[ENH] start using mypy and updating types

[Remi-Gau]

• closes use mypy to check type hints? #65

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• also applied isort to the imports

TODO:

• try to be more specific and remove most Any (probably in a follow up PR)

[codecov-commenter]

Codecov Report

Attention: 9 lines in your changes are missing coverage. Please review.

Comparison is base (22a4ae0) 92.40% compared to head (b9a59c1) 91.84%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #86      +/-   ##
==========================================
- Coverage   92.40%   91.84%   -0.56%     
==========================================
  Files          11       11              
  Lines         487      503      +16     
==========================================
+ Hits          450      462      +12     
- Misses         37       41       +4     

Files	Coverage Δ
giga_connectome/__init__.py	81.81% <100.00%> (ø)
giga_connectome/connectome.py	94.87% <100.00%> (+0.13%)	⬆️
giga_connectome/mask.py	97.00% <100.00%> (+0.03%)	⬆️
giga_connectome/run.py	96.55% <100.00%> (+0.25%)	⬆️
giga_connectome/workflow.py	90.38% <100.00%> (ø)
giga_connectome/postprocess.py	89.70% <90.90%> (ø)
giga_connectome/atlas.py	85.48% <91.30%> (+0.02%)	⬆️
giga_connectome/denoise.py	84.78% <77.77%> (-3.32%)	⬇️
giga_connectome/utils.py	93.42% <85.18%> (-1.25%)	⬇️

[Remi-Gau]

not sure it makes sense to check for type annotation in tooling scripts...

[Remi-Gau]

@htwangtw
I had to amend more than just the types because the code was in places doing things that did not match the types, so this turns into a lot more line changes than I had anticipated.

Let me know if you have questions.

[htwangtw]

I certainly learned a lot reading this PR and thank you for doing this!!!

[htwangtw]

Is this how to declare the dimension of the numpy array? That's cool

[Remi-Gau]

I need to investigate better how to use types with numpy, this is a bit of a brute force approach.

[Remi-Gau]

I certainly learned a lot reading this PR

To be honest I had to learn a lot to make it happen!!!

[Remi-Gau]

merge conflict resolved

let's see what CI says

[Remi-Gau]

merge conflicts resolved

[htwangtw]

LGTM and this is really cool. Merging....