Draft HDF5 converter

[michael-petersen]

Based on a user request, I've been thinking about how to best implement HDF5 structure for file outputs. This is a draft implementation of an HDF5 phase-space system.

Still to be done:

• Add an HDF5 reader for easier interface
• Verify that this can be used externally with static methods
• Decide if the group strategy for headers makes the most sense

[michael-petersen]

Some of this is superseded by an implementation of a standard in EXP; it makes sense to keep this but perhaps as an internal-only format.

[Copilot]

Pull request overview

This PR introduces a draft HDF5 converter for PSP format files and makes significant improvements to code documentation and style across multiple analysis modules. The changes modernize the codebase by replacing legacy file I/O with HDF5, improving docstrings to follow Google-style conventions, and refactoring calculations to use more efficient numpy methods.

Key Changes:

• Adds a new HDF5 converter class to convert PSP particle simulation files to HDF5 format
• Updates trapping analysis to use HDF5 for output instead of binary files
• Refactors kmeans implementation with improved documentation and K-means++ initialization
• Enhances pattern analysis classes with comprehensive docstrings and new BarFromCoefficients class

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 22 comments.

File	Description
exptool/io/psp_to_hdf5.py	New HDF5 converter class with methods to convert PSP files to HDF5 format, including header and phase space data handling
exptool/utils/kmeans.py	Documentation improvements, code cleanup, addition of K-means++ initialization method, and refactoring for better readability
exptool/analysis/trapping.py	Migration from binary file output to HDF5 format, documentation improvements, error message standardization, and numpy optimization
exptool/analysis/pattern.py	New BarFromCoefficients class, enhanced documentation for BarTransform and BarFromFourier classes, and improved code organization

Comments suppressed due to low confidence (2)

exptool/io/psp_to_hdf5.py:91

• Call to method HDFConverter.convert_psp_to_hdf5 with too few arguments; should be no fewer than 1.

        self.convert_psp_to_hdf5()

exptool/io/psp_to_hdf5.py:148

• Except block directly handles BaseException.

                            except:

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[Copilot]

@michael-petersen I've opened a new pull request, #48, to work on those changes. Once the pull request is ready, I'll request review from you.

[Copilot]

@michael-petersen I've opened a new pull request, #49, to work on those changes. Once the pull request is ready, I'll request review from you.

[Copilot]

@michael-petersen I've opened a new pull request, #50, to work on those changes. Once the pull request is ready, I'll request review from you.

[Copilot]

@michael-petersen I've opened a new pull request, #51, to work on those changes. Once the pull request is ready, I'll request review from you.