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Clean up exceptions and split FileFormatError in LoadError and DumpError #345

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merged 3 commits into from
Jun 21, 2024
Merged

Clean up exceptions and split FileFormatError in LoadError and DumpError #345

merged 3 commits into from
Jun 21, 2024

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tovrstra
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@tovrstra tovrstra commented Jun 21, 2024 •
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This fixes a task in #191: splitting FileFormatError and FileFormatWarning into Load... and Dump... versions, and fix formats that raise various generic exceptions. There is still a FileFormatError, but it is only used for errors related to identifying or selecting the correct file format. This fix will make error messages more informative in general, and it will make the original goal of #191 easier to achieve.

Note that there are a few more tasks related to exception handling in #191, not included in this PR, to keep it small. Cleanups like these quickly become large, so I've suppressed the usual oh-I-can-also-fix-this reflex and deferred these to future PRs instead.

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

Summary by Sourcery

Refactored exception handling to provide more specific error types for loading and dumping operations, and updated corresponding test cases.

  • Enhancements:
    • Refactored exception handling by splitting FileFormatError and FileFormatWarning into LoadError, LoadWarning, DumpError, and DumpWarning for more specific error categorization.
  • Tests:
    • Updated test cases to use LoadWarning and LoadError instead of FileFormatWarning and FileFormatError.

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sourcery-ai bot commented Jun 21, 2024 •
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Reviewer's Guide by Sourcery

This pull request addresses a task from issue #191 by splitting the FileFormatError and FileFormatWarning into more specific LoadError, LoadWarning, DumpError, and DumpWarning classes. The changes aim to make error messages more informative and specific to the context of loading or dumping data. The FileFormatError is retained but is now only used for errors related to identifying or selecting the correct file format. The changes also include updating the exception handling in various modules and tests to use the new error classes.

File-Level Changes

Files Changes
iodata/formats/json.py
iodata/api.py
iodata/utils.py
iodata/test/test_json.py
iodata/formats/mwfn.py
iodata/test/test_cp2klog.py
iodata/formats/pdb.py
iodata/test/test_pdb.py
iodata/formats/gromacs.py
iodata/formats/fchk.py
iodata/formats/mol2.py
iodata/formats/molden.py
iodata/formats/molekel.py
iodata/test/common.py
iodata/test/test_wfx.py
iodata/test/test_api.py
iodata/test/test_inputs.py
iodata/test/test_sdf.py
iodata/formats/gamess.py
iodata/formats/gaussianinput.py
iodata/test/test_mol2.py		 Replaced FileFormatError and FileFormatWarning with more specific LoadError, LoadWarning, DumpError, and DumpWarning classes. Updated exception handling in various modules and tests to use the new error classes.
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deepsource-io bot commented Jun 21, 2024 •
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Here's the code health analysis summary for commits 3f2e4fc..cfbbceb. View details on DeepSource ↗.

Analysis Summary

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DeepSource Python LogoPython✅ Success
🎯 2 occurences resolved
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sourcery-ai bot reviewed Jun 21, 2024
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Hey @tovrstra - I've reviewed your changes and they look great!

Here's what I looked at during the review
  • 🟡 General issues: 3 issues found
  • 🟢 Security: all looks good
  • 🟡 Testing: 1 issue found
  • 🟢 Complexity: all looks good
  • 🟢 Documentation: all looks good
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@tovrstra tovrstra mentioned this pull request Jun 21, 2024
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PaulWAyers
PaulWAyers approved these changes Jun 21, 2024
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I went through it quickly and it seems OK.

@tovrstra
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Thanks for checking, Paul.

I've also double-checked it, but could not spot obvious mistakes. The critical parts will be revisited in future pull requests, so I'll be taking a second look in any case.

@tovrstra tovrstra merged commit be722a9 into theochem:main Jun 21, 2024
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@tovrstra tovrstra deleted the format-exceptions branch June 21, 2024 18:32
@tovrstra tovrstra mentioned this pull request Jun 23, 2024
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@sourcery-ai-experiments-bot sourcery-ai-experiments-bot mentioned this pull request Jun 24, 2024
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@PaulWAyers PaulWAyers PaulWAyers approved these changes

@FarnazH FarnazH Awaiting requested review from FarnazH

@evohringer evohringer Awaiting requested review from evohringer

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@tovrstra @PaulWAyers