[python] Apply black/isort/flake8/mypy to all repo .py files

[johnkerl]

Previously, only within apis/python, and even then, not for apis/python/tests.

Some of our challenges with #400, #446, and #447 have had to do with typeguard, at unit-test time, reaching into .py files it had not visited before. Here we try to avoid future such surprises.

[codecov-commenter]

Codecov Report

Base: 66.87% // Head: 56.74% // Decreases project coverage by -10.12% ⚠️

Coverage data is based on head (b04f8d6) compared to base (e636da5).
Patch has no changes to coverable lines.

❗ Current head b04f8d6 differs from pull request most recent head 12fefb8. Consider uploading reports for the commit 12fefb8 to get more accurate results

Additional details and impacted files

@@             Coverage Diff             @@
##             main     #453       +/-   ##
===========================================
- Coverage   66.87%   56.74%   -10.13%     
===========================================
  Files          64       38       -26     
  Lines        3384     1542     -1842     
===========================================
- Hits         2263      875     -1388     
+ Misses       1121      667      -454     

Flag	Coverage Δ
python	?
r	56.74% <ø> (ø)

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Impacted Files	Coverage Δ
apis/python/src/tiledbsoma/dense_nd_array.py
...is/python/src/tiledbsoma/test_general_utilities.py
apis/python/src/tiledbsoma/general_utilities.py
apis/python/src/tiledbsoma/measurement.py
apis/python/src/tiledbsoma/collection.py
apis/python/src/tiledbsoma/constants.py
apis/python/src/tiledbsoma/util_arrow.py
apis/python/src/tiledbsoma/logging.py
apis/python/src/tiledbsoma/metadata_mapping.py
apis/python/src/tiledbsoma/tiledb_array.py
... and 16 more

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[johnkerl]

Closed in favor of #711