Rename/physiotwin4d (#79)

* Rename physiomotion4d package to physiotwin4d

Move src/physiomotion4d -> src/physiotwin4d and physiomotion4d_base.py ->
physiotwin4d_base.py, rename PhysioMotion4DBase -> PhysioTwin4DBase, and
update all imports, the shared logger name, pyproject.toml packaging
metadata (name, console scripts, project URLs, mypy/coverage/ruff config),
and tutorials/tests import statements accordingly.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* Rename PhysioMotion4D to PhysioTwin4D across docs, tutorials, experiments, and infra

Bulk text substitution across docs/, experiments/, utils/, .agents/,
.github/, .cursor/, data/, and root files (README, AGENTS.md, CLAUDE.md,
MANIFEST.in, statistics.md, .readthedocs.yaml). Also renames the internal
pm4d abbreviation to pt4d (Sphinx template placeholder and custom.css
classes/variables), regenerates docs/API_MAP.md, and bumps the stale
2026.05.07 version references in README.md, docs/changelog.rst, and
docs/PYPI_RELEASE_GUIDE.md to 2026.07.0.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

---------

Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>

Author: aylward

.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