Rename/physiotwin4d

.agents/agents/architecture.md

@@ -1,17 +1,17 @@
 ---
-name: PhysioMotion4D Architecture Agent
-description: Analyzes the PhysioMotion4D codebase and produces numbered design plans with trade-offs. Does not write implementation code. Flags coordinate-system and ITK/PyVista boundary risks.
+name: PhysioTwin4D Architecture Agent
+description: Analyzes the PhysioTwin4D codebase and produces numbered design plans with trade-offs. Does not write implementation code. Flags coordinate-system and ITK/PyVista boundary risks.
 tools: Read, Bash, Glob, Grep
 ---
 
-You are an architecture agent for PhysioMotion4D. Analyze the codebase and produce
+You are an architecture agent for PhysioTwin4D. Analyze the codebase and produce
 clear numbered design plans with explicit trade-offs. Do not write implementation code.
 
 ## Codebase map
 
 ```text
-src/physiomotion4d/
-  physiomotion4d_base.py      — base class with shared logger
+src/physiotwin4d/
+  physiotwin4d_base.py      — base class with shared logger
   segment_anatomy_base.py     — abstract segmentation interface
   segment_chest_*.py          — TotalSegmentator, VISTA-3D, NIM, Ensemble
   register_images_*.py        — ICON, ANTs, Greedy, time-series wrappers
@@ -27,7 +27,7 @@ Use `docs/API_MAP.md` to locate classes and signatures without manual searching.
 
 ## Design invariants to preserve
 
-- `PhysioMotion4DBase` inheritance for runtime workflow / segmentation /
+- `PhysioTwin4DBase` inheritance for runtime workflow / segmentation /
   registration / USD classes. Helper, data-container, and standalone-script
   classes do not inherit.
 - Segmenters return anatomy group masks with consistent label IDs.

.agents/agents/docs.md

@@ -1,10 +1,10 @@
 ---
-name: PhysioMotion4D Docs Agent
-description: Updates docstrings, inline comments, and docs/API_MAP.md for PhysioMotion4D. Keeps claims factual, states image shapes explicitly, and does not create new .md files.
+name: PhysioTwin4D Docs Agent
+description: Updates docstrings, inline comments, and docs/API_MAP.md for PhysioTwin4D. Keeps claims factual, states image shapes explicitly, and does not create new .md files.
 tools: Read, Edit, Bash, Glob, Grep
 ---
 
-You are a documentation agent for PhysioMotion4D. Keep docstrings, type annotations,
+You are a documentation agent for PhysioTwin4D. Keep docstrings, type annotations,
 and the API map accurate and concise.
 
 ## Scope

.agents/agents/implementation.md

@@ -1,17 +1,17 @@
 ---
-name: PhysioMotion4D Implementation Agent
-description: Implements features, bug fixes, or refactors in PhysioMotion4D. Reads source first, summarizes current behavior, proposes a numbered plan, then implements in small diffs. Calls out breaking changes.
+name: PhysioTwin4D Implementation Agent
+description: Implements features, bug fixes, or refactors in PhysioTwin4D. Reads source first, summarizes current behavior, proposes a numbered plan, then implements in small diffs. Calls out breaking changes.
 tools: Read, Edit, Write, Bash, Glob, Grep
 ---
 
-You are an implementation agent for PhysioMotion4D, an early-alpha scientific Python library
+You are an implementation agent for PhysioTwin4D, an early-alpha scientific Python library
 that converts 4D CT scans into animated USD models for NVIDIA Omniverse.
 
 ## Pipeline
 
 4D CT → Segmentation → Registration → Contour Extraction → USD Export
 
-Key modules: `physiomotion4d_base.py`, `segment_chest_*.py`, `register_images_*.py`,
+Key modules: `physiotwin4d_base.py`, `segment_chest_*.py`, `register_images_*.py`,
 `register_models_*.py`, `contour_tools.py`, `convert_vtk_to_usd.py`, `vtk_to_usd/`,
 `workflow_*.py`. Use `docs/API_MAP.md` to locate classes before searching manually.
 
@@ -27,9 +27,9 @@ Key modules: `physiomotion4d_base.py`, `segment_chest_*.py`, `register_images_*.
 ## Code rules
 
 - Runtime workflow / segmentation / registration / USD classes inherit from
-  `PhysioMotion4DBase`. Standalone scripts, data containers, and helper
+  `PhysioTwin4DBase`. Standalone scripts, data containers, and helper
   classes do not.
-- In `PhysioMotion4DBase` subclasses use `self.log_info()` / `self.log_debug()`,
+- In `PhysioTwin4DBase` subclasses use `self.log_info()` / `self.log_debug()`,
   never `print()`. Standalone scripts may use `print()`.
 - No emojis in `.py` files. Windows cp1252 has bitten this project; keep
   emojis out of code and minimize them in docs.

.agents/agents/testing.md

@@ -1,18 +1,18 @@
 ---
-name: PhysioMotion4D Testing Agent
-description: Writes and updates pytest tests for PhysioMotion4D. Strongly prefers real downloaded data via session fixtures, states tensor shapes explicitly, and uses baseline utilities for regression.
+name: PhysioTwin4D Testing Agent
+description: Writes and updates pytest tests for PhysioTwin4D. Strongly prefers real downloaded data via session fixtures, states tensor shapes explicitly, and uses baseline utilities for regression.
 tools: Read, Edit, Write, Bash, Glob, Grep
 ---
 
-You are a testing agent for PhysioMotion4D. Write correct pytest tests that
+You are a testing agent for PhysioTwin4D. Write correct pytest tests that
 exercise the library's scientific pipelines using real downloaded data
 wherever practical.
 
 ## Test architecture
 
 - `tests/conftest.py` — session-scoped fixtures chaining: download → convert → segment → register
 - `tests/baselines/` — stored via Git LFS; fetch with `git lfs pull`
-- `src/physiomotion4d/test_tools.py` — baseline comparison utilities (`TestTools`)
+- `src/physiotwin4d/test_tools.py` — baseline comparison utilities (`TestTools`)
 - Markers (all opt-in via `--run-<bucket>`): `slow`, `requires_gpu`,
   `requires_simpleware`, `experiment`, `tutorial`. The `requires_data` marker
   no longer exists — tests that need downloadable data pull it through the

.agents/skills/check-conventions/SKILL.md

@@ -1,8 +1,8 @@
 ---
-description: Audit changed files (or a given path) against PhysioMotion4D's hard project rules — base-class inheritance, logging, coordinate conventions, USD entry point, Windows multiprocessing guard, quoting, type-hint style, line length, and emoji ban. Reports violations without auto-fixing.
+description: Audit changed files (or a given path) against PhysioTwin4D's hard project rules — base-class inheritance, logging, coordinate conventions, USD entry point, Windows multiprocessing guard, quoting, type-hint style, line length, and emoji ban. Reports violations without auto-fixing.
 ---
 
-Audit PhysioMotion4D source for hard-rule violations.
+Audit PhysioTwin4D source for hard-rule violations.
 
 $ARGUMENTS
 
@@ -26,15 +26,15 @@ context such as class inheritance), then flag every occurrence of:
 
 ### Base class and logging
 - [ ] A class that orchestrates workflow / segmentation / registration / USD
-      conversion but does **not** inherit from `PhysioMotion4DBase`.
+      conversion but does **not** inherit from `PhysioTwin4DBase`.
 - [ ] A `print(` call inside the body of a class that inherits from
-      `PhysioMotion4DBase` (it must use `self.log_info()` / `self.log_debug()`).
+      `PhysioTwin4DBase` (it must use `self.log_info()` / `self.log_debug()`).
       Standalone scripts and helper / data-container classes may use `print()`.
 
 ### USD / coordinate conventions
-- [ ] An `import` of `physiomotion4d.vtk_to_usd` (or `from ... vtk_to_usd ...`)
-      from a file that is **not** `src/physiomotion4d/convert_vtk_to_usd.py`
-      and is **not** itself inside `src/physiomotion4d/vtk_to_usd/`.
+- [ ] An `import` of `physiotwin4d.vtk_to_usd` (or `from ... vtk_to_usd ...`)
+      from a file that is **not** `src/physiotwin4d/convert_vtk_to_usd.py`
+      and is **not** itself inside `src/physiotwin4d/vtk_to_usd/`.
       Experiments, CLIs, tests, and tutorials must use `ConvertVTKToUSD`.
 - [ ] A docstring or comment claiming PyVista surfaces are in **RAS** — they
       are in **LPS** internally; convert to USD Y-up only at export.

.agents/skills/commit/SKILL.md

@@ -2,7 +2,7 @@
 description: Stage all tracked modifications and deletions, draft a commit message from the diff, fix any pre-commit hook failures, and repeat until the commit succeeds.
 ---
 
-Commit all tracked pending changes in the PhysioMotion4D repository
+Commit all tracked pending changes in the PhysioTwin4D repository
 (equivalent to `git commit -a`, excluding new untracked files).
 
 $ARGUMENTS

.agents/skills/doc-feature/SKILL.md

@@ -1,8 +1,8 @@
 ---
-description: Inspect changed PhysioMotion4D code and existing docstrings, update docstrings and inline comments with accurate shape/axis information, and regenerate docs/API_MAP.md if public APIs changed.
+description: Inspect changed PhysioTwin4D code and existing docstrings, update docstrings and inline comments with accurate shape/axis information, and regenerate docs/API_MAP.md if public APIs changed.
 ---
 
-Update documentation for the following in PhysioMotion4D:
+Update documentation for the following in PhysioTwin4D:
 
 $ARGUMENTS
 

.agents/skills/impl/SKILL.md

@@ -1,8 +1,8 @@
 ---
-description: Read relevant PhysioMotion4D source files, summarize current behavior, propose a brief plan, then implement the requested feature or refactor in small diffs. Calls out breaking changes.
+description: Read relevant PhysioTwin4D source files, summarize current behavior, propose a brief plan, then implement the requested feature or refactor in small diffs. Calls out breaking changes.
 ---
 
-Implement the following in the PhysioMotion4D repository:
+Implement the following in the PhysioTwin4D repository:
 
 $ARGUMENTS
 

.agents/skills/plan/SKILL.md

@@ -1,8 +1,8 @@
 ---
-description: Inspect PhysioMotion4D source files, summarize the current design, and produce a numbered implementation plan with open questions. Does not write code unless explicitly asked.
+description: Inspect PhysioTwin4D source files, summarize the current design, and produce a numbered implementation plan with open questions. Does not write code unless explicitly asked.
 ---
 
-Analyze the following and produce a design plan for the PhysioMotion4D repository.
+Analyze the following and produce a design plan for the PhysioTwin4D repository.
 
 Task: $ARGUMENTS
 

.agents/skills/regen-api-map/SKILL.md

@@ -1,8 +1,8 @@
 ---
-description: Regenerate docs/API_MAP.md from the current source tree and report whether the public API surface changed. Run after editing any public class, method, or function signature in src/physiomotion4d.
+description: Regenerate docs/API_MAP.md from the current source tree and report whether the public API surface changed. Run after editing any public class, method, or function signature in src/physiotwin4d.
 ---
 
-Regenerate the PhysioMotion4D API map and report what changed.
+Regenerate the PhysioTwin4D API map and report what changed.
 
 $ARGUMENTS
 

.agents/skills/test-feature/SKILL.md

@@ -1,8 +1,8 @@
 ---
-description: Inspect a PhysioMotion4D implementation and its existing tests, propose a real-data-driven test plan with baseline comparisons, then create or update pytest tests. Explains how to run them.
+description: Inspect a PhysioTwin4D implementation and its existing tests, propose a real-data-driven test plan with baseline comparisons, then create or update pytest tests. Explains how to run them.
 ---
 
-Write or update tests for the following in PhysioMotion4D:
+Write or update tests for the following in PhysioTwin4D:
 
 $ARGUMENTS
 

.cursor/rules/project-standards.mdc

@@ -1,9 +1,9 @@
 ---
-description: PhysioMotion4D project standards and workflow preferences
+description: PhysioTwin4D project standards and workflow preferences
 alwaysApply: true
 ---
 
-# PhysioMotion4D Project Standards
+# PhysioTwin4D Project Standards
 
 ## File Operations
 

.github/scripts/build_dashboard.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
-Build the nightly health dashboard for PhysioMotion4D.
+Build the nightly health dashboard for PhysioTwin4D.
 
 Reads JUnit XML test results and coverage JSON from --results-dir,
 generates an HTML dashboard (index.html), a shields.io-compatible
@@ -11,7 +11,7 @@
     python .github/scripts/build_dashboard.py \\
         --results-dir results/ \\
         --output-dir dashboard/ \\
-        --run-url "https://github.com/Project-MONAI/physiomotion4d/actions/runs/123" \\
+        --run-url "https://github.com/Project-MONAI/physiotwin4d/actions/runs/123" \\
         --timestamp "2026-03-31T07:05:42Z" \\
         --health-outcome "success"
 
@@ -205,11 +205,11 @@ def build_html(data: dict) -> str:
 <head>
 <meta charset="UTF-8">
 <meta name="viewport" content="width=device-width,initial-scale=1">
-<title>PhysioMotion4D — Nightly Health</title>
+<title>PhysioTwin4D — Nightly Health</title>
 <style>{_CSS}</style>
 </head>
 <body>
-<h1>PhysioMotion4D &mdash; Nightly Health</h1>
+<h1>PhysioTwin4D &mdash; Nightly Health</h1>
 <p class="sub">
   Last run: {ts_display}&nbsp;&middot;&nbsp;
   <span class="badge {badge_class}">{badge_label}</span>&nbsp;&middot;&nbsp;
@@ -240,11 +240,11 @@ def build_html(data: dict) -> str:
 
 <footer>
   Generated by the
-  <a href="https://github.com/Project-MONAI/physiomotion4d/actions/workflows/nightly-health.yml"
+  <a href="https://github.com/Project-MONAI/physiotwin4d/actions/workflows/nightly-health.yml"
      target="_blank" rel="noopener">nightly-health</a> workflow
   &middot;
-  <a href="https://github.com/Project-MONAI/physiomotion4d"
-     target="_blank" rel="noopener">physiomotion4d</a>
+  <a href="https://github.com/Project-MONAI/physiotwin4d"
+     target="_blank" rel="noopener">physiotwin4d</a>
 </footer>
 </body>
 </html>
@@ -260,7 +260,7 @@ def build_status_json(data: dict) -> dict:
     """Return a shields.io dynamic endpoint object.
 
     Usage in README:
-        ![Health](https://img.shields.io/endpoint?url=https://project-monai.github.io/physiomotion4d/status.json)
+        ![Health](https://img.shields.io/endpoint?url=https://project-monai.github.io/physiotwin4d/status.json)
     """
     junit = data["junit"]
 
@@ -313,7 +313,7 @@ def build_summary_md(data: dict) -> str:
         status_text = "Passing"
 
     lines = [
-        f"# {status_icon} PhysioMotion4D Nightly Health — {ts_display}",
+        f"# {status_icon} PhysioTwin4D Nightly Health — {ts_display}",
         "",
         f"**Status:** {status_text} &nbsp; | &nbsp; [View run]({run_url})",
         "",
@@ -354,7 +354,7 @@ def build_summary_md(data: dict) -> str:
 
 def main() -> None:
     parser = argparse.ArgumentParser(
-        description="Build PhysioMotion4D nightly health dashboard"
+        description="Build PhysioTwin4D nightly health dashboard"
     )
     parser.add_argument(
         "--results-dir",

.github/workflows/README.md

@@ -213,7 +213,7 @@ pip install -e ".[test]"
 pytest tests/ -m "unit and not requires_gpu"
 
 # Run with coverage
-pytest tests/ -m "unit and not requires_gpu" --cov=physiomotion4d
+pytest tests/ -m "unit and not requires_gpu" --cov=physiotwin4d
 ```
 
 ### GPU Tests

.github/workflows/ci.yml

@@ -111,12 +111,12 @@ jobs:
       if: matrix.os == 'ubuntu-latest'
       run: |
         xvfb-run -a --server-args="-screen 0 1024x768x24" \
-          pytest tests/ -v --cov=physiomotion4d --cov-report=xml --cov-report=term --cov-report=html
+          pytest tests/ -v --cov=physiotwin4d --cov-report=xml --cov-report=term --cov-report=html
 
     - name: Run unit tests (fast, no GPU/slow/experiment) - Windows
       if: matrix.os == 'windows-latest'
       run: |
-        pytest tests/ -v --cov=physiomotion4d --cov-report=xml --cov-report=term --cov-report=html
+        pytest tests/ -v --cov=physiotwin4d --cov-report=xml --cov-report=term --cov-report=html
 
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v4
@@ -220,29 +220,29 @@ jobs:
 
     - name: Run data download tests
       run: |
-        pytest tests/test_download_heart_data.py -v --cov=physiomotion4d --cov-report=xml
+        pytest tests/test_download_heart_data.py -v --cov=physiotwin4d --cov-report=xml
       continue-on-error: true
 
     - name: Run data conversion tests
       run: |
-        pytest tests/test_convert_image_4d_to_3d.py -v --cov=physiomotion4d --cov-append --cov-report=xml
+        pytest tests/test_convert_image_4d_to_3d.py -v --cov=physiotwin4d --cov-append --cov-report=xml
       continue-on-error: true
 
     - name: Run contour tools tests
       run: |
-        pytest tests/test_contour_tools.py -v --cov=physiomotion4d --cov-append --cov-report=xml
+        pytest tests/test_contour_tools.py -v --cov=physiotwin4d --cov-append --cov-report=xml
       continue-on-error: true
 
     - name: Run USD conversion tests
       run: |
         xvfb-run -a --server-args="-screen 0 1024x768x24" \
-          pytest tests/test_convert_vtk_to_usd_polymesh.py -v --cov=physiomotion4d --cov-append --cov-report=xml
+          pytest tests/test_convert_vtk_to_usd_polymesh.py -v --cov=physiotwin4d --cov-append --cov-report=xml
       continue-on-error: true
 
     - name: Run USD utility tests
       run: |
         xvfb-run -a --server-args="-screen 0 1024x768x24" \
-          pytest tests/test_usd_merge.py tests/test_usd_time_preservation.py -v --cov=physiomotion4d --cov-append --cov-report=xml
+          pytest tests/test_usd_merge.py tests/test_usd_time_preservation.py -v --cov=physiotwin4d --cov-append --cov-report=xml
       continue-on-error: true
 
     - name: Run all integration tests
@@ -285,8 +285,8 @@ jobs:
       # Python 3.11 is required because the [physicsnemo] extra pulls in
       # nvidia-physicsnemo, which requires Python >= 3.11.
       run: |
-        & "C:\Program Files\Python311\python.exe" -m venv "$env:RUNNER_TEMP\physiomotion4d-venv"
-        echo "$env:RUNNER_TEMP\physiomotion4d-venv\Scripts" >> $env:GITHUB_PATH
+        & "C:\Program Files\Python311\python.exe" -m venv "$env:RUNNER_TEMP\physiotwin4d-venv"
+        echo "$env:RUNNER_TEMP\physiotwin4d-venv\Scripts" >> $env:GITHUB_PATH
 
     - name: Check GPU availability
       run: nvidia-smi
@@ -340,7 +340,7 @@ jobs:
       # aren't met on the runner will runtime-skip cleanly via their
       # internal availability guards.
       run: |
-        pytest tests/ -v --run-all --cov=physiomotion4d --cov-report=xml --cov-report=term --cov-report=html
+        pytest tests/ -v --run-all --cov=physiotwin4d --cov-report=xml --cov-report=term --cov-report=html
       env:
         CUDA_VISIBLE_DEVICES: 0
 

.github/workflows/nightly-health.yml

@@ -13,7 +13,7 @@ name: Nightly Health
 # documentation site published by docs.yml.  Use the workflow status badge
 # for a live pass/fail indicator in README:
 #
-#   [![Nightly Health](https://github.com/Project-MONAI/physiomotion4d/actions/workflows/nightly-health.yml/badge.svg)](https://github.com/Project-MONAI/physiomotion4d/actions/workflows/nightly-health.yml)
+#   [![Nightly Health](https://github.com/Project-MONAI/physiotwin4d/actions/workflows/nightly-health.yml/badge.svg)](https://github.com/Project-MONAI/physiotwin4d/actions/workflows/nightly-health.yml)
 
 on:
   schedule:
@@ -58,8 +58,8 @@ jobs:
         # Python 3.11 is required because the [physicsnemo] extra pulls in
         # nvidia-physicsnemo, which requires Python >= 3.11.
         run: |
-          & py -m venv "$env:RUNNER_TEMP\physiomotion4d-venv"
-          echo "$env:RUNNER_TEMP\physiomotion4d-venv\Scripts" >> $env:GITHUB_PATH
+          & py -m venv "$env:RUNNER_TEMP\physiotwin4d-venv"
+          echo "$env:RUNNER_TEMP\physiotwin4d-venv\Scripts" >> $env:GITHUB_PATH
 
       - name: Cache uv packages
         uses: actions/cache@v4
@@ -113,7 +113,7 @@ jobs:
         continue-on-error: true
         run: |
           pytest tests/ -v --run-all `
-            --cov=physiomotion4d `
+            --cov=physiotwin4d `
             --cov-report=xml `
             --cov-report=json `
             --junitxml=test-results.xml