Update dolphin filter cli to accept fill_value and threshold
#1388
Workflow file for this run
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| name: Pytest, build docker image, push to GHCR | |
| on: [pull_request, push] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.head_ref }} | |
| cancel-in-progress: true | |
| env: | |
| # https://github.com/pytest-dev/pytest/issues/2042#issuecomment-429289164 | |
| PY_IGNORE_IMPORTMISMATCH: 1 | |
| jobs: | |
| pytest: | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-14] | |
| deps: | |
| - label: Latest | |
| # we can't specify `tophu` for conda, not available on mac | |
| spec: >- | |
| isce3-cpu | |
| dask | |
| fail-fast: true | |
| name: ${{ matrix.os }} • ${{ matrix.deps.label }} | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Setup environment | |
| uses: mamba-org/setup-micromamba@v2 | |
| with: | |
| environment-file: conda-env.yml | |
| environment-name: dolphin-env | |
| # persist on the same day. | |
| cache-environment-key: environment-${{ steps.date.outputs.date }} | |
| cache-downloads-key: downloads-${{ steps.date.outputs.date }} | |
| generate-run-shell: false | |
| create-args: ${{ matrix.deps.spec }} | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| - name: Install | |
| run: | | |
| python -m pip install --no-deps \ | |
| "snaphu>=0.4.0" \ | |
| "opera-utils>=0.4.1" \ | |
| git+https://github.com/isce-framework/tophu@main \ | |
| git+https://github.com/isce-framework/whirlwind@40defb38d2d6deca2819934788ebbc57e418e32d | |
| python -m pip install git+https://github.com/isce-framework/spurt@bd64ed4766a668fabdff4d312fcbb0d47344f632 | |
| python -m pip install --no-deps . | |
| - name: Install test dependencies | |
| run: | | |
| micromamba install -f tests/requirements.txt -c conda-forge | |
| - name: Enable numba boundscheck for better error catching | |
| run: | | |
| echo "NUMBA_BOUNDSCHECK=1" >> $GITHUB_ENV | |
| echo "TQDM_DISABLE=1" >> $GITHUB_ENV | |
| - name: Test (with numba boundscheck on) | |
| run: | | |
| pytest -n0 -vv | |
| # https://community.codecov.com/t/numba-jitted-methods-are-not-captured-by-codecov/2649 | |
| # - name: Coverage report | |
| # uses: codecov/codecov-action@v2 | |
| dockerize: # Based on Mintpy: https://github.com/insarlab/MintPy/blob/5ca554fef324b816f9130feec567e2cf463e41d2/.github/workflows/build-n-publish-to-pypi.yml | |
| name: Build Docker image and push to GitHub Container Registry | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| packages: write | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python 3.11 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Set environment variables for docker build | |
| run: | | |
| pip install setuptools_scm # Install setuptools_scm to get version number | |
| # Save version number from CLI | |
| version=$(python -m setuptools_scm) | |
| sanitized_version=${version//+/-} # Replace all '+' with '-' | |
| echo "DOLPHIN_VERSION=${sanitized_version}" >> $GITHUB_ENV | |
| - name: Login to GitHub Container Registry | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Build, tag, and push image to Github Container Registry | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: . | |
| file: ./docker/Dockerfile | |
| push: ${{ github.event_name != 'pull_request' }} | |
| tags: | | |
| ghcr.io/${{ github.repository }}:${{ env.DOLPHIN_VERSION }} | |
| labels: | | |
| org.opencontainers.image.created=${{ env.CI_JOB_TIMESTAMP }} | |
| org.opencontainers.image.version=${{ env.DOLPHIN_VERSION }} | |
| org.opencontainers.image.revision=${{ github.sha }} | |
| - name: Add develop tag | |
| if: github.ref == 'refs/heads/main' | |
| uses: akhilerm/[email protected] | |
| with: | |
| src: ghcr.io/${{ github.repository }}:${{ env.DOLPHIN_VERSION }} | |
| dst: ghcr.io/${{ github.repository }}:develop | |
| - name: Add latest tag | |
| if: startsWith(github.ref, 'refs/tags/v') | |
| uses: akhilerm/[email protected] | |
| with: | |
| src: ghcr.io/${{ github.repository }}:${{ env.DOLPHIN_VERSION }} | |
| dst: ghcr.io/${{ github.repository }}:latest |