Replaces PyTables with H5PY as the HDF5 interface #15
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pedrocamargo wants to merge 4 commits intoosPlanning:masterfrom
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Replaces PyTables with H5PY as the HDF5 interface #15pedrocamargo wants to merge 4 commits intoosPlanning:masterfrom
pedrocamargo wants to merge 4 commits intoosPlanning:masterfrom
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refactoring refactoring refactoring refactoring refactoring debug debug debug . . . . . . . . . . . Replace two-arg super with zero-arg super Add fletcher32 option support to mirror pytables omx Some type hints WIP: add 'data' property and use it (once, more to come) Update .github/workflows/ci.yml Co-authored-by: Jake Moss <jake@outerloop.io> Update .github/workflows/ci.yml Co-authored-by: Jake Moss <jake@outerloop.io> Update tests/test_file.py Co-authored-by: Jake Moss <jake@outerloop.io> Update src/openmatrix/__init__.py Co-authored-by: Jake Moss <jake@outerloop.io> Update .github/workflows/ci.yml Co-authored-by: Jake Moss <jake@outerloop.io> Update pyproject.toml Add coverage testing Ensure data and lookup always exist, remove excessive double checks We can assume that once an OMX file is open, it's in a valid state, otherwise we should loudly complain Fix and clean up validator tests Fix and extend testing suite, reach 100% branch coverage Remove bad CI options Quotes? Forgot rename Bump CI versions Restore and update doc strings Update README documentation
Refactoring pytables out and h5py in
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Pull request overview
This pull request replaces PyTables with h5py as the HDF5 interface for the openmatrix library, addressing issue #12. The change modernizes the codebase and removes dependency on the slow-developing PyTables library.
Changes:
- Complete replacement of PyTables with h5py throughout the codebase
- Migration to modern Python packaging using pyproject.toml (replacing setup.py)
- Addition of comprehensive test suites with pytest
- Introduction of CI/CD workflow using GitHub Actions
- Updated documentation and examples to reflect h5py usage
Reviewed changes
Copilot reviewed 17 out of 18 changed files in this pull request and generated 27 comments.
Show a summary per file
| File | Description |
|---|---|
src/openmatrix/file.py |
New File class implementation extending h5py.File instead of tables.File |
src/openmatrix/__init__.py |
Updated module exports and open_file function with h5py-compatible filters |
src/openmatrix/validator.py |
Rewritten validator to work with h5py APIs |
src/openmatrix/exceptions.py |
Minimal changes - whitespace cleanup |
tests/test_file.py |
Comprehensive new test suite covering file operations |
tests/test_validator.py |
Complete test coverage for validator functionality |
pyproject.toml |
New build configuration replacing setup.py |
.github/workflows/ci.yml |
New CI workflow for automated testing across Python versions |
README.md |
Updated documentation to reference h5py instead of PyTables |
example/python-omx-sample.py |
Code formatting updates |
CHANGES.txt |
Added version 0.4.0 changelog entry |
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Author
Author
|
@billyc , any thoughts on this one? |
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Closes #12
It also adds a ton of software engineering practices, like CI/CD, modern packaging, etc.
Kudos to Jake Moss for the heavy lifting on this one.