ENH: Upaded AI agents for consistency and make physicsnemo optional (#60)

* ENH: Upaded AI agents for consistency and make physicsnemo optional

* BUG: Updated from review-pr skill

* STYLE: Typo in .gitignore

Author: aylward

.agents/agents/architecture.md

@@ -27,11 +27,18 @@ Use `docs/API_MAP.md` to locate classes and signatures without manual searching.
 
 ## Design invariants to preserve
 
-- `PhysioMotion4DBase` inheritance for all major classes.
+- `PhysioMotion4DBase` 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.
 - Image registerers follow: `set_fixed_image()` → `register(moving)` → dict with transforms.
 - ITK for images; PyVista for surfaces. Boundary is at contour extraction.
-- Coordinate system: RAS internally; Y-up only at USD export.
+- Coordinate system: LPS internally throughout (images and surfaces). Convert
+  to USD right-handed Y-up only at USD export via
+  `vtk_to_usd.lps_points_to_usd`.
+- Public entry point for VTK→USD is `ConvertVTKToUSD`. The `vtk_to_usd/`
+  subpackage is internal; experiments, CLIs, tests, and tutorials must not
+  import from it directly.
 
 ## Output format — always produce all six sections
 
@@ -42,4 +49,4 @@ Use `docs/API_MAP.md` to locate classes and signatures without manual searching.
 5. **Open questions** — decisions that need user input before coding starts.
 6. **Recommended next action** — one sentence.
 
-Flag any change at the ITK↔PyVista boundary or the RAS→Y-up transform as **high-risk**.
+Flag any change at the ITK↔PyVista boundary or the LPS→USD-Y-up transform as **high-risk**.

.agents/agents/implementation.md

@@ -26,18 +26,32 @@ Key modules: `physiomotion4d_base.py`, `segment_chest_*.py`, `register_images_*.
 
 ## Code rules
 
-- All classes inherit from `PhysioMotion4DBase`. New classes must too.
-- Use `self.log_info()` / `self.log_debug()` — never `print()`.
+- Runtime workflow / segmentation / registration / USD classes inherit from
+  `PhysioMotion4DBase`. Standalone scripts, data containers, and helper
+  classes do not.
+- In `PhysioMotion4DBase` 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.
+- Experiments, CLIs, tests, and tutorials must use `ConvertVTKToUSD`. Never
+  import directly from `vtk_to_usd` outside of `convert_vtk_to_usd.py` and
+  the `vtk_to_usd/` subpackage itself.
+- Scripts that instantiate `SegmentChestTotalSegmentator` must guard the
+  top-level invocation with `if __name__ == "__main__":` on Windows
+  (`torch.multiprocessing` requires it).
 - Single quotes for strings; double quotes for docstrings. 88-char line limit.
 - Full type hints; `Optional[X]` not `X | None` (mypy UP007 is suppressed).
 - `pathlib.Path` for all file paths. `subprocess.run(check=True, text=True)` — no `os.system`.
-- Run `ruff check . --fix && ruff format .` after every Python edit.
+- After every Python edit run `python -m ruff check . --fix && python -m ruff format .`
+  from the active `.\venv`.
 
 ## Data shapes — state them explicitly
 
 - ITK images: axes X, Y, Z [, T] in LPS world space (ITK's native frame).
 - 4D time series: shape `(X, Y, Z, T)`. Never silently squeeze or permute.
-- PyVista surfaces: RAS internally; Y-up only at USD export.
+- PyVista surfaces: LPS internally (inherited from `itk.vtk_image_from_image`).
+  Convert to USD right-handed Y-up only at USD export, via
+  `vtk_to_usd.lps_points_to_usd` (USD +X=Left, +Y=Superior, +Z=Anterior).
 - Name shape variables explicitly: `n_frames`, `spatial_shape`, not bare integer indices.
 
 ## What not to do

.agents/agents/testing.md

@@ -1,45 +1,68 @@
 ---
 name: PhysioMotion4D Testing Agent
-description: Writes and updates pytest tests for PhysioMotion4D. Prefers synthetic itk.Image and PyVista surfaces over real data, states tensor shapes explicitly, and uses baseline utilities for regression.
+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.
 tools: Read, Edit, Write, Bash, Glob, Grep
 ---
 
-You are a testing agent for PhysioMotion4D. Write correct, fast, synthetic-data-driven
-pytest tests that exercise the library's scientific pipelines.
+You are a testing agent for PhysioMotion4D. 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
+- `src/physiomotion4d/test_tools.py` — baseline comparison utilities (`TestTools`)
 - Markers (all opt-in via `--run-<bucket>`): `slow`, `requires_gpu`,
-  `requires_simpleware`, `experiment`, `tutorial`. Tests that need
-  downloadable data fetch it through the session fixtures and run by default.
-
-## Run commands (use `py`, not `python`)
-
-```bash
-py -m pytest tests/ -v                                        # fast, recommended (slow/GPU/etc auto-skipped)
-py -m pytest tests/test_contour_tools.py -v                   # single file
-py -m pytest tests/test_contour_tools.py::TestContourTools -v # single class
-py -m pytest tests/ -v --run-slow                             # opt into slow tests
-py -m pytest tests/ -v --run-gpu --run-slow                   # typical local GPU profile (CI runner adds --run-simpleware --run-experiments --run-tutorials)
-py -m pytest tests/ --create-baselines                        # create missing baselines
+  `requires_simpleware`, `experiment`, `tutorial`. The `requires_data` marker
+  no longer exists — tests that need downloadable data pull it through the
+  session fixtures and run by default.
+
+## Run commands
+
+Activate `.\venv` first (`.\venv\Scripts\Activate.ps1`); `python` then resolves
+to the project interpreter. If activation is impossible, use
+`.\venv\Scripts\python.exe -m ...` directly.
+
+```powershell
+python -m pytest tests/ -v                                        # fast, recommended (slow/GPU/etc auto-skipped)
+python -m pytest tests/test_contour_tools.py -v                   # single file
+python -m pytest tests/test_contour_tools.py::TestContourTools -v # single class
+python -m pytest tests/ -v --run-slow                             # opt into slow tests
+python -m pytest tests/ -v --run-gpu --run-slow                   # typical local GPU profile (CI runner adds --run-simpleware --run-experiments --run-tutorials)
+python -m pytest tests/ --create-baselines                        # create missing baselines
 ```
 
 ## Writing tests — rules
 
 1. Read the implementation file first; understand the public interface.
-2. Propose a test plan: what behaviors to cover, what synthetic data to create.
-3. Build synthetic `itk.Image` objects or small `pv.PolyData` surfaces — 32–64 voxels/side.
-   When real data is unavoidable, request the standard fixtures
-   (`test_directories`, `download_test_data`, `test_images`) — the data is
-   downloaded automatically on first use.
-4. State image shape and axis order in the test docstring:
-   e.g. `"""...image shape: (64, 64, 32), axes: X, Y, Z."""`
-5. Use `test_tools.py` baseline utilities for surface and image regression checks.
-6. One logical assertion per test where possible.
-7. Do not mock segmentation or registration models — test real outputs on synthetic data.
+2. Propose a test plan: what behaviors to cover, what inputs each needs.
+3. **Strongly prefer real downloaded test data over synthetic.** Request the
+   session fixtures `test_directories`, `download_test_data`, and
+   `test_images` so the standard datasets are fetched automatically on first
+   use. Real data exercises preprocessing, resampling, dtype handling, and
+   world-frame metadata paths that synthetic toy volumes silently bypass.
+4. Only fall back to synthetic `itk.Image` or `pv.PolyData` inputs when:
+   - the behavior under test is a pure unit (axis arithmetic, dict routing,
+     etc.) where real data adds no signal, or
+   - real data would push the test into a slow / GPU / Simpleware bucket
+     that does not fit the test's purpose.
+   When synthetic is unavoidable, keep volumes ≤64 voxels per side and say so
+   in the docstring.
+5. State image shape and axis order in every test docstring, e.g.
+   `"""...image shape: (X, Y, Z, T) = (64, 64, 32, 1), LPS world frame."""`.
+6. When a test produces an image or surface, compare against a baseline using
+   `test_tools.py` utilities (`TestTools`) rather than ad-hoc value asserts.
+   Store baselines under `tests/baselines/` (Git LFS-tracked).
+7. Prefer images from `ROOT/data/test/slicer_heart_small`.
+8. Prefer storing results in subdirectories under `./results/<test_name>`.
+9. Mark tests that need a GPU, slow runtime, or licensed Simpleware install
+   with `@pytest.mark.requires_gpu`, `@pytest.mark.slow`, or
+   `@pytest.mark.requires_simpleware`. Mark experiment and tutorial tests
+   with `@pytest.mark.experiment` or `@pytest.mark.tutorial`. Tests that just
+   need downloadable data need no marker.
+10. Do not mock segmentation or registration models — test real outputs.
+11. No emojis in test files (Windows cp1252 encoding has bitten this project).
 
 ## Naming
 

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

@@ -0,0 +1,76 @@
+---
+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.
+---
+
+Audit PhysioMotion4D source for hard-rule violations.
+
+$ARGUMENTS
+
+By default, audit every Python file modified since `HEAD`. If $ARGUMENTS names
+specific files or directories, audit those instead.
+
+## Determine the file set
+
+```powershell
+# Default: changed, non-deleted .py files since HEAD
+git diff --diff-filter=d --name-only HEAD -- '*.py'
+```
+
+If a path was passed in $ARGUMENTS, expand it to all `.py` files under that
+path (recursively). Skip files that no longer exist on disk.
+
+## Rules to check
+
+For each file, read the **entire file** (rules below depend on surrounding
+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`.
+- [ ] A `print(` call inside the body of a class that inherits from
+      `PhysioMotion4DBase` (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/`.
+      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.
+
+### Windows multiprocessing
+- [ ] A module-level instantiation of `SegmentChestTotalSegmentator` (or a
+      module-level call into it) that is not guarded by
+      `if __name__ == "__main__":`. Required on Windows because
+      `torch.multiprocessing` re-imports the module in child workers.
+
+### Code style
+- [ ] `X | None` in a type hint (use `Optional[X]`; ruff `UP007` is suppressed).
+- [ ] `Any` in a public signature without a comment explaining why.
+- [ ] A docstring delimited with `'''` (use `"""`).
+- [ ] A string literal using `"..."` for ordinary inline strings (use `'...'`;
+      docstrings stay on `"""`).
+- [ ] A line longer than 88 characters.
+- [ ] An emoji or other non-ASCII glyph inside a `.py` file (Windows cp1252
+      encoding has broken builds; keep emojis out of source).
+
+### Public API hygiene
+- [ ] A public method (no leading underscore) without a NumPy-style docstring.
+- [ ] An array / image parameter or return value whose docstring does not
+      state shape and axis order.
+
+## Output
+
+Group findings by file. For each finding, print:
+
+```text
+<path>:<line>  <rule short name>  <one-line excerpt>
+```
+
+End with a one-line summary: total findings per rule category.
+
+Do **not** auto-fix. The point is to surface violations the user can decide
+how to address. If `$ARGUMENTS` includes `--fix`, ask before mutating anything
+and limit fixes to the trivially mechanical rules (line length is not one of
+them — `ruff format` covers that).

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

@@ -0,0 +1,36 @@
+---
+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.
+---
+
+Regenerate the PhysioMotion4D API map and report what changed.
+
+$ARGUMENTS
+
+Instructions:
+
+1. Run the generator from the active `.\venv` (activate it first if needed,
+   or call `.\venv\Scripts\python.exe` directly):
+
+   ```powershell
+   python utils/generate_api_map.py
+   ```
+
+2. Inspect the diff:
+
+   ```powershell
+   git diff -- docs/API_MAP.md
+   ```
+
+3. Report one of:
+   - **No change** — public API surface is identical; nothing to commit.
+   - **Changed** — list each added, removed, or signature-modified entry
+     (class.method, file, one-line summary). Group by file.
+
+4. If `docs/API_MAP.md` changed, remind the user to stage it together with
+   the source changes that produced it so the API map never lags the code.
+
+5. Do not edit `docs/API_MAP.md` by hand. If the generator output looks wrong,
+   investigate `utils/generate_api_map.py` and the source it scans, not the
+   generated file.
+
+6. Do not commit. The user controls when to stage and commit.

.agents/skills/review-pr/SKILL.md

@@ -0,0 +1,84 @@
+---
+description: Screen a GitHub PR's review comments by invoking utils/ai_agent_github_reviews.py. Fetches inline threads and PR-level reviews via gh CLI, applies accepted edits as pending working-tree changes, resolves processed threads, and writes a Markdown summary tagged by PR number.
+---
+
+Process review comments on a GitHub PR using the project's PR-review driver.
+
+$ARGUMENTS
+
+## Usage shape
+
+`$ARGUMENTS` is typically just a PR number, optionally followed by flags
+forwarded to `utils/ai_agent_github_reviews.py`. Examples:
+
+- `/review-pr 42`
+- `/review-pr 42 --agent claude`
+- `/review-pr 42 --since-last-push`
+- `/review-pr 42 --prompt-only`
+- `/review-pr 42 --no-resolve`
+
+If `$ARGUMENTS` is empty, ask the user for the PR number before doing anything.
+
+## Preconditions
+
+1. Confirm `gh` is installed and authenticated:
+   ```powershell
+   gh auth status
+   ```
+   If not authenticated, stop and tell the user to run `gh auth login`.
+
+2. Confirm the current branch is **not** `main` and not detached. If it is,
+   warn the user — applied edits will land on whichever branch is checked
+   out. Ask before proceeding.
+
+3. Confirm the working tree has no unstaged Python edits the user would not
+   want mixed with applied review suggestions:
+   ```powershell
+   git status --short
+   ```
+   If there are pending changes, surface them and ask whether to continue.
+
+## Run
+
+Invoke the driver from the active `.\venv` (activate first if needed):
+
+```powershell
+python utils/ai_agent_github_reviews.py --pr <NUMBER> [flags...]
+```
+
+Defaults worth knowing:
+- `--agent codex` is the script default. Pass `--agent claude` to drive
+  Claude Code instead.
+- Without `--no-resolve`, every processed inline-comment thread is marked
+  resolved on GitHub after the agent finishes.
+- With `--since-last-push`, only comments posted after this clone last saw
+  the remote PR head branch move are included.
+- `--prompt-only` prints the prompt without invoking an agent or resolving
+  anything.
+
+## After the run
+
+1. Read `pr_<NUMBER>_review_summary.md` written to the repo root. Report:
+   - Total comments processed.
+   - APPLY / REVISE / REJECT counts.
+   - Any rejection that cited a hard rule from AGENTS.md.
+
+2. Show the resulting working-tree diff so the user can decide what to keep:
+   ```powershell
+   git diff --stat
+   git diff
+   ```
+
+3. Do **not** stage or commit. The script applies edits as pending
+   working-tree changes only; the user controls staging
+   (`git add -p`) and commit.
+
+4. Delete `pr_<NUMBER>_review_summary.md` after reporting — the working-tree
+   diff is the durable record; the summary is intermediate state.
+
+5. If the run failed:
+   - "gh CLI not found" → tell the user to install via
+     `winget install GitHub.cli` then `gh auth login`.
+   - "claude CLI not found" → tell the user to install via
+     `winget install Anthropic.ClaudeCode`, or retry with `--agent codex`.
+   - Any other error: surface the script's stderr verbatim and stop.

.github/workflows/README.md

@@ -144,12 +144,13 @@ GPU tests require self-hosted runners with:
 
 **Option 3: Run Locally**
 ```bash
-# Install with CUDA support
-uv pip install -e ".[test,cuda13]"
+# Install with CUDA + PhysicsNeMo (matches the self-hosted GPU runner).
+# Requires Python >= 3.11 (nvidia-physicsnemo does not support 3.10).
+uv pip install -e ".[test,cuda13,physicsnemo]"
 
 # Run GPU tests
-pytest tests/ -v -m "not slow"
-pytest tests/ -v -m "slow"  # For long-running tests
+pytest tests/ -v --run-gpu
+pytest tests/ -v --run-all  # Match CI: enable every --run-* bucket
 ```
 
 ### GitHub-Hosted Runners
@@ -217,14 +218,16 @@ pytest tests/ -m "unit and not requires_gpu" --cov=physiomotion4d
 
 ### GPU Tests
 ```bash
-# Install with CUDA support
-uv pip install -e ".[test,cuda13]"
+# Install with CUDA + PhysicsNeMo (matches the self-hosted GPU runner).
+# Requires Python >= 3.11 (nvidia-physicsnemo does not support 3.10).
+uv pip install -e ".[test,cuda13,physicsnemo]"
 
-# Run all tests (including GPU)
-pytest tests/ -m "not slow"
+# Run GPU tests
+pytest tests/ --run-gpu
 
-# Run slow tests
-pytest tests/ -m "slow"
+# Enable every --run-* bucket at once (slow, GPU, simpleware,
+# physicsnemo, experiments, tutorials)
+pytest tests/ --run-all
 ```
 
 ## Coverage Reports