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Merge pull request #345 from British-Oceanographic-Data-Centre/develop
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‎.github/workflows/build_package.yml

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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [3.7, 3.8]
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python-version: [ 3.7, 3.8, 3.9 ]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip virtualenv
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python -m pip install -r requirements.txt
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- name: Shell Script Permissions
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run: |
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chmod +x *.sh
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- name: Setup Environment
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run: |
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./setup_environment.sh
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- name: Build Package
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run: |
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./build.sh
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- name: Test Package Install
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run: |
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python -m pip install dist/COAsT-*.tar.gz
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- name: Generate Conda Metadata
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run: |
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./generate_conda_meta.sh
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cat conda/meta.yaml
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip virtualenv
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python -m pip install -r requirements.txt
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- name: Shell Script Permissions
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run: |
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chmod +x *.sh
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- name: Setup Environment
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run: |
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./setup_environment.sh
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- name: Build Package
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run: |
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./build.sh
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- name: Test Package Install
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run: |
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python -m pip install dist/COAsT-*.tar.gz
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- name: Generate Conda Metadata
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run: |
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./generate_conda_meta.sh
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cat conda/meta.yaml

‎.github/workflows/formatting.yml

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name: Black
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on: pull_request
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jobs:
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formatting:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [ 3.9 ]
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steps:
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- uses: actions/checkout@v1
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- name: Set up Python ${{ matrix.python-version }} for Black
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install Black
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run: pip install black
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- name: Check Formatting
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run: black --check . # Only check the formatting, don't make any changes
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- name: Apply Formatting
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if: failure() # Only run if Black suggests changes
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run: |
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black .
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git config --global user.name "BlackBot"
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git config --global author.name "BlackBot"
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git config --global user.email "bodcsoft@bodc.ac.uk"
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git config --global author.email "bodcsoft@bodc.ac.uk"
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git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY
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git checkout $GITHUB_HEAD_REF
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git commit -am "Apply Black formatting to Python code."
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git push

‎.github/workflows/publish_package.yml

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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [3.7]
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python-version: [ 3.7 ]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip virtualenv
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python -m pip install -r requirements.txt
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- name: Shell Script Permissions
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run: |
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chmod +x *.sh
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- name: Setup Environment
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run: |
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./setup_environment.sh
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- name: Build Package
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run: |
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./build.sh
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- name: Test Package Install
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run: |
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python -m pip install dist/COAsT-*.tar.gz
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- name: Publish Package to PyPi
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shell: bash
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env:
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PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
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run: |
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./publish.sh "https://upload.pypi.org/legacy/" "$PYPI_TOKEN"
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- name: Generate Conda Metadata
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run: |
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./generate_conda_meta.sh
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cat conda/meta.yaml
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- name: Publish Package to Anaconda
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uses: fcakyon/conda-publish-action@v1.3
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with:
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subdir: "conda"
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anacondatoken: ${{ secrets.ANACONDA_TOKEN }}
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platforms: 'win osx linux'
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip virtualenv
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python -m pip install -r requirements.txt
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- name: Shell Script Permissions
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run: |
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chmod +x *.sh
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- name: Setup Environment
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run: |
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./setup_environment.sh
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- name: Build Package
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run: |
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./build.sh
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- name: Test Package Install
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run: |
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python -m pip install dist/COAsT-*.tar.gz
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- name: Publish Package to PyPi
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shell: bash
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env:
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PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
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run: |
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./publish.sh "https://upload.pypi.org/legacy/" "$PYPI_TOKEN"
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- name: Generate Conda Metadata
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run: |
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./generate_conda_meta.sh
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cat conda/meta.yaml
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- name: Publish Package to Anaconda
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uses: fcakyon/conda-publish-action@v1.3
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with:
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subdir: "conda"
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anacondatoken: ${{ secrets.ANACONDA_TOKEN }}
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platforms: 'win osx linux'

‎.github/workflows/verify_package.yml

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name: Test Python Package
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on: [push]
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on: [ push ]
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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [3.7, 3.8]
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python-version: [ 3.7, 3.8, 3.9 ]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -r requirements.txt
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- name: Lint with flake8
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run: |
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pip install flake8
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# stop the build if there are Python syntax errors or undefined names
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flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
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# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
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flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
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- name: Test with pytest
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run: |
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pip install dask[complete]
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pip install -r requirements.txt
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pytest tests
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -r requirements.txt
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- name: Lint with flake8
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run: |
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pip install flake8
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# stop the build if there are Python syntax errors or undefined names
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flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
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# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
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flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
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- name: Test with pytest
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run: |
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pip install dask[complete]
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pip install -r requirements.txt
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pytest tests

‎.gitignore

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*.pyc
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*.DS_Store
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.vscode
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# development ignores
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sandbox.py
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config/nemo_tst_gridded.json
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‎README.md

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`.____ .' `.___.'|____| |____|[\__) )|_____|
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Coastal Ocean Assessment Toolbox
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https://www.nemo-ocean.eu/
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__________________________________________________________________________________________
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```
@@ -24,33 +23,35 @@ Documentation can be found [here](https://british-oceanographic-data-centre.gith
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COAsT is an object-orientated package, meaning that data is stored within Python object
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structures. In addition to data storage, these objects contain methods (subroutines)
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which allow for manipulation of this data. An example of such an object is the NEMO
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object, which allows for the storage and manipulation of NEMO output and domain data. It
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which allow for manipulation of this data. An example of such an object is the Gridded
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object, which allows for the storage and manipulation of (e.g.) NEMO output and domain data. It
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is important to understand how to load data using COAsT and the structure of the resulting
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objects.
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A NEMO object is created and initialised by passing it the paths of the domain and data
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A Gridded object is created and initialised by passing it the paths of the domain and data
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files. Ideally, the grid type should also be specified (T, U, V or F in the case of NEMO).
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For example, to load in data from a file containing data on a NEMO T-grid:
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```
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import coast
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fn_data = '<path to T-grid data file(s)>'
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fn_domain = '<path to domain file>'
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data = coast.NEMO(fn_data, fn_domain, grid_ref='t-grid')
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fn_data = "<path to T-grid data file(s)>"
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fn_domain = "<path to domain file>"
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fn_config = "<path to JSON config file>"
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data = coast.Gridded(fn_data, fn_domain, fn_config)
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```
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Ideally, NEMO output data should be in grid-specific files, i.e. containing output
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variables situated on a NEMO T, U, V or F grid. The whole domain file is supplied,
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however only grid specific variables are placed into the NEMO object. A NEMO object
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therefore contains grid-specific data and all corresponding grid variables. One of the
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file names can be omitted (to get a data-only or grid only object), however functionality
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in this case will be limited.
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Ideally, Gridded model output data should be in grid-specific files, i.e.
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containing output variables situated on a NEMO T, U, V or F grid, whereas the
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grid variables are in a single domain file. On loading into COAsT, only the
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grid specific variables appropriate for the paired data are placed into the
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Gridded object. A Gridded object therefore contains grid-specific data and all
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corresponding grid variables. One of the file names can be omitted (to get a
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data-only or grid only object), however functionality in this case will be
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limited.
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Once loaded, data is stored inside the object using an xarray.dataset object. Following
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on from the previous code example, this can be viewed by calling:
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Once loaded, data is stored inside the object using an xarray.dataset object.
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Following on from the previous code example, this can be viewed by calling:
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```
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data.dataset
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data will not. For this reason, if you require a subset of the data, it is best to
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index first.
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The names of common grid variables are standardised within the COAsT package for
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consistency and ease of use. Along with their original NEMO names, these are:
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The names of common grid variables are standardised within the COAsT package
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using JSON configuration files. For example, the following lists COAsT internal
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variable followed by the typical NEMO variable names:
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1. longitude [glamt / glamu / glamv / glamf]
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2. latitude [gphit / gphiu / gphiv / gphif]

‎coast/CLIMATOLOGY.py

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