v0.2.2

edgePython 0.2.2\n\nThis release merges recent devel updates into main and includes:\n\n- Improved exact-test group pair handling and validation.\n- Optimized Cox-Reid adjustment in dispersion estimation:\n - fast 2x2 determinant path for common bulk designs,\n - LDL fallback for near-singular cases to preserve numerical parity.\n- Updated README badges and installation guidance (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 (from edgePython) (2.2.6)
Requirement already satisfied: scipy>=1.7 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from edgePython) (1.15.3)
Requirement already satisfied: pandas>=1.3 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from edgePython) (2.3.3)
Requirement already satisfied: matplotlib>=3.4 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from edgePython) (3.10.8)
Requirement already satisfied: statsmodels>=0.13 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from edgePython) (0.14.6)
Requirement already satisfied: numba>=0.57 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from edgePython) (0.63.1)
Requirement already satisfied: contourpy>=1.0.1 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from matplotlib>=3.4->edgePython) (1.3.2)
Requirement already satisfied: cycler>=0.10 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from matplotlib>=3.4->edgePython) (0.11.0)
Requirement already satisfied: fonttools>=4.22.0 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from matplotlib>=3.4->edgePython) (4.33.3)
Requirement already satisfied: kiwisolver>=1.3.1 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from matplotlib>=3.4->edgePython) (1.4.2)
Requirement already satisfied: packaging>=20.0 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from matplotlib>=3.4->edgePython) (26.0)
Requirement already satisfied: pillow>=8 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from matplotlib>=3.4->edgePython) (9.1.1)
Requirement already satisfied: pyparsing>=3 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from matplotlib>=3.4->edgePython) (3.3.2)
Requirement already satisfied: python-dateutil>=2.7 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from matplotlib>=3.4->edgePython) (2.8.2)
Requirement already satisfied: llvmlite<0.47,>=0.46.0dev0 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from numba>=0.57->edgePython) (0.46.0)
Requirement already satisfied: pytz>=2020.1 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from pandas>=1.3->edgePython) (2022.1)
Requirement already satisfied: tzdata>=2022.7 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from pandas>=1.3->edgePython) (2025.3)
Requirement already satisfied: patsy>=0.5.6 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from statsmodels>=0.13->edgePython) (1.0.2)
Requirement already satisfied: six>=1.5 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from python-dateutil>=2.7->matplotlib>=3.4->edgePython) (1.16.0)).\n\nThese updates improve robustness and maintain strong edgeR parity while keeping bulk runtime competitive.

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.