Add pytest configuration and CI infrastructure to prevent module import errors

.github/workflows/ci-audit.yml

@@ -0,0 +1,113 @@
+name: CI Audit - Tests and Code Quality
+
+on:
+  push:
+    branches: [ main, develop ]
+  pull_request:
+    branches: [ main, develop ]
+
+# Set minimal permissions for GITHUB_TOKEN
+permissions:
+  contents: read
+
+jobs:
+  test:
+    name: Run Tests
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11"]
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive  # Initialize any git submodules if present
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+
+          # Install test dependencies
+          pip install pytest pytest-cov pytest-xdist
+
+          # Install GA_denoise_selector dependencies
+          if [ -f GA_denoise_selector/requirements.txt ]; then
+            pip install -r GA_denoise_selector/requirements.txt
+          fi
+
+          # Install Mamba-SSM-Denoise dependencies
+          if [ -f Mamba-SSM-Denoise/Track_H_cross_validation/requirements.txt ]; then
+            pip install -r Mamba-SSM-Denoise/Track_H_cross_validation/requirements.txt
+          fi
+
+          # Install GA_smoother_classic dependencies  
+          if [ -f GA_smoother_classic/requirements.txt ]; then
+            pip install -r GA_smoother_classic/requirements.txt
+          fi
+
+      - name: Set PYTHONPATH
+        run: |
+          echo "PYTHONPATH=$PYTHONPATH:$(pwd):$(pwd)/GA_denoise_selector:$(pwd)/Mamba-SSM-Denoise/Track_H_cross_validation:$(pwd)/GA_smoother_classic" >> $GITHUB_ENV
+
+      - name: Run tests
+        run: |
+          # Export PYTHONPATH for pytest (belt and suspenders approach)
+          export PYTHONPATH=$PYTHONPATH:$(pwd):$(pwd)/GA_denoise_selector:$(pwd)/Mamba-SSM-Denoise/Track_H_cross_validation:$(pwd)/GA_smoother_classic
+
+          # Run tests with quick marker if available, otherwise run all tests
+          if grep -r "pytest.mark.quick" tests/ 2>/dev/null; then
+            pytest tests -m "quick" --maxfail=1 --cov=GA_denoise_selector/smoothers --cov=Mamba-SSM-Denoise/Track_H_cross_validation/src --cov-report=term --cov-report=html
+          else
+            pytest tests --maxfail=1 --cov=GA_denoise_selector/smoothers --cov=Mamba-SSM-Denoise/Track_H_cross_validation/src --cov-report=term --cov-report=html
+          fi
+
+      - name: Upload coverage reports
+        uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: coverage-report-${{ matrix.python-version }}
+          path: htmlcov/
+          retention-days: 30
+
+  lint:
+    name: Code Quality Checks
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install linting tools
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 black isort mypy
+
+      - name: Run flake8
+        continue-on-error: true
+        run: |
+          # Stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # Exit-zero treats all errors as warnings
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+      - name: Check code formatting with black
+        continue-on-error: true
+        run: |
+          black --check --diff .
+
+      - name: Check import ordering with isort
+        continue-on-error: true
+        run: |
+          isort --check-only --diff .

.gitignore

@@ -0,0 +1,93 @@
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyTorch
+*.pth
+*.pt
+checkpoints/
+runs/
+lightning_logs/
+
+# Testing
+.pytest_cache/
+.coverage
+.coverage.*
+htmlcov/
+.tox/
+.nox/
+coverage.xml
+*.cover
+.hypothesis/
+pytest_cache/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+*.ipynb
+
+# Environment
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# IDEs
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+.DS_Store
+
+# Data
+*.csv
+*.h5
+*.hdf5
+*.pkl
+*.pickle
+data/
+datasets/
+output/
+outputs/
+results/
+
+# Logs
+*.log
+logs/
+tensorboard/
+
+# Git submodules (if any future submodules are added)
+external/
+
+# Temporary files
+tmp/
+temp/
+*.tmp
+
+# OS-specific
+.DS_Store
+Thumbs.db

README.md

@@ -3,3 +3,58 @@
 This repository collects quick experiments and reusable components for transformer architectures and state-space model (SSM) projects. Expect lightweight prototypes, training scripts, and utility code that make it easy to compare and iterate on modern sequence modeling ideas.
 
 Jump in, explore the models, and use the pieces that help you move faster on your own AI workflows.
+
+## Projects
+
+- **GA_denoise_selector**: Genetic algorithm-based smoother selection with 13+ filter implementations
+- **Mamba-SSM-Denoise**: Deep learning denoising using Mamba state-space models
+- **GA_smoother_classic**: Classic genetic algorithm smoother implementation
+
+## Testing
+
+This repository includes a test infrastructure to ensure code quality and prevent import errors.
+
+### Running Tests
+
+```bash
+# Install test dependencies
+pip install pytest pytest-cov
+
+# Run all tests
+pytest tests/
+
+# Run quick tests only
+pytest tests/ -m "quick"
+
+# Run with coverage
+pytest tests/ --cov=GA_denoise_selector/smoothers --cov=Mamba-SSM-Denoise/Track_H_cross_validation/src
+```
+
+### Configuration
+
+- **pytest configuration**: `setup.cfg` - Configures Python path for all projects
+- **Test directory**: `tests/` - All test files
+- **CI/CD**: `.github/workflows/ci-audit.yml` - Automated testing on push/PR
+
+For more details, see [tests/README.md](tests/README.md).
+
+## Development
+
+### Prerequisites
+
+Each project has its own dependencies. Install them as needed:
+
+```bash
+# GA_denoise_selector
+pip install -r GA_denoise_selector/requirements.txt
+
+# Mamba-SSM-Denoise
+pip install -r Mamba-SSM-Denoise/Track_H_cross_validation/requirements.txt
+
+# GA_smoother_classic
+pip install -r GA_smoother_classic/requirements.txt
+```
+
+### Python Path
+
+The repository uses a multi-project structure. When importing modules, the Python path is configured via `setup.cfg` to include all project directories. This prevents `ModuleNotFoundError` issues in tests.

setup.cfg

@@ -0,0 +1,38 @@
+[tool:pytest]
+# Configure pytest to find source modules for all projects
+pythonpath = 
+    .
+    GA_denoise_selector
+    Mamba-SSM-Denoise/Track_H_cross_validation
+    GA_smoother_classic
+
+# Test discovery patterns
+testpaths = tests
+python_files = test_*.py
+python_classes = Test*
+python_functions = test_*
+
+# Custom markers
+markers =
+    quick: marks tests as quick (deselect with '-m "not quick"')
+
+# Coverage configuration
+[coverage:run]
+source = 
+    GA_denoise_selector/smoothers
+    Mamba-SSM-Denoise/Track_H_cross_validation/src
+
+omit =
+    */tests/*
+    */test_*.py
+    */__pycache__/*
+
+[coverage:report]
+exclude_lines =
+    pragma: no cover
+    def __repr__
+    raise AssertionError
+    raise NotImplementedError
+    if __name__ == '__main__':
+    if TYPE_CHECKING:
+    @abstractmethod