Add a test and fix for invalid geometry #3872
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| # yamllint disable-file | |
| name: Run Code Checks | |
| on: | |
| pull_request: | |
| push: | |
| # Only run on push to `develop` branch to prevent double execution of | |
| # all the code checks. | |
| # Everything should be merged through PRs anyway. | |
| branches: | |
| - develop | |
| - test-ci-* | |
| - pypi/publish | |
| paths: | |
| - '**' | |
| - '!notebooks/**' | |
| - '!docs/**' | |
| - '!old/**' | |
| - '!README.md' | |
| jobs: | |
| build-wheels: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Setup Python | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: 3.8 | |
| - uses: actions/cache@v3 | |
| id: wheels_cache | |
| with: | |
| path: ./wheels | |
| key: wheels-${{ github.sha }} | |
| - name: Install Dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install --upgrade setuptools | |
| python -m pip install --upgrade \ | |
| toml \ | |
| wheel \ | |
| packaging \ | |
| twine | |
| python -m pip freeze | |
| - name: Build Clean Packages | |
| run: | | |
| mkdir -p ./wheels/clean | |
| ./scripts/build-wheels.sh ./wheels/clean | |
| find ./wheels/clean -type f | |
| - name: Patch Package Versions | |
| run: | | |
| grep -R --files-with-matches --include '*.py' '__version__ =' \ | |
| | xargs python ./scripts/patch_version.py ${GITHUB_RUN_NUMBER:-0} | |
| - name: Build Dev Packages | |
| run: | | |
| mkdir -p ./wheels/dev | |
| ./scripts/build-wheels.sh ./wheels/dev | |
| find ./wheels/dev -type f | |
| build-test-env-base: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: actions/cache@v3 | |
| id: conda_cache | |
| with: | |
| path: | | |
| tests/env | |
| key: ${{ runner.os }}-test-env-py38-${{ hashFiles('tests/test-env-py38.yml') }} | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| if: steps.conda_cache.outputs.cache-hit != 'true' | |
| with: | |
| channels: conda-forge,defaults | |
| channel-priority: true | |
| activate-environment: "" | |
| # mamba-version: "*" | |
| use-mamba: true | |
| miniforge-variant: Mambaforge | |
| - name: Dump Conda Environment Info | |
| shell: bash -l {0} | |
| if: steps.conda_cache.outputs.cache-hit != 'true' | |
| run: | | |
| conda info | |
| conda list | |
| mamba -V | |
| conda config --show-sources | |
| conda config --show | |
| printenv | sort | |
| - name: Build Python Environment for Testing | |
| shell: bash -l {0} | |
| if: steps.conda_cache.outputs.cache-hit != 'true' | |
| run: | | |
| mamba env create -f tests/test-env-py38.yml -p tests/env | |
| - name: Check Python Env | |
| shell: bash -l {0} | |
| if: steps.conda_cache.outputs.cache-hit != 'true' | |
| run: | | |
| mamba env export -p tests/env | |
| test-with-coverage: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - build-test-env-base | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Get Conda Environment from Cache | |
| uses: actions/cache@v3 | |
| id: conda_cache | |
| with: | |
| path: | | |
| tests/env | |
| key: ${{ runner.os }}-test-env-py38-${{ hashFiles('tests/test-env-py38.yml') }} | |
| - name: Update PATH | |
| shell: bash | |
| run: | | |
| echo "$(pwd)/tests/env/bin" >> $GITHUB_PATH | |
| export PATH="$(pwd)/tests/env/bin" | |
| - name: Install in Edit mode | |
| shell: bash | |
| run: | | |
| which python | |
| which createdb | |
| which datacube | |
| ./scripts/dev-install.sh --no-deps | |
| - name: Start Test DB | |
| shell: bash | |
| run: | | |
| echo "Launching test db" | |
| pgdata=$(pwd)/.dbdata | |
| initdb -D ${pgdata} --auth-host=md5 --encoding=UTF8 | |
| pg_ctl -D ${pgdata} -l "${pgdata}/pg.log" start | |
| createdb datacube | |
| datacube system init | |
| pip list --format=freeze | |
| env: | |
| DATACUBE_DB_URL: postgresql:///datacube | |
| - name: Run Tests | |
| shell: bash | |
| run: | | |
| datacube system check | |
| datacube metadata add "https://raw.githubusercontent.com/GeoscienceAustralia/dea-config/master/product_metadata/eo3_sentinel_ard.odc-type.yaml" | |
| echo "Running Tests" | |
| pytest --cov=. \ | |
| --cov-report=html \ | |
| --cov-report=xml:coverage.xml \ | |
| --timeout=30 \ | |
| libs apps | |
| env: | |
| AWS_DEFAULT_REGION: us-west-2 | |
| DASK_TEMPORARY_DIRECTORY: /tmp/dask | |
| DATACUBE_DB_URL: postgresql:///datacube | |
| - name: Upload Coverage | |
| if: | | |
| github.repository == 'opendatacube/odc-tools' | |
| uses: codecov/codecov-action@v1 | |
| with: | |
| fail_ci_if_error: false | |
| verbose: false | |
| test-wheels: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - build-test-env-base | |
| - build-wheels | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Get Wheels from Cache | |
| uses: actions/cache@v3 | |
| id: wheels_cache | |
| with: | |
| path: ./wheels | |
| key: wheels-${{ github.sha }} | |
| - name: Get Conda Environment from Cache | |
| uses: actions/cache@v3 | |
| id: conda_cache | |
| with: | |
| path: | | |
| tests/env | |
| key: ${{ runner.os }}-test-env-py38-${{ hashFiles('tests/test-env-py38.yml') }} | |
| - name: Update PATH | |
| shell: bash | |
| run: | | |
| echo "$(pwd)/tests/env/bin" >> $GITHUB_PATH | |
| - name: Install wheels for testing | |
| shell: bash | |
| run: | | |
| which python | |
| which createdb | |
| which datacube | |
| ls -lh wheels/clean | |
| python -m pip install --no-deps wheels/clean/*whl | |
| python -m pip check || true | |
| - name: Start Test DB | |
| shell: bash | |
| run: | | |
| echo "Launching test db" | |
| pgdata=$(pwd)/.dbdata | |
| initdb -D ${pgdata} --auth-host=md5 --encoding=UTF8 | |
| pg_ctl -D ${pgdata} -l "${pgdata}/pg.log" start | |
| createdb datacube | |
| datacube system init | |
| env: | |
| DATACUBE_DB_URL: postgresql:///datacube | |
| - name: Run Tests | |
| shell: bash | |
| run: | | |
| datacube system check | |
| datacube metadata add "https://raw.githubusercontent.com/GeoscienceAustralia/dea-config/master/product_metadata/eo3_sentinel_ard.odc-type.yaml" | |
| echo "Running Tests" | |
| pytest --timeout=30 libs apps | |
| env: | |
| AWS_DEFAULT_REGION: us-west-2 | |
| DASK_TEMPORARY_DIRECTORY: /tmp/dask | |
| DATACUBE_DB_URL: postgresql:///datacube | |
| publish-pypi: | |
| if: | | |
| github.event_name == 'push' | |
| && github.repository == 'opendatacube/odc-tools' | |
| && (github.ref == 'refs/heads/stable' || github.ref == 'refs/heads/pypi/publish') | |
| strategy: | |
| matrix: | |
| pkg: | |
| - odc-algo | |
| - odc-cloud | |
| - odc-io | |
| - odc-ui | |
| - odc-apps-cloud | |
| - odc-apps-dc-tools | |
| needs: | |
| - build-wheels | |
| - test-wheels | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Config | |
| if: | | |
| github.event_name == 'push' | |
| && github.repository == 'opendatacube/odc-tools' | |
| && (github.ref == 'refs/heads/stable' || github.ref == 'refs/heads/pypi/publish') | |
| id: cfg | |
| env: | |
| PKG: ${{ matrix.pkg }} | |
| run: | | |
| tk="pypi_token_${PKG//-/_}" | |
| echo "tk=${tk}" >> $GITHUB_OUTPUT | |
| echo "publish=yes" >> $GITHUB_OUTPUT | |
| - name: Setup Python | |
| if: steps.cfg.outputs.publish == 'yes' | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: 3.8 | |
| - name: Install Twine | |
| if: steps.cfg.outputs.publish == 'yes' | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install --upgrade setuptools | |
| python -m pip install --upgrade \ | |
| toml \ | |
| wheel \ | |
| twine | |
| python -m pip freeze | |
| - uses: actions/cache@v3 | |
| id: wheels_cache | |
| if: steps.cfg.outputs.publish == 'yes' | |
| with: | |
| path: ./wheels | |
| key: wheels-${{ github.sha }} | |
| - name: Prepare for upload | |
| if: steps.cfg.outputs.publish == 'yes' | |
| run: | | |
| mkdir -p ./pips | |
| ./scripts/mk-pip-tree.sh ./wheels/clean ./pips | |
| find ./pips -type f | |
| - name: Upload to PyPI | |
| if: steps.cfg.outputs.publish == 'yes' | |
| env: | |
| TWINE_PASSWORD: ${{ secrets[ steps.cfg.outputs.tk ] }} | |
| TWINE_USERNAME: __token__ | |
| PKG: ${{ matrix.pkg }} | |
| run: | | |
| ls pips/${PKG} | |
| twine upload --non-interactive --skip-existing pips/${PKG}/* |