[Feature request]: Add --extend, --shift Options To flepimop-calibrate

[TimothyWillard]

Label

enhancement, gempyor, inference

Priority Label

high priority

Is your feature request related to a problem? Please describe.

Updating forecasting configurations with new data is currently complex and relies on manual processes or elaborate scripts (e.g., modifying R scripts to adjust dates and fitting targets). This makes iterative updates cumbersome and error-prone, lacking a streamlined, automated workflow. See this slack thread for the original discussion: https://uncreturntocampus.slack.com/archives/CU0SBC2AC/p1731689410476909.

Is your feature request related to a new application, scenario round, pathogen? Please describe.

n/a

Describe the solution you'd like

Add two options to the flepimop-calibrate tool:

1. --extend: Adjusts the end dates and fitting targets in the configuration file while incorporating new target data, and
2. --shift: Offsets both start and end dates for recalibration.

Both options:

• Reuse conserved parameters from the base configuration,
• Transform output data into an updated configuration file for iterative use, and
• Simplify forecasting workflows with a single command.

[pearsonca]

So roughly practically: on the first iteration, we run:

flepimop calibrate someconfig.yml

that yields the first set of outputs. The second invocation would be

flepimop calibrate someconfig.yml --extend="2 weeks" > config_2.yml

and subsequently would look iteratively like:

flepimop calibrate config_n.yml --extend="2 weeks" > config_n+1.yml