Filter known warnings in tests and raise on others

[mwouts]

Closes #823

[codecov]

Codecov Report

Merging #893 (73b4a1e) into main (0662680) will increase coverage by 0.15%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main     #893      +/-   ##
==========================================
+ Coverage   98.89%   99.04%   +0.15%     
==========================================
  Files         114      114              
  Lines       10690    10699       +9     
==========================================
+ Hits        10572    10597      +25     
+ Misses        118      102      -16     

Impacted Files	Coverage Δ
tests/test_cli.py	100.00% <100.00%> (ø)
tests/test_cm_config.py	100.00% <100.00%> (ø)
tests/test_pre_commit_scripts.py	100.00% <100.00%> (ø)
jupytext/cli.py	95.68% <0.00%> (-0.19%)	⬇️
jupytext/myst.py	97.19% <0.00%> (+0.46%)	⬆️
jupytext/contentsmanager.py	97.61% <0.00%> (+1.02%)	⬆️
tests/test_read_empty_text_notebook.py	100.00% <0.00%> (+5.88%)	⬆️
tests/test_ipynb_to_myst.py	100.00% <0.00%> (+13.33%)	⬆️

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