Replace lit.error by raise LoadError

[tovrstra]

This is another step in #191. As a sideline in fixing that issue, the IOData error handling is improved in general, not just for errors and warnings when data is converted before writing it out.

The old code used a wrapper function lit.error to raise an exception when a file cannot be read for some reason. This function adds some info (filename and line number) to the error message. This was a bad idea for several reasons:

• It does not allow raise LoadError(...) from exc calls.
• It is less readable than a plain raise LoadError(....
• Static code analysis does realize that lit.error(...) interrupts the control flow, leaving poor code undetected. (We had some of that in the gro and cp2klog formats, fixed in this PR.)

The logic that was in LineIterator.error has now been implemented in the LoadError exception, and has been generalized to work well for all use cases.

I will YOLO-merge this on Friday, June 28, unless reviewed earlier.

Summary by Sourcery

This pull request refactors error handling by replacing the custom lit.error function with direct raise LoadError calls. This change improves code readability, allows for better exception chaining, and enhances error reporting by including filename and line number information in the LoadError exception. Additionally, test cases have been updated to reflect these changes.

• Enhancements:
  • Replaced the custom lit.error function with direct raise LoadError calls to improve readability and allow raise ... from syntax.
  • Generalized the LoadError exception to include filename and line number information, enhancing error reporting across various file formats.
• Tests:
  • Updated test cases to check for LoadError exceptions instead of lit.error messages.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request replaces the lit.error method with raise LoadError across multiple files to improve error handling and readability. The LoadError class now includes enhanced error message handling, providing more context in error messages. Test cases have also been updated to reflect these changes.

File-Level Changes

Files	Changes
iodata/formats/mwfn.py iodata/formats/gromacs.py iodata/formats/json.py iodata/formats/molden.py iodata/formats/wfx.py iodata/formats/molekel.py iodata/formats/fchk.py iodata/formats/wfn.py iodata/formats/charmm.py iodata/formats/cp2klog.py iodata/formats/fcidump.py iodata/formats/gamess.py iodata/formats/sdf.py iodata/formats/gaussianinput.py iodata/formats/mol2.py iodata/formats/pdb.py	Replaced lit.error calls with raise LoadError in multiple locations and updated error messages to include more context.
iodata/test/test_wfx.py iodata/test/test_gaussianinput.py	Updated test cases to check for LoadError instead of lit.error.

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[deepsource-io]

Here's the code health analysis summary for commits be722a9..84e8f8f. View details on DeepSource ↗.

Analysis Summary

Analyzer	Status	Summary	Link
Shell	✅ Success		View Check ↗
Python	✅ Success		View Check ↗

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[sourcery-ai]

Hey @tovrstra - I've reviewed your changes and they look great!

Here's what I looked at during the review

• 🟡 General issues: 5 issues found
• 🟢 Security: all looks good
• 🟡 Testing: 4 issues found
• 🟢 Complexity: all looks good
• 🟡 Documentation: 1 issue found

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[PaulWAyers]

Seems OK to me.

[tovrstra]

Thanks for checking Paul!