VEC function integration into smact.properties with a test file to serve as an example for its use.

[ryannduma]

VEC function Pull Request

Description

Hey, I hope this PR finds you well, I have now completed the integration of the VEC function succintly into the smact.properties.py module and attached a relevant example of it's use. I would also like to indicate that the function takes two arguments - the compound in question and a valence file - allowing for the user to select any file say magpie, or any existing valence file that they would like to use, in this case the example uses the modified file you shared.

I would like to highlight that this is a New feature (non-breaking change which adds functionality)

How Has This Been Tested?

Test Configuration: VECexample.py

• Python version: 3.12.0
• Operating System: MacOS

Reviewers

@AntObi - Admin and Maintainer

Checklist:

• [y ] My code follows the style guidelines of this project
• [ y] I have performed a self-review of my own code
• [ y] I have commented my code, particularly in hard-to-understand areas
• [n ] I have made corresponding changes to the documentation
• [y ] My changes generate no new warnings
• [ y] I have added tests that prove my fix is effective or that my feature works
• [ n] New and existing unit tests pass locally with my changes
• [ y] Any dependent changes have been merged and published in downstream modules
• [ y] I have checked my code and corrected any misspellings

Summary by CodeRabbit

• New Features

  • Introduced scripts for calculating the Valence Electron Count (VEC) for specified compounds.
  • Added a function to compute VEC from a compound formula with enhanced parsing capabilities.

• Bug Fixes

  • Implemented error handling for invalid chemical elements in the compound formula.

• Tests

  • Enhanced test coverage to validate the accuracy of the VEC calculations for various compounds.

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Commits

Files that changed from the base of the PR and between f8b7a8aec513830870e987f19df1e93998c8e153 and 55ba0db43bdfd38e5c8388a6921e874791ca9b3d.

Walkthrough

The changes introduce two new scripts, VECexample.py and examples/vec_example.py, for calculating the Valence Electron Count (VEC) of different chemical compounds. This functionality is facilitated by the new valence_electron_count function in the smact/properties.py module, which includes parsing capabilities and error handling. Test coverage is enhanced with a new test function in the smact/tests/test_core.py file, ensuring proper validation of the new functionality.

Changes

Files	Change Summary
VECexample.py, examples/vec_example.py	Introduced scripts for VEC calculation for "Ba5In4Bi5" and "Fe2O3" using the valence_electron_count function from smact.properties.
smact/properties.py	Added valence_electron_count function for computing VEC with parsing and error handling.
smact/tests/test_core.py	Added test_valence_electron_count to validate the functionality of the valence_electron_count function, including expected outputs and error handling.
.pre-commit-config.yaml	Updated pre-commit hooks, modifying nbQA version and Python compatibility argument.
examples/Crystal_Space/1_reduction.ipynb	Changed import of Iterable from typing to collections.abc for better compatibility.

Poem

In a garden of formulas, oh what a sight,
A rabbit hops joyfully, under moonlight.
Valence counts dancing, a new script in play,
For compounds and elements, come join the fray!
With data from CSV, the VEC's now bright,
A leap for the science, oh what pure delight! 🐇✨

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[AntObi]

Thank you for submitting this PR @ryannduma . A few things before I can accept this PR.

• [x] Install pre-commit (pip install pre-commit) and run pre-commit run --all-files: This automatically lints and formats any updated code to make it compliant with some coding conventions/styles. This will make the PR pass the QA stage of the CI
• [x] Add a unit test for this function in smact/tests/test_core.py
• [x] While allowing the user to supply their own valence files is option to have, the function should work with data that's already built into SMACT, so default behaviour should be to access the valence data through Element('Fe').num_valence_modified, which is available on this develop branch.
• [x] Move the example into the example folders for now

[ryannduma]

Hey Anthony,

I have resolved all conflicts and the code now passes the qa stage of the CI except its failing all the other tests of the CI, how can I resolve that?

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 75.67%. Comparing base (f7a72b7) to head (55ba0db). Report is 206 commits behind head on develop.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## develop #305 +/- ## =========================================== + Coverage 75.47% 75.67% +0.19% =========================================== Files 24 24 Lines 2361 2183 -178 =========================================== - Hits 1782 1652 -130 + Misses 579 531 -48 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

---

🚨 Try these New Features:

• Flaky Tests Detection - Detect and resolve failed and flaky tests

[AntObi]

Merged!

[ryannduma]

Hey @AntObi , the code passed the tests after a bunch of minor tweaks here and there to the types of errors raised, I noticed the Lr0 element check passed as a ValueError when passed to the function instead of a TypeError as presumed so I edited that part of the test to match, and it passed, though I dont know if thats exactly right, same to the Xx which isnt a valid element but I guess when parsed over is accepted because of the following codeblock, which ofc down the line, is found to not have a Valence number and then returns a ValueError instead of a NameError - please let me know what your thoughts are on this and whether additional tweaks need to be made.

Thank you and have a good evening

def parse_formula(formula): pattern = re.compile(r'([A-Z][a-z]*)(\d*)') elements = pattern.findall(formula) element_stoich = defaultdict(int) for (element, count) in elements: count = int(count) if count else 1 element_stoich[element] += count return element_stoich