From 6303d62c7ade83b19e37246807e66b9bea80356f Mon Sep 17 00:00:00 2001 From: Jakub Recman Date: Mon, 13 Apr 2026 15:36:23 +0200 Subject: [PATCH 1/7] Update workflows and their structure --- .github/workflows/notebook-qa.yml | 785 ++++++++++-------- process-notebooks/action.yml | 235 ------ process-notebooks/checkers/__init__.py | 1 - .../checkers/accessibility_checker.py | 109 --- .../checkers/data_source_checker.py | 113 +++ process-notebooks/checkers/doi_checker.py | 163 ---- process-notebooks/checkers/figure_checker.py | 108 +-- .../checkers/metadata_checker.py | 190 ++--- process-notebooks/checkers/qa_config.py | 212 +++++ process-notebooks/checkers/test_checker.py | 125 --- process-notebooks/checkers/utils.py | 66 +- .../checkers/write_gha_config.py | 88 ++ 12 files changed, 998 insertions(+), 1197 deletions(-) delete mode 100644 process-notebooks/action.yml delete mode 100755 process-notebooks/checkers/__init__.py delete mode 100755 process-notebooks/checkers/accessibility_checker.py create mode 100644 process-notebooks/checkers/data_source_checker.py delete mode 100755 process-notebooks/checkers/doi_checker.py mode change 100755 => 100644 process-notebooks/checkers/metadata_checker.py create mode 100644 process-notebooks/checkers/qa_config.py delete mode 100755 process-notebooks/checkers/test_checker.py mode change 100755 => 100644 process-notebooks/checkers/utils.py create mode 100644 process-notebooks/checkers/write_gha_config.py diff --git a/.github/workflows/notebook-qa.yml b/.github/workflows/notebook-qa.yml index 4a65d8f..3df1fcc 100644 --- a/.github/workflows/notebook-qa.yml +++ b/.github/workflows/notebook-qa.yml @@ -4,405 +4,490 @@ on: workflow_call: inputs: notebooks: - description: 'Comma-separated list of notebook paths to check (e.g., ./notebook1.ipynb,./folder/notebook2.ipynb). Leave empty to check all notebooks.' + description: "Space-separated list of notebook paths to check (default: all *.ipynb)" required: false type: string - default: '' + default: "" + execution_runner: + description: "Runner for notebook execution (supports self-hosted)" + required: false + type: string + default: "ubuntu-latest" + execution_timeout: + description: "Timeout in minutes for notebook execution job" + required: false + type: number + default: 60 + qa_tools_repo: + description: "Repository containing QA tools" + required: false + type: string + default: "ecmwf-training/reusable-workflows" + jira_create_ticket: + description: "Create Jira ticket on failure (requires JIRA_* secrets)" + required: false + type: boolean + default: false + jira_issue_type: + description: "Jira issue type for failure tickets" + required: false + type: string + default: "Bug" + jira_labels: + description: "Comma-separated labels for Jira ticket" + required: false + type: string + default: "notebook-qa,automated" + secrets: + JIRA_BASE_URL: + required: false + JIRA_USER_EMAIL: + required: false + JIRA_API_TOKEN: + required: false + JIRA_PROJECT_KEY: + required: false +env: + QA_OUTPUT_DIR: qa_outputs${{ github.run_id }} jobs: - checks: - strategy: - matrix: - os: [ubuntu-24.04] - python-version: [3.13] - fail-fast: false - runs-on: ${{ matrix.os }} - defaults: - run: - shell: bash -l {0} - env: - QA_OUTPUT_DIR: qa_outputs${{ github.run_id }} + # Job 0: Collect notebooks to check (shared by all jobs) + collect: + runs-on: ubuntu-latest + outputs: + notebooks: ${{ steps.notebooks.outputs.files }} steps: - - name: Checkout code - uses: actions/checkout@v5 - - - name: Set up Conda environment - uses: conda-incubator/setup-miniconda@v3 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 with: - miniforge-version: "latest" - environment-file: "environment.yml" - activate-environment: notebook-qa - auto-activate-base: false - use-mamba: true - channels: conda-forge - use-only-tar-bz2: true - python-version: ${{ matrix.python-version }} + persist-credentials: false + + - name: Fetch PR base for diff + if: github.event.pull_request.base.sha != '' + run: git fetch --depth=1 origin "$BASE_SHA" + env: + BASE_SHA: ${{ github.event.pull_request.base.sha }} - - name: Install QA dependencies + - name: Get notebooks + id: notebooks + env: + INPUT_NOTEBOOKS: ${{ inputs.notebooks }} + BASE_SHA: ${{ github.event.pull_request.base.sha }} run: | - conda install pip - # Pin click to <8.3 to avoid issues with pynblint bool flags - pip install nbqa ruff pynblint 'click<8.3' pytest-check-links ploomber-engine psutil matplotlib \ - beautifulsoup4 lxml pytest pytest-cov - - if command -v apt-get &> /dev/null; then - echo "Installing jq via apt-get..." - sudo apt-get -y update && sudo apt-get -y --no-install-recommends install jq - elif command -v brew &> /dev/null; then - echo "Installing jq via brew..." - brew install jq - elif command -v choco &> /dev/null; then - echo "Installing jq via choco..." - choco install jq + if [ -n "$INPUT_NOTEBOOKS" ]; then + NBS=$(printf '%s\n' $INPUT_NOTEBOOKS) + elif [ -n "$BASE_SHA" ]; then + NBS=$(git diff --name-only --diff-filter=ACMR "$BASE_SHA" HEAD -- '*.ipynb' \ + | grep -v '\.ipynb_checkpoints/' \ + | sed 's|^|./|' || true) else - echo "Error: No package manager found (apt-get, brew, or choco)" - exit 1 + NBS=$(find . -name '*.ipynb' -not -path '*/.ipynb_checkpoints/*') + fi + if [ -z "$NBS" ]; then + echo "files=" >> "$GITHUB_OUTPUT" + echo "No notebooks found." + else + { + echo "files<<__NB_EOF__" + echo "$NBS" + echo "__NB_EOF__" + } >> "$GITHUB_OUTPUT" + echo "Notebooks:" + echo "$NBS" fi - - name: Collect notebooks - id: collect_notebooks - shell: python + # Job 1: Static checks (fast, run on default runner) + lint: + needs: collect + runs-on: ubuntu-latest + outputs: + linter_result: ${{ steps.linter.outcome }} + formatter_result: ${{ steps.formatter.outcome }} + pynblint_result: ${{ steps.pynblint.outcome }} + link_result: ${{ steps.link_checker.outcome }} + test_result: ${{ steps.test_checker.outcome }} + figure_result: ${{ steps.figure_checker.outcome }} + metadata_result: ${{ steps.metadata_checker.outcome }} + accessibility_result: ${{ steps.accessibility_checker.outcome }} + license_result: ${{ steps.license.outcome }} + changelog_result: ${{ steps.changelog.outcome }} + steps: + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + with: + persist-credentials: false + + - name: Checkout QA tools + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + with: + repository: ${{ inputs.qa_tools_repo }} + path: .tmp/${{ github.run_id }}-qa-tools + persist-credentials: false + + - name: Set up uv + uses: astral-sh/setup-uv@cec208311dfd045dd5311c1add060b2062131d57 # v8.0.0 + + - name: Install QA tools + working-directory: .tmp/${{ github.run_id }}-qa-tools + run: | + uv sync --frozen --no-install-project + echo "$PWD/.venv/bin" >> $GITHUB_PATH + + # Load QA configuration + - name: Load QA config + id: config env: - MANUAL_NOTEBOOKS: ${{ inputs.notebooks }} + ALL_NOTEBOOKS: ${{ needs.collect.outputs.notebooks }} run: | - import json - import os - import sys - - manual_notebooks = os.environ.get('MANUAL_NOTEBOOKS', '').strip() - - if manual_notebooks: - # Parse comma-separated notebook paths - notebooks = [nb.strip() for nb in manual_notebooks.split(',') if nb.strip()] - - # Validate that all specified notebooks exist - missing_notebooks = [] - for notebook in notebooks: - if not os.path.isfile(notebook): - missing_notebooks.append(notebook) - - if missing_notebooks: - print(f"Error: The following notebooks do not exist:", file=sys.stderr) - for nb in missing_notebooks: - print(f" - {nb}", file=sys.stderr) - sys.exit(1) - - print(f"Using manually specified notebooks: {notebooks}") - else: - # Default behavior: find all notebooks - notebooks = [] - for root, dirs, files in os.walk('.'): - for filename in files: - if filename.endswith('.ipynb'): - notebook_path = os.path.join(root, filename) - notebooks.append(notebook_path) - - print(f"Found {len(notebooks)} notebooks in repository") - - notebooks_json = json.dumps(notebooks) - with open(os.environ['GITHUB_OUTPUT'], 'a') as fh: - fh.write(f"notebooks={notebooks_json}\n") + python .tmp/${{ github.run_id }}-qa-tools/process-notebooks/checkers/write_gha_config.py \ + --checks linter formatter pynblint links tests figures metadata data_source accessibility license changelog \ + --config .github/notebook-qa.yml \ + --extras + # Linting checks - name: (2.2.3) Run linter id: linter - if: success() || failure() - uses: ecmwf-training/gha-ci-notebook-checks/process-notebooks@main - with: - command: linter - notebooks: ${{ steps.collect_notebooks.outputs.notebooks }} + if: (success() || failure()) && steps.config.outputs.skip_linter != 'true' && steps.config.outputs.notebooks_linter != '' + env: + NOTEBOOKS: ${{ steps.config.outputs.notebooks_linter }} + run: | + mapfile -t nbs <<< "$NOTEBOOKS" + ruff check "${nbs[@]}" - name: (2.2.3) Run formatter id: formatter - if: success() || failure() - uses: ecmwf-training/gha-ci-notebook-checks/process-notebooks@main - with: - command: formatter - notebooks: ${{ steps.collect_notebooks.outputs.notebooks }} + if: (success() || failure()) && steps.config.outputs.skip_formatter != 'true' && steps.config.outputs.notebooks_formatter != '' + env: + NOTEBOOKS: ${{ steps.config.outputs.notebooks_formatter }} + run: | + mapfile -t nbs <<< "$NOTEBOOKS" + ruff format --check --diff "${nbs[@]}" - name: (2.2.3) Run pynblint id: pynblint - if: success() || failure() - uses: ecmwf-training/gha-ci-notebook-checks/process-notebooks@main - with: - command: pynblint - notebooks: ${{ steps.collect_notebooks.outputs.notebooks }} - pynblint_include_violations: 'non-linear-execution,untitled-notebook,on-portable-chars-in-nb-name,missing-h1-MD-heading,missing-opening-MD-text,missing-closing-MD-text,too-few-MD-cells,duplicate-notebook-not-renamed,non-executed-notebook,non-executed-cells,empty-cells' - - - name: (1.2.5) Check for DOI references - id: doi_checker - if: success() || failure() - uses: ecmwf-training/gha-ci-notebook-checks/process-notebooks@main - with: - command: doi_checker - notebooks: ${{ steps.collect_notebooks.outputs.notebooks }} - - - name: (1.2.3) Run link checker - id: link_checker - if: success() || failure() - uses: ecmwf-training/gha-ci-notebook-checks/process-notebooks@main - with: - command: link_checker - notebooks: ${{ steps.collect_notebooks.outputs.notebooks }} - - - name: (2.2.1, 2.2.4, 2.2.6) Execute notebooks - id: execute_notebooks - if: success() || failure() - uses: ecmwf-training/gha-ci-notebook-checks/process-notebooks@main + if: (success() || failure()) && steps.config.outputs.skip_pynblint != 'true' && steps.config.outputs.notebooks_pynblint != '' env: - CDSAPI_KEY: ${{ secrets.CDSAPI_KEY || '' }} - with: - command: execute - notebooks: ${{ steps.collect_notebooks.outputs.notebooks }} - - - name: (1.2.6) Check version metadata - id: metadata_checker - if: success() || failure() - uses: ecmwf-training/gha-ci-notebook-checks/process-notebooks@main + NOTEBOOKS: ${{ steps.config.outputs.notebooks_pynblint }} + PYNBLINT_EXCLUDE: ${{ steps.config.outputs.pynblint_exclude }} + run: | + mapfile -t nbs <<< "$NOTEBOOKS" + failed=0 + for nb in "${nbs[@]}"; do + echo "Checking: $nb" + output_file="/tmp/pynblint_$(basename "$nb" .ipynb).json" + if [ -n "$PYNBLINT_EXCLUDE" ]; then + pynblint "$nb" -o "$output_file" --exclude "$PYNBLINT_EXCLUDE" + else + pynblint "$nb" -o "$output_file" + fi + + # Parse JSON to check for lints (pynblint always exits 0) + lint_count=$(python -c "import json; print(len(json.load(open('$output_file'))['lints']))") + if [ "$lint_count" -gt 0 ]; then + echo "❌ $nb has $lint_count pynblint issue(s):" + python -c " + import json + data = json.load(open('$output_file')) + for lint in data['lints']: + print(f\" - ({lint['slug']}) {lint['description']}\") + " + failed=1 + else + echo "✅ $nb passed pynblint" + fi + done + exit $failed + + # Link checking with lychee (fast, Rust-based) + - name: (1.2.3) Check links + id: link_checker + if: (success() || failure()) && steps.config.outputs.skip_links != 'true' && steps.config.outputs.notebooks_links != '' + uses: lycheeverse/lychee-action@8646ba30535128ac92d33dfc9133794bfdd9b411 # v2.8.0 with: - command: metadata_checker - notebooks: ${{ steps.collect_notebooks.outputs.notebooks }} + args: --verbose --no-progress ${{ steps.config.outputs.notebooks_links }} + fail: true + # Test coverage (direct pytest-cov) - name: (2.3.1, 2.3.2) Check tests and coverage id: test_checker - if: success() || failure() - uses: ecmwf-training/gha-ci-notebook-checks/process-notebooks@main - with: - command: test_checker - notebooks: ${{ steps.collect_notebooks.outputs.notebooks }} - coverage_threshold: '80' - - - name: (3.1.3) Check accessibility - alt text - id: accessibility_checker - if: success() || failure() - uses: ecmwf-training/gha-ci-notebook-checks/process-notebooks@main - with: - command: accessibility_checker - notebooks: ${{ steps.collect_notebooks.outputs.notebooks }} + if: (success() || failure()) && steps.config.outputs.skip_tests != 'true' + env: + REQUIRE_TESTS: ${{ steps.config.outputs.require_tests }} + COVERAGE_THRESHOLD: ${{ steps.config.outputs.coverage_threshold }} + run: | + if ls test_*.py *_test.py tests/*.py 2>/dev/null; then + pytest --cov=. --cov-report=term --cov-fail-under="$COVERAGE_THRESHOLD" + else + echo "::warning::No test files found" + if [ "$REQUIRE_TESTS" = "true" ]; then + echo "Tests are required by configuration (require_tests: true)" + exit 1 + fi + fi + # Custom checks - name: (3.3.2) Check figure labels and sources id: figure_checker - if: success() || failure() - uses: ecmwf-training/gha-ci-notebook-checks/process-notebooks@main - with: - command: figure_checker - notebooks: ${{ steps.collect_notebooks.outputs.notebooks }} + if: (success() || failure()) && steps.config.outputs.skip_figures != 'true' && steps.config.outputs.notebooks_figures != '' + env: + NOTEBOOKS: ${{ steps.config.outputs.notebooks_figures }} + run: | + mapfile -t nbs <<< "$NOTEBOOKS" + python .tmp/${{ github.run_id }}-qa-tools/process-notebooks/checkers/figure_checker.py \ + --config .github/notebook-qa.yml \ + "${nbs[@]}" - - name: Upload notebook outputs - if: always() - uses: actions/upload-artifact@v4 + # Metadata version check + - name: (1.2.6) Check version metadata + id: metadata_checker + if: (success() || failure()) && steps.config.outputs.skip_metadata != 'true' && steps.config.outputs.notebooks_metadata != '' + env: + NOTEBOOKS: ${{ steps.config.outputs.notebooks_metadata }} + run: | + mapfile -t nbs <<< "$NOTEBOOKS" + python .tmp/${{ github.run_id }}-qa-tools/process-notebooks/checkers/metadata_checker.py \ + --config .github/notebook-qa.yml \ + "${nbs[@]}" + + # Data source check (warning only, criterion 1.2.8) + - name: (1.2.8) Check data sources + id: data_source_checker + if: (success() || failure()) && steps.config.outputs.skip_data_source != 'true' && steps.config.outputs.notebooks_data_source != '' + env: + NOTEBOOKS: ${{ steps.config.outputs.notebooks_data_source }} + run: | + mapfile -t nbs <<< "$NOTEBOOKS" + python .tmp/${{ github.run_id }}-qa-tools/process-notebooks/checkers/data_source_checker.py \ + --config .github/notebook-qa.yml \ + "${nbs[@]}" + + # Accessibility check + - name: (3.1.3) Check accessibility + id: accessibility_checker + if: (success() || failure()) && steps.config.outputs.skip_accessibility != 'true' && steps.config.outputs.notebooks_accessibility != '' + uses: berkeley-dsep-infra/jupyterlab-a11y-checker@c77482165508460d671cdad6ecdff5ac72ab6063 with: - name: notebook-outputs-${{ github.run_id }} - path: ${{ env.QA_OUTPUT_DIR }} - if-no-files-found: warn + files: ${{ steps.config.outputs.notebooks_accessibility }} + # File existence checks - name: (1.2.4) Check LICENSE id: license - if: success() || failure() + if: (success() || failure()) && steps.config.outputs.skip_license != 'true' run: | - if [[ ! -f "LICENSE" ]]; then - echo "LICENSE file is missing" - exit 1 + if [ -s LICENSE ]; then + echo "✅ LICENSE file is present and non-empty" else - echo "LICENSE file is present" - fi - if [ ! -s "LICENSE" ]; then - echo "LICENSE file is empty" + echo "❌ LICENSE file is missing or empty" exit 1 - else - echo "LICENSE file is not empty" fi - name: (4.2.3) Check CHANGELOG id: changelog - if: success() || failure() + if: (success() || failure()) && steps.config.outputs.skip_changelog != 'true' run: | - if [[ ! -f "CHANGELOG.md" ]]; then - echo "CHANGELOG.md file is missing" - exit 1 + if [ -s CHANGELOG.md ]; then + echo "✅ CHANGELOG.md file is present and non-empty" else - echo "CHANGELOG.md file is present" - fi - if [ ! -s "CHANGELOG.md" ]; then - echo "CHANGELOG.md file is empty" + echo "❌ CHANGELOG.md file is missing or empty" exit 1 - else - echo "CHANGELOG.md file is not empty" fi - - name: Generate Workflow Summary - if: always() - shell: python + # Job 2: Notebook execution (resource-intensive, configurable runner) + execute: + needs: collect + runs-on: ${{ inputs.execution_runner }} + timeout-minutes: ${{ inputs.execution_timeout }} + outputs: + execute_result: ${{ steps.execute_notebooks.outcome }} + defaults: + run: + shell: bash -el {0} + env: + CDSAPI_KEY: ${{ secrets.CDSAPI_KEY }} # zizmor: ignore[secrets-outside-env] + steps: + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + with: + persist-credentials: false + + - name: Checkout QA tools + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + with: + repository: ${{ inputs.qa_tools_repo }} + path: .tmp/${{ github.run_id }}-qa-tools + persist-credentials: false + + # Load QA config to check if execute is disabled + - name: Load QA config + id: config + env: + ALL_NOTEBOOKS: ${{ needs.collect.outputs.notebooks }} run: | - import csv - import json + python3 .tmp/${{ github.run_id }}-qa-tools/process-notebooks/checkers/write_gha_config.py \ + --checks execute \ + --config .github/notebook-qa.yml + + - name: Skip execution check + if: steps.config.outputs.skip_execute == 'true' || steps.config.outputs.notebooks_execute == '' + run: echo "Notebook execution skipped by configuration" + + - name: Set up Conda + if: steps.config.outputs.skip_execute != 'true' && steps.config.outputs.notebooks_execute != '' + uses: conda-incubator/setup-miniconda@fc2d68f6413eb2d87b895e92f8584b5b94a10167 # v3.3.0 + with: + miniforge-version: latest + activate-environment: notebook-qa + environment-file: environment.yml + use-mamba: true + + - name: Install execution tools + if: steps.config.outputs.skip_execute != 'true' && steps.config.outputs.notebooks_execute != '' + run: pip install ploomber-engine psutil matplotlib pyyaml + + - name: Configure CDS API + if: steps.config.outputs.skip_execute != 'true' && steps.config.outputs.notebooks_execute != '' && env.CDSAPI_KEY != '' + run: | + echo "url: https://cds.climate.copernicus.eu/api" > ~/.cdsapirc + echo "key: $CDSAPI_KEY" >> ~/.cdsapirc + + - name: (2.2.1, 2.2.4, 2.2.6) Execute notebooks with memory profiling + id: execute_notebooks + if: steps.config.outputs.skip_execute != 'true' && steps.config.outputs.notebooks_execute != '' + env: + NOTEBOOKS_EXECUTE: ${{ steps.config.outputs.notebooks_execute }} + run: | + python << 'EOF' import os + import csv from pathlib import Path + from ploomber_engine import execute_notebook + from ploomber_engine.profiling import get_profiling_data + + notebooks = [nb for nb in os.environ['NOTEBOOKS_EXECUTE'].splitlines() if nb.strip()] + output_dir = os.environ.get('QA_OUTPUT_DIR', 'qa_outputs') + Path(output_dir).mkdir(parents=True, exist_ok=True) + + failed = [] + for nb in notebooks: + if not nb.strip(): + continue + print(f"\n{'='*60}") + print(f"Executing: {nb}") + print('='*60) + try: + result = execute_notebook( + nb, + output_path=nb, + profile_memory=True, + progress_bar=False + ) + # Save profiling data from cell metadata + data = get_profiling_data(result) + if data.get('memory') or data.get('runtime'): + csv_path = Path(output_dir) / f"{Path(nb).stem}-profiling-data.csv" + with open(csv_path, 'w', newline='') as f: + writer = csv.DictWriter(f, fieldnames=['cell', 'memory', 'runtime']) + writer.writeheader() + for i, (mem, time) in enumerate(zip( + data.get('memory', []), + data.get('runtime', []) + )): + writer.writerow({'cell': i, 'memory': mem, 'runtime': time}) + else: + print(f"::warning::No profiling data returned for {nb}") + print(f"✅ {nb} executed successfully") + except Exception as e: + print(f"❌ {nb} failed: {e}") + failed.append(nb) + + if failed: + print(f"\n❌ {len(failed)} notebook(s) failed to execute:") + for nb in failed: + print(f" - {nb}") + exit(1) + EOF + + - name: Upload profiling artifacts + if: always() + uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7.0.0 + with: + name: notebook-profiling-${{ github.run_id }} + path: ${{ env.QA_OUTPUT_DIR }} + if-no-files-found: ignore + + # Job 3: Create Jira ticket on failure (optional) + notify-failure: + needs: [lint, execute] + runs-on: ubuntu-latest + if: >- + always() && + inputs.jira_create_ticket == true && + (needs.lint.result == 'failure' || needs.execute.result == 'failure') + steps: + - name: Login to Jira + uses: atlassian/gajira-login@ca13f8850ea309cf44a6e4e0c49d9aa48ac3ca4c # v3 + env: + JIRA_BASE_URL: ${{ secrets.JIRA_BASE_URL }} # zizmor: ignore[secrets-outside-env] + JIRA_USER_EMAIL: ${{ secrets.JIRA_USER_EMAIL }} # zizmor: ignore[secrets-outside-env] + JIRA_API_TOKEN: ${{ secrets.JIRA_API_TOKEN }} # zizmor: ignore[secrets-outside-env] - # Get step outcomes - outcomes = { - '(1.2.3) Link Checker': '${{ steps.link_checker.outcome }}', - '(1.2.4) License Check': '${{ steps.license.outcome }}', - '(1.2.5) DOI Checker': '${{ steps.doi_checker.outcome }}', - '(1.2.6) Metadata Check': '${{ steps.metadata_checker.outcome }}', - '(2.2.3) Linter': '${{ steps.linter.outcome }}', - '(2.2.3) Formatter': '${{ steps.formatter.outcome }}', - '(2.2.3) Pynblint': '${{ steps.pynblint.outcome }}', - '(2.2.1, 2.2.4, 2.2.6) Execute Notebooks': '${{ steps.execute_notebooks.outcome }}', - '(2.3.1, 2.3.2) Test & Coverage': '${{ steps.test_checker.outcome }}', - '(3.1.3) Accessibility': '${{ steps.accessibility_checker.outcome }}', - '(3.3.2) Figure Labels': '${{ steps.figure_checker.outcome }}', - '(4.2.3) Changelog Check': '${{ steps.changelog.outcome }}', - } - - # Map outcomes to status icons - status_map = { - 'success': '✅ Pass', - 'failure': '❌ Fail', - 'skipped': '⏭️ Skipped', - 'cancelled': '🚫 Cancelled', - '': '⏭️ Skipped' - } - - # Map individual notebook statuses to icons - notebook_status_map = { - 'success': '✅', - 'failure': '❌', - 'skipped': '⏭️', - } - - summary = [] - summary.append('# Notebook QA Summary\n') - - # Add overall status table - summary.append('## Overall Check Results\n') - summary.append('| Check | Status |') - summary.append('|-------|--------|') - - for check_name, outcome in outcomes.items(): - status = status_map.get(outcome, outcome) - summary.append(f'| {check_name} | {status} |') - - summary.append('\n') - - # Read per-notebook results - qa_output_dir = os.getenv('QA_OUTPUT_DIR', 'qa_outputs') - output_path = Path(qa_output_dir) - - # Command mapping for table headers - command_headers = { - 'link_checker': 'Links', - 'doi_checker': 'DOI', - 'metadata_checker': 'Metadata', - 'linter': 'Linter', - 'formatter': 'Formatter', - 'pynblint': 'Pynblint', - 'execute': 'Execute', - 'test_checker': 'Tests', - 'accessibility_checker': 'Alt-text', - 'figure_checker': 'Figures' - } - - # Collect all notebook results - all_notebooks = set() - results_by_command = {} - - if output_path.exists(): - # Read all result JSON files - for result_file in output_path.glob('*-results.json'): - try: - with open(result_file, 'r') as f: - data = json.load(f) - command = data.get('command', '') - results = data.get('results', {}) - results_by_command[command] = results - all_notebooks.update(results.keys()) - except Exception as e: - print(f"Warning: Failed to read {result_file}: {e}") - - # Generate per-notebook results table if we have results - if all_notebooks and results_by_command: - summary.append('## Per-Notebook Results\n') - - # Create table header - header = '| Notebook |' - separator = '|----------|' - for cmd in ['linter', 'formatter', 'pynblint', 'doi_checker', 'link_checker', 'execute', - 'metadata_checker', 'test_checker', 'accessibility_checker', 'figure_checker']: - if cmd in results_by_command: - header += f' {command_headers[cmd]} |' - separator += '--------|' - - summary.append(header) - summary.append(separator) - - # Create table rows for each notebook - for notebook in sorted(all_notebooks): - row = f'| {notebook} |' - - for cmd in ['linter', 'formatter', 'pynblint', 'doi_checker', 'link_checker', 'execute', - 'metadata_checker', 'test_checker', 'accessibility_checker', 'figure_checker']: - if cmd in results_by_command: - status = results_by_command[cmd].get(notebook, 'skipped') - icon = notebook_status_map.get(status, '⏭️') - row += f' {icon} |' - - summary.append(row) - - summary.append('\n') - - # Add memory profiling section - - if output_path.exists(): - # Add CSV memory profiling data tables - profiling_csvs = sorted(output_path.glob('*-profiling-data.csv')) - - if profiling_csvs: - for csv_path in profiling_csvs: - # Extract notebook name from CSV filename - # Format: .output-profiling-data.csv - notebook_name = csv_path.stem.replace('.output-profiling-data', '') - - # Parse CSV file - try: - with open(csv_path, 'r') as csvfile: - reader = csv.DictReader(csvfile) - rows = list(reader) - - if rows: - # Create collapsible section for each notebook - summary.append(f'\n
\n{notebook_name} ({len(rows)} cells)\n\n') - - # Create table header - summary.append('| Cell | Memory (MB) | Time (s) |') - summary.append('|------|-------------|----------|') - - # Add rows for each cell - for row in rows: - cell = row.get('cell', 'N/A') - memory_mb = row.get('memory', 'N/A') - if memory_mb != 'N/A': - try: - memory_mb = f"{float(memory_mb):.2f}" - except ValueError: - pass - exec_time_s = row.get('runtime', 'N/A') - if exec_time_s != 'N/A': - try: - exec_time_s = f"{float(exec_time_s):.2f}" - except ValueError: - pass - - summary.append(f'| {cell} | {memory_mb} | {exec_time_s} |') - - summary.append('\n
\n') - except Exception as e: - print(f'Warning: Failed to parse {csv_path}: {e}') - summary.append(f'\n*Could not parse profiling data for {notebook_name}*\n') - - summary.append('\n**View the generated memory profile charts by downloading the workflow artifacts.**\n') - - summary_text = '\n'.join(summary) - github_summary = os.getenv('GITHUB_STEP_SUMMARY') - with open(github_summary, 'a') as f: - f.write(summary_text) + - name: Build failure summary + id: summary + env: + LINT_LINTER: ${{ needs.lint.outputs.linter_result }} + LINT_FORMATTER: ${{ needs.lint.outputs.formatter_result }} + LINT_PYNBLINT: ${{ needs.lint.outputs.pynblint_result }} + LINT_LINKS: ${{ needs.lint.outputs.link_result }} + LINT_TESTS: ${{ needs.lint.outputs.test_result }} + LINT_FIGURES: ${{ needs.lint.outputs.figure_result }} + LINT_METADATA: ${{ needs.lint.outputs.metadata_result }} + LINT_A11Y: ${{ needs.lint.outputs.accessibility_result }} + LINT_LICENSE: ${{ needs.lint.outputs.license_result }} + LINT_CHANGELOG: ${{ needs.lint.outputs.changelog_result }} + EXEC_RESULT: ${{ needs.execute.outputs.execute_result }} + JIRA_LABELS_INPUT: ${{ inputs.jira_labels }} + run: | + # Build a list of failed checks + FAILED_CHECKS="" + + # Lint job checks + [ "$LINT_LINTER" = "failure" ] && FAILED_CHECKS="${FAILED_CHECKS}- Linter (ruff check)\n" + [ "$LINT_FORMATTER" = "failure" ] && FAILED_CHECKS="${FAILED_CHECKS}- Formatter (ruff format)\n" + [ "$LINT_PYNBLINT" = "failure" ] && FAILED_CHECKS="${FAILED_CHECKS}- Pynblint\n" + [ "$LINT_LINKS" = "failure" ] && FAILED_CHECKS="${FAILED_CHECKS}- Link checker\n" + [ "$LINT_TESTS" = "failure" ] && FAILED_CHECKS="${FAILED_CHECKS}- Tests/coverage\n" + [ "$LINT_FIGURES" = "failure" ] && FAILED_CHECKS="${FAILED_CHECKS}- Figure labels/sources\n" + [ "$LINT_METADATA" = "failure" ] && FAILED_CHECKS="${FAILED_CHECKS}- Version metadata\n" + [ "$LINT_A11Y" = "failure" ] && FAILED_CHECKS="${FAILED_CHECKS}- Accessibility\n" + [ "$LINT_LICENSE" = "failure" ] && FAILED_CHECKS="${FAILED_CHECKS}- LICENSE file\n" + [ "$LINT_CHANGELOG" = "failure" ] && FAILED_CHECKS="${FAILED_CHECKS}- CHANGELOG\n" + + # Execute job + [ "$EXEC_RESULT" = "failure" ] && FAILED_CHECKS="${FAILED_CHECKS}- Notebook execution\n" + + echo "failed_checks<> $GITHUB_OUTPUT + echo -e "$FAILED_CHECKS" >> $GITHUB_OUTPUT + echo "EOF" >> $GITHUB_OUTPUT + + # Convert comma-separated labels to JSON array + LABELS_JSON=$(echo "$JIRA_LABELS_INPUT" | tr ',' '\n' | sed 's/^[[:space:]]*//;s/[[:space:]]*$//' | jq -R . | jq -s .) + echo "labels_json=$LABELS_JSON" >> $GITHUB_OUTPUT + + - name: Create Jira ticket + uses: atlassian/gajira-create@1ff0b6bd115a780592b47bfbb63fc4629132e6ec # v3 + with: + project: ${{ secrets.JIRA_PROJECT_KEY }} # zizmor: ignore[secrets-outside-env] + issuetype: ${{ inputs.jira_issue_type }} + summary: "[Notebook QA] Checks failed in ${{ github.repository }} (${{ github.ref_name }})" + description: | + h2. Notebook QA Workflow Failure + + *Repository:* ${{ github.repository }} + *Branch:* ${{ github.ref_name }} + *Commit:* ${{ github.sha }} + *Workflow Run:* [View logs|${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}] + + h3. Failed Checks + ${{ steps.summary.outputs.failed_checks }} + + h3. Triggered By + ${{ github.event.head_commit.message || github.event.pull_request.title || 'Manual run' }} + fields: '{"labels": ${{ steps.summary.outputs.labels_json }}}' diff --git a/process-notebooks/action.yml b/process-notebooks/action.yml deleted file mode 100644 index 8600bba..0000000 --- a/process-notebooks/action.yml +++ /dev/null @@ -1,235 +0,0 @@ -name: 'Process Notebooks' -description: 'Run QA tools on Jupyter notebooks cross-platform' -inputs: - command: - description: 'Command to run (linter, formatter, pynblint, link_checker, doi_checker, execute, metadata_checker, test_checker, accessibility_checker, figure_checker)' - required: true - notebooks: - description: 'JSON array of notebook paths' - required: true - pynblint_include_violations: - description: 'List of violations to include when running pynblint (comma-separated)' - required: false - default: '' - coverage_threshold: - description: 'Minimum code coverage percentage for test_checker (default: 80)' - required: false - default: '80' -runs: - using: 'composite' - steps: - - name: Process notebooks - shell: bash -l {0} - run: | - python3 - << 'EOF' - import json - import os - import subprocess - import sys - - from pathlib import Path - from ploomber_engine import execute_notebook - - command = "${{ inputs.command }}" - notebooks_json = """${{ inputs.notebooks }}""".strip() - - valid_commands = ['linter', 'formatter', 'pynblint', 'link_checker', 'doi_checker', 'execute', - 'metadata_checker', 'test_checker', 'accessibility_checker', 'figure_checker'] - if command not in valid_commands: - print(f"Error: Invalid command '{command}'") - print(f"Valid commands: {', '.join(valid_commands)}") - sys.exit(1) - - if not notebooks_json: - notebooks = [] - else: - try: - notebooks = json.loads(notebooks_json) - except json.JSONDecodeError: - print(f"Error: Invalid JSON format") - sys.exit(1) - - # Get action path for checker scripts - action_path = os.environ.get('GITHUB_ACTION_PATH', str(Path(__file__).parent)) - output_dir = os.getenv("QA_OUTPUT_DIR", "qa_outputs") - - result = 0 - notebook_results = {} - - for notebook in notebooks: - if not notebook: - continue - - print(f"Processing {notebook} with {command}") - - if command == "linter": - cmd = ["nbqa", "ruff check", notebook] - elif command == "formatter": - cmd = ["nbqa", "ruff format --diff", notebook] - elif command == "pynblint": - notebook_name = Path(notebook).name - lint_file = f"lint.{notebook_name}.json" - cmd = ["pynblint", "--output", lint_file, notebook] - include_violations_str = "${{ inputs.pynblint_include_violations }}".strip() - if include_violations_str: - include_violations = [v.strip() for v in include_violations_str.split(',') if v.strip()] - if include_violations: - violations_json = '[' + ','.join(f'"{v}"' for v in include_violations) + ']' - cmd.extend(["--include", violations_json]) - elif command == "link_checker": - cmd = ["pytest-check-links", notebook] - elif command == "doi_checker": - cmd = [ - 'python3', - os.path.join(action_path, 'checkers', 'doi_checker.py'), - '--notebooks', json.dumps([notebook]), - '--output-dir', output_dir - ] - try: - subprocess.run(cmd, check=True) - notebook_results[notebook] = "success" - except subprocess.CalledProcessError: - notebook_results[notebook] = "failure" - result = 1 - # Results are written by the checker script, skip default processing - continue - elif command == "execute": - # Create cdsapi config file if needed - cdsapi_key = os.getenv("CDSAPI_KEY") - if cdsapi_key: - print("Creating .cdsapirc file") - cdsapi_rc = Path.home() / ".cdsapirc" - if not cdsapi_rc.exists(): - with open(cdsapi_rc, 'w') as f: - f.write("url: https://cds.climate.copernicus.eu/api\n") - f.write(f"key: {cdsapi_key}") - - output_dir = os.getenv("QA_OUTPUT_DIR", "qa_outputs") - Path(output_dir).mkdir(parents=True, exist_ok=True) - - notebook_path = Path(notebook) - output_name = notebook_path.stem + ".output" + notebook_path.suffix - output_path = Path(output_dir) / output_name - - # Execute notebook with memory profiling and CSV output - try: - execute_notebook( - input_path=notebook, - output_path=str(output_path), - profile_memory=True, - save_profiling_data=True - ) - print(f"✅ {command} finished successfully for {notebook}") - notebook_results[notebook] = "success" - except Exception as e: - print(f"❌ {command} failed for {notebook}: {e}") - notebook_results[notebook] = "failure" - result = 1 - # Skip subprocess call for execute - continue - elif command == "metadata_checker": - cmd = [ - 'python3', - os.path.join(action_path, 'checkers', 'metadata_checker.py'), - '--notebooks', json.dumps([notebook]), - '--output-dir', output_dir, - '--check-readme' - ] - try: - subprocess.run(cmd, check=True) - notebook_results[notebook] = "success" - except subprocess.CalledProcessError: - notebook_results[notebook] = "failure" - result = 1 - # Results are written by the checker script, skip default processing - continue - elif command == "test_checker": - coverage_threshold_str = "${{ inputs.coverage_threshold }}".strip() - cmd = [ - 'python3', - os.path.join(action_path, 'checkers', 'test_checker.py'), - '--notebooks', json.dumps([notebook]), - '--output-dir', output_dir, - '--coverage-threshold', coverage_threshold_str if coverage_threshold_str else '80' - ] - try: - subprocess.run(cmd, check=True) - notebook_results[notebook] = "success" - except subprocess.CalledProcessError: - notebook_results[notebook] = "failure" - result = 1 - # Results are written by the checker script, skip default processing - continue - elif command == "accessibility_checker": - # Call external checker script - cmd = [ - 'python3', - os.path.join(action_path, 'checkers', 'accessibility_checker.py'), - '--notebooks', json.dumps([notebook]), - '--output-dir', output_dir - ] - try: - subprocess.run(cmd, check=True) - notebook_results[notebook] = "success" - except subprocess.CalledProcessError: - notebook_results[notebook] = "failure" - result = 1 - # Results are written by the checker script, skip default processing - continue - elif command == "figure_checker": - cmd = [ - 'python3', - os.path.join(action_path, 'checkers', 'figure_checker.py'), - '--notebooks', json.dumps([notebook]), - '--output-dir', output_dir - ] - try: - subprocess.run(cmd, check=True) - notebook_results[notebook] = "success" - except subprocess.CalledProcessError: - notebook_results[notebook] = "failure" - result = 1 - # Results are written by the checker script, skip default processing - continue - - try: - subprocess.run(cmd, check=True) - - # Handle pynblint recommendations - if command == "pynblint" and Path(lint_file).exists(): - with open(lint_file, 'r') as f: - lint_data = json.load(f) - if any('recommendation' in lint for lint in lint_data.get('lints', [])): - print(f"❌ pynblint failed for {notebook}") - notebook_results[notebook] = "failure" - result = 1 - else: - print(f"✅ {command} finished successfully for {notebook}") - notebook_results[notebook] = "success" - else: - print(f"✅ {command} finished successfully for {notebook}") - notebook_results[notebook] = "success" - except subprocess.CalledProcessError: - print(f"❌ {command} failed for {notebook}") - notebook_results[notebook] = "failure" - result = 1 - except Exception as e: - print(f"❌ Error processing {notebook}: {e}") - notebook_results[notebook] = "failure" - result = 1 - - # Write results to JSON file for workflow summary to parse - output_dir = os.getenv("QA_OUTPUT_DIR", "qa_outputs") - Path(output_dir).mkdir(parents=True, exist_ok=True) - results_file = Path(output_dir) / f"{command}-results.json" - - results_data = { - "command": command, - "results": notebook_results - } - - with open(results_file, 'w') as f: - json.dump(results_data, f, indent=2) - - sys.exit(result) - EOF diff --git a/process-notebooks/checkers/__init__.py b/process-notebooks/checkers/__init__.py deleted file mode 100755 index 4fb06be..0000000 --- a/process-notebooks/checkers/__init__.py +++ /dev/null @@ -1 +0,0 @@ -"""Notebook checker modules for QA validation.""" diff --git a/process-notebooks/checkers/accessibility_checker.py b/process-notebooks/checkers/accessibility_checker.py deleted file mode 100755 index 56562c5..0000000 --- a/process-notebooks/checkers/accessibility_checker.py +++ /dev/null @@ -1,109 +0,0 @@ -#!/usr/bin/env python3 -""" -Accessibility Checker for Jupyter Notebooks - -Checks for alt-text on all images (Criterion 3.1.3). -""" - -import argparse -import json -import re -import sys -from pathlib import Path - -from bs4 import BeautifulSoup - -sys.path.insert(0, str(Path(__file__).parent)) -from utils import read_notebook, extract_cell_source, write_results - - -def check_accessibility(notebook_path: str) -> str: - """ - Check for alt-text on all images in a notebook. - - Args: - notebook_path: Path to the notebook file - - Returns: - Result status: "success" or "failure" - """ - nb_data = read_notebook(notebook_path) - - issues = [] - - for cell_idx, cell in enumerate(nb_data.get('cells', [])): - # Check markdown cells for images - if cell.get('cell_type') == 'markdown': - source = extract_cell_source(cell) - - # Check HTML img tags - soup = BeautifulSoup(source, 'html.parser') - for img in soup.find_all('img'): - alt = img.get('alt', '').strip() - if not alt: - issues.append(f"Cell {cell_idx}: tag missing alt text") - - # Check markdown image syntax: ![alt](url) - md_images = re.findall(r'!\[(.*?)\]\([^)]*\)', source) - ref_images = re.findall(r'!\[(.*?)\]\[[^\]]*\]', source) - for idx, alt_text in enumerate(md_images + ref_images): - if not alt_text.strip(): - issues.append(f"Cell {cell_idx}: Markdown image missing alt text") - - # Check output cells for figures - elif cell.get('cell_type') == 'code': - outputs = cell.get('outputs', []) - for output in outputs: - if output.get('output_type') in ['display_data', 'execute_result']: - # Check for image outputs - data = output.get('data', {}) - if 'image/png' in data or 'image/jpeg' in data or 'image/jpg' in data: - metadata = output.get('metadata', {}) - # Check for alt text in metadata - if not metadata.get('alt_text') and not metadata.get('alt'): - issues.append(f"Cell {cell_idx}: Figure output missing alt text metadata") - - if not issues: - print(f"✅ All images have alt-text in {notebook_path}") - return "success" - else: - print(f"❌ Found {len(issues)} accessibility issue(s) in {notebook_path}:") - for issue in issues: - print(f" - {issue}") - print("\nAdd alt-text to all images for screen reader compatibility") - return "failure" - - -def main(): - parser = argparse.ArgumentParser(description='Check for image alt-text in notebooks') - parser.add_argument('--notebooks', required=True, help='JSON array of notebook paths') - parser.add_argument('--output-dir', required=True, help='Directory to write results') - args = parser.parse_args() - - try: - notebooks = json.loads(args.notebooks) - except json.JSONDecodeError as e: - print(f"Error: Invalid JSON format for notebooks: {e}") - sys.exit(1) - - notebook_results = {} - overall_result = 0 - - for notebook in notebooks: - if not notebook: - continue - - print(f"Processing {notebook} with accessibility_checker") - result = check_accessibility(notebook) - notebook_results[notebook] = result - - if result == "failure": - overall_result = 1 - - write_results("accessibility_checker", notebook_results, args.output_dir) - - sys.exit(overall_result) - - -if __name__ == "__main__": - main() diff --git a/process-notebooks/checkers/data_source_checker.py b/process-notebooks/checkers/data_source_checker.py new file mode 100644 index 0000000..29f9dfd --- /dev/null +++ b/process-notebooks/checkers/data_source_checker.py @@ -0,0 +1,113 @@ +#!/usr/bin/env python3 +""" +Data Source Checker for Jupyter Notebooks (Warning Only) + +Checks that notebooks source data via cdsapi and/or earthkit (Criterion 1.2.8). + +If data sourcing is detected but NOT via cdsapi/earthkit, emits a ::warning:: +annotation. This check NEVER fails the job — it always exits 0. + +Usage: + python data_source_checker.py [--config CONFIG] notebook1.ipynb notebook2.ipynb ... +""" + +import argparse +import re +import sys + +from qa_config import filter_notebooks, is_check_disabled, load_config +from utils import extract_cell_source, read_notebook + +# Patterns indicating data sourcing via approved sources +APPROVED_PATTERNS = [ + r"import\s+cdsapi", + r"from\s+cdsapi", + r"import\s+earthkit", + r"from\s+earthkit", + r"cds\.climate\.copernicus\.eu", + r"ads\.atmosphere\.copernicus\.eu", +] + +# Patterns indicating data sourcing via other methods +OTHER_SOURCE_PATTERNS = [ + r"requests\.get\s*\(", + r"urllib\.request", + r"wget", + r"curl", + r'open_dataset\s*\(["\']https?://', + r'read_csv\s*\(["\']https?://', + r"download\s*\(", +] + + +def check_data_source(notebook_path: str) -> str: + """ + Check data sourcing patterns in a notebook's code cells. + + Returns: "success" | "warning" | "skipped" + """ + try: + nb_data = read_notebook(notebook_path) + except Exception as e: + print(f"::warning file={notebook_path}::Could not read notebook: {e}") + return "skipped" + + code_cells = [ + extract_cell_source(cell) + for cell in nb_data.get("cells", []) + if cell.get("cell_type") == "code" + ] + all_code = "\n".join(code_cells) + + has_approved = any(re.search(p, all_code) for p in APPROVED_PATTERNS) + has_other = any(re.search(p, all_code) for p in OTHER_SOURCE_PATTERNS) + + if has_approved: + print(f" {notebook_path}: Data sourced via cdsapi/earthkit") + return "success" + + if has_other: + print( + f"::warning file={notebook_path}::" + f"Data sourcing detected but not via cdsapi or earthkit. " + f"Consider using cdsapi or earthkit for CDS data access." + ) + return "warning" + + # No data sourcing detected + return "skipped" + + +def main(): + parser = argparse.ArgumentParser( + description="Check data sourcing patterns in Jupyter notebooks (warning only)" + ) + parser.add_argument("notebooks", nargs="*", help="Notebook files to check") + parser.add_argument( + "--config", + default=".github/notebook-qa.yml", + help="Path to QA configuration file (default: .github/notebook-qa.yml)", + ) + args = parser.parse_args() + + config = load_config(args.config) + + if is_check_disabled(config, "data_source"): + print("Data source check is disabled by configuration") + sys.exit(0) + + notebooks = filter_notebooks(config, "data_source", args.notebooks) + + if not notebooks: + print("All notebooks skipped by configuration") + sys.exit(0) + + for notebook in notebooks: + check_data_source(notebook) + + # Warning-only check: always exit 0 + sys.exit(0) + + +if __name__ == "__main__": + main() diff --git a/process-notebooks/checkers/doi_checker.py b/process-notebooks/checkers/doi_checker.py deleted file mode 100755 index a23b3e8..0000000 --- a/process-notebooks/checkers/doi_checker.py +++ /dev/null @@ -1,163 +0,0 @@ -#!/usr/bin/env python3 -""" -DOI Checker for Jupyter Notebooks - -Checks if notebooks that use datasets with DOI metadata properly cite those DOIs (Criterion 1.2.5). -""" - -import argparse -import json -import re -import sys -from pathlib import Path - -sys.path.insert(0, str(Path(__file__).parent)) -from utils import read_notebook, extract_cell_source, write_results - - -def check_doi(notebook_path: str) -> str: - """ - Check for DOI citations in a notebook. - - Args: - notebook_path: Path to the notebook file - - Returns: - Result status: "success", "failure", or "skipped" - """ - # DOI regex patterns - doi_patterns = [ - r'10\.\d{4,9}/[-._;()/:A-Z0-9]+', # Standard DOI format - r'doi\.org/(10\.\d{4,9}/[-._;()/:A-Z0-9]+)', # doi.org URLs - r'https?://(?:dx\.)?doi\.org/(10\.\d{4,9}/[-._;()/:A-Z0-9]+)' # Full DOI URLs - ] - - # Metadata fields that might contain DOI references - metadata_fields = ['references', 'citation', 'doi', 'reference', 'Attributes'] - - nb_data = read_notebook(notebook_path) - - # First, check if dataset metadata contains DOI references - has_dataset_doi_metadata = False - - for cell in nb_data.get('cells', []): - if cell.get('cell_type') == 'code': - for output in cell.get('outputs', []): - # Check text outputs for dataset metadata with DOIs - if 'text' in output: - text = output['text'] - if isinstance(text, list): - text = ''.join(text) - # Check if this looks like xarray/dataset output with metadata - if any(field in text for field in metadata_fields): - # Check if metadata contains DOI patterns - for pattern in doi_patterns: - if re.search(pattern, text, re.IGNORECASE): - has_dataset_doi_metadata = True - break - - # Check data outputs for metadata - data = output.get('data', {}) - for key, value in data.items(): - if isinstance(value, (str, list)): - if isinstance(value, list): - value = ''.join(value) - if any(field in value for field in metadata_fields): - for pattern in doi_patterns: - if re.search(pattern, value, re.IGNORECASE): - has_dataset_doi_metadata = True - break - - if has_dataset_doi_metadata: - break - - if has_dataset_doi_metadata: - break - - if not has_dataset_doi_metadata: - print(f"INFO: No dataset DOI metadata found in {notebook_path}, skipping DOI check") - return "skipped" - - found_dois = set() - - # Search in all cells for DOI citations - for cell in nb_data.get('cells', []): - # Check markdown cells - if cell.get('cell_type') == 'markdown': - source = extract_cell_source(cell) - for pattern in doi_patterns: - matches = re.findall(pattern, source, re.IGNORECASE) - found_dois.update(matches) - - # Check code cell outputs - if cell.get('cell_type') == 'code': - for output in cell.get('outputs', []): - # Check text outputs - if 'text' in output: - text = output['text'] - if isinstance(text, list): - text = ''.join(text) - for pattern in doi_patterns: - matches = re.findall(pattern, text, re.IGNORECASE) - found_dois.update(matches) - - # Check data outputs (HTML, plain text, etc.) - data = output.get('data', {}) - for key, value in data.items(): - if isinstance(value, (str, list)): - if isinstance(value, list): - value = ''.join(value) - for pattern in doi_patterns: - matches = re.findall(pattern, value, re.IGNORECASE) - found_dois.update(matches) - - # Validate DOI format - valid_doi_pattern = re.compile(r'^10\.\d{4,9}/[-._;()/:A-Z0-9]+$', re.IGNORECASE) - valid_dois = [doi for doi in found_dois if valid_doi_pattern.match(doi)] - - if not valid_dois: - print(f"ERROR: No valid DOI found in {notebook_path}") - print(" Notebook uses dataset with DOI metadata but doesn't cite the DOI") - print(" Please add DOI citation in markdown or ensure dataset metadata is visible") - print(" Expected format: 10.xxxx/xxxxx") - return "failure" - else: - print(f"Found {len(valid_dois)} valid DOI(s) in {notebook_path}:") - for doi in sorted(valid_dois): - print(f" - {doi}") - return "success" - - -def main(): - parser = argparse.ArgumentParser(description='Check for DOI citations in notebooks') - parser.add_argument('--notebooks', required=True, help='JSON array of notebook paths') - parser.add_argument('--output-dir', required=True, help='Directory to write results') - args = parser.parse_args() - - try: - notebooks = json.loads(args.notebooks) - except json.JSONDecodeError as e: - print(f"Error: Invalid JSON format for notebooks: {e}") - sys.exit(1) - - notebook_results = {} - overall_result = 0 - - for notebook in notebooks: - if not notebook: - continue - - print(f"Processing {notebook} with doi_checker") - result = check_doi(notebook) - notebook_results[notebook] = result - - if result == "failure": - overall_result = 1 - - write_results("doi_checker", notebook_results, args.output_dir) - - sys.exit(overall_result) - - -if __name__ == "__main__": - main() diff --git a/process-notebooks/checkers/figure_checker.py b/process-notebooks/checkers/figure_checker.py index 93ddc33..6013032 100755 --- a/process-notebooks/checkers/figure_checker.py +++ b/process-notebooks/checkers/figure_checker.py @@ -3,56 +3,56 @@ Figure Checker for Jupyter Notebooks Checks for figure labels and source attribution (Criterion 3.3.2). + +Usage: + python figure_checker.py [--config CONFIG] notebook1.ipynb notebook2.ipynb ... """ import argparse -import json import re import sys -from pathlib import Path -sys.path.insert(0, str(Path(__file__).parent)) -from utils import read_notebook, extract_cell_source, write_results +from qa_config import filter_notebooks, is_check_disabled, load_config +from utils import extract_cell_source, read_notebook def check_figures(notebook_path: str) -> str: """ Check for figure labels and source attribution in a notebook. - Args: - notebook_path: Path to the notebook file - - Returns: - Result status: "success" or "failure" + Returns: "success" or "failure" """ - nb_data = read_notebook(notebook_path) - - issues = [] - # Source attribution patterns source_patterns = [ - r'source:?\s+\S+', - r'data\s+from:?\s*', - r'doi:?\s*10\.\d+', - r'https?://\S+', - r'credit:?\s*', - r'attribution:?\s*', - r'reference:?\s*', - r'dataset:?\s*', + r"source:?\s+\S+", + r"data\s+from:?\s*", + r"doi:?\s*10\.\d+", + r"https?://\S+", + r"credit:?\s*", + r"attribution:?\s*", + r"reference:?\s*", + r"dataset:?\s*", ] - cells = nb_data.get('cells', []) + try: + nb_data = read_notebook(notebook_path) + except Exception as e: + print(f"❌ Error reading {notebook_path}: {e}") + return "failure" + + issues = [] + cells = nb_data.get("cells", []) for cell_idx, cell in enumerate(cells): - if cell.get('cell_type') == 'code': - outputs = cell.get('outputs', []) + if cell.get("cell_type") == "code": + outputs = cell.get("outputs", []) for output in outputs: - if output.get('output_type') in ['display_data', 'execute_result']: - data = output.get('data', {}) + if output.get("output_type") in ["display_data", "execute_result"]: + data = output.get("data", {}) # Check if this is a figure output - if 'image/png' in data or 'image/jpeg' in data or 'image/jpg' in data: + if "image/png" in data or "image/jpeg" in data or "image/jpg" in data: # Check nearby markdown cells for source attribution has_source = False @@ -61,7 +61,7 @@ def check_figures(notebook_path: str) -> str: check_idx = cell_idx + offset if 0 <= check_idx < len(cells): check_cell = cells[check_idx] - if check_cell.get('cell_type') == 'markdown': + if check_cell.get("cell_type") == "markdown": source = extract_cell_source(check_cell) # Check for source patterns @@ -74,51 +74,53 @@ def check_figures(notebook_path: str) -> str: break if not has_source: - issues.append( - f"Cell {cell_idx}: Figure missing source attribution " - f"(expected in nearby markdown cell)" - ) + issues.append(f"Cell {cell_idx}: Figure missing source attribution") if not issues: - print(f"✅ All figures have proper labels and sources in {notebook_path}") + print(f"✅ {notebook_path}: All figures have proper labels and sources") return "success" else: - print(f"❌ Found {len(issues)} figure labeling issue(s) in {notebook_path}:") + print(f"❌ {notebook_path}: {len(issues)} figure labeling issue(s)") for issue in issues: print(f" - {issue}") - print("\nAdd source attribution in markdown cells near figures") - print("Expected patterns: 'Source:', 'Data from:', DOI, URL, 'Credit:', etc.") + print(" Add source attribution in markdown cells near figures") + print(" Patterns: 'Source:', 'Data from:', DOI, URL, 'Credit:', etc.") return "failure" def main(): - parser = argparse.ArgumentParser(description='Check for figure labels and sources in notebooks') - parser.add_argument('--notebooks', required=True, help='JSON array of notebook paths') - parser.add_argument('--output-dir', required=True, help='Directory to write results') + parser = argparse.ArgumentParser( + description="Check for figure labels and source attribution in Jupyter notebooks" + ) + parser.add_argument("notebooks", nargs="*", help="Notebook files to check") + parser.add_argument( + "--config", + default=".github/notebook-qa.yml", + help="Path to QA configuration file (default: .github/notebook-qa.yml)", + ) args = parser.parse_args() - try: - notebooks = json.loads(args.notebooks) - except json.JSONDecodeError as e: - print(f"Error: Invalid JSON format for notebooks: {e}") - sys.exit(1) + config = load_config(args.config) + + # Check if figures check is globally disabled + if is_check_disabled(config, "figures"): + print("Figure check is disabled by configuration") + sys.exit(0) + + # Filter notebooks based on config + notebooks = filter_notebooks(config, "figures", args.notebooks) + + if not notebooks: + print("All notebooks skipped by configuration") + sys.exit(0) - notebook_results = {} overall_result = 0 for notebook in notebooks: - if not notebook: - continue - - print(f"Processing {notebook} with figure_checker") result = check_figures(notebook) - notebook_results[notebook] = result - if result == "failure": overall_result = 1 - write_results("figure_checker", notebook_results, args.output_dir) - sys.exit(overall_result) diff --git a/process-notebooks/checkers/metadata_checker.py b/process-notebooks/checkers/metadata_checker.py old mode 100755 new mode 100644 index 96d84d4..5463cfd --- a/process-notebooks/checkers/metadata_checker.py +++ b/process-notebooks/checkers/metadata_checker.py @@ -2,133 +2,113 @@ """ Metadata Checker for Jupyter Notebooks -Checks for version date information in notebooks or README files (Criterion 1.2.6). +Checks that notebooks have a 'Last updated' date in the first markdown cell (Criterion 1.2.6). + +Expected format in first markdown cell: + **Last updated:** YYYY-MM-DD + +Usage: + python metadata_checker.py [--config CONFIG] notebook1.ipynb notebook2.ipynb ... """ import argparse -import json import re import sys from pathlib import Path -sys.path.insert(0, str(Path(__file__).parent)) -from utils import read_notebook, extract_cell_source, write_results +from qa_config import filter_notebooks, is_check_disabled, load_config +from utils import extract_cell_source, read_notebook -def check_metadata(notebook_path: str, check_readme: bool = True) -> str: +def check_metadata(notebook_path: str) -> tuple[str, str | None]: """ - Check for version date metadata in a notebook. - - Args: - notebook_path: Path to the notebook file - check_readme: Whether to check README.md if not found in notebook + Check for 'Last updated' date in a notebook's first markdown cell. - Returns: - Result status: "success" or "failure" + Returns: ("success"|"failure"|"warning", date_found_or_None) """ - # Date patterns to search for - date_patterns = [ - r'last\s+updated:?\s*(\d{4}-\d{2}-\d{2})', - r'version:?\s*[\d.]+\s*\((\d{4}-\d{2}-\d{2})\)', - r'modified:?\s*(\d{4}-\d{2}-\d{2})', - r'date:?\s*(\d{4}-\d{2}-\d{2})', - r'updated:?\s*(\d{4}-\d{2}-\d{2})', - ] - - nb_data = read_notebook(notebook_path) - - found_date = None - found_location = None - - # Check notebook metadata - metadata = nb_data.get('metadata', {}) - for field in ['date', 'modified', 'version', 'last_updated']: - if field in metadata: - value = str(metadata[field]) - # Try to extract date from the metadata field - for pattern in date_patterns: - match = re.search(pattern, value, re.IGNORECASE) - if match: - found_date = match.group(1) - found_location = f"metadata.{field}" - break - if found_date: - break - - # Check markdown cells if not found in metadata - if not found_date: - for cell_idx, cell in enumerate(nb_data.get('cells', [])): - if cell.get('cell_type') == 'markdown': - source = extract_cell_source(cell) - - # Search for date patterns - for pattern in date_patterns: - match = re.search(pattern, source, re.IGNORECASE) - if match: - found_date = match.group(1) - found_location = f"markdown cell {cell_idx}" - break - - if found_date: - break - - # Check for README.md if not found in notebook - if not found_date and check_readme: - readme_path = Path(notebook_path).parent / "README.md" - if readme_path.exists(): - try: - with open(readme_path, 'r', encoding='utf-8') as f: - readme_content = f.read() - - for pattern in date_patterns: - match = re.search(pattern, readme_content, re.IGNORECASE) - if match: - found_date = match.group(1) - found_location = "README.md" - break - except Exception: - pass - - if found_date: - print(f"✅ Found version date for {notebook_path}: {found_date} (in {found_location})") - return "success" - else: - print(f"❌ No version date found for {notebook_path}") - print(" Add 'Last updated: YYYY-MM-DD' to notebook markdown or README.md") - return "failure" + date_pattern = r"\*\*Last updated:\*\*\s*(\d{4}-\d{2}-\d{2})" + + try: + nb_data = read_notebook(notebook_path) + except Exception as e: + print(f"❌ Error reading {notebook_path}: {e}") + return ("failure", None) + + cells = nb_data.get("cells", []) + + # Check all markdown cells before the first code cell + for cell in cells: + if cell.get("cell_type") == "code": + break # Stop searching once we hit code + if cell.get("cell_type") == "markdown": + source = extract_cell_source(cell) + match = re.search(date_pattern, source) + if match: + date = match.group(1) + print(f"✅ {notebook_path}: Last updated {date}") + return ("success", date) + + # Fallback: check README.md in same directory + readme_path = Path(notebook_path).parent / "README.md" + if readme_path.exists(): + try: + readme_text = readme_path.read_text(encoding="utf-8") + match = re.search(date_pattern, readme_text) + if match: + date = match.group(1) + print(f"✅ {notebook_path}: Last updated {date} (from README.md)") + return ("success", date) + except Exception: + pass + + print(f"❌ {notebook_path}: No 'Last updated' date found") + print("") + print(" To fix this, add the following to the FIRST markdown cell of your notebook:") + print("") + print(" **Last updated:** YYYY-MM-DD") + print("") + print(" Example:") + print(" **Last updated:** 2025-01-15") + print("") + return ("failure", None) def main(): - parser = argparse.ArgumentParser(description='Check for version date metadata in notebooks') - parser.add_argument('--notebooks', required=True, help='JSON array of notebook paths') - parser.add_argument('--output-dir', required=True, help='Directory to write results') - parser.add_argument('--check-readme', action='store_true', default=True, - help='Check README.md if not found in notebook') + parser = argparse.ArgumentParser( + description="Check for Last updated metadata in Jupyter notebooks" + ) + parser.add_argument("notebooks", nargs="*", help="Notebook files to check") + parser.add_argument( + "--config", + default=".github/notebook-qa.yml", + help="Path to QA configuration file (default: .github/notebook-qa.yml)", + ) args = parser.parse_args() - try: - notebooks = json.loads(args.notebooks) - except json.JSONDecodeError as e: - print(f"Error: Invalid JSON format for notebooks: {e}") - sys.exit(1) - - notebook_results = {} - overall_result = 0 + config = load_config(args.config) - for notebook in notebooks: - if not notebook: - continue + # Check if metadata check is globally disabled + if is_check_disabled(config, "metadata"): + print("Metadata check is disabled by configuration") + sys.exit(0) - print(f"Processing {notebook} with metadata_checker") - result = check_metadata(notebook, args.check_readme) - notebook_results[notebook] = result + # Filter notebooks based on config + notebooks = filter_notebooks(config, "metadata", args.notebooks) - if result == "failure": - overall_result = 1 + if not notebooks: + print("All notebooks skipped by configuration") + sys.exit(0) - write_results("metadata_checker", notebook_results, args.output_dir) + results = [] + for notebook in notebooks: + result, _ = check_metadata(notebook) + results.append(result) - sys.exit(overall_result) + # Exit 0 even for warnings (non-blocking check) + # Change to exit(1) if this should be a blocking check + if "failure" in results: + sys.exit(1) + sys.exit(0) if __name__ == "__main__": diff --git a/process-notebooks/checkers/qa_config.py b/process-notebooks/checkers/qa_config.py new file mode 100644 index 0000000..b33a6cc --- /dev/null +++ b/process-notebooks/checkers/qa_config.py @@ -0,0 +1,212 @@ +#!/usr/bin/env python3 +""" +QA Configuration Parser for Notebook Checks + +Loads and parses .github/notebook-qa.yml configuration file to support +disabling specific checks globally, per-notebook, or skipping notebooks entirely. + +Config file format: + # .github/notebook-qa.yml + + # Globally disable specific checks (applies to all notebooks) + disabled_checks: + - linter + - formatter + + # Notebooks to skip entirely (all checks) + skip_notebooks: + - "notebooks/draft.ipynb" + - "notebooks/experimental/**" # glob patterns supported + + # Per-notebook check configuration + notebooks: + "notebooks/example.ipynb": + skip: + - figures +""" + +import json +import os +from fnmatch import fnmatch +from typing import Any + +# Optional YAML import - falls back gracefully if not available +try: + import yaml + + HAS_YAML = True +except ImportError: + HAS_YAML = False + +# Baseline pynblint rules to exclude across all consuming repos. +PYNBLINT_DEFAULT_EXCLUDE = ["missing-h1-MD-heading", "imports-beyond-first-cell"] + + +def load_config(config_path: str = ".github/notebook-qa.yml") -> dict[str, Any]: + """ + Load QA configuration from YAML file. + + Args: + config_path: Path to the configuration file + + Returns: + Configuration dictionary, or empty dict if file doesn't exist + """ + if not os.path.exists(config_path): + return {} + + if not HAS_YAML: + print(f"Warning: PyYAML not installed, cannot load {config_path}") + return {} + + try: + with open(config_path, encoding="utf-8") as f: + config = yaml.safe_load(f) + return config if config else {} + except Exception as e: + print(f"Warning: Failed to load {config_path}: {e}") + return {} + + +def is_check_disabled(config: dict[str, Any], check_id: str) -> bool: + """ + Check if a specific check is globally disabled. + + Args: + config: Configuration dictionary + check_id: Check identifier (e.g., 'linter', 'figures', 'metadata') + + Returns: + True if check is globally disabled, False otherwise + """ + disabled_checks = config.get("disabled_checks", []) + return check_id in disabled_checks + + +def is_notebook_skipped(config: dict[str, Any], notebook: str) -> bool: + """ + Check if a notebook should be skipped entirely (all checks). + + Args: + config: Configuration dictionary + notebook: Path to the notebook file + + Returns: + True if notebook should be skipped, False otherwise + """ + skip_patterns = config.get("skip_notebooks", []) + return any(fnmatch(notebook, pattern) for pattern in skip_patterns) + + +def is_check_skipped_for_notebook(config: dict[str, Any], check_id: str, notebook: str) -> bool: + """ + Check if a specific check should be skipped for a specific notebook. + + Args: + config: Configuration dictionary + check_id: Check identifier + notebook: Path to the notebook file + + Returns: + True if check should be skipped for this notebook, False otherwise + """ + per_notebook = config.get("notebooks", {}) + for pattern, settings in per_notebook.items(): + if fnmatch(notebook, pattern): + skip_checks = settings.get("skip", []) + if check_id in skip_checks: + return True + return False + + +def filter_notebooks(config: dict[str, Any], check_id: str, notebooks: list[str]) -> list[str]: + """ + Filter a list of notebooks based on configuration. + + Removes notebooks that should be skipped either: + - Entirely (via skip_notebooks) + - For this specific check (via per-notebook skip) + + Note: Does NOT check if the check is globally disabled. + Use is_check_disabled() separately for that. + + Args: + config: Configuration dictionary + check_id: Check identifier + notebooks: List of notebook paths + + Returns: + Filtered list of notebooks that should be checked + """ + result = [] + for notebook in notebooks: + # Skip if notebook matches skip_notebooks patterns + if is_notebook_skipped(config, notebook): + continue + + # Skip if per-notebook config says skip this check + if is_check_skipped_for_notebook(config, check_id, notebook): + continue + + result.append(notebook) + + return result + + +def get_filtered_notebooks_for_check( + config: dict[str, Any], check_id: str, notebooks: list[str] +) -> tuple[bool, list[str]]: + """ + Get filtered notebooks for a check, including global disable check. + + This is a convenience function that combines is_check_disabled() + and filter_notebooks() for typical use cases. + + Args: + config: Configuration dictionary + check_id: Check identifier + notebooks: List of notebook paths + + Returns: + Tuple of (should_skip_entirely, filtered_notebooks) + - should_skip_entirely: True if check is globally disabled + - filtered_notebooks: List of notebooks to check (empty if skipped) + """ + if is_check_disabled(config, check_id): + return (True, []) + + filtered = filter_notebooks(config, check_id, notebooks) + return (False, filtered) + + +def get_pynblint_exclude(config: dict[str, Any]) -> str: + """ + Build the pynblint --exclude JSON string from baseline + user config. + + Config format in .github/notebook-qa.yml: + pynblint: + exclude: + - untitled-notebook + exclude_mode: extend # "extend" (default) or "override" + + Returns: + JSON array string for pynblint --exclude, or empty string if no exclusions. + """ + pynblint_config = config.get("pynblint", {}) + if not isinstance(pynblint_config, dict): + pynblint_config = {} + + user_exclude = pynblint_config.get("exclude", []) + if not isinstance(user_exclude, list): + user_exclude = [] + + mode = pynblint_config.get("exclude_mode", "extend") + + if mode == "override": + exclude = user_exclude + else: + exclude = sorted(set(PYNBLINT_DEFAULT_EXCLUDE + user_exclude)) + + if not exclude: + return "" + return json.dumps(exclude) diff --git a/process-notebooks/checkers/test_checker.py b/process-notebooks/checkers/test_checker.py deleted file mode 100755 index 4858c43..0000000 --- a/process-notebooks/checkers/test_checker.py +++ /dev/null @@ -1,125 +0,0 @@ -#!/usr/bin/env python3 -""" -Test Checker for Jupyter Notebooks - -Checks for test files and runs coverage analysis. -Validates criteria 2.3.1 (test existence) and 2.3.2 (coverage threshold). -""" - -import argparse -import json -import subprocess -import sys -import xml.etree.ElementTree as ET -from pathlib import Path - -sys.path.insert(0, str(Path(__file__).parent)) -from utils import write_results - - -def check_tests(notebook_path: str, coverage_threshold: float = 80.0) -> str: - """ - Check for test files and run coverage analysis. - - Args: - notebook_path: Path to the notebook file - coverage_threshold: Minimum coverage percentage required - - Returns: - Result status: "success" or "failure" - """ - # Check for test files (Criterion 2.3.1) - test_patterns = ['test_*.py', '*_test.py', 'tests/**/*.py'] - test_files = [] - - for pattern in test_patterns: - test_files.extend(Path('.').glob(pattern)) - - if not test_files: - print(f"❌ No test files found for {notebook_path}") - print(" Create test_*.py or tests/ directory with test files") - return "failure" - - print(f"✅ Found {len(test_files)} test file(s)") - for test_file in test_files: - print(f" - {test_file}") - - # Run tests with coverage (Criterion 2.3.2) - print(f"\nRunning tests with coverage (threshold: {coverage_threshold}%)...") - - try: - pytest_result = subprocess.run( - ['pytest', '--cov=.', '--cov-report=xml', '--cov-report=term'], - capture_output=True, - text=True, - timeout=300 # 5 minute timeout - ) - - print(pytest_result.stdout) - if pytest_result.stderr: - print(pytest_result.stderr) - - coverage_xml = Path('coverage.xml') - if not coverage_xml.exists(): - print("❌ Coverage report not generated") - return "failure" - - tree = ET.parse('coverage.xml') - root = tree.getroot() - coverage_pct = float(root.attrib.get('line-rate', 0)) * 100 - - print(f"\nCode coverage: {coverage_pct:.1f}%") - - if coverage_pct < coverage_threshold: - print(f"❌ Coverage {coverage_pct:.1f}% below threshold {coverage_threshold}%") - return "failure" - else: - print(f"✅ Coverage {coverage_pct:.1f}% meets threshold {coverage_threshold}%") - return "success" - - except subprocess.TimeoutExpired: - print("❌ Tests timed out after 5 minutes") - return "failure" - except FileNotFoundError: - print("❌ pytest not found. Install pytest and pytest-cov") - return "failure" - except Exception as e: - print("❌ Error running tests: {e}") - return "failure" - - -def main(): - parser = argparse.ArgumentParser(description='Check for tests and coverage in notebooks') - parser.add_argument('--notebooks', required=True, help='JSON array of notebook paths') - parser.add_argument('--output-dir', required=True, help='Directory to write results') - parser.add_argument('--coverage-threshold', type=float, default=80.0, - help='Minimum coverage percentage (default: 80)') - args = parser.parse_args() - - try: - notebooks = json.loads(args.notebooks) - except json.JSONDecodeError as e: - print(f"Error: Invalid JSON format for notebooks: {e}") - sys.exit(1) - - notebook_results = {} - overall_result = 0 - - for notebook in notebooks: - if not notebook: - continue - - print(f"Processing {notebook} with test_checker") - result = check_tests(notebook, args.coverage_threshold) - notebook_results[notebook] = result - - if result == "failure": - overall_result = 1 - - write_results("test_checker", notebook_results, args.output_dir) - - sys.exit(overall_result) - - -if __name__ == "__main__": - main() diff --git a/process-notebooks/checkers/utils.py b/process-notebooks/checkers/utils.py old mode 100755 new mode 100644 index 5c07e24..9ef89ec --- a/process-notebooks/checkers/utils.py +++ b/process-notebooks/checkers/utils.py @@ -1,64 +1,18 @@ -"""Shared utility functions for notebook checkers.""" +#!/usr/bin/env python3 +"""Shared utilities for notebook QA checkers.""" import json -import sys -from pathlib import Path -from typing import Dict, Any -def read_notebook(notebook_path: str) -> Dict[str, Any]: - """ - Read and parse a Jupyter notebook file. +def read_notebook(notebook_path: str) -> dict: + """Read and parse a Jupyter notebook file.""" + with open(notebook_path, encoding="utf-8") as f: + return json.load(f) - Args: - notebook_path: Path to the notebook file - Returns: - Parsed notebook data as dictionary - - Raises: - SystemExit: If the notebook cannot be read - """ - try: - with open(notebook_path, 'r', encoding='utf-8') as f: - return json.load(f) - except Exception as e: - print(f"❌ Error reading notebook {notebook_path}: {e}") - sys.exit(1) - - -def extract_cell_source(cell: Dict[str, Any]) -> str: - """ - Extract source code/markdown from a cell as a single string. - - Args: - cell: Notebook cell dictionary - - Returns: - Cell source as a single string - """ - source = cell.get('source', []) +def extract_cell_source(cell: dict) -> str: + """Extract source code/markdown from a cell as a single string.""" + source = cell.get("source", []) if isinstance(source, list): - return ''.join(source) + return "".join(source) return str(source) - - -def write_results(command_name: str, notebook_results: Dict[str, str], output_dir: str) -> None: - """ - Write standardized JSON results file. - - Args: - command_name: Name of the command/checker - notebook_results: Dictionary mapping notebook paths to results (success/failure/skipped) - output_dir: Directory to write the results file - """ - Path(output_dir).mkdir(parents=True, exist_ok=True) - results_file = Path(output_dir) / f"{command_name}-results.json" - - results_data = { - "command": command_name, - "results": notebook_results - } - - with open(results_file, 'w') as f: - json.dump(results_data, f, indent=2) diff --git a/process-notebooks/checkers/write_gha_config.py b/process-notebooks/checkers/write_gha_config.py new file mode 100644 index 0000000..9184535 --- /dev/null +++ b/process-notebooks/checkers/write_gha_config.py @@ -0,0 +1,88 @@ +#!/usr/bin/env python3 +"""Write QA config filtering results to GITHUB_OUTPUT for GitHub Actions. + +Replaces the inline Python config-loading blocks in notebook-qa.yml. +Uses qa_config.py as a library to filter notebooks per check and write +the results as GitHub Actions step outputs. + +Usage (lint job — all checks + extras): + python write_gha_config.py \ + --checks linter formatter pynblint links tests figures \ + metadata accessibility license changelog \ + --config .github/notebook-qa.yml \ + --extras + +Usage (execute job — single check): + python3 write_gha_config.py \ + --checks execute \ + --config .github/notebook-qa.yml + +Reads the notebook list from the ALL_NOTEBOOKS environment variable +(newline-separated paths). +""" + +import argparse +import os +import sys + +from qa_config import get_filtered_notebooks_for_check, get_pynblint_exclude, load_config + + +def parse_notebook_list(raw: str) -> list[str]: + """Parse notebook list from newline-separated (or space-separated) string.""" + if "\n" in raw: + return [nb.strip() for nb in raw.splitlines() if nb.strip()] + return raw.split() + + +def write_multiline_output(fh, key: str, lines: list[str]) -> None: + """Write a value to GITHUB_OUTPUT, using multiline syntax when needed.""" + if not lines: + fh.write(f"{key}=\n") + return + fh.write(f"{key}<<__NB_EOF__\n") + for line in lines: + fh.write(f"{line}\n") + fh.write("__NB_EOF__\n") + + +def main(): + parser = argparse.ArgumentParser(description="Write QA config outputs for GitHub Actions") + parser.add_argument( + "--checks", nargs="+", required=True, help="Check IDs to produce output for" + ) + parser.add_argument( + "--config", default=".github/notebook-qa.yml", help="Path to QA config file" + ) + parser.add_argument( + "--extras", action="store_true", help="Also write require_tests and coverage_threshold" + ) + args = parser.parse_args() + + raw_notebooks = os.environ.get("ALL_NOTEBOOKS", "") + notebooks = parse_notebook_list(raw_notebooks) + config = load_config(args.config) + + output_path = os.environ.get("GITHUB_OUTPUT") + if not output_path: + print("Error: GITHUB_OUTPUT environment variable not set", file=sys.stderr) + sys.exit(1) + + with open(output_path, "a") as out: + for check in args.checks: + skip, filtered = get_filtered_notebooks_for_check(config, check, notebooks) + out.write(f"skip_{check}={'true' if skip else 'false'}\n") + write_multiline_output(out, f"notebooks_{check}", filtered) + + if args.extras: + require = config.get("require_tests", False) + threshold = config.get("coverage_threshold", 80) + out.write(f"require_tests={'true' if require else 'false'}\n") + out.write(f"coverage_threshold={threshold}\n") + + pynblint_exclude = get_pynblint_exclude(config) + out.write(f"pynblint_exclude={pynblint_exclude}\n") + + +if __name__ == "__main__": + main() From a9d5b3bbd95dffd007fc1cc468ad37e45e40a9db Mon Sep 17 00:00:00 2001 From: Jakub Recman Date: Mon, 13 Apr 2026 15:37:30 +0200 Subject: [PATCH 2/7] Update README --- README.md | 104 ++++++++++++++++++++++++++++++++++++++++++++---------- 1 file changed, 86 insertions(+), 18 deletions(-) diff --git a/README.md b/README.md index f110c4d..0b6ac07 100644 --- a/README.md +++ b/README.md @@ -1,24 +1,35 @@ -## gha-ci-notebook-checks +## reusable workflows This repository contains reusable GitHub Actions workflows for C3S projects. There is currently one CI workflow for Jupyter Notebook QA automation. ### notebook-qa -This workflow implements QA automation for Jupyter Notebooks with following automation checks: - -1. Code linting with `nbqa` and `ruff` -2. Code formatting with `nbqa` and `ruff` -3. Notebook linting with `pynblint` -4. Custom DOI checker -5. Link availability testing with `pytest-check-links` -6. Notebook execution and memory profilling with `ploomber-engine` -7. Custom metadata version check -8. Custom test and coverage checks -9. Custom accessibility check -10. Custom figure labels check -11. License file check -12. Changelog file check +This workflow implements QA automation for Jupyter Notebooks. The checks below run automatically — all checks that are not skipped or disabled must pass for the workflow to succeed. + +#### Checks + +**Code linting** (`linter`) — Runs `ruff check` on all code cells. No Python lint violations allowed. + +**Code formatting** (`formatter`) — Runs `ruff format --check` on code cells. Code cells must conform to `ruff` formatting rules. + +**Notebook linting** (`pynblint`) — Runs `pynblint` on each notebook. Checks notebook-level quality issues such as non-linear execution order, empty cells, or untitled notebooks. + +**Link availability** (`links`) — Runs `lychee` against all notebooks. Every URL in markdown and code cells must be reachable. + +**Notebook execution** (`execute`) — Executes each notebook end-to-end with `ploomber-engine`. The notebook must run without errors. Memory usage and runtime are profiled per cell and uploaded as an artifact. + +**Version metadata** (`metadata`) — Looks for `**Last updated:** YYYY-MM-DD` (e.g. `**Last updated:** 2025-01-15`) in the first markdown cell(s) before any code cell. Falls back to a `README.md` in the same directory if not found in the notebook. + +**Tests & coverage** (`tests`) — If test files exist (`test_*.py`, `*_test.py`, `tests/*.py`), runs `pytest` with coverage. Coverage must meet the configured threshold (default 80%). When no test files exist the check passes by default, unless `require_tests: true` is set in the config. + +**Accessibility** (`accessibility`) — Runs WCAG compliance checks on notebooks using `jupyterlab-a11y-checker`. + +**Figure attribution** (`figures`) — Every figure output (PNG/JPEG) in code cells must have source attribution in a nearby markdown cell (within 2 cells). Recognized attribution patterns include `source:`, `credit:`, `data from:`, `attribution:`, `reference:`, `dataset:`, a DOI, or a URL. + +**License file** (`license`) — A non-empty `LICENSE` file must exist in the repository root. + +**Changelog file** (`changelog`) — A non-empty `CHANGELOG.md` file must exist in the repository root. #### How to use `notebook-qa.yml` workflow @@ -48,13 +59,70 @@ on: jobs: notebook-qa: - uses: ecmwf-training/gha-ci-notebook-checks/.github/workflows/notebook-qa.yml@main + uses: ecmwf-training/reusable-workflows/.github/workflows/notebook-qa.yml@main with: notebooks: ${{ inputs.notebooks || '' }} secrets: inherit ``` -This sets up automated checks on new pull requests and merges/pushes into `develop` branch. It also allow manual Action run in GitHub Actions UI. +This sets up automated checks on new pull requests and merges/pushes into `develop` branch. It also allows manual Action runs in the GitHub Actions UI. + + +#### Configuration + +You can customize check behavior by adding a `.github/notebook-qa.yml` config file in the consuming repository: + +```yaml +# Globally disable specific checks +disabled_checks: + - linter + - formatter + +# Notebooks to skip entirely (all checks), supports glob patterns +skip_notebooks: + - "notebooks/draft.ipynb" + - "notebooks/experimental/**" + +# Per-notebook check configuration +notebooks: + "notebooks/example.ipynb": + skip: + - figures + +# Test configuration +require_tests: false # Set true to fail when no test files exist +coverage_threshold: 80 # Minimum coverage percentage for pytest-cov + +# Pynblint rule configuration +pynblint: + exclude: # Additional rules to suppress (extends baseline) + - untitled-notebook + exclude_mode: extend # "extend" (default) or "override" +``` + +The baseline pynblint exclusion list suppresses `missing-h1-MD-heading` (MyST notebooks use YAML frontmatter for titles). In `extend` mode (default), your `exclude` list is merged with the baseline. In `override` mode, your list fully replaces the baseline. + +Available pynblint rule slugs: `non-linear-execution`, `notebook-too-long`, `untitled-notebook`, `non-portable-chars-in-nb-name`, `notebook-name-too-long`, `imports-beyond-first-cell`, `missing-h1-MD-heading`, `missing-opening-MD-text`, `missing-closing-MD-text`, `too-few-MD-cells`, `duplicate-notebook-not-renamed`, `invalid-python-syntax`, `non-executed-notebook`, `non-executed-cells`, `empty-cells`, `long-multiline-python-comment`, `cell-too-long` + +Valid check IDs: `linter`, `formatter`, `pynblint`, `links`, `tests`, `figures`, `metadata`, `accessibility`, `license`, `changelog`, `execute` + + +#### QA criteria reference + +| ID | Description | Tool / Check | +|-------|---------------------------|------------------------| +| 1.2.3 | Link availability | lychee | +| 1.2.4 | License file | LICENSE existence | +| 1.2.6 | Version metadata | metadata_checker.py | +| 2.2.1 | Code execution | ploomber-engine | +| 2.2.3 | Code style | ruff, pynblint | +| 2.2.4 | Execution profiling | ploomber-engine | +| 2.2.6 | Memory profiling | ploomber-engine | +| 2.3.1 | Test existence | pytest | +| 2.3.2 | Coverage threshold | pytest-cov | +| 3.1.3 | Accessibility | jupyterlab-a11y-checker| +| 3.3.2 | Figure attribution | figure_checker.py | +| 4.2.3 | Changelog | CHANGELOG.md existence | ### How to configure access to cdsapi for notebook execution check @@ -62,7 +130,7 @@ This sets up automated checks on new pull requests and merges/pushes into `devel The action responsible for notebook execution allows setting a `cdsapi` key via `CDSAPI_KEY` secret set either on repository or organisation level. -### How to setup gha-ci-notebook-checks repository in GitHub organisation +### How to setup reusable-workflows repository in GitHub organisation 1. Fork this repository into your organisation 2. 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.github/workflows/lint.yml diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml new file mode 100644 index 0000000..1ec04a3 --- /dev/null +++ b/.github/workflows/lint.yml @@ -0,0 +1,37 @@ +name: Lint + +on: + push: + branches: [main] + pull_request: + +permissions: + contents: read + +jobs: + ruff: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + with: + persist-credentials: false + + - uses: astral-sh/setup-uv@cec208311dfd045dd5311c1add060b2062131d57 # v8.0.0 + + - name: Ruff check + run: uvx ruff check process-notebooks/ + + - name: Ruff format check + run: uvx ruff format --check process-notebooks/ + + zizmor: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + with: + persist-credentials: false + + - uses: astral-sh/setup-uv@cec208311dfd045dd5311c1add060b2062131d57 # v8.0.0 + + - name: Zizmor + run: uvx zizmor .github/workflows/ From 9203078878a1b246352f21dc342f709a4f97a004 Mon Sep 17 00:00:00 2001 From: Jakub Recman Date: Mon, 13 Apr 2026 15:39:24 +0200 Subject: [PATCH 5/7] Add pre-commit --- .pre-commit-config.yaml | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 .pre-commit-config.yaml diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..35500cf --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,12 @@ +repos: + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.15.9 + hooks: + - id: ruff + args: [--fix] + - id: ruff-format + + - repo: https://github.com/zizmorcore/zizmor-pre-commit + rev: v1.23.1 + hooks: + - id: zizmor From b8b37bff8a0f6cff276a89fae76bd8679f8582d1 Mon Sep 17 00:00:00 2001 From: Jakub Recman Date: Mon, 13 Apr 2026 15:39:44 +0200 Subject: [PATCH 6/7] Add dependabot --- .github/dependabot.yaml | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 .github/dependabot.yaml diff --git 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