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Fixed lint errors after running flake8

Loic Huder requested to merge lint-fix into master

I ran flake8 --ignore=E501,E226,E203,W503 on the project and tried to correct as many warnings/errors I could. To help me, I used black to format a few files (mostly tests).

The following warnings remain:

./pygeodyn/utilities.py:121:61: E741 ambiguous variable name 'l'
./pygeodyn/__init__.py:2:1: F401 'pygeodyn._version.__version__' imported but unused
./pygeodyn/zonkf/algo.py:178:100: E126 continuation line over-indented for hanging indent
./pygeodyn/augkf/forecaster.py:105:41: E128 continuation line under-indented for visual indent
./pygeodyn/augkf/analyser.py:36:17: E123 closing bracket does not match indentation of opening bracket's line
./pygeodyn/augkf/analyser.py:40:17: E123 closing bracket does not match indentation of opening bracket's line

but we can live with them.

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