Deprecate positional boolean arguments

[flying-sheep]

For reference: #1241

[codecov]

Codecov Report

Attention: Patch coverage is 91.83673% with 8 lines in your changes missing coverage. Please review.

Project coverage is 84.63%. Comparing base (df213f6) to head (1021b1f).

Files with missing lines	Patch %	Lines
src/anndata/tests/helpers.py	91.17%	3 Missing ⚠️
src/anndata/compat/__init__.py	66.66%	2 Missing ⚠️
...anndata/experimental/multi_files/_anncollection.py	90.00%	1 Missing ⚠️
src/anndata/experimental/pytorch/_annloader.py	90.00%	1 Missing ⚠️
src/anndata/logging.py	87.50%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1694      +/-   ##
==========================================
- Coverage   87.06%   84.63%   -2.44%     
==========================================
  Files          40       40              
  Lines        6101     6129      +28     
==========================================
- Hits         5312     5187     -125     
- Misses        789      942     +153     

Files with missing lines	Coverage Δ
src/anndata/_core/anndata.py	83.86% <100.00%> (+0.13%)	⬆️
src/anndata/_core/file_backing.py	91.07% <100.00%> (ø)
src/anndata/_core/merge.py	84.07% <100.00%> (-10.96%)	⬇️
src/anndata/_io/specs/methods.py	88.18% <100.00%> (-0.43%)	⬇️
src/anndata/_io/write.py	77.52% <100.00%> (+0.78%)	⬆️
src/anndata/utils.py	84.72% <ø> (-0.93%)	⬇️
...anndata/experimental/multi_files/_anncollection.py	70.91% <90.00%> (+0.23%)	⬆️
src/anndata/experimental/pytorch/_annloader.py	23.52% <90.00%> (+3.12%)	⬆️
src/anndata/logging.py	50.00% <87.50%> (+4.83%)	⬆️
src/anndata/compat/__init__.py	81.14% <66.66%> (-4.21%)	⬇️
... and 1 more

... and 3 files with indirect coverage changes