Oxidation states

[AntObi]

Fix oxidation states module

Description

oxidation_states.py fixes:

• Fixed pymatgen import Specie to Species fixing the error of oxidation states not being recognised in Structures

• Fixed getting species from iterating over a structure

• Added example of computing compound probability for a pymatgen Structure

• Updated test_core.py to test the oxidation_states with a pymatgen Structure

Fixes #190

Type of change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)

How Has This Been Tested?

Added test in test_core.py that tests Oxidation_state_probability_finder().compound_probability(structure)

Test Configuration:

• Python version: 3.10
• Operating System: Ubuntu

Reviewers

N/A

Checklist:

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

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (7d1ee94) 72.80% compared to head (bc9c44b) 73.10%.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #191      +/-   ##
==========================================
+ Coverage   72.80%   73.10%   +0.30%     
==========================================
  Files          24       24              
  Lines        1945     1952       +7     
==========================================
+ Hits         1416     1427      +11     
+ Misses        529      525       -4     

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