Milestones
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mkdocs-material docs site + mkdocstrings API docs, tutorials/notebooks (headline: compare apo vs holo), PyPI + conda-forge packaging, mypy/ruff pre-commit, codecov coverage, stable semver public API, Zenodo DOI per release. See ROADMAP.md sections 6-7.
No due daterich CLI (progress bars, tables, pretty --plan), 'mdforge config init' scaffolder, user-extensible detection dictionaries (custom lipid/ion/ligand resnames), missing-hydrogen handling for H-bond analyses, benchmark suite + performance regression guard. See ROADMAP.md section 6.
No due dateDihedral-PCA (dPCA), linear mutual-information DCCM (nonlinear coupling), porcupine mode plots, optional Markov State Models (deeptime: implied timescales, macrostates), water analyses (residence time, bridging waters, hydration density), interactive plotly HTML reports (zoom/hover/collapsible). See ROADMAP.md section 6.
No due dateMembrane suite (area-per-lipid, bilayer thickness, S_CD order parameters, lipid-protein contacts, insertion depth/tilt). Multi-engine support (AMBER prmtop/nc, NAMD psf/dcd, CHARMM, OpenMM) via MDAnalysis. Validate & ship interface/ligand/nucleic modules with committed fixture trajectories + golden-file CI. Chunked streaming reader default for solvent analyses. See ROADMAP.md sections 4.3, 6.
No due dateFlagship 'mdforge compare' — overlay control vs protein-ligand / protein-protein on shared axes: delta-RMSF maps, common-subspace PCA, FEL/DCCM/contact difference maps, KS/Welch/Cohen statistics, ensemble similarity (CES/DRES/HES). Plus FrameAnalysis lifecycle + parallel --threads backend, functional mdforge.compute API, content-addressed cache/resume, 'mdforge reproduce', and expanded options (reference/units/frames/selections). See ROADMAP.md sections 3, 4.1-4.2, 5, 6.
No due date