Remove merge_ts

[claudio525]

No description provided.

[gemini-code-assist]

Summary of Changes

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This pull request systematically removes the merge_ts functionality from the project. This comprehensive cleanup involves deleting the core Python script and its Cython-optimized loop, updating project build configurations to reflect the removal, and eliminating all related documentation and workflow stage definitions. The change streamlines the codebase by removing a component that is no longer needed or has been superseded, though the specific reason for its deprecation is not explicitly stated in the provided context.

Highlights

• Core Functionality Removal: The primary merge_ts script, responsible for merging EMOD3D timeslices, along with its underlying Cython-optimized merge_ts_loop component, has been completely removed from the project.
• Build Configuration Cleanup: The pyproject.toml file has been updated to remove the merge-ts entry point, and the entire setup.py file, which handled Cython compilation for merge_ts_loop, has been deleted.
• Documentation and Workflow Updates: All documentation related to 'Merge Timeslices' in wiki/Stages.md has been removed, and the MergeTimeslices entry has been eliminated from the workflow components table in workflow/__init__.py and the StageIdentifier enum in workflow/scripts/plan_workflow.py.

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[gemini-code-assist]

Code Review

This pull request aims to remove the merge_ts functionality. The changes are mostly correct, removing the script, its Cython helper, documentation, and project configuration entries. However, I've found a critical issue in workflow/scripts/plan_workflow.py where references to the removed StageIdentifier.MergeTimeslices enum still exist, which will lead to runtime errors. I've left a specific comment on this. Additionally, it appears that the template files workflow/templates/hypocentre/merge_ts.cylc and workflow/templates/nesi/merge_ts.cylc are now unused and should also be removed to complete the cleanup.

[Copilot]

Pull request overview

This PR removes the "merge_ts" (Merge Timeslices) functionality from the workflow system. The merge_ts stage was used to merge output timeslice files from EMOD3D simulations. The removal includes deleting the Python implementation, Cython optimization code, CLI entry points, and associated documentation.

Key changes:

• Removed the MergeTimeslices stage identifier from the workflow planning system
• Deleted the merge_ts Python module and Cython loop implementation
• Removed CLI entry point and build configuration for the merge-ts command
• Updated documentation to remove references to the Merge Timeslices stage

Reviewed changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
workflow/scripts/plan_workflow.py	Removed MergeTimeslices enum value from StageIdentifier class
workflow/scripts/merge_ts_loop.pyx	Deleted Cython implementation for efficient file descriptor merging
workflow/scripts/merge_ts.py	Deleted Python module containing merge_ts CLI with XYTS and HDF5 merge functions
workflow/__init__.py	Removed "Merge Timeslices" entry from the workflow stages documentation table
wiki/Stages.md	Removed complete documentation section for the Merge Timeslices stage
setup.py	Deleted setup.py file that was used to build the Cython extension
pyproject.toml	Removed merge-ts CLI entry point from project scripts

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[lispandfound]

Also delete the templates folder in the workflow package.

[lispandfound]

You also need to remove the cython requirement at the top of the pyproject.toml file. This is added to build merge-ts but is no longer needed.