Fix flake8 config and update flake8 to 6.0

[flying-sheep]

Fixes our broken config discovered due to PyCQA/flake8#1760.

In the long run, we should go away from all INI config. Ruff is very promising, we should probably get rid of flake8 completely.

Closes #862

updates:

• github.com/PyCQA/flake8: 5.0.4 → 6.0.0

[codecov]

Codecov Report

Merging #863 (b99d0d4) into master (9ee3616) will decrease coverage by 45.18%.
The diff coverage is 80.00%.

❗ Current head b99d0d4 differs from pull request most recent head 03d679d. Consider uploading reports for the commit 03d679d to get more accurate results

Additional details and impacted files

@@             Coverage Diff             @@
##           master     #863       +/-   ##
===========================================
- Coverage   83.60%   38.41%   -45.19%     
===========================================
  Files          32       32               
  Lines        4362     4365        +3     
===========================================
- Hits         3647     1677     -1970     
- Misses        715     2688     +1973     

Impacted Files	Coverage Δ
anndata/_io/read.py	15.84% <0.00%> (-62.27%)	⬇️
anndata/_io/specs/registry.py	62.76% <ø> (-31.92%)	⬇️
anndata/experimental/multi_files/_anncollection.py	19.95% <0.00%> (-50.61%)	⬇️
anndata/_core/index.py	42.40% <100.00%> (-50.52%)	⬇️
anndata/_core/views.py	65.85% <100.00%> (-23.50%)	⬇️
anndata/_io/specs/methods.py	47.61% <100.00%> (-36.78%)	⬇️
anndata/compat/__init__.py	37.34% <100.00%> (-51.07%)	⬇️
anndata/tests/conftest.py	87.50% <100.00%> (-12.50%)	⬇️
anndata/tests/helpers.py	46.72% <100.00%> (-49.07%)	⬇️
anndata/_io/h5ad.py	17.89% <0.00%> (-74.74%)	⬇️
... and 19 more