diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index 13c398aca..69b0659a6 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -9,25 +9,20 @@ on: workflow_dispatch: env: - CONDA_ENV: echopype NUM_WORKERS: 2 jobs: test: name: ${{ matrix.python-version }}-build - runs-on: ubuntu-20.04 + runs-on: ubuntu-latest if: ${{ !contains(github.event.head_commit.message, '[skip ci]') }} continue-on-error: ${{ matrix.experimental }} strategy: fail-fast: false matrix: - python-version: ["3.9", "3.10"] # TODO: add back 3.11 once parsed2zarr is fixed + python-version: ["3.9", "3.10", "3.11"] runs-on: [ubuntu-latest] experimental: [false] - include: - - runs-on: ubuntu-latest - python-version: "3.11" - experimental: true services: # TODO: figure out how to update tag when there's a new one minio: @@ -46,30 +41,20 @@ jobs: - name: Set environment variables run: | echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV - - name: Setup micromamba - uses: mamba-org/setup-micromamba@v1 + - name: Set up Python + uses: actions/setup-python@v4.7.1 with: - environment-file: .ci_helpers/py${{ matrix.python-version }}.yaml - environment-name: ${{ env.CONDA_ENV }} - cache-environment: true - post-cleanup: 'all' - - name: Print conda environment - shell: bash -l {0} - run: | - micromamba info - micromamba list + python-version: ${{ matrix.python-version }} + - name: Upgrade pip + run: python -m pip install --upgrade pip - name: Remove docker-compose python - if: ${{ matrix.python-version == '3.10' || matrix.python-version == '3.11' }} - shell: bash -l {0} run: sed -i "/docker-compose/d" requirements-dev.txt - name: Install dev tools - shell: bash -l {0} - run: | - micromamba install -c conda-forge -n ${{ env.CONDA_ENV }} --yes --file requirements-dev.txt + run: python -m pip install -r requirements-dev.txt - name: Install echopype - shell: bash -l {0} - run: | - python -m pip install -e .[plot] + run: python -m pip install -e ".[plot]" + - name: Print installed packages + run: python -m pip list - name: Copying test data to services shell: bash -l {0} run: | diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index 800a1e96f..b44acb8b7 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -5,7 +5,6 @@ on: paths-ignore: ["**/docker.yaml", "docs"] env: - CONDA_ENV: echopype NUM_WORKERS: 2 jobs: @@ -17,16 +16,9 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.9", "3.10"] # TODO: add back 3.11 once parsed2zarr is fixed + python-version: ["3.9", "3.10", "3.11"] runs-on: [ubuntu-latest] experimental: [false] - include: - - runs-on: ubuntu-latest - python-version: "3.11" - experimental: true - defaults: - run: - shell: bash -l {0} services: # TODO: figure out how to update tag when there's a new one minio: @@ -42,35 +34,28 @@ jobs: uses: actions/checkout@v4 with: fetch-depth: 0 # Fetch all history for all branches and tags. + - name: Set up Python + uses: actions/setup-python@v4.7.1 + with: + python-version: ${{ matrix.python-version }} + - name: Upgrade pip + run: python -m pip install --upgrade pip - name: Set environment variables run: | echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV - - name: Setup micromamba - uses: mamba-org/setup-micromamba@v1 - with: - environment-file: .ci_helpers/py${{ matrix.python-version }}.yaml - environment-name: ${{ env.CONDA_ENV }} - cache-environment: true - post-cleanup: 'all' - - name: Print conda environment - run: | - micromamba info - micromamba list - name: Remove docker-compose python - if: ${{ matrix.python-version == '3.10' || matrix.python-version == '3.11' }} run: sed -i "/docker-compose/d" requirements-dev.txt - name: Install dev tools - run: | - micromamba install -c conda-forge -n ${{ env.CONDA_ENV }} --yes --file requirements-dev.txt + run: python -m pip install -r requirements-dev.txt # We only want to install this on one run, because otherwise we'll have # duplicate annotations. - name: Install error reporter if: ${{ matrix.python-version == '3.9' }} - run: | - python -m pip install pytest-github-actions-annotate-failures + run: python -m pip install pytest-github-actions-annotate-failures - name: Install echopype - run: | - python -m pip install -e .[plot] + run: python -m pip install -e ".[plot]" + - name: Print installed packages + run: python -m pip list - name: Copying test data to services run: | python .ci_helpers/docker/setup-services.py --deploy --data-only --http-server ${{ job.services.httpserver.id }} diff --git a/echopype/tests/convert/test_parsed_to_zarr.py b/echopype/tests/convert/test_parsed_to_zarr.py index 9b836753c..1fb30ebc4 100644 --- a/echopype/tests/convert/test_parsed_to_zarr.py +++ b/echopype/tests/convert/test_parsed_to_zarr.py @@ -15,6 +15,8 @@ from echopype.echodata.convention import sonarnetcdf_1 from echopype.convert.api import _check_file, SONAR_MODELS +pytestmark = pytest.mark.skip(reason="Removed Parsed2Zarr") + test_bucket_name = "echopype-test" port = 5555 endpoint_uri = "http://127.0.0.1:%s/" % port