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Automation: Generate both global and wa-state phylogenetic trees #54

Merged
merged 4 commits into from
Jan 20, 2025
Merged

Automation: Generate both global and wa-state phylogenetic trees #54

merged 4 commits into from
Jan 20, 2025

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j23414
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@j23414 j23414 commented Jan 10, 2025 •
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Description of proposed changes

During automated building, kick off both global and wa (washington-state) phylogenetic trees.

Main changes include:

  • Configuration updates: Modifies the phylogenetic workflow such that the "global" and "wa" pipeline-generated files are placed in subfolders and do not overwrite each other. Build names are explicitly specified from the config YAML files.
  • Automation: Adds a phylogenetic_wa GitHub Action to support building both global and Washington state phylogenetic trees and deploys them to WNV_global and WNV_wa respectively. See commits for details.

Checklist

  • Checks pass
  • Manual checks pass

@j23414 j23414 force-pushed the multi-builds branch 3 times, most recently from b50253f to 8c9b810 Compare January 10, 2025 22:28
@j23414 j23414 changed the title [draft] Multi builds Automation: Generate both global and wa-state phylogenetic trees Jan 11, 2025
@j23414 j23414 marked this pull request as ready for review January 13, 2025 20:47
j23414 added 2 commits January 20, 2025 11:20
@j23414
Phylogenetic: Allow specification of global verses Washington state (…
e14df28 
…wa) builds

This is a prerequisite to automating both global and washington state builds
so that they do not overwrite to the same files.
@j23414
Phylogenetic: Put default files in separate build directories
e942c7f
j23414 added 2 commits January 20, 2025 14:02
@j23414
Phylogenetic: Update metadata fields in auspice config
6e71b1d
@j23414
Automation: Build global and wa-state phylogenetic trees
f360cd6 
Added a `phylogenetic_wa` GitHub Action in order to support building both
global and Washington state phylogenetic trees. Since both define custom_rules,
which would overwrite each other, we defined a config-public.yaml that combines
deploy-related and Washington state-specific custom rules, merging them into
a unified array.

For the Washington state build, the public-facing configuration required
additional overrides to access data from the public site, as opposed to
the original configuration, which relied on privately processed ingest.
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j23414 commented Jan 20, 2025 •
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Merging this, since:

@j23414 j23414 merged commit 19f50ac into main Jan 20, 2025
4 checks passed
@j23414 j23414 deleted the multi-builds branch January 20, 2025 22:14
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