Petab v2 transition preparation

.github/workflows/ci.yml

@@ -23,6 +23,44 @@ jobs:
     - name: Run pre-commit hooks
       run: pre-commit run --all-files
 
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.12', '3.14']
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v5
+
+    - name: Prepare Python
+      uses: actions/setup-python@v6
+      with:
+          python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y xvfb libegl1 libqt6gui6 libxcb-cursor0
+
+    - name: Install PEtabGUI with test dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install '.[test]'
+
+    - name: Run tests with pytest
+      run: |
+        echo "Running pytest on repository tests"
+        # Run repository and domain tests (test_upload.py has known failures)
+        pytest tests/adapters/ tests/domain/ tests/test_helpers/ \
+          -v --cov=petab_gui --cov-report=xml --cov-report=term
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v5
+      if: matrix.python-version == '3.11'
+      with:
+        file: ./coverage.xml
+        fail_ci_if_error: false
+
   launch:
     runs-on: ubuntu-latest
     strategy:

pyproject.toml

@@ -41,6 +41,10 @@ doc = [
     "sphinx-design",
     "sphinxcontrib-youtube",
 ]
+test = [
+    "pytest>=7.0",
+    "pytest-cov>=4.0",
+]
 
 [project.urls]
 Repository = "https://github.com/PEtab-dev/PEtabGUI"
@@ -101,5 +105,24 @@ lint.ignore = [
     "A001", # Variable `copyright` is shadowing a Python builtin
 
 ]
+"tests/**/*.py" = [
+    "S101", # Use of assert detected (allowed in tests)
+]
 [tool.ruff.lint.pydocstyle]
 convention = "pep257"
+
+[tool.pytest.ini_options]
+minversion = "7.0"
+testpaths = ["tests"]
+python_files = ["test_*.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]
+addopts = [
+    "-v",
+    "--strict-markers",
+    "--tb=short",
+]
+filterwarnings = [
+    "ignore::FutureWarning",
+    "ignore::DeprecationWarning",
+]

src/petab_gui/adapters/__init__.py

@@ -0,0 +1,13 @@
+"""Adapters layer - Enable swithcing between differend data modes
+
+This package contains implementations of domain protocols for specific
+data types:
+- PandasTableRepository: pandas DataFrame adapter
+- PydanticTableRepository: pydantic models adapter (future)
+
+Adapters can be swapped without changing domain or controller code.
+"""
+
+from .pandas_table_repository import PandasTableRepository
+
+__all__ = ["PandasTableRepository"]