Add prepare_segmented function

[tovrstra]

This addresses another task from #191: conversion to segmented basis functions is now also implemented through in the prepare and convert modules. In addition to reorganizing how this was done previously, the FCHK format now also makes use of this feature. (For FCHK, SP shells are left in place, but other types of generalized contractions are converted.) This also addresses the last point in #256 .

This is API breaking because the MolecularBasis.get_segmented method was removed and replaced by functions in separate modules. This improves overall modularity: separating utilities from the core data structures. Related unit tests were also moved for consistency.

⚠️ I will YOLO-merge this on Thursday, July 18, unless reviewed earlier.

Summary by Sourcery

This pull request introduces the prepare_segmented function to convert generalized contractions to segmented ones, enhancing modularity by moving this functionality to separate modules. It also updates various format modules to utilize this new feature and refactors related tests for consistency.

• New Features:
  • Introduced the prepare_segmented function to convert generalized contractions to segmented ones in the prepare module.
  • Added convert_to_segmented function in the convert module for converting basis sets with generalized contractions to single contractions.
• Enhancements:
  • Removed the MolecularBasis.get_segmented method and replaced it with functions in separate modules to improve modularity.
  • Updated the FCHK format to utilize the new segmented basis conversion feature.
  • Modified the prepare_dump functions in various format modules (Molden, Molekel, WFN, WFX) to include calls to prepare_segmented.
  • Refactored tests to use the new prepare_segmented and convert_to_segmented functions, ensuring consistency and modularity.
• Tests:
  • Added unit tests for the new prepare_segmented function in test_prepare.py.
  • Added unit tests for the new convert_to_segmented function in test_convert.py.
  • Updated existing tests to remove references to the deprecated MolecularBasis.get_segmented method and replace them with the new functions.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request introduces the prepare_segmented function to convert generalized contractions to segmented ones, enhancing modularity by moving the MolecularBasis.get_segmented method to separate modules. The changes affect multiple files, including the addition of new tests and modifications to existing ones to ensure compatibility with the new function. The FCHK format now also utilizes this feature, and related unit tests have been updated accordingly.

File-Level Changes

Files	Changes
iodata/formats/molden.py iodata/formats/molekel.py iodata/formats/wfn.py iodata/formats/wfx.py iodata/formats/fchk.py	Updated prepare_dump and dump_one functions to handle segmented basis and call prepare_segmented.
iodata/test/test_convert.py iodata/test/test_prepare.py iodata/test/test_basis.py iodata/test/test_molden.py iodata/test/test_molekel.py iodata/test/test_wfx.py iodata/test/test_fchk.py iodata/test/test_wfn.py	Added new tests for prepare_segmented and convert_to_segmented functions, and updated existing tests to use convert_to_segmented instead of get_segmented.

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[deepsource-io]

Here's the code health analysis summary for commits cdb30cc..62dc5dd. View details on DeepSource ↗.

Analysis Summary

Analyzer	Status	Summary	Link
Shell	✅ Success		View Check ↗
Python	✅ Success	❗ 1 occurence introduced 🎯 2 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: 8 issues found
• 🟢 Security: all looks good
• 🟡 Testing: 8 issues found
• 🟡 Complexity: 2 issues found
• 🟢 Documentation: all looks good

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[PaulWAyers]

It seems clear to me.

[tovrstra]

Thanks for checking Paul! Let's see if merging works from a phone...

[FarnazH]

@tovrstra This API change breaks the from_iodata function of gbasis. I have reported this at theochem/gbasis#195.

[PaulWAyers]

Sorry @FarnazH , I should have caught this.