Merge pull request #181 from Daylily-Informatics/codex/bloom-legacy-r… #10
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| name: CI | |
| on: | |
| push: | |
| branches: ['*'] | |
| pull_request: | |
| branches: [main] | |
| permissions: | |
| contents: read | |
| env: | |
| PYTHON_VERSION: "3.12" | |
| jobs: | |
| lint: | |
| name: Code Quality (Ruff) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION }} | |
| - name: Install ruff | |
| run: pip install ruff | |
| - name: Collect changed Python files | |
| id: changed | |
| run: | | |
| python - <<'PY' | |
| import json | |
| import os | |
| import subprocess | |
| def collect_files(command): | |
| result = subprocess.run(command, capture_output=True, check=False, text=True) | |
| if result.returncode == 0: | |
| return [line.strip() for line in result.stdout.splitlines() if line.strip()] | |
| return None | |
| event = os.environ["GITHUB_EVENT_NAME"] | |
| if event == "pull_request": | |
| with open(os.environ["GITHUB_EVENT_PATH"], encoding="utf-8") as fh: | |
| payload = json.load(fh) | |
| base_sha = payload["pull_request"]["base"]["sha"] | |
| head_sha = payload["pull_request"]["head"]["sha"] | |
| files = collect_files(["git", "diff", "--name-only", f"{base_sha}...{head_sha}", "--", "*.py"]) | |
| if files is None: | |
| files = collect_files(["git", "diff", "--name-only", f"{base_sha}..{head_sha}", "--", "*.py"]) | |
| if files is None: | |
| files = [] | |
| else: | |
| has_parent = subprocess.run( | |
| ["git", "rev-parse", "--verify", "HEAD^"], | |
| stdout=subprocess.DEVNULL, | |
| stderr=subprocess.DEVNULL, | |
| ).returncode == 0 | |
| if has_parent: | |
| files = collect_files(["git", "diff", "--name-only", "HEAD^", "HEAD", "--", "*.py"]) or [] | |
| else: | |
| files = collect_files(["git", "ls-files", "*.py"]) or [] | |
| with open(os.environ["GITHUB_OUTPUT"], "a", encoding="utf-8") as fh: | |
| fh.write(f"files={json.dumps(files)}\n") | |
| fh.write(f"count={len(files)}\n") | |
| PY | |
| - name: Run ruff check | |
| if: steps.changed.outputs.count != '0' | |
| run: ruff check ${{ join(fromJson(steps.changed.outputs.files), ' ') }} | |
| - name: Run ruff format check | |
| if: steps.changed.outputs.count != '0' | |
| run: ruff format --check ${{ join(fromJson(steps.changed.outputs.files), ' ') }} | |
| - name: Skip ruff when no Python files changed | |
| if: steps.changed.outputs.count == '0' | |
| run: echo "No Python file changes detected." | |
| security: | |
| name: Security Scanning (Bandit) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION }} | |
| - name: Install bandit | |
| run: pip install "bandit[toml]" | |
| - name: Collect changed Python files | |
| id: changed | |
| run: | | |
| python - <<'PY' | |
| import json | |
| import os | |
| import subprocess | |
| def collect_files(command): | |
| result = subprocess.run(command, capture_output=True, check=False, text=True) | |
| if result.returncode == 0: | |
| return [line.strip() for line in result.stdout.splitlines() if line.strip()] | |
| return None | |
| event = os.environ["GITHUB_EVENT_NAME"] | |
| if event == "pull_request": | |
| with open(os.environ["GITHUB_EVENT_PATH"], encoding="utf-8") as fh: | |
| payload = json.load(fh) | |
| base_sha = payload["pull_request"]["base"]["sha"] | |
| head_sha = payload["pull_request"]["head"]["sha"] | |
| files = collect_files(["git", "diff", "--name-only", f"{base_sha}...{head_sha}", "--", "*.py"]) | |
| if files is None: | |
| files = collect_files(["git", "diff", "--name-only", f"{base_sha}..{head_sha}", "--", "*.py"]) | |
| if files is None: | |
| files = [] | |
| else: | |
| has_parent = subprocess.run( | |
| ["git", "rev-parse", "--verify", "HEAD^"], | |
| stdout=subprocess.DEVNULL, | |
| stderr=subprocess.DEVNULL, | |
| ).returncode == 0 | |
| if has_parent: | |
| files = collect_files(["git", "diff", "--name-only", "HEAD^", "HEAD", "--", "*.py"]) or [] | |
| else: | |
| files = collect_files(["git", "ls-files", "*.py"]) or [] | |
| with open(os.environ["GITHUB_OUTPUT"], "a", encoding="utf-8") as fh: | |
| fh.write(f"files={json.dumps(files)}\n") | |
| fh.write(f"count={len(files)}\n") | |
| PY | |
| - name: Run bandit security scan | |
| if: steps.changed.outputs.count != '0' | |
| run: bandit -c pyproject.toml ${{ join(fromJson(steps.changed.outputs.files), ' ') }} | |
| - name: Skip bandit when no Python files changed | |
| if: steps.changed.outputs.count == '0' | |
| run: echo "No Python file changes detected." | |
| test: | |
| name: Beta Tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ env.PYTHON_VERSION }} | |
| activate-environment: BLOOM | |
| environment-file: bloom_env.yaml | |
| auto-activate-base: false | |
| - name: Install bloom in editable mode | |
| shell: bash -el {0} | |
| run: | | |
| pip install -e . | |
| - name: Initialize local Bloom database | |
| shell: bash -el {0} | |
| run: | | |
| bloom db init | |
| - name: Run beta-critical tests | |
| shell: bash -el {0} | |
| run: | | |
| pytest --no-cov \ | |
| tests/test_config_runtime.py \ | |
| tests/test_api_atlas_bridge.py \ | |
| tests/test_atlas_lookup_resilience.py \ | |
| tests/test_queue_flow.py \ | |
| tests/test_run_resolver.py |