Add updated CLI and workflow

[samueljackson92]

Cannot be merged before #35

Closes #37 #36

[jameshod5]

There's a lot of changes but generally seems okay to me, do you have an example command that I can test?

[samueljackson92]

Sorry @jameshod5, I forgot to add that to the PR, and I think the README is updated in the next one.

I think something like:

python3 -m src.level1.main -v -n 1 --facility MAST --shot 28028 -i amc  

Should work. You will need a config.yml file which will look something like this:

metadatabase_file: /common/tmp/sjackson/level1.ukaea.db
readers:
  uda:
    type: 'uda'

writer:
  type: "zarr"
  options:
    zarr_format: 2
    output_path: "/common/tmp/sjackson/upload-tmp/zarr/level1"

[jameshod5]

Looks good to me.

Passed tests and works well for various shots/signals. Nothing sticks out to me