Support Numpy 1 and Numpy 2 #6802
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| name: ASPIRE Python Pip CI | |
| on: | |
| pull_request: | |
| types: [opened, synchronize, reopened, ready_for_review] | |
| push: | |
| jobs: | |
| check: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.9' | |
| - name: Install dependencies | |
| run: | | |
| pip install tox tox-gh-actions | |
| - name: Run Tox Check | |
| run: tox -e check | |
| build: | |
| needs: check | |
| runs-on: ubuntu-latest | |
| # Run on every code push, but only on review ready PRs | |
| if: ${{ github.event_name == 'push' || github.event.pull_request.draft == false }} | |
| strategy: | |
| matrix: | |
| python-version: ['3.9', '3.10', '3.11', '3.12'] | |
| pyenv: [pip] | |
| exclude: | |
| # Exclude 3.9-pip so we can add pre/post tasks to that environment. | |
| - python-version: '3.9' | |
| pyenv: pip | |
| include: | |
| # Re-include 3.9 with additional tox tasks. | |
| - python-version: '3.9' | |
| pyenv: pip,docs | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} ${{ matrix.pyenv }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| pip install tox tox-gh-actions | |
| # Optional packages | |
| pip install pyfftw # `test_fft` runs for pyfftw when installed | |
| - name: Test with tox | |
| run: tox --skip-missing-interpreters false -e py${{ matrix.python-version }}-${{ matrix.pyenv }} | |
| - name: Upload Coverage to CodeCov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| conda-build: | |
| needs: check | |
| runs-on: ${{ matrix.os }} | |
| # Only run on review ready pull_requests | |
| if: ${{ github.event_name == 'pull_request' && github.event.pull_request.draft == false }} | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, ubuntu-20.04, macOS-latest, macOS-13] | |
| backend: [default, openblas] | |
| python-version: ['3.9'] | |
| include: | |
| - os: ubuntu-latest | |
| backend: intel | |
| - os: macOS-latest | |
| backend: accelerate | |
| - os: windows-2019 | |
| backend: default | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Conda ${{ matrix.os }} Python ${{ matrix.python-version }} | |
| uses: conda-incubator/[email protected] | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: aspire | |
| environment-file: environment-${{ matrix.backend }}.yml | |
| auto-activate-base: false | |
| - name: Complete Install and Log Environment ${{ matrix.os }} Python ${{ matrix.python-version }} | |
| run: | | |
| conda info | |
| conda list | |
| pip install -e ".[dev]" | |
| pip freeze | |
| python -c "import numpy; numpy.show_config()" | |
| - name: Execute Pytest Conda ${{ matrix.os }} Python ${{ matrix.python-version }} | |
| run: | | |
| export OMP_NUM_THREADS=2 | |
| # -n runs test in parallel using pytest-xdist | |
| pytest -n2 --durations=50 -s | |
| # Build and Deploy production (main) docs. | |
| docs_deploy: | |
| if: github.ref == 'refs/heads/main' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.9' | |
| - name: Install Dependencies | |
| run: | | |
| pip install -e ".[dev]" | |
| - name: Run Sphinx doc build script | |
| env: | |
| GITHUB_ACTOR: ${{ github.actor }} | |
| GITHUB_REPOSITORY: ${{ github.repository }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: "docs/buildsite.sh" | |
| shell: bash | |
| ampere_gpu: | |
| needs: check | |
| runs-on: self-hosted | |
| # Run on every code push, but only on review ready PRs | |
| if: ${{ github.event_name == 'push' || github.event.pull_request.draft == false }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install dependencies | |
| run: | | |
| pip install -e ".[dev,gpu-12x]" | |
| - name: Customize config | |
| run: | | |
| echo "Setup tmp dirs and chmod so others can cleanup." | |
| CI_TMP_DIR=/var/ci/tmp | |
| mkdir -p ${CI_TMP_DIR} | |
| chmod g+rwx ${CI_TMP_DIR} | |
| CI_CACHE_DIR=${CI_TMP_DIR}/cache | |
| mkdir -p ${CI_CACHE_DIR} | |
| chmod g+rwx ${CI_CACHE_DIR} | |
| echo "Create and assign a unique temp dir to hold our config." | |
| WORK_DIR=$(mktemp -d -p "${CI_TMP_DIR}") | |
| echo "WORK_DIR=${WORK_DIR}" | |
| echo "Stash the WORK_DIR to GitHub env so we can clean it up later." | |
| echo "WORK_DIR=${WORK_DIR}" >> $GITHUB_ENV | |
| echo -e "ray:\n temp_dir: ${WORK_DIR}\n" > ${WORK_DIR}/config.yaml | |
| echo -e "common:" >> ${WORK_DIR}/config.yaml | |
| echo -e " cache_dir: ${CI_CACHE_DIR}" >> ${WORK_DIR}/config.yaml | |
| echo -e " numeric: cupy" >> ${WORK_DIR}/config.yaml | |
| echo -e " fft: cupy\n" >> ${WORK_DIR}/config.yaml | |
| echo "Log the config: ${WORK_DIR}/config.yaml" | |
| cat ${WORK_DIR}/config.yaml | |
| - name: Cache Data | |
| run: | | |
| ASPIREDIR=${{ env.WORK_DIR }} python -c \ | |
| "import aspire; print(aspire.config['common']['cache_dir']); import aspire.downloader; aspire.downloader.emdb_2660()" | |
| - name: Run | |
| run: | | |
| ASPIREDIR=${{ env.WORK_DIR }} python -c \ | |
| "import aspire; print(aspire.config['ray']['temp_dir'])" | |
| ASPIREDIR=${{ env.WORK_DIR }} PYTHONWARNINGS=error python -m pytest --durations=50 --cov=aspire --cov-report=xml | |
| - name: Upload Coverage to CodeCov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| - name: Cleanup | |
| run: rm -rf ${{ env.WORK_DIR }} | |
| # Create cache and download data for Github Actions CI. | |
| data-cache: | |
| needs: check | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.9' | |
| - name: Install Dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -e ".[dev]" | |
| - name: Create Cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/ASPIRE-data | |
| key: ${{ runner.os }}-cached-data | |
| - name: Download EMDB 2660 | |
| run: | | |
| python -c \ | |
| "from aspire.downloader import emdb_2660; emdb_2660()" | |
| # Build branch's docs and gallery. | |
| docs: | |
| needs: [check, data-cache] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.9' | |
| - name: Install Dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -e ".[dev]" | |
| - name: Restore Cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/ASPIRE-data | |
| key: ${{ runner.os }}-cached-data | |
| - name: Build Sphinx docs | |
| run: | | |
| make distclean | |
| sphinx-apidoc -f -o ./source ../src -H Modules | |
| make html | |
| working-directory: ./docs | |
| - name: Archive Sphinx docs | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: sphinx-docs | |
| path: docs/build | |
| retention-days: 7 | |
| osx_arm: | |
| needs: check | |
| runs-on: macos-14 | |
| # Run on every code push, but only on review ready PRs | |
| if: ${{ github.event_name == 'push' || github.event.pull_request.draft == false }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Complete Install and Log Environment | |
| run: | | |
| python --version | |
| pip install -e ".[dev]" # install aspire | |
| pip freeze | |
| - name: Test | |
| run: python -m pytest -n3 --durations=50 |