[Feature request]: Templating With `flepimop patch`

[TimothyWillard]

Label

cli, config, enhancement

Priority Label

medium priority

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

It would be helpful if there was a way to provide templated variables to flepimop patch, either directly as key value pairs or by importing from a YAML file (or similar). Could use jinja2 templates since that is already a dependency of gempyor.

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

Would have been extremely helpful with the Flu SMH 2025/26 round.

Describe the solution you'd like

Suppose input.yaml is:

name: 'Example'
start_date: '{{ year }}-01-01'
end_date: '{{ year }}-12-31'

Then calling

flepimop patch --data="year=2025" input.yaml > output.yaml

Would produce a output.yaml file of:

name: 'Example'
start_date: '2025-01-01'
end_date: '2025-12-31'

CLI interface could use some polishing/thinking before implmenting.

[pearsonca]

I like it.

One practice we might want to adopt here: distinguish between yaml vs to-be-templated yaml. Maybe via extension - yatl? yamt? somename.yaml.tmp?