v0.2.4

What's Changed

• Add fast options to estimate_disp
• Fix estimate_disp crash when called without a design matrix (integer group labels were being mishandled due to drop_empty_levels returning a pd.Categorical)
• Revert pair index change that broke exact_test with integer group labels

v0.2.3

What's Changed

• Validate nonnegative dispersion in GLM fitting
• Harden numerical edge cases in GLM and dispersion paths
• Remove external kallisto H5 test dependency

v0.2.2

edgePython 0.2.2

This release merges recent devel updates into main and includes:

Improvements

• Improved exact-test group pair handling and validation.
• Optimized Cox–Reid adjustment in dispersion estimation:
  • Fast 2×2 determinant path for common bulk designs.
  • LDL fallback for near-singular cases to preserve numerical parity with edgeR.

Documentation

• Updated README badges and installation guidance.

Example Installation Output

Requirement already satisfied: edgePython in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (0.1.0)
Requirement already satisfied: numpy>=1.21 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (2.2.6)
Requirement already satisfied: scipy>=1.7 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (1.15.3)
Requirement already satisfied: pandas>=1.3 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (2.3.3)
Requirement already satisfied: matplotlib>=3.4 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (3.10.8)
Requirement already satisfied: statsmodels>=0.13 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (0.14.6)
Requirement already satisfied: numba>=0.57 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (0.63.1)
Requirement already satisfied: contourpy>=1.0.1 (1.3.2)
Requirement already satisfied: cycler>=0.10 (0.11.0)
Requirement already satisfied: fonttools>=4.22.0 (4.33.3)
Requirement already satisfied: kiwisolver>=1.3.1 (1.4.2)
Requirement already satisfied: packaging>=20.0 (26.0)
Requirement already satisfied: pillow>=8 (9.1.1)
Requirement already satisfied: pyparsing>=3 (3.3.2)
Requirement already satisfied: python-dateutil>=2.7 (2.8.2)
Requirement already satisfied: llvmlite<0.47,>=0.46.0dev0 (0.46.0)
Requirement already satisfied: pytz>=2020.1 (2022.1)
Requirement already satisfied: tzdata>=2022.7 (2025.3)
Requirement already satisfied: patsy>=0.5.6 (1.0.2)
Requirement already satisfied: six>=1.5 (1.16.0)

**Full Changelog**: https://github.com/pachterlab/edgePython/compare/v0.2.1...v0.2.2

edgePython v0.2.1

edgePython 0.2.1

What's new

• Added full voom workflow support, including voom, voom_lmfit, voom_basic, array_weights, and duplicate_correlation.
• Added robust GLM dispersion estimation with estimate_glm_robust_disp (estimateGLMRobustDisp compatibility alias).
• Improved dispersion parity with edgeR by matching Cox-Reid adjustment behavior more closely (LDL-style factorization path), reducing BCV discrepancies.
• Expanded test coverage with dedicated voom tests and R parity checks.

Documentation and MCP updates

• Updated docs/api.yaml to document voom and robust GLM dispersion APIs.
• Updated MCP server with:
  • robust GLM dispersion tool support,
  • voom transform tool support,
  • DTU tool support for diff_splice_dge and splice_variants,
  • updated workflow guidance and status reporting.

Examples

• Refreshed the main example notebooks in examples/ with updated outputs.
• Added explicit DE count reporting in the mammary R-vs-Python notebook output.

v0.2.0

First release of edgePython.