Create python-app.yml

.github/workflows/python-app.yml

@@ -0,0 +1,57 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python application
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.11"
+    - name: Install Poetry
+      uses: snok/install-poetry@v1.4.1
+      with:
+        version: 2.1.1
+        virtualenvs-create: true
+    - name: Configure poetry
+      run: |
+        poetry config virtualenvs.in-project true
+
+    - name: Poetry Cache
+      uses: actions/cache@v4
+      id: poetry-cache
+      with:
+        path: .venv
+        key: venv-${{ hashFiles('**/poetry.lock', '**/pyproject.toml') }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        poetry install --no-root
+        pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 --exclude=.venv/ . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 --exclude=.venv/ . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        poetry install --no-root
+        poetry run python -m pip list
+        poetry run python -m pytest

gen_inroom_rtss.py

@@ -9,7 +9,7 @@
 from typing import Dict, List
 
 import numpy as np
-from pydicom import Dataset, Sequence, read_file, uid, write_file
+from pydicom import Dataset, Sequence, dcmread as read_file, uid, dcmwrite as write_file
 
 #  Copied and modified from ImageLoading.py from OnkoDICOM, which was LGPL 2.1 at the time
 

pyproject.toml

@@ -9,10 +9,19 @@ license = "Apache-2.0"
 readme = "README.md"
 requires-python = ">=3.11"
 dependencies = [
-    "pydicom >=3.0.1",
-    "numpy >= 2.2.3"
+    "pydicom ~=3.0.1",
+    "numpy ~= 2.2.3"
 ]
+package-mode = false
 
 [build-system]
 requires = ["poetry-core>=2.0"]
 build-backend = "poetry.core.masonry.api"
+
+[tool.pytest]
+testpaths = ["rtregistrationcalc/tests"]
+python_files = "test_*.py"
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^8.3.5"
+pytest-cov = "^6.0.0"

test_gen_inroom_rtss.py

@@ -16,7 +16,7 @@ def test_valid_orientation_and_position(self):
 
     # Handles empty or incomplete orientation and position lists gracefully
     def test_empty_or_incomplete_lists(self):
-        with pytest.raises(IndexError):
+        with pytest.raises((IndexError, ValueError)):
             img_stack_displacement([], [])
-        with pytest.raises(IndexError):
+        with pytest.raises((IndexError, ValueError)):
             img_stack_displacement(["1.0", "0.0"], ["0.0"])