MAINT: Use flake8 pre-commit hook over pep8speaks

[ghisvail]

This PR sets up flake8 with pre-commit and drops pep8speaks.

The latter did let a few pycodestyle errors and warnings pass by, which gives me little trust in the tool for the long term. Instead, let's rely on the official pre-commit hook for flake8 and use the same config used with pep8speaks. It might be worth adding some more checks later (the select option) than just pycodestyle errors (E) and warnings (W).

[ghisvail]

I fixed the errors and warnings reported:

flake8...................................................................Failed
- hook id: flake8
- exit code: 1

<unknown>:1594: SyntaxWarning: invalid escape sequence '\d'
<unknown>:70: SyntaxWarning: invalid escape sequence '\s'
<unknown>:374: SyntaxWarning: invalid escape sequence '\d'
<unknown>:36: SyntaxWarning: invalid escape sequence '\s'
clinica/iotools/converters/adni_to_bids/adni_utils.py:1594:29: W605 invalid escape sequence '\d'
clinica/iotools/converters/adni_to_bids/adni_utils.py:1594:47: W605 invalid escape sequence '\d'
clinica/iotools/converters/adni_to_bids/adni_utils.py:1606:5: E722 do not use bare 'except'
clinica/iotools/converters/genfi_to_bids/genfi_to_bids_utils.py:110:5: E722 do not use bare 'except'
clinica/iotools/converters/habs_to_bids/habs_to_bids.py:72:23: E226 missing whitespace around arithmetic operator
clinica/iotools/converters/habs_to_bids/habs_to_bids.py:245:35: E226 missing whitespace around arithmetic operator
clinica/iotools/converters/oasis3_to_bids/oasis3_utils.py:117:5: E722 do not use bare 'except'
clinica/iotools/converters/oasis3_to_bids/oasis3_utils.py:126:5: E722 do not use bare 'except'
clinica/iotools/converters/oasis3_to_bids/oasis3_utils.py:171:31: E201 whitespace after '{'
clinica/iotools/converters/oasis3_to_bids/oasis3_utils.py:171:34: E226 missing whitespace around arithmetic operator
clinica/iotools/converters/oasis3_to_bids/oasis3_utils.py:197:27: E226 missing whitespace around arithmetic operator
clinica/pipelines/engine.py:641:48: E226 missing whitespace around arithmetic operator
clinica/pipelines/machine_learning/input.py:42:16: E721 do not compare types, for exact checks use `is` / `is not`, for instance checks use `isinstance()`
clinica/pipelines/t1_freesurfer_longitudinal/t1_freesurfer_template_pipeline.py:322:17: E124 closing bracket does not match visual indentation
clinica/pipelines/t1_volume_create_dartel/t1_volume_create_dartel_pipeline.py:205:17: E124 closing bracket does not match visual indentation
clinica/pipelines/t1_volume_dartel2mni/t1_volume_dartel2mni_pipeline.py:207:17: E124 closing bracket does not match visual indentation
clinica/utils/freesurfer.py:70:24: W605 invalid escape sequence '\s'
test/unittests/iotools/converters/adni_to_bids/test_adni_utils.py:374:18: W605 invalid escape sequence '\d'
test/unittests/iotools/converters/adni_to_bids/test_adni_utils.py:374:36: W605 invalid escape sequence '\d'
test/unittests/utils/test_nipype.py:36:56: W605 invalid escape sequence '\s'

[NicolasGensollen]

LGTM, thanks @ghisvail !