FastMDAnalysis: Software for Automated Analysis of Molecular Dynamics Trajectories

Highlights

• Added Dihedral analysis with Ramachandran plots (including error bars and per-residue frame plots) and improved CLI support (e.g., --residues handling and aliases). (#16, #18, #19, #20)
• Added Fraction of Native Contacts (Q-value) analysis module. (Q-Value module + test discovery update)
• Improved MDS dimensionality reduction to robustly detect and adapt to scikit-learn API differences, avoiding deprecated parameters and handling multiple versions cleanly.

Analysis & plotting improvements

• Enhanced time-series/statistical reporting with compute_stat summaries; refined plot bounds and visual defaults. (#21)
• Improved clustering visualizations (layout/whitespace, dendrogram x-axis cleanup, label styling).
• Added adaptive plotting helpers for slide-ready figures and expanded plotting regression coverage (including slide style helpers).

Reliability & compatibility

• Major scikit-learn compatibility work for MDS: exhaustive parameter fallbacks, warning suppression, and version-robust behavior.
• Filtered pyparsing deprecation warnings originating from MDTraj; fixed pytest warning filtering to avoid failures across pyparsing versions.
• Increased test coverage across analyze helpers, plotting, options forwarding/passthrough, and specific analysis modules.

CLI & workflow

• Fixed CLI -o/--output flag issue. (#7)
• Added permissive options passthrough and test coverage for the options forwarder.

Documentation & metadata

• Documentation updates for plotting and outputs.
• Added CODE_OF_CONDUCT.md.
• Updated Zenodo DOI metadata (pyproject.toml, CITATION, README).