Add option to analysis export for exporting predictions for all frames including those with no predictions #1915
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| # Continuous integration using conda installation | |
| name: CI | |
| on: | |
| pull_request: | |
| types: [opened, reopened, synchronize] | |
| paths: | |
| - "sleap/**" | |
| - "tests/**" | |
| - ".github/workflows/ci.yml" | |
| - "environment_no_cuda.yml" | |
| - "requirements.txt" | |
| - "dev_requirements.txt" | |
| push: | |
| branches: | |
| - master | |
| - develop | |
| paths: | |
| - "sleap/**" | |
| - "tests/**" | |
| - ".github/workflows/ci.yml" | |
| - "environment_no_cuda.yml" | |
| - "requirements.txt" | |
| - "dev_requirements.txt" | |
| jobs: | |
| type_check: | |
| name: Type Check | |
| runs-on: "ubuntu-22.04" | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v3 | |
| - name: Set up Python 3.7 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.7 | |
| - name: Install Dependencies | |
| run: | | |
| pip install mypy | |
| - name: Run MyPy | |
| # TODO: remove this once all MyPy errors get fixed | |
| continue-on-error: true | |
| run: | | |
| mypy --follow-imports=skip --ignore-missing-imports sleap tests | |
| lint: | |
| name: Lint | |
| runs-on: "ubuntu-22.04" | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v3 | |
| - name: Set up Python 3.7 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.7 | |
| - name: Install Dependencies | |
| run: | | |
| pip install click==8.0.4 | |
| pip install black==21.6b0 | |
| - name: Run Black | |
| run: | | |
| black --check sleap tests | |
| tests: | |
| name: Tests (${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-22.04", "windows-2022", "macos-latest"] | |
| include: | |
| # Default values | |
| - env_file: environment_no_cuda.yml | |
| - test_args: --durations=-1 tests/ | |
| # Mac specific values | |
| - os: macos-latest | |
| env_file: environment_mac.yml | |
| # Ubuntu specific values | |
| - os: ubuntu-22.04 | |
| test_args: --cov=sleap --cov-report=xml --durations=-1 tests/ | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v3 | |
| - name: Setup Micromamba | |
| # https://github.com/mamba-org/setup-micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| micromamba-version: '1.4.6-0' | |
| environment-file: ${{ matrix.env_file }} | |
| environment-name: sleap_ci | |
| init-shell: >- | |
| bash | |
| powershell | |
| post-cleanup: all | |
| # Print environment info | |
| - name: Print environment info | |
| shell: bash -l {0} | |
| run: | | |
| which python | |
| micromamba info | |
| micromamba list | |
| pip freeze | |
| # Test environment | |
| - name: Test with pytest | |
| shell: bash -l {0} | |
| run: | | |
| pytest ${{ matrix.test_args }} | |
| # Upload coverage | |
| - name: Upload coverage | |
| uses: codecov/codecov-action@v1 | |
| if: matrix.os == 'ubuntu-22.04' | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| fail_ci_if_error: true | |
| verbose: false |