Fix io.cp2k.input.DataFile

[DanielYang59]

Summary

Fixed a flawed change in io.cp2k.input.DataFile.from_file made by me in #3705, discussed in #3705 (comment). Also added comment to prevent this from happening again.

[coderabbitai]

Walkthrough

The recent changes in the pymatgen library bring enhancements to file handling and data consistency across various modules. These updates aim to streamline processes and improve clarity in code structure.

Changes

File Path	Change Summary
.../io/cp2k/inputs.py	Updated from_file method for improved file loading, data processing, object naming, and added type hints.
.../electronic_structure/plotter.py	Refactored variable names for consistency in power factor plotting functions.
tests/io/test_openff.py	Replaced np.allclose with assert_allclose for clearer partial charge assertions in tests.
tests/io/cp2k/test_inputs.py	Various changes including imports, variable renaming, and improved clarity in test functions.

Poem

🐰🌟
Code changes flutter like leaves in the wind,
Bringing order where chaos once grinned.
Test assertions now shine bright and clear,
In the land of bytes, with nary a tear.
Cheers to the updates, a dance so sweet,
In the world of pymatgen, where changes meet.
🌟🐰

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Recent Review Details

Configuration used: CodeRabbit UI

Commits

Files that changed from the base of the PR and between 21461f4 and 8e3a692.

Files selected for processing (3)

• pymatgen/electronic_structure/plotter.py (3 hunks)
• pymatgen/io/cp2k/inputs.py (2 hunks)
• tests/io/cp2k/test_inputs.py (12 hunks)

Files skipped from review as they are similar to previous changes (1)

• pymatgen/io/cp2k/inputs.py

Additional comments not posted (15)

tests/io/cp2k/test_inputs.py (15)

4-4: Added pytest import.

This import is necessary for using pytest.raises in the test cases.

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27-27: Renamed Si_structure to si_struct.

This change aligns with Python's naming conventions for variables, which prefer lowercase with underscores.

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39-39: Renamed molecule to ch_mol.

The new name ch_mol provides a clearer indication of the molecule's composition, improving code readability.

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41-41: Introduced BASIS_FILE_STR as a constant.

Using a constant for the basis file string is a good practice as it enhances maintainability and reusability of the code.

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53-53: Introduced ALL_HYDROGEN_STR as a constant.

Defining string constants for configuration or data blocks like this one improves clarity and reduces the risk of typos in multiple uses.

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58-58: Introduced POT_HYDROGEN_STR as a constant.

Similar to other string constants, this change helps in managing the data more efficiently and makes the code cleaner.

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64-69: Added CP2K_INPUT_STR constant.

Storing configuration strings as constants is a good practice. It centralizes the configuration data, making it easier to manage and modify.

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75-92: Updated test_basis_info to use new constants and improved assertions.

The updates in the test function make use of the newly introduced constants and enhance the assertions for better test coverage and clarity.

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101-104: Enhanced test_potential_info with soft-matching checks.

The addition of soft-matching checks is a good improvement, providing more robust testing for the potential information functionality.

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133-154: > 📝 NOTE

This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [108-147]

Refined tests for basis and potential files to use new constants and improved assertions.

The changes in these test functions are well-made, utilizing the new constants and enhancing the assertions to ensure the functionality is thoroughly tested.

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165-179: Updated test_basic_sections and test_section_list to use new CP2K_INPUT_STR and improved section handling.

These updates improve the structure and clarity of the tests, making them more maintainable and robust.

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191-198: Enhanced test_coords and test_kind functions with better structure handling and assertions.

The improvements in these test functions enhance the clarity and effectiveness of the tests, ensuring that the coordinate and kind functionalities are correctly implemented.

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215-228: Introduced a new test scenario in test_odd_file to handle scrambled input.

This test is innovative as it checks the robustness of the input handling against non-standard and scrambled inputs, ensuring the parser's resilience.

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243-249: > 📝 NOTE

This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [246-256]

Updated test_mongo to use new CP2K_INPUT_STR and enhanced keyword handling.

The updates to this test function improve the testing of the configuration handling, ensuring that the keyword manipulations are correctly implemented.

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259-264: Added a test case to ensure DataFile.from_file raises NotImplementedError.

This test case is crucial as it verifies that the expected exception is raised for unimplemented functionality, which is important for avoiding runtime errors.

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[DanielYang59]

Can you please review this fix? @janosh Apologize again for the trouble.

[janosh]

thanks for this fix. i added several new tests and made the DataFile.from_file an abstractmehod

[coderabbitai]

Actionable comments posted: 4

[DanielYang59]

Thanks for reviewing and making it a real "fix" 😄

[DanielYang59]

Wondering what is the advantage here? (thought the original syntax is more consistent with the assert condition syntax)

From the assert_allclose documentation, these two seems equivalent:

The test is equivalent to allclose(actual, desired, rtol, atol) (note that allclose has different default values). It compares the difference between actual and desired to atol + rtol * abs(desired).

[janosh]

compare the error messages when they each fail. assert_allclose gives a much more informative message

[DanielYang59]

Thanks for the input! Appreciate that.