refactor: Improve code readability and reducing code duplications

[Anselmoo]

• Using tuples to reperesent the non-diagonal elements via dictionary

Summary by Sourcery

Enhancements:

• Refactor matrix construction by introducing a new method 'construct_matrix' to handle diagonal and off-diagonal elements, improving code readability and reducing duplication.

[semanticdiff-com]

Review changes with  

Changed Files

File	Status
tanabesugano/test/test_front.py	100% smaller
tanabesugano/batch.py	100% smaller
tanabesugano/cmd.py	93% smaller
tanabesugano/tools.py	76% smaller
tanabesugano/matrices.py	42% smaller
tanabesugano/test/test_num.py	2% smaller
.github/dependabot.yml	Unsupported file format
.github/workflows/docker-image.yml	Unsupported file format
CHANGELOG.md	Unsupported file format
poetry.lock	Unsupported file format
pyproject.toml	Unsupported file format
tanabesugano/__init__.py	0% smaller
tanabesugano/test/test_matrices.py	0% smaller

[sourcery-ai]

Reviewer's Guide by Sourcery

The pull request refactors matrix construction in ligand field theory calculations by introducing a new helper method construct_matrix that centralizes the creation of symmetric matrices from diagonal and off-diagonal elements. This change eliminates code duplication across multiple state calculation methods.

Class diagram for LigandFieldTheory refactor

classDiagram
    class LigandFieldTheory {
        +Dq: float
        +B: float
        +C: float
        +solver() Dict~str, Float64Array~
        +construct_matrix(diag_elements: List~float~, off_diag_elements: Dict~Tuple~int, int~, float~) Float64Array
    }
    class d2 {
        +A_1_1_states() Float64Array
        +E_1_states() Float64Array
        +T_1_2_states() Float64Array
        +T_3_1_states() Float64Array
        +solver() Dict~str, Float64Array~
    }
    LigandFieldTheory <|-- d2
    note for LigandFieldTheory "Added construct_matrix method to centralize matrix creation"

Loading

File-Level Changes

Change	Details	Files
Added a new helper method to construct symmetric matrices	Introduced construct_matrix method that takes diagonal and off-diagonal elements as input Method automatically handles matrix symmetry by mirroring off-diagonal elements Returns a numpy array representing the constructed matrix	tanabesugano/matrices.py
Refactored state calculation methods to use the new matrix construction helper	Replaced direct matrix construction with calls to construct_matrix Separated diagonal and off-diagonal elements into distinct dictionaries Removed redundant symmetric element assignments Simplified matrix construction code across all state calculation methods	tanabesugano/matrices.py
Improved code organization and readability	Removed redundant comments marking diagonal and non-diagonal sections Eliminated duplicate variable assignments for symmetric matrix elements Standardized the structure of state calculation methods	tanabesugano/matrices.py

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[sourcery-ai]

Hey @Anselmoo - I've reviewed your changes and they look great!

Here's what I looked at during the review

• 🟡 General issues: 1 issue found
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

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[sourcery-ai]

suggestion: Document the symmetry assumption and consider skipping zero elements

The docstring should mention that the method assumes off_diag_elements contains values for a symmetric matrix. Also, consider skipping zero values in off_diag_elements to avoid unnecessary operations.