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FastMDXplora v2.1.0

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@ainaadekunle ainaadekunle released this 01 Aug 20:01
· 1365 commits to main since this release
v2.1.0
7172cf6

FastMDXplora 2.1.0

A graphical interface, publication-ready figures, and Python 3.13 support.
An exploration can now be designed, launched, watched, and reviewed from a
browser, and the figures it produces are drawn for print.

Added

  • Graphical interface. fastmdx gui opens a local browser interface with
    sections for building an exploration, starting it, watching it run, viewing
    the structure and trajectory, browsing analyses, and reaching the report.
  • Config files from the GUI. The builder can save its selection as a
    FastMDXplora .yml file instead of starting a run, so an exploration
    designed in the browser can be submitted anywhere, including on a cluster
    where the GUI cannot run. The GUI guide documents the rsync pattern for
    watching a cluster job from a workstation.
  • Live telemetry. A dependency-free localhost server that watches an
    output directory while an exploration is in progress: phase progress, live
    trajectory frames, an interactive 3D molecular viewer with playback, and
    per-analysis charts. It observes and starts explorations; it does not
    reimplement any phase science.
  • Report content in the GUI. Summary cards, per-phase progress including
    phases that did not run, trajectory statistics with means and standard
    deviations, categorised analysis sections, and quick-action links. These are
    computed once and shown identically in the browser and in the report.
  • v1 analysis compatibility profile (--compat v1): reproduces the
    scope, selection, stride, analysis set, and per-analysis options of the
    published BPTI case study from FastMDXplora version 1.
  • PDB smoke campaign (scripts/run_pdb_smoke_campaign.py) for exercising
    the pipeline across many structures.
  • Report additions: region highlights and a single-figure run summary.
  • Python 3.13 support across the whole supported range (3.9 to 3.13).
  • Documentation: a beginner's guide, a CLI reference, a GUI guide, a
    production-run guide, region-highlight and smoke-campaign pages, and a
    substantially expanded installation guide.

Changed

  • Publication-ready figures. The palette is now Okabe-Ito, which stays
    distinguishable under common colour vision deficiencies and in greyscale;
    the previous palette's red and green converged in both. Axes are closed with
    inward major and minor ticks, and tick density adapts to each panel's
    physical size, so long trajectories no longer crowd their axes. Legends get
    a translucent backing and headroom so they stay readable over dense data.
  • One interface module. All user-interface code now lives in
    fastmdxplora.gui: the localhost server, the browser application and its
    assets, and the static dashboard written into a report. Both surfaces share
    one set of design tokens and display the same figures.
  • Explorer nomenclature throughout. An exploration is started rather than a
    job launched: Start Exploration in the interface, /api/explore/*
    endpoints, fastmdxplora.gui.exploration in the Python API, and exploration
    wording in the terminal.
  • Each analysis has its own section. Sections used to be merged when they
    held three figures or fewer, so an analysis appeared under its own name or a
    catch-all depending on how many plots that run produced.
  • The startup banner is one left-aligned block; info carries the version,
    authors, DOI, phase availability, and backend status.
  • CI runs on Python 3.9 through 3.13 across Linux, macOS, and Windows, with
    actions updated to Node 24 compatible versions.
  • STRUCTURE.md rewritten to match the current tree.

Fixed

  • Simulation robustness, with clearer diagnostics when an integration step
    produces a NaN.
  • Batch early-stop behaviour when an exploration fails.
  • Report-only invocation and phase validation.
  • Windows: path comparison, server port reuse, and platform-specific commands.
  • The CLI degrades cleanly when the chemistry backends are absent rather than
    failing mid-phase.
  • The startup banner printed twice, and advertised a GUI address even when no
    GUI was running.
  • Figures were listed twice, once for the PNG and once for the SVG of the same
    plot.
  • CLI tests asserted the exit code of a machine without OpenMM, so they passed
    in CI and failed on a working install.
  • Documentation examples are covered by drift tests so they cannot go stale.

Removed

  • The bundled installer and repository doctor. Installation now follows
    standard routes: pip for analysis and reporting, pip plus conda-forge for the
    full chemistry stack, or a clone with the bundled environment.yml.
  • The dashboard subcommand; fastmdx gui --output DIR opens the same
    interface pointed at an existing run.
  • The curated chart pipeline, which redrew 17 figures in a second style that
    nothing displayed once both surfaces settled on the analysis figures.
  • The live pressure metric. OpenMM's StateDataReporter cannot supply it, so
    the card could only ever read zero; the barostat setpoint remains in the run
    summary.
  • driftmd_workbench, a separate package that duplicated the analysis and
    report pipeline without using it.

Install

pip install fastmdxplora

For the full four-phase workflow you also need the chemistry stack:

conda install -c conda-forge openmm pdbfixer openmmforcefields

See the installation guide.

Links

Citation

Aina, A.; Kwan, D. FastMDAnalysis: Software for Automated Analysis of Molecular Dynamics Trajectories. J. Comput. Chem. 2026, 47, e70350. DOI: 10.1002/jcc.70350

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