• pdb1tff.ent: is looking for a residue at position 6 on chain A, but it doesn't exist in the .ent file
  • either remove entry 20 from the csv file, or fix the data file
• for multiple files, the code throws an exception regarding position 112 on chain A, even though it does exist
  • investigate why this is and resolve
• cell 2 fails if the folder already exists.
  • Either add a comment asking users to skip the cell in this case, or rewrite it so that it does not fail.
  • Add a warning or code to avoid overwriting pre-existing data.
• provide clearer message/warning about "failing entries", so that it is clear that the code can still be run, but that certain data points are skipped. Now it can look like the code crashed, even though it didn't.
• consider linting the notebooks as well
  • add extend-include = ["*.ipynb"] to [tool.ruff] in pyproject.toml
  • ruff v6.something does this by default, so consider upgrading to that version. However, new rules seem to be added as well, so unsure whether we want to fix those as well atm.

also, see #613