[Feature request]: refactor flepimop_sample into flepimop/examples, provide example project auto copy-paste

[pearsonca]

Label

documentation, meta/workflow

Priority Label

low priority

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

In the gitbook, several of the guides suggest using a "flepimop_sample" repository, which appears to be approximately the same as the /examples folder.

This is duplicating code in multiple places, and increases work when documenting new library features with examples.

It complicates the future addition of CI to verify that examples run according to the associated instructions, because it would have to span repositories.

In the future, we intend the library to also include partial config files that specify typical models + a project skeleton builder. The examples should be driven by that.

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

No response

Describe the solution you'd like

Consolidate from flepimop_sample into examples. Update the current documentation to a copy operation from the examples folder (possibly also including a git init to turn that copy into a repo, if there are git actions with the example), rather than a clone operation from flepimop_sample.

[emprzy]

@pearsonca Is it flepimop/examples flat, or is it flepimop/examples/tutorials? Asking because I think I can address some of this as I update documentation for user installation.

[pearsonca]

i'm not entirely clear myself. what could use some investigating: is there a standard (or even just preferred / typical) way to distribute examples with a python package / application?

in an R package, these would be vignettes or more free-form content in inst/ or data/ - what's the pythonic equivalent?

[emprzy]

@pearsonca mmm interesting. I can definitely look into that after pushing this first documentation change (just need to get it to correctly reflect how we want users to engage with flepiMoP). FWIW, I think the answer to the question is flepiMoP/examples/tutorials. Not just flepiMoP/examples

[emprzy]

I believe #460 addresses this issue!