Add docker-build to default build #361
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| name: build | |
| on: | |
| pull_request: | |
| branches: | |
| - main | |
| workflow_dispatch: | |
| push: | |
| branches: | |
| - 'main' | |
| - 'test-build' | |
| - 'docker-build' | |
| tags: | |
| - "v*" | |
| env: | |
| PARTICIPANT_DATA: | |
| REGISTRY: ghcr.io | |
| ORG: nbisweden | |
| IMAGE: workshop-pgip/workshop-pgip:latest | |
| jobs: | |
| build: | |
| name: Build site | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 60 | |
| permissions: | |
| contents: write | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Set time zone | |
| uses: szenius/set-timezone@v1.0 | |
| with: | |
| timezoneLinux: "Europe/Stockholm" | |
| timezoneMacos: "Europe/Stockholm" | |
| timezoneWindows: "W. Europe Standard Time" | |
| - name: Cancel Previous Runs | |
| if: ${{ !env.ACT }} | |
| uses: styfle/cancel-workflow-action@0.11.0 | |
| with: | |
| access_token: ${{ github.token }} | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Pull image | |
| run: docker pull ${{ env.REGISTRY }}/${{ env.ORG }}/${{ env.IMAGE }} | |
| # - name: Install micromamba | |
| # uses: mamba-org/setup-micromamba@v1 | |
| # with: | |
| # micromamba-version: "1.3.1-0" | |
| # environment-file: conda-linux-64.lock | |
| # environment-name: pgip | |
| # init-shell: bash | |
| # cache-environment: true | |
| # - name: Test git installation | |
| # run: | | |
| # git --help | |
| # echo Listing branches | |
| # git branch -l | |
| # echo Fetching branches | |
| # git fetch --all | |
| # echo Listing branches again | |
| # git branch --list | |
| - name: Install pgip dependencies | |
| run: | | |
| python -m ipykernel install --user --name pgip --display-name "Population Genomics in Practice (Python)" | |
| python -m pip install git+https://github.com/NBISweden/pgip-tools | |
| python -m pip install git+https://github.com/ksamuk/pixy.git | |
| - name: Install dotenv | |
| run: | | |
| R -e "install.packages('dotenv', repos=c(CRAN = 'https://cran.rstudio.com/'))" | |
| - name: Install TeXLive | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install texlive texlive-latex-extra | |
| - name: Install local pgip R package | |
| run: | | |
| R -e "library(devtools); devtools::install_local('src/R/pgip', upgrade=F)" | |
| - name: Setup Quarto | |
| uses: quarto-dev/quarto-actions/setup@v2 | |
| with: | |
| version: 1.3.450 | |
| - run: | | |
| quarto --version | |
| - name: Add miniconda path | |
| run: | | |
| echo "$(dirname $(which R))" >> $GITHUB_PATH | |
| quarto check | |
| - name: "Set environment variables" | |
| run: | | |
| echo "TEXINPUTS=$TEXINPUTS:$GITHUB_WORKSPACE/src/latex" >> $GITHUB_ENV | |
| - name: Install dvisvgm | |
| run: | | |
| sudo apt-get install dvisvgm | |
| - name: Render project without publishing | |
| uses: quarto-dev/quarto-actions/render@v2 | |
| if: ${{ github.event_name == 'pull_request' }} | |
| with: | |
| path: docs | |
| - name: Publish to GitHub Pages | |
| uses: quarto-dev/quarto-actions/publish@v2 | |
| if: ${{ github.ref_name == 'main' || github.ref_name == 'test-build' }} | |
| with: | |
| target: gh-pages | |
| path: docs | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Create archive branch | |
| if: startsWith(github.ref, 'refs/tags/v') | |
| run: | | |
| echo "Creating archive branch archive-${{ github.ref_name }}" | |
| if git show-ref --quiet "refs/heads/archive-${{ github.ref_name }}"; then | |
| echo "archive-${{ github.ref_name }}" branch exists | |
| else | |
| echo "Running git branch archive-${{ github.ref_name }}" | |
| git branch "archive-${{ github.ref_name }}" | |
| fi | |
| - name: Render tag and save rendered state in separate branch | |
| if: startsWith(github.ref, 'refs/tags/v') | |
| env: | |
| GITHUB_EMAIL: do_not_email@example.com | |
| GITHUB_USERNAME: gh_action | |
| TARGET: "archive-${{ github.ref_name }}" | |
| run: | | |
| # Add git info | |
| git config --global user.email "${{ env.GITHUB_EMAIL }}" | |
| git config --global user.name "${{ env.GITHUB_USERNAME }}" | |
| git clone --single-branch --branch ${{ env.TARGET }} "https://${{ secrets.GITHUB_TOKEN }}@github.com/${GITHUB_REPOSITORY}.git" tmprepo | |
| # - name: Render tag and save rendered state in separate branch | |
| # uses: quarto-dev/quarto-actions/publish@v2 | |
| # if: startsWith(github.ref, 'refs/tags/v') | |
| # with: | |
| # target: "archive-${{ github.ref_name }}" | |
| # path: docs | |
| # env: | |
| # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Checkout archived course versions | |
| env: | |
| GITHUB_EMAIL: do_not_email@example.com | |
| GITHUB_USERNAME: gh_action | |
| TARGET: gh-pages | |
| run: | | |
| # Add git info | |
| git config --global user.email "${{ env.GITHUB_EMAIL }}" | |
| git config --global user.name "${{ env.GITHUB_USERNAME }}" | |
| git clone --single-branch --branch ${{ env.TARGET }} "https://${{ secrets.GITHUB_TOKEN }}@github.com/${GITHUB_REPOSITORY}.git" tmprepo | |
| cd tmprepo | |
| mkdir -p archive | |
| cd archive | |
| git branch -l | |
| ls -lh | |
| # Add archive index page | |
| cat .header.html > index.html | |
| # Loop tags that match v\d+ | |
| for tag in $(git tag --list v[0-9][0-9][0-9][0-9]); do | |
| if [ -d $tag ]; then | |
| echo "Directory ${tag} already exsists. Removing" | |
| git rm -f $tag | |
| fi | |
| git clone --depth 1 --branch "archive-$tag" "https://${{ secrets.GITHUB_TOKEN }}@github.com/${GITHUB_REPOSITORY}.git" $tag | |
| git add -f $tag | |
| contents=$(git tag -n 100 $tag --format "%(contents)") | |
| echo "<section id=\"$tag\" class=\"level3\">" >> index.html | |
| echo "<h3 class=\"anchored\" data-anchor-id=\"$tag\">" >> index.html | |
| echo "<a href=\"$link\">$tag</a>" >> index.html | |
| echo "</h3>" >> index.html | |
| echo "<p>$contents</p>" >> index.html | |
| echo "</section>" >> index.html | |
| done | |
| cat .footer.html >> index.html | |
| git add -f index.html |