CI & documentation improvements

[danielkovtun]

Test suite

• Replaces custom action runner with default ubuntu-latest
• Removes inefficient test behavior where entire metadata was being cast to dict
• removes pin on scikit-learn in top-level package and only installs pinned version in CI with prodigy-cryst installed (optional)
• Silent failures due to invalid assert syntax addressed
• Misleading filter behavior when performing logical checks on literals (e.g., is not None to check for NaN)
• dtype and deprecation warnings encountered in test suite
• Increases required coverage to 80%

Documentation

• New example notebook added to illustrate one of the FAQ about cropped monomer superposition
• FAQ example on using pinder eval outside of pinder context
• Formatting

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 69.76744% with 13 lines in your changes missing coverage. Please review.

Files	Coverage Δ
src/pinder-core/pinder/core/loader/structure.py	84.31% <100.00%> (-0.10%)	:arrow_down:
src/pinder-core/pinder/core/structure/atoms.py	70.78% <100.00%> (+0.44%)	:arrow_up:
src/pinder-core/pinder/core/structure/contacts.py	87.34% <ø> (ø)
...c/pinder-core/pinder/core/structure/superimpose.py	87.71% <ø> (ø)
src/pinder-core/pinder/core/utils/cloud.py	77.11% <ø> (ø)
src/pinder-core/pinder/core/utils/log.py	98.03% <ø> (ø)
src/pinder-core/pinder/core/utils/paths.py	95.96% <ø> (ø)
src/pinder-data/pinder/data/alignment_utils.py	80.74% <100.00%> (ø)
...a/pinder/data/annotation/contact_classification.py	83.63% <ø> (ø)
...data/pinder/data/annotation/detached_components.py	79.31% <ø> (+20.77%)	:arrow_up:
... and 14 more

... and 6 files with indirect coverage changes