flepimop.org documentation updates for information pertaining to new users

[emprzy]

Describe your changes.

This pull request changes documentation to reflect imminent changes in user local installation processes (affecting 'before any run' and 'quick start guide' sections of the flepimop.org documentation). It also attempts to move towards a new user start-up process that does not involve the flepimop_sample repository: looking to instead use the examples in the flepiMoP/examples/tutorial directory. All references to flepimop_sample in 'before any run' and 'quick start guide' have been corrected.

For now, this pull request does NOT fully eradicate mention/use of flepimop_sample throughout the entire documentation base for flepiMoP. I know that there are still references to flepimop_sample in the "Model Output" section of documentation, and likely in other places as well.

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

New users will be able to install flepiMoP (all packages and dependencies along with initialization of a conda environment) with a single script that they can run from CL.

What does your pull request address? Tag relevant issues.

This pull request addresses necessary documentation changes resulting from issue GH #401 and pull request GH #418.
If we can fully convert away from flepimop_sample to flepiMoP/examples/tutorials as a base for first-run examples, this pull request can also serve GH #368.

[emprzy]

My question to reviewers is: should I go ahead and search for all references to flepimop_sample in other places in the documentation and replace them with flepiMoP/examples/tutorials, or should I do that in another PR?

[TimothyWillard]

My question to reviewers is: should I go ahead and search for all references to flepimop_sample in other places in the documentation and replace them with flepiMoP/examples/tutorials, or should I do that in another PR?

My vote would be to do it all in one pass as to minimize confusion.

[emprzy]

places where flepimop_sample is referenced (need to be resolved):

HOW TO RUN

• before any run
• quick start guide
• advanced run guides ->
• running with a docker locally
• running locally in a conda environment
• running on a HPC with slurm

GEMPYOR: MODELING INFECTIOUS DISEASE DYNAMICS

• model output

MODEL INFERENCE

• inference model output

[TimothyWillard]

places where flepimop_sample is referenced (need to be resolved):

I'm going to hold off on reviewing until this, unless you want me to review now @emprzy?

[emprzy]

A question for @pearsonca (or anyone else that cares to chime in). We are very close to purging data_path as a config key from the flepiMoP codebase, but DATA_PATH as an environmental variable referring to a place where data exists is still present in the documentation and code. How would we feel about universally moving towards using PROJECT_PATH to refer to these instances (unless there is a distinction between PROJECT_PATH and DATA_PATH that I am not familiar with)? I've included an example each of where PROJECT_PATH exists in the documentation, and where DATA_PATH does, and you can let me know what you think:

from how-to-run quick start guide from how-to-run useful commands