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GitHub Action workflows clean up #218

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merged 4 commits into from
Oct 31, 2023
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joverlee521
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@joverlee521 joverlee521 commented Oct 30, 2023

Clean up GitHub Action workflows, see commits for details.

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Recently learned that Snakemake no longer overwrites the entire config
when providing nested config values via the `--config` option.¹ This
allows us to remove the set-branch-ingest-config script and directly set
branch config values via the command line option in our GitHub Action
workflows.

I've opted to use `jq` to interpolate the branch name into the S3_DST
because I didn't want to fiddle with escaping quotes in the JSON string.

¹ nextstrain/dengue#13 (comment)
Since we've removed the need to run set-branch-ingest-config in the
GitHub Action workflow in the previous commit, we can refactor the
fetch-and-ingest-branch workflow to use the shared pathogen-repo-build
workflow.
The AWS_DEFAULT_REGION envvar is not required for AWS S3 interactions,
so remove it from our workflows and documentation.

This will allow us to remove AWS_DEFAULT_REGION from the repo secrets
so that our pathogen-repo-build summary no longer points to a masked
URL for the AWS Batch console
(e.g. https://console.aws.amazon.com/batch/home?region=***#jobs/detail/0d66a150-a010-4761-9561-8085ef1d7ea3).
@joverlee521 joverlee521 force-pushed the remove-set-branch-config branch from 0d0154f to a20d021 Compare October 30, 2023 20:57
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As part of this PR, I've already removed the AWS_DEFAULT_REGION secret from the repo.

@joverlee521 joverlee521 marked this pull request as ready for review October 30, 2023 21:02
@joverlee521 joverlee521 changed the title Remove set-branch-ingest-config GitHub Action workflows clean up Oct 30, 2023
@joverlee521 joverlee521 requested review from corneliusroemer and a team and removed request for corneliusroemer October 30, 2023 21:04
The GITHUB_RUN_ID environment variable is only used for Slack
notification messages, so it is not needed for the branch workflows
that run without Slack notifications.
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Test run completed successfully and uploaded files to s3://nextstrain-data/files/workflows/monkeypox/branch/remove-set-branch-config/.

@joverlee521 joverlee521 merged commit 9ff822f into master Oct 31, 2023
@joverlee521 joverlee521 deleted the remove-set-branch-config branch October 31, 2023 15:46
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