scfix behaviour change

[csbrasnett]

opening this as a PR for changing the default for -scfix.

Obviously atm this makes a bunch of tests fail. Is the best way to fix the test to:

1. change the command being used as the input
2. change the expected output of the test

or both?

Do we change the flag description too, to something like -[no]scfix, ie. when the flag is applied scfix gets turned off?

[pckroon]

Thanks.

I'm happy to see that the integration tests fail :)
The "best" fix would be to change all the integration tests to reflect the new default, but that sounds rather painful. I think more feasible would be to indeed change the command invocation of those tests, and in addition maybe add one more case with the new defaults.

Do we change the flag description too, to something like -[no]scfix, ie. when the flag is applied scfix gets turned off?

Yes. Users need to have an option to switch the feature off.

Finally, you can combine #622 with this PR, otherwise changing the tests will result in a bunch of merge conflicts (I expect) and double work.

[csbrasnett]

Unfortunately, I think we'll have to change (at least some of) the tests. I've noticed a couple of the tests don't actually reflect the default applications. I don't think it should take too long to do 🤞

[pckroon]

Yes, excellent!
Just some teenie tiny nitpicks

[csbrasnett]

Not sure why the lint is still failing?

[pckroon]

Probably because 9.0 is not more than 9.0 or something dumb. We need to update the pylint config file as well it seems, lots of deprecated options.
Doesn't really matter at the moment though.
Excellent work!

[csbrasnett]

aha thanks! I'll have a look at #616 to check if that's ready to merge too and then we're set