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Merge pull request #164 from ACCESS-Community-Hub/prerelease
Release of v1.0
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‎.github/workflows/mopper-conda-release.yaml‎

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name: Build of mopper conda package for new release
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# Controls when the action will run.
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on:
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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jobs:
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conda_deployment_with_new_tag:
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name: Test conda deployment of package with Python ${{ matrix.python-version }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.10", "3.11", "3.12"]
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steps:
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- uses: actions/checkout@v4.1.7
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with:
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fetch-depth: 0
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- name: Set env
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run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
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- name: Conda environment creation and activation
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uses: conda-incubator/setup-miniconda@v3.0.4
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with:
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python-version: ${{ matrix.python-version }}
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activate-environment: mopper_env
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environment-file: conda/environment.yaml # Path to the build conda environment
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show-channel-urls: true #
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- name: Build but do not upload the conda packages
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uses: uibcdf/action-build-and-upload-conda-packages@v1.3.0
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with:
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meta_yaml_dir: conda
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python-version: ${{ matrix.python-version }} # Values previously defined in `matrix`
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user: coecms
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label: auto
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upload: true
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token: ${{ secrets.ANACONDA_TOKEN }} # Replace with the right name of your secret

‎.github/workflows/mopper-pytest.yaml‎

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name: mopper-all-tests
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#on: [push]
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on:
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push:
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branches:
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- prerelease
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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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- prerelease
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jobs:
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build-linux:
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runs-on: ubuntu-latest
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timeout-minutes: 60
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strategy:
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max-parallel: 5
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matrix:
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python-version: ["3.10", "3.11", "3.12"]
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steps:
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- uses: actions/checkout@v4.1.7
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- name: Set up Python 3.10/3.11
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uses: actions/setup-python@v5.1.1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install Miniconda
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uses: conda-incubator/setup-miniconda@v3.0.4
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with:
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activate-environment: testenv
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environment-file: conda/testenv.yaml
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python-version: ${{ matrix.python-version }}
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channels: conda-forge
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- name: Lint with ruff
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shell: bash -el {0}
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run: |
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ruff check --output-format=github .
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continue-on-error: true
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# making sure we are testing installed package
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- name: Install package
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shell: bash -el {0}
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run: |
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conda activate testenv
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pip install -e .
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- name: Test with pytest
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shell: bash -el {0}
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run: |
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conda run python -m pytest
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#conda run coverage run --source src -m py.test
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# - name: Upload to codecov
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# shell: bash -el {0}
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# if: steps.build.outcome == 'success'
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# run: |
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# curl -Os https://uploader.codecov.io/latest/linux/codecov
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# chmod +x codecov
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# ./codecov
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‎.github/workflows/mopper-test-calcs.yaml‎

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# this workflow can be used as a template for a worklfow
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# that runs automatically only specific tests when pushing
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# to a selected branch.
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name: mopper-specific-tests
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on:
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push:
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branches:
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- class
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jobs:
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build-linux:
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runs-on: ubuntu-latest
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timeout-minutes: 60
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strategy:
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max-parallel: 5
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matrix:
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python-version: ["3.10", "3.11", "3.12"]
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steps:
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- uses: actions/checkout@v4.1.7
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- name: Set up Python 3.10/3.11
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uses: actions/setup-python@v5.1.1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install Miniconda
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uses: conda-incubator/setup-miniconda@v3.0.4
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with:
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activate-environment: testenv
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environment-file: conda/testenv.yaml
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python-version: ${{ matrix.python-version }}
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channels: conda-forge
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- name: Lint with ruff
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shell: bash -el {0}
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run: |
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ruff check --output-format=github .
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continue-on-error: true
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# making sure we are testing installed package
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- name: Install package
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shell: bash -el {0}
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run: |
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conda activate testenv
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pip install -e .
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- name: Test with pytest
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shell: bash -el {0}
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run: |
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conda run python -m pytest -q tests/test_calculations.py

‎.github/workflows/mopper-test-conda.yaml‎

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name: Test Build of mopper conda package
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# Controls when the action will run.
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on:
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# Triggers the workflow on push or pull request events but only for the prerelase branch
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push:
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branches: [ prerelease ]
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pull_request:
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branches: [ prerelease ]
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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jobs:
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conda_deployment_with_new_tag:
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name: Test conda deployment of package with Python ${{ matrix.python-version }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.10", "3.11", "3.12"]
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steps:
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- uses: actions/checkout@v4.1.7
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with:
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fetch-depth: 0
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- name: Set env
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run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
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- name: Conda environment creation and activation
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uses: conda-incubator/setup-miniconda@v3.0.4
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with:
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python-version: ${{ matrix.python-version }}
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activate-environment: mopper_env
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environment-file: conda/environment.yaml # Path to the build conda environment
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show-channel-urls: true #
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- name: Build but do not upload the conda packages
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uses: uibcdf/action-build-and-upload-conda-packages@v1.3.0
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with:
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meta_yaml_dir: conda
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python-version: ${{ matrix.python-version }} # Values previously defined in `matrix`
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user: coecms
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label: auto
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upload: false
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token: ${{ secrets.ANACONDA_TOKEN }} # Replace with the right name of your secret

‎.gitignore‎

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custom_app4_*.sh
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__pycache__/
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build/
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mopper_venv/
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*.csv
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*.yaml
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*.json
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localdata/
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src/mopper.egg-info/
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extras/
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*.txt

‎ACDD_conf.yaml‎

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grids: "ACDD_grids.json"
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# Additional NCI information:
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# NCI project to charge compute; $PROJECT = your default project
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# NCI queue to use; hugemem is recommended
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project: v45
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# additional NCI projects to be included in the storage flags
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addprojs: []
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# queue and memory (GB) per CPU (depends on queue)
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# queue and memory (GB) per CPU (depends on queue),
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# hugemem is reccomended for high reoslution data and/or derived variables
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# hugemem requires a minimum of 6 cpus this is handled by the code
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queue: hugemem
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mem_per_cpu: 32
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# walltime in "hh:mm:ss"
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walltime: '8:00:00'
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mode: custom
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# conda_env to use by default hh5 analysis3-unstable
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# as this has the code and all dependecies installed
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# you can override that by supplying the env to pass to "source"
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# Ex
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# conda_env: <custom-env-path>/bin/activate
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# or you can set "test: true" and modify mopper_job.sh manually
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conda_env: default
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#
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# Global attributes: these will be added to each files comment unwanted ones
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# Using ACDD CV vocab to check validity of global attributes
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parent: !!bool false
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# CMOR will add a tracking_id if you want to define a prefix add here
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tracking_id_prefix:
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comment: "post-processed using ACCESS-MOPPeR v0.6.0 https://doi.org/10.5281/zenodo.10346216"
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comment: "post-processed using ACCESS-MOPPeR v1.0.0 https://doi.org/10.5281/zenodo.10346216"

‎CMIP6_conf.yaml‎

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# additional NCI projects to be included in the storage flags
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addprojs: []
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# queue and memory (GB) per CPU (depends on queue)
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# hugemem is reccomended for high reoslution data and/or derived variables
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# hugemem requires a minimum of 6 cpus this is handled by the code
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queue: hugemem
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mem_per_cpu: 30
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# walltime in "hh:mm:ss"
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walltime: '8:00:00'
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mode: cmip6
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# conda_env: <custom-env-path>/bin/activate
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conda_env: default
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# Global attributes: these will be added to each files comment unwanted ones
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# the labels CMIP6/ACDD indicates which ones are necessary to comply with respective standards
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#CMOR will add a tracking_id if you want to define a prefix add here
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tracking_id_prefix:
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Conventions: "CF-1.7 CMIP-6.2"
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comment: "post-processed using ACCESS-MOPPeR v0.6.0 https://doi.org/10.5281/zenodo.10346216"
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comment: "post-processed using ACCESS-MOPPeR v1.0.0 https://doi.org/10.5281/zenodo.10346216"

‎README.md‎

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# [ACCESS Model Output Post-Processor (MOPPeR)](https://access-mopper.readthedocs.io/en/latest)
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[![Read the docs](https://readthedocs.org/projects/access-mopper/badge/?version=latest)](https://access-mopper.readthedocs.io/en/latest/)
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[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10976467.svg)](https://doi.org/10.5281/zenodo.10976467)
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[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12747219.svg)](https://doi.org/10.5281/zenodo.12747219)
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This code is derived from the [APP4](https://doi.org/10.5281/zenodo.7703469), initially created by Peter Uhe for CMIP5, and further developed for CMIP6-era by Chloe Mackallah from CSIRO, O&A Aspendale.
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Although we retained a differentiation between `custom` and `cmip` mode the main workflow is the same and `mode` is now only another field in the main configuration file.
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See [MOPPeR ReadtheDocs](https://access-mopper.readthedocs.io/en/stable/) for the full documentation.
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### Install
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You can install the latest version of `mopper` directly from conda (accessnri channel)::
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conda install -c accessnri mopper
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conda install -c coecms mopper
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If you want to install an unstable version or a different branch:
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MOPPeR is pre-installed into a Conda environment at NCI. Load it with::
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module use /g/data3/hh5/public/modules
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module load conda/analysis3-unstable
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module load conda/analysis3
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NB. You need to be a member of the hh5 project to load the modules.

‎conda/environment.yaml‎

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name: mopper_env
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channels:
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- conda-forge
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- coecms
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- default
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dependencies:
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- anaconda-client
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- conda-build
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- conda-verify

‎conda/meta.yaml‎

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{% set version = "0.6.1" %}
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package:
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name: mopper
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version: {{ version }}
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version: "{{ environ.get('GIT_DESCRIBE_TAG', '1.0') }}"
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#source:
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# path: ./
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source:
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#url: https://github.com/ACCESS-Hive/ACCESS-MOPPeR/archive/refs/tags/{{version}}.tar.gz
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git_url: https://github.com/ACCESS-Hive/ACCESS-MOPPeR.git
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git_rev: {{ version }}
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git_depth: 1 # (Defaults to -1/not shallow)
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#git_tag: prerelease
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git_rev: "{{ version }}"
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#git_depth: 1 # (Defaults to -1/not shallow)
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build:
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number: 0
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number: 1
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noarch: python
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script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed"
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entry_points:
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host:
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- python
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- pip
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- pbr
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run:
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- python
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- click
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- pyyaml
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- cftime
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- python-dateutil
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test:
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#imports:
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# - mopdb
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# - mopper
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source_files:
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- tests
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- tests/testdata
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requires:
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- cmor
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- xarray
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- numpy
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- dask
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- pyyaml
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- cftime
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- python-dateutil
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- pytest
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- pyfakefs
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- coverage
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- codecov
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about:
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home: https://github.com/ACCESS-Hive/ACCESS-MOPPeR
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license: Apache 2.0
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#license_file: LICENSE.txt
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summary: 'ACCESS-MOPPeR post-process ACCESS raw model output to ESGF data standards'
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summary: 'ACCESS-MOPPeR post-process ACCESS raw model output using CMOR and pre-defined data standards'

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