chat gpt for elegance on Will's functions and carrying the output file input through

[wcornwell]

Check out how good Chat-GPT is at decomposing functions. Worked the first time.

[fontikar]

Totally nitpicky, do we want to allow users to save the output when full = FALSE? Lines 528 - 537.

If so, may need another if statement with the else on line 527

[dfalster]

Before accepting a refactoring like this, we need some more tests to check specific outputs. Most/all of our existing tests just check that there was output created, with easy-to-pass tests like n >100

I'm unwilling to approve until we can show it produces the same results.

I'm very sceptical the new code for state-diversity will produce the same results
In any case, we don't know as we don't have any tests that would tell us. the current tests are very lenient,int

[fontikar]

most_likely_species defaults to the original_name if that name is accepted by the APC; this will be right for certain species subsets, but make errors in other cases, use with caution.

That worries me a little as an argument. Let's keep for now, but we should come up with use cases for each of these methods for documentation and clever code to avoid errors. If its too hard maybe collpase to most_likely_species is too risky as an option!

[dfalster]

Before accepting a refactoring like this, we need some more tests to check specific outputs. Most/all of our existing tests just check that there was output created, with easy-to-pass tests like n >100

I'm unwilling to approve until we can show it produces the same results.

I'm very sceptical the new code for state-diversity will produce the same results In any case, we don't know as we don't have any tests that would tell us. the current tests are very lenient,int

Regarding workflow, these tests should be added on a seperate branch off master, then be merged in here

added tests to address

[fontikar]

I forced rerun of jobs, once they pass I am happy for this to merge in :)

[fontikar]

Passing all new tests! Approved! Great work

[fontikar]

@wcornwell could you please squash and merge and delete branch once thats done :)