to get back to nextstrain/public#39 |
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Description of proposed changes
Searches the Nextstrain GitHub org to find repos that have the
.gitrepofile with the nextstrain/shared or nextstrain/ingest remote to create a matrix of repos to potentially update. Installs and usesgit subrepoto pull in the latest changes with the--forceflag to avoid merge conflicts to due rebasing in the downstream repo. If there are changes pulled down, thengit subrepowill create a single commit. If there is a single commit, then push up the changes to a branch and create or update the PR in the downstream repo. Nothing happens if there were no changes and workflow exits with error if it encounters more than one commit.Related issue(s)
Prompted by nextstrain/public#39 (comment)
Checklist
If adding a script, add an entry for it in the README.