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),
• Fully eradicates flepimop_sample from code and documentation; replacing it with the flepiMoP/examples/tutorials directory,
• Replaces all environmental variable instances of DATA_PATH with PROJECT_PATH. It does not attempt to adjust the command line option --data_path, as I believe @TimothyWillard said he was working on editing the CLI options.

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.
Because of eradication of flepimop_sample, it also serves 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

[emprzy]

Sorry for the mid-way expansion of what this PR covers, but it's ready for review now!

[pearsonca]

progress, but seems like several open items.

[pearsonca]

probably shouldn't suggest people env - going to spam them confusingly.

[pearsonca]

I don't mind a live TODO, but it should be in a comment, rather than actively displayed. Probably a better version is to convert this to an item on an explicit issue, e.g. the new environmental variables one. Basically an explicit note "in file XYZ, section ABC, ..."

[pearsonca]

needs the one fix, then fine to merge