Revive merge-ts hdf5 merging

[lispandfound]

When @claudio525 created the very helpful PR to remove merge-ts we might've gone a little overboard... We removed the merging code that needed Cython, but then the full python xarray xyts->hdf5 logic was also deleted! This PR re-adds merge-ts with just the HDF5 output. I also slightly refactored the reading logic by extracting out helper functions instead of one big main function. At some point, these helper functions will be extracted into the qcore.xyts module.

[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 restores the merge-ts utility, which was previously removed, specifically focusing on its HDF5 output capabilities. It re-implements the merging of EMOD3D timeslice files into a single HDF5 file using Python's xarray library. The implementation also includes a refactoring of the data reading logic into several dedicated helper functions, improving code organization and maintainability.

Highlights

• Re-introduction of merge-ts: The merge-ts utility has been re-added to the project, specifically restoring its functionality for merging EMOD3D timeslice files into HDF5 format.
• Refactored Reading Logic: The data reading and processing logic within merge-ts has been refactored into several modular helper functions, enhancing code organization and maintainability. These functions are intended for future extraction into the qcore.xyts module.
• Xarray Integration for HDF5 Output: The script now leverages the xarray library for robust handling of N-dimensional data, coordinate generation, and efficient saving of the merged timeslice data to HDF5 files with compression.

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[gemini-code-assist]

Code Review

This pull request revives the merge-ts script for HDF5 merging, which was accidentally removed. The new implementation is a pure Python script using xarray and typer. The refactoring into helper functions is a good improvement for readability and future reuse.

My review focuses on improving correctness, robustness, and maintainability. I've identified a critical issue where the script would crash if no input files are found, a data type inconsistency that could lead to errors, and some minor improvements regarding a magic number and docstring correctness. Overall, this is a great addition and the refactoring is well done.

[Copilot]

Pull request overview

This PR revives the merge-ts HDF5 merging functionality that was previously removed. The implementation is now purely Python-based (no Cython dependencies) and provides a command-line tool to merge EMOD3D timeslice files into a single HDF5 output file with quantized waveform data.

Key changes:

• Re-introduces workflow/scripts/merge_ts.py with a refactored architecture using helper functions
• Adds merge-ts command-line entry point in pyproject.toml
• Implements XYTS file reading, waveform magnitude calculation, and HDF5 output generation with compression

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 7 comments.

File	Description
workflow/scripts/merge_ts.py	New script implementing XYTS file merging with helper functions for reading component files, extracting metadata, calculating coordinates, and creating compressed HDF5 output
pyproject.toml	Adds merge-ts command-line entry point mapping to the new merge_ts module

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[Copilot]

Pull request overview

Copilot reviewed 2 out of 2 changed files in this pull request and generated 7 comments.

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