v1.0.0

MPP v1.0.0 — First stable release

Install via pip:

pip install mpp-lumping

Full documentation: https://moldyn.github.io/MPP/

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Highlights

• Documentation site — MkDocs Material site at https://moldyn.github.io/MPP/ with CLI, Python API, and Snakemake workflow guides
• Stable public API — MPP.Lumping, MPP.kernel.LumpingKernel, MPP.kernel.FeatureKernel
• src/ layout — package restructured to src/MPP/; core module renamed from MPP.py to lumping.py
• PyPI package — installable as mpp-lumping

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Changes since 0.9.1

Interface & UX

• Improved CLI argument descriptions, error messages, and validation (TASK-4.4)
• Standardized deterministic output directory structure and file naming (TASK-4.3)
• Resolved 11 cross-interface consistency issues between CLI, Python API, and Snakemake workflow (TASK-4.2)
• Aligned terminology across code, docs, and CLI (TASK-3.7)

Naming & Conventions

• YAML config keys migrated from space-separated to snake_case (e.g. microstate_trajectory, frame_length) — legacy keys still accepted with a deprecation warning (TASK-2.2)
• Kernel parameters renamed for clarity (TASK-2.3)
• Naming conventions documented and applied consistently across all interfaces (TASK-2.1)

Documentation

• NumPy-style docstrings added and standardized across all modules (TASK-3.1 – 3.4)
• Outdated and incorrect docstrings removed (TASK-3.6)
• CLI, Python API, and Snakemake usage guides added to docs/ (TASK-3.5)

Code Quality

• Dead code and unused imports removed (TASK-1.10)
• Line length and formatting enforced project-wide (TASK-1.11)
• Docstring formatting standardized to NumPy style (TASK-1.12)
• Deterministic regression test suite stabilized against scientific baselines (TASK-1.7 – 1.9)