[Feature request]: incorporate update / init capabilities into flepimop CLI

[pearsonca]

Label

batch, enhancement, meta/workflow, operations

Priority Label

medium priority

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

Getting consistent environment for multiple users to replicate (or independently run) jobs.

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

No response

Describe the solution you'd like

See #330 and comments against #329. Depends on merge of #329 and #336

Desire support for command line actions that handle:

• update / upgrade of flepimop, using syntax flepimop update or similar
• initializing of a flepimop project directory / environment (activating environment variables, HPC modules, etc) at the start of some action, using syntax like flepimop init

[TimothyWillard]

I like the concept, but I'm not sure if this implementation is feasible as outlined.

• The flepimop update command seems fine to me, can do vaguely what the build/hpc_install_or_update.sh script does. But users would have to have the conda environment with flepiMoP installed already activated to use so it wouldn't replace that install script, so the value add is a bit unclear to me. We could also have a similar script to accompany local installs.
• I don't see a great way to do a flepimop init type command. I'm fairly certain that when using the flepimop CLI it creates a child process to run python, but child processes can't modify the environment variables (and by extensions modules) of a parent process. You could do something that generates a shell script you could source, but I don't see what value this adds over the current process of sourcing batch/hpc_init.sh. I suppose we need to add a version of that script for use in local installs?