The amount of changes is a bit overwhelming for a review, so I'm afraid I can only make some general comments.
I see a lot of variable and method name changes, and even a config name change (max_intrinsic_pka_diff). I suppose PROPKA 3.1 API compatibility is not a goal of this refactoring, and this will become PROPKA 4.0 when refactoring is complete? If this is a conscious decision, then I see no issue with that.
For multi-line statements, I think PEP8 prefers parentheses around the expression instead of a backslash, if possible.
Python 3.5 supports str.format which is a bit more "modern" than %-formatted strings, and uses the same syntax like the Python 3.6 f-strings.
sobolevnrm
commented
4 years ago
The amount of changes is a bit overwhelming for a review, so I'm afraid I can only make some general comments.
I see a lot of variable and method name changes, and even a config name change (
max_intrinsic_pka_diff). I suppose PROPKA 3.1 API compatibility is not a goal of this refactoring, and this will become PROPKA 4.0 when refactoring is complete? If this is a conscious decision, then I see no issue with that.For multi-line statements, I think PEP8 prefers parentheses around the expression instead of a backslash, if possible.
Python 3.5 supports str.format which is a bit more "modern" than
%-formatted strings, and uses the same syntax like the Python 3.6 f-strings.Originally posted by @speleo3 in https://github.com/jensengroup/propka-3.1/pull/40#issuecomment-633659044