Fix empty instance handling #1435
Workflow file for this run
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| name: CI | |
| on: | |
| pull_request: | |
| types: [opened, reopened, synchronize] | |
| paths: | |
| - "sleap_nn/**" | |
| - "tests/**" | |
| - ".github/workflows/ci.yml" | |
| - "pyproject.toml" | |
| jobs: | |
| lint: | |
| name: Lint | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Set up uv | |
| uses: astral-sh/setup-uv@v5 | |
| with: | |
| enable-cache: false | |
| - name: Set up Python | |
| run: uv python install 3.13 | |
| - name: Install dev dependencies and torch | |
| run: uv sync --extra dev --extra torch-cpu | |
| - name: Run Black | |
| run: uv run black --check sleap_nn tests | |
| - name: Run Ruff | |
| run: uv run ruff check sleap_nn/ | |
| tests: | |
| timeout-minutes: 30 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu", "windows", "mac", "self-hosted-gpu"] | |
| include: | |
| - os: ubuntu | |
| runs-on: ubuntu-latest | |
| - os: windows | |
| runs-on: windows-latest | |
| - os: mac | |
| runs-on: macos-14 | |
| - os: self-hosted-gpu | |
| runs-on: [self-hosted, puma, gpu, 2xgpu] | |
| python: [3.13] | |
| name: Tests (${{ matrix.os }}, Python ${{ matrix.python }}) | |
| runs-on: ${{ matrix.runs-on }} | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Set up uv | |
| uses: astral-sh/setup-uv@v5 | |
| with: | |
| enable-cache: false | |
| - name: Set up Python (non-self-hosted GPU) | |
| if: matrix.os != 'self-hosted-gpu' | |
| run: uv python install ${{ matrix.python }} | |
| - name: Install dev dependencies and torch (self-hosted GPU) | |
| if: matrix.os == 'self-hosted-gpu' | |
| run: uv sync --python 3.13 --extra dev --extra torch-cuda128 | |
| - name: Install dev dependencies and torch (non-self-hosted GPU) | |
| if: matrix.os != 'self-hosted-gpu' | |
| run: uv sync --extra dev --extra torch-cpu | |
| - name: Print environment info | |
| run: | | |
| echo "=== UV Environment ===" | |
| uv run python --version | |
| uv run python -c "import sys; print('Python executable:', sys.executable)" | |
| echo "=== UV Environment NumPy Check ===" | |
| uv run python -c "import numpy; print('NumPy version:', numpy.__version__); print('NumPy location:', numpy.__file__)" || echo "NumPy import failed in uv environment" | |
| echo "=== CUDA Availability Check ===" | |
| uv run python -c " | |
| import torch | |
| print(f'PyTorch version: {torch.__version__}') | |
| print(f'CUDA available: {torch.cuda.is_available()}') | |
| print(f'CUDA device count: {torch.cuda.device_count()}') | |
| if torch.cuda.is_available(): | |
| print(f'CUDA version: {torch.version.cuda}') | |
| print(f'Current device: {torch.cuda.current_device()}') | |
| print(f'Device name: {torch.cuda.get_device_name(0)}') | |
| else: | |
| print('CUDA is not available') | |
| " || echo "CUDA check failed" | |
| echo "=== PIP EXECUTABLE COMPARISON ===" | |
| uv run python -c "import subprocess; print('pip from uv run python:', subprocess.check_output(['pip', '--version']).decode().strip())" || echo "pip not found from python" | |
| uv run pip --version || echo "uv run pip failed" | |
| echo "=== UV pip list vs python -m pip list ===" | |
| echo "--- uv run pip list ---" | |
| uv run pip list | head -20 | |
| echo "--- uv run python -m pip list ---" | |
| uv run python -m pip list | head -20 | |
| echo "=== UV ENVIRONMENT CHECK ===" | |
| uv run python -c "import os; print('VIRTUAL_ENV:', os.environ.get('VIRTUAL_ENV', 'Not set'))" | |
| echo "=== Import Test ===" | |
| uv run python -c "import torch; import lightning; import kornia; print('All imports successful')" || echo "Import test failed" | |
| - name: Check MPS backend (macOS only) | |
| if: runner.os == 'macOS' | |
| run: | | |
| echo "=== macOS MPS Backend Check ===" | |
| uv run python -c " | |
| import torch | |
| print(f'PyTorch version: {torch.__version__}') | |
| print(f'MPS available: {torch.backends.mps.is_available()}') | |
| print(f'MPS built: {torch.backends.mps.is_built()}') | |
| if torch.backends.mps.is_available(): | |
| print('MPS backend is available and ready to use!') | |
| device = torch.device('mps') | |
| test_tensor = torch.randn(3, 3).to(device) | |
| print(f'Test tensor on MPS: {test_tensor.device}') | |
| else: | |
| print('MPS backend is not available on this macOS system') | |
| " | |
| - name: Run pytest | |
| run: | | |
| echo "=== Final environment check before tests ===" | |
| uv run python -c "import numpy, torch, lightning, kornia; print(f'All packages available: numpy={numpy.__version__}, torch={torch.__version__}')" | |
| echo "=== Running pytest ===" | |
| uv run pytest --cov=sleap_nn --cov-report=xml --durations=-1 tests/ | |
| - name: Upload coverage | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| fail_ci_if_error: true | |
| verbose: false | |
| token: ${{ secrets.CODECOV_TOKEN }} |