Update pathogen-repo-ci to better support CI [#63]
#86
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This adds the following features to the `pathogen-repo-ci` workflow: * defines a `build-target` argument that will get passed to `nextstrain build` as a target directory — this allows the targeting of sub-dir based workflows, which was the main original issue in #63 * defines arguments (`download-previous-artifact`, `previous-artifact-name`) and a conditional step (`Dowload previous step artifact`) to support the downloading of the build artifact from a previous step to allow testing of later steps in a complete pathogen repo build This combination of features was all that was needed to support [a CI workflow for `seasonal-cov`](nextstrain/seasonal-cov#11) that: 1. runs an ingest workflow for a subset of the regular build data 2. uploads an artifact with the ingest output 3. downloads that artifact into a phylogenetic workflow 4. runs the phylogenetic workflow for the same subset of data
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I think it would be good to talk through if CI should be flexible (using the work in this PR) or follow more rigid requirements described in #84. |
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This will need to be further extended, and will be re-oriented to the still-to-be-written ticket summarizing today's meeting. |
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Supplanted by #89 ; closing this issue in favor of that one. |
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This adds the following features to the
pathogen-repo-ciworkflow:build-targetargument that will get passed tonextstrain buildas a target directory — this allows the targeting of sub-dir based workflows, which was the main original issue in ENH: Allow pathogen-repo-ci to invoke workflow in subfolder #63download-previous-artifact,previous-artifact-name) and a conditional step (Dowload previous step artifact) to support the downloading of the build artifact from a previous step to allow testing of later steps in a complete pathogen repo buildThis combination of features was all that was needed to support a CI workflow for
seasonal-covthat:Description of proposed changes
This is an attempt to address the issues in #63 , which I also ended up running in to while trying to add CI to the
seasonal-covrepo. I made a copy of this workflow into theseasonal-covrepo, and made the minimum viable set of changes needed to support the CI work I wanted to add.Related issue(s)
seasonal-cov/#8
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