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.github/workflows/cgatcore_python.yml

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@@ -1,16 +1,10 @@
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name: cgatcore
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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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on: [push, pull_request]
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jobs:
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build:
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name: "Ex1 (${{ matrix.python-version }}, ${{ matrix.os }})"
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name: Ex1 (${{ matrix.python-version }}, ${{ matrix.os }})
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runs-on: ${{ matrix.os }}
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strategy:
@@ -25,48 +19,41 @@ jobs:
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steps:
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- uses: actions/checkout@v3
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- name: Cache conda
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uses: actions/cache@v3
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with:
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path: ~/conda_pkgs_dir
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key: ${{ runner.os }}-conda-${{ hashFiles('conda/environments/cgat-core.yml') }}
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env:
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# Adjust this value if the conda environment changes
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# Increase this value to reset cache if conda/environments/cgat-core.yml has not changed
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CACHE_NUMBER: 0
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with:
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path: ~/conda_pkgs_dir
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key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('conda/environments/cgat-core.yml') }}
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- name: Set installer URL
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id: set-installer-url
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run: |
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if [ "${{ matrix.os }}" = "ubuntu-latest" ]; then
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if [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then
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echo "installer-url=https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh" >> $GITHUB_ENV
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elif [ "${{ matrix.os }}" = "macos-latest" ]; then
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elif [[ "${{ matrix.os }}" == "macos-latest" ]]; then
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echo "installer-url=https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-arm64.sh" >> $GITHUB_ENV
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fi
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- name: Set up Miniconda
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uses: conda-incubator/setup-miniconda@v2
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- uses: conda-incubator/setup-miniconda@v2
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with:
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installer-url: ${{ env.installer-url }}
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python-version: ${{ matrix.python-version }}
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channels: conda-forge, bioconda, defaults
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channel-priority: true
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activate-environment: cgat-core
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environment-file: conda/environments/cgat-core.yml
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- name: Configure Conda Paths
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run: echo "$(conda info --base)/condabin" >> $GITHUB_PATH
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- name: Show Conda Information
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run: echo "/usr/share/miniconda3/condabin" >> $GITHUB_PATH
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- name: Show conda
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run: |
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conda info
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conda list
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- name: Test
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run: |
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pip install .
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./all-tests.sh
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deploy_docs:
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name: Deploy MkDocs Documentation
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runs-on: ubuntu-latest
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- name: Build and Deploy MkDocs Site
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run: mkdocs gh-deploy --force --clean
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env:
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GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

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