Replace asserts by errors or warnings

[tovrstra]

An item on the list of cleanups in #204. This PR builds on the error and warning features added in the course of fixing #191.

The bad practice of using assert outside unit tests is removed. Such asserts are ignored by Python when running in optimized mode, meaning that possible errors when loading or dumping files go unnoticed. Each assert was checked and one of the following changes was made (roughly in order of decreasing prevalence):

• Converted to raising a suitable error. (some moved to an earlier part of the code)
• Converted to raising a warning.
• Removed if the assertion was blocking something that was actually fine.

Other related changes:

• Extended a few docstrings.
• Improved some of the checks in the Molekel format (and removed a few bogus ones).
• Moved tests for tools/harmonics.py to a separate file.

I will YOLO-merge this on Wednesday, July 10, unless reviewed earlier.

Summary by Sourcery

This pull request replaces assert statements with appropriate error or warning raises to ensure proper error handling in optimized mode. It also includes improvements to error messages and checks in the Molekel format, extends some docstrings, and moves tests for tools/harmonics.py to a separate file.

• Bug Fixes:
  • Replaced assert statements with error or warning raises to ensure proper error handling in optimized mode.
• Enhancements:
  • Improved error messages and checks in the Molekel format.
  • Extended docstrings for better clarity and documentation.
• Tests:
  • Moved tests for tools/harmonics.py to a separate file tools/test_harmonics.py.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request replaces the use of assert statements with appropriate error or warning handling in various files. The changes ensure that potential issues are not ignored when Python is run in optimized mode. Additionally, some docstrings were extended, checks in the Molekel format were improved, and tests for tools/harmonics.py were moved to a separate file.

File-Level Changes

Files	Changes
iodata/formats/extxyz.py iodata/formats/molekel.py iodata/formats/fchk.py iodata/formats/cp2klog.py iodata/formats/molden.py iodata/formats/fcidump.py iodata/formats/qchemlog.py iodata/formats/wfx.py iodata/formats/mwfn.py iodata/formats/wfn.py	Replaced assert statements with appropriate error or warning handling to ensure potential issues are not ignored in optimized mode.
tools/harmonics.py tools/test_harmonics.py	Moved tests for harmonics.py to a separate file and added new unit tests.

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[deepsource-io]

Here's the code health analysis summary for commits b08f401..37a67f1. View details on DeepSource ↗.

Analysis Summary

Analyzer	Status	Summary	Link
Shell	✅ Success		View Check ↗
Python	❌ Failure	❗ 7 occurences introduced 🎯 44 occurences resolved	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: 17 issues found
• 🟢 Security: all looks good
• 🟡 Testing: 1 issue found
• 🟡 Complexity: 1 issue found
• 🟢 Documentation: all looks good

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[tovrstra]

The 7 deepsource issues already exists. This PR actually fixes 37 issues detected by deepsource and touched code related to those 7 other ones.

[PaulWAyers]

I took a very fast look and it seems Ok to me.

[tovrstra]

Thanks for checking Paul! Merging...