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Allow build-specific --narrow-bandwidth param in frequencies

Open trvrb opened this issue 7 months ago • 0 comments

Description of proposed changes

This is a bug fix PR. There was a bug in the current behavior where the rule frequencies was calling config["frequencies"]["narrow_bandwidth"]. This resulted in --narrow-bandwidth to be fixed to whatever was specified in parameters.yaml. However, we were relying on build-specific settings to differentiate behavior in the all-time vs 6m vs 2m vs 1m builds, ala:

frequencies
    global_1m:
      narrow_bandwidth: 0.019

This PR fixes this issue and allows overriding of narrow_bandwidth in parameters.yaml by build-specific settings. It also provides a genuine default (equal to augur default) so that parameters.yaml doesn't have to always specify narrow_bandwidth.

Additionally, this PR removes the build-specific setting for recent_days_to_censor. This setting wasn't actually being applied in a build-specific fashion and so we had been always using the workflow default of 0. I decided to stick with this.

Testing

I've tested locally and via trial build. Trail builds are visible at:

trvrb avatar Jul 26 '24 20:07 trvrb