Clean up workflows #62
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Trim back CI jobs for reasons stated in nextstrain/cli@fab709a
Remove the copy in this repo and update references. The supporting scripts `sha256sum` and `cloudfront-invalidate` can also be removed.
Remove the copies in this repo and update references.
No longer need to create an envdir with ingest/bin/write-envdir to use with --exec env + `envdir env.d snakemake`. Moves the env variables in the GitHub Action workflow to the step that needs them to limit scope of their availability. Note the `PAT_GITHUB_DISPATCH` envvar was removed because we no longer trigger any downstream actions since b5fc2b9
The model results are expected to be uploaded to the same AWS S3 bucket, so remove the unnecessary complexity caused by the nested `s3_dst` config param. This will make it easier to transition to using the pathogen-repo-build workflow for the run-model GitHub Action.
Since the workflow config has been updated in the previous commit to use a top level `s3_dst` param, we can now easily override it in the GH Action workflow with input values for trial runs. This allows us to directly use the reusable pathogen-repo-build workflow. Note that `DATA_PROVENANCES` and `S3_DST` are passed as envvars to the reusable workflow so they can be interpolated in the build command, but they do _not_ need to be passed to the build runtime. Removed `bin/set-trial-optional-config` since we are no longer using a full config file to override the workflow configs.
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This was referenced Sep 7, 2023
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Merging since test runs worked fine, will monitor automated runs tomorrow. |
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Following up here that all automated workflows ran as expected last night and this morning. |
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Description of proposed changes
General clean up of workflows that includes:
s3_dstconfig paramSee commits for details
Checklist