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Same as #30 but the PR is opened from upstream repository instead of fork (#32)
See PR #30 for more details. This PR is open to check if ci runs on the repository. --------- Co-authored-by: Franz Király <fkiraly@gcos.ai>
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‎.github/workflows/ci.yml‎

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# MAWS CI/CD Workflow
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# Runs tests on Linux with AmberTools and OpenMM across Python 3.10-3.13
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# Includes optional GPU testing when self-hosted runners with GPU are available
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name: CI
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on:
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push:
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branches:
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- main
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pull_request:
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branches:
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- main
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workflow_dispatch: # Allow manual trigger
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jobs:
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# ============================================================================
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# Full integration tests with AmberTools (CPU)
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# ============================================================================
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test:
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name: Test Python ${{ matrix.python-version }}
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.10", "3.11", "3.12", "3.13"]
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defaults:
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run:
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shell: bash -el {0} # Required for conda activate
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Setup Miniconda
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uses: conda-incubator/setup-miniconda@v3
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with:
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miniforge-version: latest
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python-version: ${{ matrix.python-version }}
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channels: conda-forge,bioconda,defaults
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channel-priority: strict
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activate-environment: maws
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auto-activate-base: false
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- name: Install dependencies via conda
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run: |
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conda activate maws
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conda install -y openmm ambertools mpmath numba pandas numpy
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- name: Install package and dev dependencies
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run: |
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conda activate maws
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pip install -e ".[dev]"
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- name: Verify AmberTools installation
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run: |
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conda activate maws
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which tleap
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tleap -h || echo "tleap help displayed"
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- name: Run tests
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run: |
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conda activate maws
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pytest tests/ -v --tb=short
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- name: Run tests with coverage
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if: matrix.python-version == '3.10'
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run: |
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conda activate maws
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pytest tests/ --cov=maws --cov-report=term-missing --cov-report=xml
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- name: Upload coverage to Codecov
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if: matrix.python-version == '3.10'
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uses: codecov/codecov-action@v4
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with:
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files: ./coverage.xml
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fail_ci_if_error: false
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verbose: true
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# ============================================================================
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# Fast unit tests (no AmberTools needed)
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# ============================================================================
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unit-tests:
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name: Unit Tests Python ${{ matrix.python-version }}
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.10", "3.11", "3.12", "3.13"]
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Setup Python
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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cache: pip
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- name: Install minimal dependencies
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run: |
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pip install numpy openmm mpmath pandas pytest pytest-cov
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- name: Install package
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run: pip install -e .
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- name: Run unit tests only
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run: |
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pytest tests/ -v --tb=short \
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--ignore=tests/test_chain_complex.py \
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--ignore=tests/test_run.py
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# ============================================================================
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# GPU tests (only runs on self-hosted runners with NVIDIA GPU)
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# To enable: add a self-hosted runner with GPU and label 'gpu'
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# ============================================================================
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gpu-test:
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name: GPU Test
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runs-on: [self-hosted, gpu]
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if: github.event_name == 'workflow_dispatch' || contains(github.event.head_commit.message, '[gpu]')
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continue-on-error: true # Don't fail the whole workflow if GPU tests fail
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defaults:
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run:
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shell: bash -el {0}
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Check NVIDIA GPU
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run: |
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nvidia-smi
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echo "CUDA devices found:"
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nvidia-smi --query-gpu=name,driver_version,memory.total --format=csv
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- name: Setup Miniconda
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uses: conda-incubator/setup-miniconda@v3
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with:
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miniforge-version: latest
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python-version: "3.10"
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channels: conda-forge,bioconda,defaults
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channel-priority: strict
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activate-environment: maws-gpu
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auto-activate-base: false
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- name: Install dependencies with CUDA support
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run: |
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conda activate maws-gpu
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# Install OpenMM with CUDA support
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conda install -y openmm cudatoolkit ambertools mpmath numba pandas numpy
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- name: Install package
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run: |
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conda activate maws-gpu
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pip install -e ".[dev]"
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- name: Verify CUDA platform
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run: |
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conda activate maws-gpu
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python -c "
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import openmm as mm
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print('Available platforms:')
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for i in range(mm.Platform.getNumPlatforms()):
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p = mm.Platform.getPlatform(i)
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print(f' {p.getName()}')
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try:
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cuda = mm.Platform.getPlatformByName('CUDA')
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print(f'CUDA platform found!')
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except Exception as e:
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print(f'CUDA not available: {e}')
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"
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- name: Run all tests including GPU
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env:
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MAWS_OPENMM_PLATFORM: CUDA
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run: |
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conda activate maws-gpu
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pytest tests/ -v --tb=short -m "not slow"
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# ============================================================================
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# Linting
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# ============================================================================
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lint:
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name: Lint
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Setup Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.10"
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- name: Install ruff
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run: pip install ruff
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- name: Run ruff check
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run: ruff check maws/
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- name: Run ruff format check
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run: ruff format --check maws/

‎.gitignore‎

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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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cython_debug/
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#MAWS pdf files
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maws_*.pdb
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.maws_cache/
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*.in
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*.mdp
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*.mdp
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*.log
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*.lib
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# We have to correct all this before release

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