ENH: Rename *_tools modules and classes to process_* naming convention (#139)

Standardize the object-first `*_tools.py`/`*Tools` naming used throughout
src/monai_physio/ to the verb-first convention used elsewhere in the project
(workflow_train_physicsnemo.py, register_images_ants.py,
segment_chest_total_segmentator.py).

contour_tools/ContourTools -> process_contours/ProcessContours, and similarly
for transform, test, image, physicsnemo, usd_anatomy, usd, labelmap, and
landmark tools. data_download_tools/DataDownloadTools -> download_data/
DownloadData as a naming exception.

Only import paths and PascalCase class names changed; lowercase instance
attributes and pytest fixtures (self.image_tools, the contour_tools fixture,
etc.) are unaffected. Corresponding Sphinx API pages and toctrees were moved
and retargeted to match.

Adds utils/rename_tools_to_process.py, a reusable git-mv + regex migration
script, and records the break in docs/developer/migration_next.md per
project policy.

Author: aylward

.agents/agents/architecture.md

@@ -22,10 +22,10 @@ src/monai_physio/
   segment_chest_*.py          - TotalSegmentator, VISTA-3D, NIM, Ensemble
   register_images_*.py        - ICON, ANTs, Greedy, time-series wrappers
   register_models_*.py        - ICP, PCA, distance-map registerers
-  contour_tools.py            - surface extraction from ITK masks
+  process_contours.py            - surface extraction from ITK masks
   convert_vtk_to_usd.py       - high-level VTK→USD (in-memory, PyVista)
   vtk_to_usd/                 - file-based VTK→USD subpackage
-  usd_tools.py / usd_anatomy_tools.py - USD stage utilities
+  process_usd.py / process_usd_anatomy.py - USD stage utilities
   workflow_*.py               - top-level orchestration
 ```
 

.agents/agents/implementation.md

@@ -19,7 +19,7 @@ tutorials may require a GPU.
 4D CT → Segmentation → Registration → Contour Extraction → USD Export
 
 Key modules: `monai_physio_base.py`, `segment_chest_*.py`, `register_images_*.py`,
-`register_models_*.py`, `contour_tools.py`, `convert_vtk_to_usd.py`, `vtk_to_usd/`,
+`register_models_*.py`, `process_contours.py`, `convert_vtk_to_usd.py`, `vtk_to_usd/`,
 `workflow_*.py`. Use `graphify query "<question>"` to locate classes before
 searching manually.
 

.agents/agents/testing.md

@@ -17,7 +17,7 @@ test off the GPU bucket.
 
 - `tests/conftest.py` - session-scoped fixtures chaining: download → convert → segment → register
 - `tests/baselines/` - stored via Git LFS; fetch with `git lfs pull`
-- `src/monai_physio/test_tools.py` - baseline comparison utilities (`TestTools`)
+- `src/monai_physio/process_tests.py` - baseline comparison utilities (`ProcessTests`)
 - Markers (all opt-in via `--run-<bucket>`): `slow`, `requires_gpu`,
   `requires_simpleware`, `tutorial`. The `requires_data` marker
   no longer exists - tests that need downloadable data pull it through the
@@ -32,7 +32,7 @@ to the project interpreter. If activation is impossible, use
 ```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/test_contour_tools.py::TestProcessContours -v # single class
 python -m pytest tests/ -v --run-slow                             # opt into slow tests
 # typical local GPU profile; CI adds --run-simpleware --run-tutorials
 python -m pytest tests/ -v --run-gpu --run-slow
@@ -59,7 +59,7 @@ python -m pytest tests/ --create-baselines                        # create missi
    those are fixed conventions. State only what is specific to the test, such
    as the size of a synthetic volume.
 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.
+   `process_tests.py` utilities (`ProcessTests`) 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>`.

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

@@ -25,7 +25,7 @@ Instructions:
    When using synthetic inputs anyway, keep volumes ≤64 voxels per side and
    say so in the docstring.
 5. **When a test produces an image or surface as output, compare against a
-   baseline** using the `test_tools.py` utilities (e.g. `TestTools`) rather
+   baseline** using the `process_tests.py` utilities (e.g. `ProcessTests`) rather
    than ad-hoc value assertions. Store baselines under `tests/baselines/`
    (Git LFS-tracked). Run with `--create-baselines` to materialize missing
    baselines on first use; afterward, regression compares to the stored

.github/scripts/build_dashboard.py

@@ -32,10 +32,9 @@
 import argparse
 import json
 import xml.etree.ElementTree as ET
-from datetime import datetime, timezone
+from datetime import UTC, datetime
 from pathlib import Path
 
-
 # ──────────────────────────────────────────────────────────────────────────────
 # Parsers
 # ──────────────────────────────────────────────────────────────────────────────
@@ -54,7 +53,7 @@ def parse_junit(xml_path: Path) -> dict:
         }
 
     try:
-        tree = ET.parse(xml_path)  # noqa: S314
+        tree = ET.parse(xml_path)
         root = tree.getroot()
 
         suites = root.findall("testsuite") if root.tag == "testsuites" else [root]
@@ -401,9 +400,7 @@ def main() -> None:
     output_dir = Path(args.output_dir)
     output_dir.mkdir(parents=True, exist_ok=True)
 
-    timestamp = args.timestamp or datetime.now(timezone.utc).strftime(
-        "%Y-%m-%dT%H:%M:%SZ"
-    )
+    timestamp = args.timestamp or datetime.now(UTC).strftime("%Y-%m-%dT%H:%M:%SZ")
 
     data = {
         "junit": parse_junit_dir(results_dir),

.github/workflows/README.md

@@ -197,21 +197,25 @@ Tests should be marked appropriately:
 ```python
 import pytest
 
+
 @pytest.mark.unit
 def test_simple_function():
     """Fast unit test"""
     pass
 
+
 @pytest.mark.integration
 def test_full_pipeline():
     """Integration test"""
     pass
 
+
 @pytest.mark.slow
 def test_long_running():
     """Long-running test"""
     pass
 
+
 @pytest.mark.requires_gpu
 def test_gpu_function():
     """Test requiring GPU"""

AGENTS.md

@@ -249,7 +249,7 @@ graphify update .               # refresh after code changes (AST-only, no API c
   those are fixed conventions (see Data Conventions above). State only what is
   specific to the test, such as the size of a synthetic volume.
 - When a test produces an image or surface, compare against a baseline using
-  `src/monai_physio/test_tools.py` utilities such as `TestTools`.
+  `src/monai_physio/process_tests.py` utilities such as `ProcessTests`.
 - Store baselines under `tests/baselines/`, which is tracked by Git LFS. Run
   `git lfs pull` after cloning.
 - Run with `--create-baselines` to materialize missing baselines on first use.

CLAUDE.md

@@ -156,7 +156,7 @@ came from.
 - Baselines in `tests/baselines/` via Git LFS - run `git lfs pull` after cloning
 - `tests/conftest.py`: session-scoped fixtures chaining
   download → convert → segment → register
-- `src/monai_physio/test_tools.py`: baseline comparison utilities (`TestTools`, etc.)
+- `src/monai_physio/process_tests.py`: baseline comparison utilities (`ProcessTests`, etc.)
 - Markers (all opt-in via `--run-<bucket>`): `slow`, `requires_gpu`,
   `requires_simpleware`, `tutorial`. Data-dependent tests no
   longer use a marker - they pull data through fixtures and run by default.

CONTRIBUTING.md

@@ -228,6 +228,7 @@ Add tests in the `tests/` directory:
 import pytest
 from monai_physio import MyNewFeature
 
+
 def test_my_feature():
     feature = MyNewFeature()
     result = feature.do_something()

data/CHOP-Valve4D/README.md

@@ -11,10 +11,10 @@ monai-physio-download-data CHOP-Valve4D --directory data/CHOP-Valve4D
 or from Python:
 
 ```python
-from monai_physio import DataDownloadTools
+from monai_physio import DownloadData
 
-DataDownloadTools.DownloadCHOPValve4DData("data/CHOP-Valve4D")
-assert DataDownloadTools.VerifyCHOPValve4DData("data/CHOP-Valve4D")
+DownloadData.DownloadCHOPValve4DData("data/CHOP-Valve4D")
+assert DownloadData.VerifyCHOPValve4DData("data/CHOP-Valve4D")
 ```
 
 This downloads and extracts three zip archives attached to the