Move SP config to yaml file

[xinaxu]

No description provided.

[rvagg]

Nice, so do we still need the env file after this, can we move all the config to this so we don't have to describe two config files? And is singularity able to handle all of these config options on a per-SP basis or is there work to do on the singularity side coming out of this too?

[xinaxu]

Nice, so do we still need the env file after this, can we move all the config to this so we don't have to describe two config files? And is singularity able to handle all of these config options on a per-SP basis or is there work to do on the singularity side coming out of this too?

We still need the env file. Lots of env vars are referenced in docker compose, e.g. db user/pass, singularity version, etc.

So I only split out settings related to SP to a config file which will be hot loaded.

[rvagg]

Lots of env vars are referenced in docker compose

OK, but a lot of them are not too; maybe we just mark this as a future TODO item - move as much as possible into a config file, leaving the .env being only something we an ship as a default for users - items such as SINGULARITY_REF. A lot of these variables just end up being commandline arguments to motion itself, which we could easily ship in the same way as sps.yml.

So in light of that, maybe we could make it config.yml instead of sps.yml with an eye to evolving it into the single place that a user has to edit their stuff?

[xinaxu]

Saving the current state of the work here.

[codecov-commenter]

Codecov Report

Merging #234 (f96e775) into main (421fde2) will increase coverage by 3.19%.
The diff coverage is 25.17%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #234      +/-   ##
==========================================
+ Coverage   44.00%   47.19%   +3.19%     
==========================================
  Files           9        9              
  Lines        1009      945      -64     
==========================================
+ Hits          444      446       +2     
+ Misses        513      444      -69     
- Partials       52       55       +3     

Files	Coverage Δ
integration/singularity/options.go	34.72% <50.00%> (+11.25%)	⬆️
integration/singularity/store.go	36.63% <23.25%> (+0.75%)	⬆️