Updated sample/tutorial files

[alsnhll]

Describe your changes.

I copied changes over that were made in the flepimop_sample repository during testing.

I just made some super simple updates the example configs. There was a small error in the outcomes section of two. Updated some parameters to give more reasonable results. Added one with vaccination. Updated file for turning simulated data to fake ground truth data.

Does this pull request make any user interface changes? If so please describe.

No

What does your pull request address? Tag relevant issues.

NA

Tag relevant team members.

[TimothyWillard]

Just so I understand, the contents of examples/tutorials is copied directly from https://github.com/HopkinsIDD/flepimop_sample? Have we considered just folding in that repo into this repo? Or at least make the syncing not manual with the use of submodules?

Unless this is important to get done ASAP I have a preference for merging this into dev instead of main.

[alsnhll]

Hi @TimothyWillard , thanks for reviewing! For workflow reasons whenever I make or test tutorial material I always do it from that sample repo, because we always run things from project repos, and having one for this purpose is very useful. But we purposefully decided to fold those tutorials into the core flepimop repo to make sure it stays up to date with code changes there and can be accessed along with that code.
I am fine with merging this into dev instead of main (though these are really trivial changes that have zero effect on any flepi function ... it's just example configs). It would also be amazing if this syncing could be automatic!

[TimothyWillard]

For workflow reasons whenever I make or test tutorial material I always do it from that sample repo, because we always run things from project repos, and having one for this purpose is very useful. But we purposefully decided to fold those tutorials into the core flepimop repo to make sure it stays up to date with code changes there and can be accessed along with that code.

I'm not entirely sure I follow, is there a known issue with setting the project path to a subdirectory of the flepi path? I think:

export PROJECT_PATH=$FLEPI_PATH/examples/tutorials

works and is close to what we do in the gempyor CLI tests on the dev branch: https://github.com/HopkinsIDD/flepiMoP/blob/2c73f388692ef2aefd02a8668aa8631f713eb022/flepimop/gempyor_pkg/tests/shared_cli/test_cli.py. Having duplicate sets of code/config under version control makes it difficult to keep these in sync.

I think for now let's just change the target branch to dev and we'll address further improvements after this release cycle.

[anjalika-nande]

This seems fine to me. I don't have a strong preference between merging it initially in dev versus main so we can do whatever is cleanest!

[pearsonca]

Seems fine, but: are there any knock on changes to the partial configuration examples?

[saraloo]

I don't think there would be any changes to the config parts you worked on. If they worked before they should still work fine. Makes sense to me to merge into dev.

[alsnhll]

I changed the base branch to dev instead of main. I am fine with removing the flepimop_sample repo and just having this single location for the example code within flepimop repo, as long as we make sure the documentation is updated to match, as running things from this tutorials folder is how we want new users to get started

[TimothyWillard]

LGTM