Bump version 2026.05.07 -> 2026.05.8

[aylward]

PhysioMotion4D 2026.5.8 — Initial PyPI Release

PhysioMotion4D generates anatomic models with physiological motion in NVIDIA Omniverse from 4D medical images. This is the first beta release on PyPI; the package is ready for evaluation, research, and visualization workflows but is not validated for clinical use.

What's included

End-to-end pipeline

A complete 4D CT → USD pipeline composed of small, focused modules:

4D CT → segmentation → registration → contour extraction → USD export

All public classes inherit from PhysioMotion4DBase for unified logging and debug controls.

Workflows

• WorkflowConvertHeartGatedCTToUSD — full cardiac CT → animated USD pipeline.
• WorkflowCreateStatisticalModel — build a PCA statistical shape model from a population of meshes.
• WorkflowFitStatisticalModelToPatient — fit a PCA model to a patient image or surface.

Segmentation

• SegmentChestTotalSegmentator — AI-based chest segmentation via TotalSegmentator (nnUNetv2).
• SegmentHeartSimpleware — wraps Simpleware ASCardio for cardiac segmentation (external license required).
• SegmentAnatomyBase — extensible base class, now driven by the new AnatomyTaxonomy data type that both segmenters and renderers consume.

Registration

• Image-to-image: RegisterImagesICON (deep-learning, GPU), RegisterImagesANTs (classical SyN), RegisterTimeSeriesImages (4D series).
• Model-to-image / model-to-model: RegisterModelsPCA, RegisterModelsICP, RegisterModelsDistanceMaps.

VTK ↔ USD

• High-level: ConvertVTKToUSD — the recommended entry point for experiments, CLIs, tutorials, and tests. Supports time-series animation, anatomical labeling, colormap visualization, automatic topology-change detection, and both surface and volumetric meshes.
• Low-level: physiomotion4d.vtk_to_usd subpackage (advanced users only) — convert_vtk_file(), MeshData, ConversionSettings, MaterialData, MaterialManager, and an add_framing_camera() helper that authors a look-at camera respecting the stage up axis.
• USDTools provides USD inspection, merging, and a load_usd_as_vtk() round-tripping helper.
• USDAnatomyTools paints anatomy meshes with surgical-style materials driven by the shared AnatomyTaxonomy.

CLI commands

Seven installable console commands:

• physiomotion4d-convert-ct-to-vtk
• physiomotion4d-heart-gated-ct
• physiomotion4d-convert-vtk-to-usd
• physiomotion4d-create-statistical-model
• physiomotion4d-fit-statistical-model-to-patient
• physiomotion4d-reconstruct-highres-4d-ct
• physiomotion4d-visualize-pca-modes

Tutorials and examples

• Nine end-to-end tutorial scripts under tutorials/ covering each major workflow.
• 35 percent-cell (# %%) experiment scripts under experiments/ for research and exploratory work.
• All scripts run either as plain python <script>.py or interactively cell-by-cell in VS Code / Cursor .

Other quality-of-life features

• Calendar versioning via bumpver.
• Trusted-publishing release pipeline (GitHub Actions → PyPI, no token in repo).
• Sphinx documentation at https://project-monai.github.io/physiomotion4d/.
• Test suite with baseline regression comparison; Git LFS for binary baselines.

Installation

# CPU-only — works out of the box
pip install physiomotion4d

# CUDA 13 (recommended for production)
uv pip install "physiomotion4d[cuda13]"

The [cuda13] extra installs CuPy. In uv-managed source environments, PyTorch (torch, torchvision, torchaudio) resolves from the CUDA 13.0 wheel index automatically.

Compatibility

• Python: 3.11 or 3.12
• OS: Linux (Ubuntu 20.04+) and Windows 10/11
• GPU (optional but recommended): NVIDIA GPU with CUDA 13 support (e.g. RTX 3090+) for AI segmentation, ICON registration, and reconstruction
• Visualization: NVIDIA Omniverse, USD-aware viewers, or any OpenUSD-compatible 3D tool

Known limitations

• Some tutorial datasets (DirLab-4DCT, KCL-Heart-Model, CHOP-Valve4D) must be downloaded manually; only Slicer-Heart-CT downloads automatically.
• Headless rendering for tests on Windows hosted CI is disabled (no software OpenGL fallback). Linux runners use Xvfb + Mesa.
• API may change between beta releases as the project stabilizes.

Documentation

• Home: https://project-monai.github.io/physiomotion4d/
• Quickstart, tutorials, CLI guide, API reference, developer guides are all linked from the documentation home.

License

Apache-2.0.

Acknowledgments

PhysioMotion4D builds on excellent open work: MONAI, DirLab, TotalSegmentator, Icon-Registration / UniGradICON, ITK, TubeTK, VTK / PyVista, OpenUSD, and ANTs.

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Disclaimer: PhysioMotion4D is a research and visualization toolkit. It is not a medical device and must not be used for diagnosis, treatment planning, or clinical decision-making.

Summary by CodeRabbit

• Chores
  • Package version updated to 2026.05.8.

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No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 4a56d2b2-55c1-4a37-a041-8a76b586d2c1

📥 Commits

Reviewing files that changed from the base of the PR and between 2c9ffa7 and 7530ef7.

📒 Files selected for processing (2)

• pyproject.toml
• src/physiomotion4d/__init__.py

---

Walkthrough

Package version updated from 2026.05.07 to 2026.05.8 across three metadata locations: the project version field, bumpver configuration, and the public __version__ variable.

Changes

Version Number Synchronization

Layer / File(s)	Summary
Version metadata update pyproject.toml, src/physiomotion4d/__init__.py	Version string synchronized to 2026.05.8 in the project metadata ([project].version), bumpver configuration ([tool.bumpver].current_version), and the public package __version__ variable.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~2 minutes

Poem

🐰 A hop, a bump, a number's change,
From .07 to .8, a simple range,
Three places marked, now in sync,
The version flows without a blink! ✨

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The pull request title accurately describes the main change: bumping the package version from 2026.05.07 to 2026.05.8 in pyproject.toml and init.py.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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• Create PR with unit tests

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[Copilot]

Pull request overview

Routine calendar-version bump from 2026.05.07 to 2026.05.8, updating the version string in the package __init__.py and pyproject.toml (including the bumpver current_version). The bumpver pattern YYYY.0M.PATCH[PYTAGNUM] uses an unpadded PATCH, so the new 8 is consistent with the configured pattern, and PEP 440 normalization keeps ordering correct (2026.5.8 > 2026.5.7).

Changes:

• Bump __version__ in src/physiomotion4d/__init__.py.
• Bump project.version and tool.bumpver.current_version in pyproject.toml.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

File	Description
src/physiomotion4d/init.py	Updates package __version__ to 2026.05.8.
pyproject.toml	Updates project version and bumpver current_version to 2026.05.8.

---

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 29.64%. Comparing base (2c9ffa7) to head (7530ef7).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

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  Coverage   29.64%   29.64%           
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  Files          48       48           
  Lines        6611     6611           
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  Hits         1960     1960           
  Misses       4651     4651           

Flag	Coverage Δ
unittests	29.64% <100.00%> (ø)

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