hotfix: inference with PDB files via JSON API #76
Workflow file for this run
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| name: lint_and_test | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - production | |
| paths: | |
| - 'src/**' | |
| - 'tests/**' | |
| - '.github/workflows/**' | |
| pull_request: | |
| branches: | |
| - main | |
| - dev | |
| - staging | |
| - production | |
| paths: | |
| - 'src/**' | |
| - 'tests/**' | |
| - '.github/workflows/**' | |
| pull_request_target: | |
| types: [ready_for_review] | |
| paths: | |
| - 'src/**' | |
| - 'tests/**' | |
| - '.github/workflows/**' | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| permissions: | |
| contents: read | |
| jobs: | |
| lint: | |
| name: ruff | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Extract ruff version from pyproject.toml | |
| run: | | |
| echo "RUFF_VERSION=$(grep -E 'ruff.*=' pyproject.toml | sed -E 's/.*\"ruff==([^\"]+)\".*/\1/')" >> $GITHUB_ENV | |
| echo "Extracted Ruff version: ${{ env.RUFF_VERSION }}" | |
| - name: Install ruff | |
| run: pip install ruff==${{ env.RUFF_VERSION }} | |
| - name: ruff format (check code formatting) | |
| run: ruff format --diff | |
| - name: ruff check (lint code base) | |
| run: ruff check src tests | |
| test_digs: | |
| name: pytest (jojo) | |
| runs-on: [self-hosted] | |
| timeout-minutes: 30 | |
| needs: lint | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Run tests | |
| run: | | |
| export N_CPU=8 | |
| srun --chdir=$PWD -p cpu -c $N_CPU -t 00:30:00 --mem=32G bash ./.github/ci/run_tests.sh | |
| - name: Upload coverage report | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-report | |
| path: coverage.xml | |
| test_github: | |
| name: pytest (github) | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 45 | |
| needs: lint | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Install system dependencies | |
| run: | | |
| # Check if rsync is already installed | |
| if ! command -v rsync &> /dev/null; then | |
| echo "Installing rsync..." | |
| sudo apt-get update | |
| sudo apt-get install -y rsync | |
| else | |
| echo "rsync is already available" | |
| fi | |
| - name: Setup uv | |
| uses: astral-sh/setup-uv@v4 | |
| with: | |
| version: "latest" | |
| - name: Install dependencies with uv | |
| run: | | |
| uv pip install -e ".[ml,openbabel,dev]" --system | |
| - name: Setup test data | |
| run: | | |
| atomworks setup tests | |
| - name: Run pytest | |
| run: | | |
| export OPENBLAS_NUM_THREADS=1 | |
| export OMP_NUM_THREADS=1 | |
| # Get number of CPUs available | |
| N_CPU=$(nproc) | |
| echo "Running tests with max $N_CPU CPUs" | |
| # Run the tests with coverage | |
| if [ "$N_CPU" -eq 1 ]; then | |
| PDB_MIRROR_PATH=tests/data/pdb CCD_MIRROR_PATH=tests/data/ccd pytest -m "not benchmark" tests/io | |
| PDB_MIRROR_PATH=tests/data/pdb CCD_MIRROR_PATH=tests/data/ccd pytest -m "not benchmark and not slow" tests/ml | |
| # NOTE: The slow tests below are currently skipped on github runners due to low memory. | |
| # PDB_MIRROR_PATH=tests/data/pdb CCD_MIRROR_PATH=tests/data/ccd pytest -m "not benchmark and slow" tests/ml | |
| else | |
| PDB_MIRROR_PATH=tests/data/pdb CCD_MIRROR_PATH=tests/data/ccd pytest -m "not benchmark" -n auto --maxprocesses=$N_CPU --dist=worksteal --cov=atomworks --cov-report=xml --cov-report=term --cov-report=term-missing tests/ | |
| fi | |
| - name: Upload coverage report | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-report-github | |
| path: coverage.xml | |
| if: always() |