Fix type-checking errors for workflow

[lispandfound]

Fixes a few bugs spotted by the type-checker:

1. Type checking failures in realisation-to-srf relating to handling Plane and Fault sources,
2. Incorrect calculation of area in the point-source case,

[gemini-code-assist]

Summary of Changes

Hello @lispandfound, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request resolves several type-checking errors and a logical bug across various workflow scripts. The changes improve the robustness and accuracy of the workflow by correctly handling different source types during SRF generation, ensuring precise area calculations for point sources, and addressing type compatibility issues with external libraries.

Highlights

• Type Checking Fixes: Addressed type-checking failures in realisation_to_srf related to handling Plane and Fault sources, ensuring correct attribute access based on source type.
• Point Source Area Calculation: Corrected the calculation of fault area for point sources in realisation_to_srf to use length * width for accuracy.
• External Library Type Ignores: Added type: ignore comments for qcore related tobytes() calls in merge_ts.py to resolve current type-checking issues, with a note for future removal.
• Stage Parent Property Refinement: Updated the Stage.parent property in plan_workflow.py to use deepcopy when creating a parent stage, ensuring proper object state preservation.

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[gemini-code-assist]

Code Review

This pull request addresses several type-checking errors and a bug in area calculation. The changes look good overall. In generate_velocity_model_parameters.py and realisation_to_srf.py, the handling of different source types (Fault, Plane, Point) is now more robust, fixing potential AttributeErrors. The correction to the fault area calculation in realisation_to_srf.py for point sources is also a good fix. The addition of type: ignore in merge_ts.py is a reasonable temporary solution for upstream type hint issues. I have one suggestion in plan_workflow.py to use a more idiomatic and efficient way to copy a dataclass instance.

[Copilot]

Pull Request Overview

This PR fixes type-checking errors in the workflow codebase, specifically addressing issues in SRF generation, velocity model parameter generation, workflow planning, and timeslice merging.

• Fixed type-checking failures when handling different source types (Fault, Plane, Point) by adding proper isinstance checks and using appropriate properties
• Corrected the area calculation for point sources from (length_m / 1000) ** 2 to length * width
• Improved the Stage.parent property implementation to use deepcopy for better maintainability
• Added type: ignore comments for qcore type annotation issues that will be resolved upstream

Reviewed Changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated no comments.

File	Description
workflow/scripts/realisation_to_srf.py	Added Fault import and isinstance checks to properly handle multi-plane faults vs single planes; fixed point source area calculation to multiply length by width instead of squaring length
workflow/scripts/plan_workflow.py	Improved Stage.parent property to use deepcopy instead of manual instantiation for better maintainability
workflow/scripts/merge_ts.py	Added type: ignore comments for tobytes() calls pending qcore type annotation updates
workflow/scripts/generate_velocity_model_parameters.py	Changed from computing mean dip across fault planes to using fault.dip property directly for type-checker compatibility

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[lispandfound]

Failing test case is because of a bug in zarr that I have just opened: zarr-developers/zarr-python#3592

[lispandfound]

Type check will fail until my PR to scipy is merged: scipy/scipy-stubs#992

[lispandfound]

I've decided to ignore the scipy type bug, with a TODO to remove this after scipy-stubs updates.