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castcollab / tesserae2

Tesserae2: Fast recombination-aware global and local alignment.
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Adds mypy testing and type hints for sequence.py #32

Closed winni2k closed 4 years ago

winni2k commented 4 years ago

Closes #19

One particular question for review: Are we removing assert statements of types now that we are using mypy for typing instead? I think that that could work.

winni2k commented 4 years ago

We should annotate all function arguments and return types going forward.

winni2k commented 4 years ago

This has become quite a substantial PR, so in order to avoid lots of merge conflicts going forward, I am keen to get this merged quickly.

winni2k commented 4 years ago

I am also quite excited about mypy now. In 61f1f2a it allowed me to detect a mismatch between the documentation of a method and what the method was actually doing.

winni2k commented 4 years ago

I renamed Sequence because that is already a class in the python typing system/collections. I thought it would avoid confusion in the future to use something else.

winni2k commented 4 years ago

I have squashed and rebased onto master. I will merge this on Friday morning unless I get comments by then.