Updates on Voxel-S Dosimetry Pipeline

.github/workflows/ci.yml

@@ -28,4 +28,4 @@ jobs:
         run: pre-commit run --all-files
 
       - name: Run pytest
-        run: pytest
+        run: pytest -rs

.gitignore

@@ -129,6 +129,8 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
+# VS Code settings
+.vscode
 
 # Other
 Notebooks
@@ -137,4 +139,5 @@ pytheranostics/local
 pytheranostics/.vscode
 
 pytheranostics/data/s-values
-pytheranostics/data/ICRP_phantom_masses
+pytheranostics/data/ICRP_phantom_masses
+pytheranostics/data/voxel_kernels

CONTRIBUTING.md

@@ -99,6 +99,9 @@ Once your environment is set up, you can use these commands:
 # Run all tests
 pytest
 
+# Run the external voxel dosimetry validation test before opening a PR
+pytest tests/test_voxel_dosimetry_validation.py -rs
+
 # Run only smoke tests (fast)
 pytest -m smoke
 
@@ -121,6 +124,13 @@ pre-commit run --all-files
 pytest -m smoke && black --check . && isort --check-only . && flake8 && mypy pytheranostics
 ```
 
+The voxel dosimetry validation test downloads the SNMMI Deep Blue dataset and
+RT-STRUCT files from Zenodo. GitHub Actions may skip this test if Deep Blue
+rejects CI-hosted downloads, so contributors should run it locally before
+opening a pull request. Outside CI, SNMMI data-fetch failures are treated as
+test failures rather than skips. Zenodo RT-STRUCT download or validation
+failures are always test failures when the validation test runs.
+
 ### Type Checking with Mypy
 
 Mypy is configured in `pyproject.toml` to be development-friendly (ignores missing imports by default). For focused development:

docs/source/tutorials/Data_Ingestion_Examples/Data_Ingestion_Examples.ipynb

@@ -25,7 +25,7 @@
     "# Imports\n",
     "from pathlib import Path\n",
     "import pytheranostics as tx\n",
-    "from pytheranostics.ImagingDS.dicom_ingest import auto_setup_dosimetry_study, extract_patient_metadata\n",
+    "from pytheranostics.imaging_ds.dicom_ingest import auto_setup_dosimetry_study, extract_patient_metadata\n",
     "\n",
     "print('PyTheranostics version:', getattr(tx, '__version__', 'unknown'))"
    ]
@@ -201,8 +201,14 @@
   }
  ],
  "metadata": {
+  "kernelspec": {
+   "display_name": ".pyThera-DBG",
+   "language": "python",
+   "name": "python3"
+  },
   "language_info": {
-   "name": "python"
+   "name": "python",
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,