minor updates to v0.8.1 for compatability with numpy 2.0+ and pandas 2.0+ #267
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This file provides comprehensive guidance for future Claude Code instances working with the HyperTools codebase, including: - Key commands for testing, development, and documentation - High-level architecture overview and data flow - Core component descriptions and design patterns - Testing strategy and development notes 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <noreply@anthropic.com>
The test was failing because t-SNE's default perplexity (30) was larger than the number of samples (10) in the test data. Fixed by explicitly setting perplexity=5 which is less than the sample count. This ensures the test passes while maintaining the same test coverage for t-SNE dimensionality reduction functionality. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <noreply@anthropic.com>
Critical fixes: - Replace deprecated pkg_resources with importlib.metadata in config.py - Fix scipy.stats.stats.pearsonr import to use scipy.stats.pearsonr - Add comprehensive compatibility review tracking in notes/ All 129 tests pass with numpy 2.0.2 and pandas 2.2.3. The codebase is now fully compatible with: - NumPy ≥ 2.0.0 (already specified in requirements.txt) - Pandas ≥ 2.2.0 (already specified in requirements.txt) - Python 3.9+ (as specified in setup.py) 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <noreply@anthropic.com>
Features: - Test matrix across Python 3.9, 3.10, 3.11, 3.12 - Cross-platform testing: Ubuntu, Windows, macOS - Dependency caching for faster builds - System dependencies (FFmpeg) installation - Coverage reporting on Ubuntu Python 3.12 - Parallel execution with fail-fast disabled - Triggers on push/PR to master and dev branches The workflow runs 12 parallel jobs (4 Python versions × 3 OS) to ensure comprehensive compatibility testing across all supported environments. Also added importlib_metadata fallback dependency for Python < 3.8 compatibility in requirements.txt. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <noreply@anthropic.com>
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Pull Request Overview
This PR updates compatibility with NumPy 2.0+ and pandas 2.0+ and adds a GitHub Actions CI workflow.
- Tests: updated
test_reduce_TSNEto use the newreducedict signature - Code: fixed deprecated imports (
scipy.stats.stats,pkg_resources) - CI: added GitHub Actions workflow and related documentation files
Reviewed Changes
Copilot reviewed 7 out of 8 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| tests/test_reduce.py | Updated TSNE test to use reduce={'model': ..., 'params': {...}} |
| hypertools/tools/describe.py | Changed import from scipy.stats.stats to scipy.stats |
| hypertools/config.py | Switched from pkg_resources to importlib.metadata for version |
| notes/numpy_pandas_compatibility_review.csv | Added compatibility notes for NumPy 2.0+ and pandas 2.0+ |
| notes/github_actions_info.md | Documented GitHub Actions CI/CD setup |
| .github/workflows/test.yml | Added GitHub Actions workflow for tests and coverage reporting |
| CLAUDE.md | Added AI guidance documentation |
Comments suppressed due to low confidence (3)
tests/test_reduce.py:95
- Consider adding tests for other
reducealgorithms with parameter dicts and edge cases to ensure the new API signature is consistently handled across different configurations.
reduced_data_3d = reducer(data, reduce={'model': 'TSNE', 'params': {'perplexity': 5}}, ndims=3)
.github/workflows/test.yml:50
- The
continue-on-error: truesetting for Windows ffmpeg installation may mask failures and lead to inconsistent test environments; consider removing it to surface installation issues.
continue-on-error: true
tests/test_reduce.py:95
- [nitpick] The inline nested dict for
reducearguments is verbose; consider extracting it into a named variable or fixture to improve readability and reuse.
reduced_data_3d = reducer(data, reduce={'model': 'TSNE', 'params': {'perplexity': 5}}, ndims=3)
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also added github actions tests (they run automatically on pull requests to master or dev)