reverts to Mambaforge #8
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| name: Build Dissertation | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # os: [ubuntu-latest, macos-latest, windows-latest] | |
| os: [ubuntu-latest] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| # Checkout the repository | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Create environment with Mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge # mamba is faster than base conda | |
| miniforge-version: latest | |
| channels: conda-forge, bioconda | |
| auto-activate-base: false | |
| activate-environment: 2025-dotson-thesis | |
| environment-file: environment.yml | |
| use-mamba: true | |
| use-only-tar-bz2: true | |
| - run: | | |
| conda config --env --set pip_interop_enabled True | |
| # Set up caching to speed up subsequent runs | |
| - name: Set up cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| ~/.texlive | |
| ~/.miktex | |
| /usr/local/texlive | |
| ${{ runner.temp }}/latex_cache | |
| key: ${{ runner.os }}-latex-${{ hashFiles('**/Snakefile') }} | |
| restore-keys: | | |
| ${{ runner.os }}-latex- | |
| # Install LaTeX on each OS | |
| - name: Install LaTeX | |
| run: | | |
| if [[ ${{ matrix.os }} == 'ubuntu-latest' ]]; then | |
| sudo apt-get update | |
| sudo apt-get install -y texlive-full biber | |
| elif [[ ${{ matrix.os }} == 'macos-latest' ]]; then | |
| brew install --cask mactex-no-gui | |
| sudo tlmgr update --self && sudo tlmgr install biber | |
| elif [[ ${{ matrix.os }} == 'windows-latest' ]]; then | |
| choco install miktex -y | |
| miktexsetup finish | |
| initexmf --update-fndb | |
| initexmf --mklinks | |
| initexmf --mklangs | |
| fi | |
| # Execute the Snakemake workflow | |
| - name: Run Snakemake workflow | |
| run: | | |
| cd analysis && snakemake -j2 | |
| # Upload the generated PDF as an artifact | |
| - name: Upload PDF artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: thesis-pdf | |
| path: docs/thesis.pdf |