Refactor/helpers

[ryanmccann1024]

📝 Description

This PR refactors the module responsible for input file generation. The logic from setup_helpers.py has been moved to a more semantically appropriate location within the simulation package at fusion/sim/input_setup.py.

This change improves the project's organization by grouping simulation-specific logic together. The PR also includes linting fixes for the fusion package and updates the top-level tests to align with the new file structure.

Fixes: # (issue number) ---

🧐 Type of Change

• 🐛 Bug fix (non-breaking change which fixes an issue)
• ✨ New feature (non-breaking change which adds functionality)
• 💥 Breaking change (fix or feature that would cause existing functionality to not work as expected)
• 💅 UI/UX change (improves the user interface or experience)
• 📚 Documentation update
• ⚙️ Chore (refactoring, dependency updates, etc.)

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💥 Impact of Breaking Change

This is a minor breaking change due to the file relocation. Any internal modules that were importing directly from the old setup_helpers.py will be broken. This PR resolves the immediate impact on the top-level tests, but other areas could be affected. Any dependencies must be updated to import from the new path (fusion.sim.input_setup).

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🧪 How Has This Been Tested?

The refactoring has been verified with the following steps:

• The top-level test suite was run, and all tests affected by the file move have been fixed and confirmed to pass.
• The linter was run on the fusion package to ensure code style and quality are maintained.

Test Configuration:

• Operating System: [Please fill in]
• Python version: [Please fill in]
• Other Dependencies: [Please fill in]

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📸 Screenshots / Screen Recordings

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✅ Final 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.
• I have checked that my commit message follows the project's formatting guidelines.

[ryanmccann1024]

@bozo-bud @arashr88 I'm not sure if we should try and pass the Cross-platform as the refactor of phase 2 is for the sim/core scripts.

What do you think?

[bozo-bud]

Ideally I'd think we'd want each update to have them working, but all things considered its probably fine. I'm more curious why two of them were cancelled.

[ryanmccann1024]

Ideally I'd think we'd want each update to have them working, but all things considered its probably fine. I'm more curious why two of them were cancelled.

I think they're a part of one pipeline so if one fails the others are cancelled. I'm not sure if this is a good idea but could potentially save a lot of pipeline time (not any limits but if you submit multiple times they'll queue and take much longer).

Let's say we forgot to put a variable in the example config that these run on, all pipelines would fail and it wouldn't be worth it to run the others.

But, let's say it's an OS specific error, we'd have to fix one before moving onto the other...Not sure what's ideal here.