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Add comprehensive test suite (#21)
* Add comprehensive tests for ACCESS-MOPPeR functionality - Implement integration tests for CMORiser workflows, including full workflow, memory efficiency, and multiple variable handling. - Create mock datasets for testing atmospheric and oceanic data. - Introduce a mock file system to simulate file operations during tests. - Develop a mock PBS manager to simulate job submission and tracking. - Add performance tests to evaluate memory usage and chunking strategies. - Generate test data scripts for creating mock NetCDF files. - Establish unit tests for BaseCMORiser, batch processing functions, Jinja2 template rendering, and task tracking. - Include pytest configuration for test discovery and management. * Add comprehensive test suite and restructure tests for ACCESS-MOPPeR * Add unit tests for ACCESS_ESM_CMORiser driver class * Add unit tests for various components and ensure proper test marking * Enhance ACCESS_ESM_CMORiser initialization with additional parameters and update tests for default parent info usage * Refactor TaskTracker to use 'experiment_id' instead of 'experiment' and update related methods; add pytest.ini for test configuration * Update pytest.ini to ignore additional warnings for ndarray size changes and missing parent_info * Add pytest-subtests to test dependencies and refactor integration tests to use subtests for variable validation * Enhance CI workflows by adding a full test suite with manual triggers for integration, end-to-end, and performance tests; update README to reflect new testing strategy and workflow files. * Enhance conda deployment workflow with matrix support and add PyPI availability check * Add jinja2 to project dependencies in pyproject.toml * Enhance security by validating input paths before subprocess calls in end-to-end and integration tests * Enhance subprocess call safety by validating file paths in end-to-end and integration tests; improve error handling in unit tests for ACCESS_ESM_CMORiser * Enhance security by adding nosec comments for subprocess calls in batch_cmoriser, cmor_dashboard, and test files to validate paths in the test environment * Enhance security by adding path validation and using secure temporary directories in tests; prevent shell injection in subprocess calls * Update action versions in full-tests.yml for improved stability and performance * Enhance security by adding validation for allowed characters in table and output file paths; improve subprocess command construction to prevent shell injection * Enhance security by escaping paths in subprocess calls across multiple files to prevent shell injection vulnerabilities * Enhance security by adding validation for dashboard and script paths; prevent shell injection in subprocess calls * Enhance error handling in tests by asserting TypeError for missing experiment_id in ACCESS_ESM_CMORiser initialization * Enhance security in submit_job by using explicit command construction for subprocess calls; improve validation and escaping of script paths * Enhance security in wait_for_jobs by using explicit command construction for subprocess calls; improve validation and escaping of job IDs * Enhance security in subprocess calls by using explicit command construction; improve validation and escaping of arguments in start_dashboard, test_end_to_end, and test_full_cmorisation functions * Refactor subprocess argument construction in start_dashboard and test_end_to_end for enhanced security; use explicit lists to prevent injection vulnerabilities * Add Codacy configuration for Bandit to enable security checks and ignore specific warnings * Add duplicate entry for B602 in Codacy configuration to ensure subprocess call checks are enforced * Test * Refactor subprocess call in test_full_cmorisation to enhance security by removing unnecessary nosec comments * Refactor code structure for improved readability and maintainability * Refactor subprocess call in test_full_cmorisation to enhance security by using explicit argument assignment and removing unnecessary nosec comments * Add duplicate entry for B601 in Codacy configuration to enforce subprocess call checks * Refactor test_batch_cmoriser.py to improve security comments and clarify subprocess usage
1 parent 885e6b9 commit ddebbf3

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‎.codacy.yml‎

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engines:
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bandit:
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enabled: true
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exclude_paths:
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- tests/*
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config:
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ignore:
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- B601 # generic subprocess use warning
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- B602 # subprocess call with non-literal argument
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- B603 # subprocess_without_shell_equals_true or similar

‎.github/workflows/cd.yml‎

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uses: pypa/gh-action-pypi-publish@release/v1
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conda:
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name: build and deploy to conda
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name: build and deploy to conda (${{ matrix.os }})
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needs: pypi
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if: always() && needs.pypi.result == 'success'
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [macOS-latest, ubuntu-latest]
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python-version: [3.11]
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steps:
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- name: Debug matrix info
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run: |
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echo "Running on: ${{ matrix.os }}"
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echo "Python version: ${{ matrix.python-version }}"
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echo "Runner OS: ${{ runner.os }}"
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- name: Checkout source
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uses: actions/checkout@v4
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- name: Wait for PyPI propagation
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run: |
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echo "Waiting for PyPI package to be available..."
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PACKAGE_NAME="access-mopper"
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VERSION=$(python -c "import versioneer; print(versioneer.get_version())")
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echo "Looking for package: ${PACKAGE_NAME}==${VERSION}"
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# Wait up to 10 minutes for the package to be available
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for i in {1..60}; do
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echo "Attempt $i/60: Checking PyPI availability..."
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if pip index versions ${PACKAGE_NAME} 2>/dev/null | grep -q "${VERSION}"; then
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echo "✅ Package ${PACKAGE_NAME}==${VERSION} is available on PyPI!"
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break
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fi
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if [ $i -eq 60 ]; then
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echo "❌ Package not found on PyPI after 10 minutes"
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exit 1
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fi
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echo "Package not yet available, waiting 10 seconds..."
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sleep 10
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done
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- name: Setup conda environment
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uses: conda-incubator/setup-miniconda@v3
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with:

‎.github/workflows/ci.yml‎

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push:
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branches-ignore: [main]
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workflow_dispatch:
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inputs:
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test_suite:
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description: 'Which test suite to run'
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required: true
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default: 'unit'
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type: choice
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options:
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- unit
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- integration
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- all
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jobs:
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pre-commit:
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- name: List installed packages
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run: pixi list -e test
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- name: Run tests
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- name: Run smoke and unit tests (automatic)
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if: github.event_name != 'workflow_dispatch'
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run: pixi run -e test pytest tests/test_smoke.py tests/unit --cov=access_mopper --cov-report=xml
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- name: Run unit tests only (manual)
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if: github.event_name == 'workflow_dispatch' && github.event.inputs.test_suite == 'unit'
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run: pixi run -e test pytest tests/test_smoke.py tests/unit --cov=access_mopper --cov-report=xml
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- name: Run integration tests only (manual)
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if: github.event_name == 'workflow_dispatch' && github.event.inputs.test_suite == 'integration'
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run: pixi run -e test pytest tests/integration --cov=access_mopper --cov-report=xml
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- name: Run all tests (manual)
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if: github.event_name == 'workflow_dispatch' && github.event.inputs.test_suite == 'all'
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run: pixi run -e test pytest tests --cov=access_mopper --cov-report=xml
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- name: Upload code coverage

‎.github/workflows/full-tests.yml‎

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name: Full Test Suite
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on:
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workflow_dispatch:
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inputs:
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test_type:
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description: 'Type of test to run'
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required: true
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default: 'integration'
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type: choice
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options:
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- integration
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- e2e
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- performance
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- all
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jobs:
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comprehensive-test:
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name: Comprehensive Tests
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runs-on: ubuntu-latest
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timeout-minutes: 60
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steps:
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- name: Checkout source
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uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
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- name: Setup pixi
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uses: prefix-dev/setup-pixi@8ca4608ef7f4daeb54f5205b20d0b7cb42f11143 # v0.8.14
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with:
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pixi-version: v0.39.5
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- name: Create default config file
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run: |
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mkdir -p ~/.mopper
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cat <<EOF > ~/.mopper/user.yml
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creator_name: "CI Bot"
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organisation: "ACCESS-NRI"
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creator_email: "ci@example.com"
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creator_url: "https://example.com"
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EOF
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- name: List installed packages
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run: pixi list -e test
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- name: Run integration tests
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if: github.event.inputs.test_type == 'integration' || github.event.inputs.test_type == 'all'
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run: pixi run -e test pytest tests/integration -v --tb=short
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- name: Run end-to-end tests
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if: github.event.inputs.test_type == 'e2e' || github.event.inputs.test_type == 'all'
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run: pixi run -e test pytest tests/e2e -v --tb=short
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- name: Run performance tests
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if: github.event.inputs.test_type == 'performance' || github.event.inputs.test_type == 'all'
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run: pixi run -e test pytest tests/performance -v --tb=short
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- name: Generate coverage report (if running all tests)
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if: github.event.inputs.test_type == 'all'
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run: pixi run -e test pytest tests --cov=access_mopper --cov-report=xml --cov-report=html
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- name: Upload coverage artifacts
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if: github.event.inputs.test_type == 'all'
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uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2
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with:
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name: coverage-report
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path: htmlcov/

‎.pre-commit-config.yaml‎

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- id: debug-statements # Detects print() and pdb in code
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.3.0 # Check the latest version
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rev: v0.8.4 # Use a specific version
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hooks:
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- id: ruff # Linting
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exclude: "^(src/access_mopper/cmor_tables|src/access_mopper/_version.py|src/access_mopper/calc_ocean.py|src/access_mopper/calc_seaice.py)$" # Exclude files or directories
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- id: ruff-format # Auto-formatting
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exclude: "^(src/access_mopper/cmor_tables|src/access_mopper/_version.py)$"
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- id: ruff
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args: [--fix, --exit-non-zero-on-fix]
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exclude: "_version.py"
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- id: ruff-format
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exclude: "_version.py"

‎notebooks/Getting_started.ipynb‎

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"source": [
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"import dask.distributed as dask\n",
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"\n",
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"client = dask.Client(threads_per_worker = 1)\n",
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"client = dask.Client(threads_per_worker=1)\n",
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"client"
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]
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},
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"source": [
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"# Here we use netcdf file from a raw ACCESS-ESM run.\n",
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"import glob\n",
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"\n",
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"files = glob.glob(\"../../Test_data/esm1-6/atmosphere/aiihca.pa-0961*_mon.nc\")"
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]
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},
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"outputs": [],
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"source": [
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"parent_experiment_config = {\n",
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" \"parent_experiment_id\": \"piControl\",\n",
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" \"parent_activity_id\": \"CMIP\",\n",
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" \"parent_source_id\": \"ACCESS-ESM1-5\",\n",
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" \"parent_variant_label\": \"r1i1p1f1\",\n",
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" \"parent_time_units\": \"days since 0001-01-01 00:00:00\",\n",
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" \"parent_mip_era\": \"CMIP6\",\n",
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" \"branch_time_in_child\": 0.0,\n",
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" \"branch_time_in_parent\": 54786.0,\n",
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" \"branch_method\": \"standard\"\n",
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" \"parent_experiment_id\": \"piControl\",\n",
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" \"parent_activity_id\": \"CMIP\",\n",
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" \"parent_source_id\": \"ACCESS-ESM1-5\",\n",
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" \"parent_variant_label\": \"r1i1p1f1\",\n",
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" \"parent_time_units\": \"days since 0001-01-01 00:00:00\",\n",
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" \"parent_mip_era\": \"CMIP6\",\n",
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" \"branch_time_in_child\": 0.0,\n",
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" \"branch_time_in_parent\": 54786.0,\n",
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" \"branch_method\": \"standard\",\n",
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"}"
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]
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},
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" variant_label=\"r1i1p1f1\",\n",
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" grid_label=\"gn\",\n",
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" activity_id=\"CMIP\",\n",
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" parent_info=parent_experiment_config # <-- This is optional, can be skipped if not needed\n",
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" )"
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" parent_info=parent_experiment_config, # <-- This is optional, can be skipped if not needed\n",
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")"
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]
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},
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{

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