Change pwd brackets #365
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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: | |
| runs-on: ubuntu-latest | |
| name: Build site | |
| 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 }}/${{ env.IMAGE }} | |
| - name: Define variables | |
| run: | | |
| echo "REPO=$(basename ${GITHUB_REPOSITORY})" >> $GITHUB_ENV | |
| cd docs | |
| echo "PATH_REPO=$(pwd)" >> $GITHUB_ENV | |
| echo "PATH_EXPORT=$(grep -E 'output-dir' _quarto.yml | xargs | sed 's/output-dir://' | xargs)" >> $GITHUB_ENV | |
| - name: Check docker and variables | |
| run: | | |
| docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/qmd ${{ env.REGISTRY }}/${{ env.ORG }}/${{ env.IMAGE }} Rscript -e "print('R in docker works!')" | |
| echo "GITHUB_ACTOR: ${GITHUB_ACTOR}" | |
| echo "GITHUB_REPOSITORY: ${GITHUB_REPOSITORY}" | |
| echo "REPO: ${REPO}" | |
| echo "env.PATH_REPO: ${{ env.PATH_REPO }}" | |
| echo "PATH_EXPORT: ${PATH_EXPORT}" | |
| echo "PATH_EXPORT_CANVAS: ${PATH_EXPORT_CANVAS}" | |
| echo "GITHUB_REPOSITORY_OWNER: ${GITHUB_REPOSITORY_OWNER}" | |
| echo "---------------------------------------------------------------------------------------------" | |
| echo "Folder contents at $(pwd):" | |
| ls -lh | |
| echo "---------------------------------------------------------------------------------------------" | |
| printenv | |
| sed --version | |
| - name: Render site | |
| run: | | |
| # Add git info | |
| git config --global user.email "do_not_email@example.com" | |
| git config --global user.name "gh_action" | |
| # Render website | |
| echo "Rendering qmd files ..." | |
| echo "pwd: ${pwd}" | |
| echo "PWD: ${PWD}" | |
| docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${pwd}/scripts:/scripts -v ${pwd}/src:/src -v ${pwd}/docs:/qmd --env TEXINPUTS="../src/latex:$TEXINPUTS" ${{ env.REGISTRY }}/${{ env.ORG }}/${{ env.IMAGE }} | |
| # - name: Install pgip dependencies | |
| # run: | | |
| # python -m ipykernel install --user --name pgip --display-name "Population Genomics in Practice (Python)" | |
| # python -m pip install git+https://github.com/NBISweden/pgip-tools | |
| # python -m pip install git+https://github.com/ksamuk/pixy.git | |
| # - name: Install dotenv | |
| # run: | | |
| # R -e "install.packages('dotenv', repos=c(CRAN = 'https://cran.rstudio.com/'))" | |
| # - name: Install TeXLive | |
| # run: | | |
| # sudo apt-get update | |
| # sudo apt-get install texlive texlive-latex-extra | |
| # - name: Install local pgip R package | |
| # run: | | |
| # R -e "library(devtools); devtools::install_local('src/R/pgip', upgrade=F)" | |
| # - name: Setup Quarto | |
| # uses: quarto-dev/quarto-actions/setup@v2 | |
| # with: | |
| # version: 1.3.450 | |
| # - run: | | |
| # quarto --version | |
| # - name: Add miniconda path | |
| # run: | | |
| # echo "$(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 |