test: increase test coverage to 98% and fix slab/defect edge cases

[ToAmano]

Description

This PR resolves the remaining untested lines in cli.py and core.py, bringing the overall code coverage to 98% (exceeding the target of 80%). It also fixes a critical bug in surface slab generation and adds robust edge-case validation.

Changes

• Slab Generation Bug Fix: Corrected the return statement in generate_surface_slab to return the Slab object directly instead of attempting to call the non-existent generate_unique_slab_structs method.
• Miller Index Validation: Added validation in generate_surface_slab to raise a ValueError if crystallographically invalid zero indices ([0, 0, 0]) are provided.
• Improved Coverage Tests:
  • Added warning path coverage for mismatching target elements during substitutions and vacancies.
  • Added exception handling path coverage for EspressoAdapter parsing and file reading.
  • Added integration tests for CLI error paths (substitutions, vacancies, and slabs).
  • Added tests for CLI default output filename generation logic.
• Corrected Existing Tests: Fixed percentage substitutions (reducing composition formula) and random vacancies lattice sizing issues.

[cr-gpt]

Seems you are using me but didn't get OPENAI_API_KEY seted in Variables/Secrets for this repo. you could follow readme for more information

[codecov-commenter]

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Codecov Report

✅ All modified and coverable lines are covered by tests.

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