`--water_entropy` `CLI` argument ignored when matching default value

[harryswift01]

When using argparse.parse_known_args() and merging CLI args with YAML config, boolean arguments like --water_entropy are ignored if their value matches the default (True). This causes YAML overrides (e.g. water_entropy: False) to be skipped unintentionally.

Cause:

• The logic assumes that if args.water_entropy == default, then the CLI didn’t override it, but this fails when the CLI did pass --water_entropy True.

[jimboid]

Great spot! You should be able to write a generic test to ensure this type of bug doesn't reoccur

[skfegan]

Currently it seems to print blanks for some options (including start, verbose, and water_entropy) when using the default values. Maybe make the code print out the actual value used for each input (after YAML and CLI overrides) and not leave a blank even when it is using the default value to make it easier for the user to check that they got the options they wanted.

[jimboid]

That is a good point Sarah, you can probably then write tests that check this happens and happens correctly too. Obvs these are not strictly unit tests so you might want to think how to structure these.

[harryswift01]

Currently it seems to print blanks for some options (including start, verbose, and water_entropy) when using the default values. Maybe make the code print out the actual value used for each input (after YAML and CLI overrides) and not leave a blank even when it is using the default value to make it easier for the user to check that they got the options they wanted.

This is also something I have noticed, I am planning on changing the way the input options are outputted within the #38 issue to ensure that it is consistent and looks more structured.