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Allow build-specific --narrow-bandwidth param in frequencies #1130

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merged 3 commits into from
Oct 3, 2024

Commits on Sep 26, 2024

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

    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 commit 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.
    trvrb committed Sep 26, 2024
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  2. Remove recent_days_to_censor from GISAID/21L and open builds

    This removes `recent_days_to_censor` from GISAID/21L and open builds to match removal from GISAID builds.
    trvrb committed Sep 26, 2024
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Commits on Sep 27, 2024

  1. Specify build defaults with "default" key

    This follows recommendation in issue #1131 to use the pattern
    
    frequencies:
      default:
        min_date: "6M"
        narrow_bandwidth: 0.038
    
    This use of "default" extends just to min_date, max_date and narrow_bandwidth. This behavior is now documented in parameters.yaml as well as workflow-config-file.rst.
    
    The specification of frequencies parameters in builds.yaml now follows this pattern.
    trvrb committed Sep 27, 2024
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