Merge main and align python layout

Author: Morningliumengkun

.github/workflows/test.yml

@@ -0,0 +1,38 @@
+name: Tests
+
+on:
+  push:
+    branches: [ main, feat/* ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      run: uv python install ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: uv sync --dev
+
+    - name: Run tests with coverage
+      run: uv run pytest --verbose --cov=bpdecoderplus --cov-report=xml --cov-report=term
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        files: ./coverage.xml
+        flags: unittests
+        name: codecov-umbrella
+        fail_ci_if_error: false

.gitignore

@@ -1,9 +1,34 @@
-__pycache__/
-*.pyc
+# macOS
 .DS_Store
+
+# Jupyter
 .ipynb_checkpoints/
+
+# Julia
 Manifest.toml
+
+# IDE
 .vscode/
+.idea/
+
+# Python
+.venv/
+__pycache__/
+*.py[cod]
+*$py.class
+*.egg-info/
+dist/
+build/
+.eggs/
+*.egg
+.pytest_cache/
+.coverage
+coverage.xml
+htmlcov/
+.uv/
+uv.lock
+
+# LaTeX
 *.aux
 *.fls
 *.log

Makefile

@@ -0,0 +1,37 @@
+.PHONY: help install setup test test-cov generate-dataset clean
+
+help:
+	@echo "Available targets:"
+	@echo "  install          - Install uv package manager"
+	@echo "  setup            - Set up development environment with uv"
+	@echo "  generate-dataset - Generate noisy circuit dataset"
+	@echo "  test             - Run tests"
+	@echo "  test-cov         - Run tests with coverage report"
+	@echo "  clean            - Remove generated files and caches"
+
+install:
+	@command -v uv >/dev/null 2>&1 || { \
+		echo "Installing uv..."; \
+		curl -LsSf https://astral.sh/uv/install.sh | sh; \
+	}
+
+setup: install
+	uv sync --dev
+
+generate-dataset:
+	uv run generate-noisy-circuits --distance 3 --p 0.01 --rounds 3 5 7 --task z --output datasets/noisy_circuits
+
+test:
+	uv run pytest
+
+test-cov:
+	uv run pytest --cov=bpdecoderplus --cov-report=html --cov-report=term
+
+clean:
+	rm -rf .pytest_cache
+	rm -rf __pycache__
+	rm -rf htmlcov
+	rm -rf .coverage
+	rm -rf coverage.xml
+	find . -type d -name "__pycache__" -exec rm -rf {} + 2>/dev/null || true
+	find . -type f -name "*.pyc" -delete