2.0.0b2

A quality and robustness release on top of 2.0.0b1, focused on the density-profile bilayer fitting (mesh refinement and thickness measurement), a forgiving centralized config system, and packaging fixes.

Added

• Per-triangle bilayer_resolution score (0–1) in the thickness CSV — a reliability flag separating strictly-resolved leaflets from prior-recovered (slightly thin) measurements.
• morphometrics new_config --simple — a minimal, fully-runnable starter config (--verbose still gives the full annotated template).
• Centralized config defaults so partial/stripped configs run; per-command required-key validation with clean errors; trailing slashes on directory paths no longer required.
• Distance/orientation measurements default to all-vs-all when intra/inter are omitted.
• Plugins can contribute morphometrics subcommands via a morphometrics.commands entry point.
• GitHub Actions test workflow and unit tests.

Changed

• Dual-Gaussian bilayer fitting overhaul (refinement + thickness): height-above-base leaflet detection, shared-width centered fit over a symmetric window (removes a ~0.1 nm centering bias and the collapse failure mode), and a two-tier gate that recovers locally-merged bilayers from the global prior while rejecting genuine single/skewed peaks.
• Thickness measurement applies a real quality gate (resolution + R² + physical range), reporting NaN for unmeasurable triangles.
• accept_refinement falls back to a surface's last available iteration when it converged early.
• mesh_refinement defaults now match the documented template.
• export_obj: --angstroms → --scale_to_angstroms with config-aware units.

Fixed

• pycurv fork deadlock on Linux (OMP_NUM_THREADS=1).
• export_obj reads legacy/empty VTP surfaces.
• NumPy 2.x compatibility (np.trapz); deprecated matplotlib.cm.get_cmap.

Full changelog: https://github.com/GrotjahnLab/surface_morphometrics/blob/main/CHANGELOG.md

2.0.0b1

See CHANGELOG.MD for extensive breaking changes in 2.0 version.

v1.2

What's Changed

• Ensure compatibility with pymeshlab 2022.2.post3 by @m-albert in #26
• Update xyz2ply.py by @Kate-G-stem in #28
• Downgrade Python to 3.7.9 and adjust related dependencies by @hemanthkapa in #31
• Implemented Docker container and updated documentation by @hemanthkapa in #32
• fixing docker import pymeshlab error by @hemanthkapa in #34
• Fix description of point_weight config parameter by @m-albert in #37
• adding new dependancies for GUI by @hemanthkapa in #49
• Create quantifications_documentation.md by @hemanthkapa in #51
• Revert "Create quantifications_documentation.md" by @hemanthkapa in #52
• Initial Thickness Measurements by @bbarad in #53
• Fix pycurv multifile hang by @bbarad in #55
• Mesh refinement by @bbarad in #56

New Contributors

• @m-albert made their first contribution in #26
• @Kate-G-stem made their first contribution in #28
• @hemanthkapa made their first contribution in #31

Full Changelog: 1.1...1.2

v1.1

New version to support updated pymeshlab API and to deal with missing pyto dependencies.

1.0beta1

Beta release of 1.0 - needs installer testing and updated citation, but this will be the final "feature release" for Barad, Medina et al JCB 2023 paper.

v0.2

Version 0.2 is the fully pipelined and configurable version of the surface morphometrics pipeline. Tutorial data and config file included so you can really jump in! This is the version prepared in response to review, and I anticipate that v1.0 (released with the final manuscript) will look very similar to this (With some extra polishing of the visualization side of the workflow, and bugfixes of course)

v0.1

Scripts for implicit surface reconstruction, tensor-voting based curvature analysis, and morphometric quantification. Release includes final surface reconstruction workflow but incomplete visualizations and quantifications.