Update index.md #46
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Test template | |
| on: | |
| push: | |
| branches: gh-pages | |
| pull_request: | |
| jobs: | |
| check-template: | |
| name: ${{ matrix.lesson-name }} (${{ matrix.os-name }}) | |
| if: github.repository == 'carpentries/styles' | |
| runs-on: ${{ matrix.os }} | |
| continue-on-error: ${{ matrix.experimental }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| lesson: [swcarpentry/shell-novice, datacarpentry/r-intro-geospatial, librarycarpentry/lc-git] | |
| os: [ubuntu-20.04, macos-latest, windows-latest] | |
| experimental: [false] | |
| include: | |
| - os: ubuntu-20.04 | |
| os-name: Linux | |
| - os: macos-latest | |
| os-name: macOS | |
| - os: windows-latest | |
| os-name: Windows | |
| - lesson: swcarpentry/shell-novice | |
| lesson-name: (SWC) Shell novice | |
| - lesson: datacarpentry/r-intro-geospatial | |
| lesson-name: (DC) R Intro Geospatial | |
| - lesson: librarycarpentry/lc-git | |
| lesson-name: (LC) Intro to Git | |
| - lesson: datacarpentry/astronomy-python | |
| lesson-name: (DC) Foundations of Astronomical Data Science | |
| experimental: true | |
| os: ubuntu-20.04 | |
| os-name: Linux | |
| - lesson: carpentries/lesson-example | |
| lesson-name: (CP) Lesson Example | |
| experimental: false | |
| os: ubuntu-20.04 | |
| os-name: Linux | |
| defaults: | |
| run: | |
| shell: bash # forces 'Git for Windows' on Windows | |
| env: | |
| RSPM: 'https://packagemanager.rstudio.com/cran/__linux__/focal/latest' | |
| steps: | |
| - name: Set up Ruby | |
| uses: ruby/setup-ruby@v1 | |
| with: | |
| ruby-version: '2.7' | |
| bundler-cache: true | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.x' | |
| - name: Install GitHub Pages, Bundler, and kramdown gems | |
| run: | | |
| gem install github-pages bundler kramdown kramdown-parser-gfm | |
| - name: Install Python modules | |
| run: | | |
| if [[ $RUNNER_OS == macOS || $RUNNER_OS == Linux ]]; then | |
| python3 -m pip install --upgrade pip setuptools wheel pyyaml==5.3.1 requests | |
| elif [[ $RUNNER_OS == Windows ]]; then | |
| python -m pip install --upgrade pip setuptools wheel pyyaml==5.3.1 requests | |
| fi | |
| - name: Checkout the ${{ matrix.lesson }} lesson | |
| uses: actions/checkout@master | |
| with: | |
| repository: ${{ matrix.lesson }} | |
| path: lesson | |
| fetch-depth: 0 | |
| - name: Sync lesson with carpentries/styles | |
| working-directory: lesson | |
| run: | | |
| echo "::group::Fetch Styles" | |
| if [[ -n "${{ github.event.pull_request.number }}" ]] | |
| then | |
| ref="refs/pull/${{ github.event.pull_request.number }}/head" | |
| else | |
| ref="gh-pages" | |
| fi | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "The Carpentries Bot" | |
| git remote add styles https://github.com/carpentries/styles.git | |
| git fetch styles $ref:styles-ref | |
| echo "::endgroup::" | |
| echo "::group::Synchronize Styles" | |
| # Sync up only if necessary | |
| if [[ $(git rev-list --count HEAD..styles-ref) != 0 ]] | |
| then | |
| # The merge command below might fail for lessons that use remote theme | |
| # https://github.com/carpentries/carpentries-theme | |
| echo "Testing merge using recursive strategy, accepting upstream changes without committing" | |
| if ! git merge -s recursive -Xtheirs --no-commit styles-ref | |
| then | |
| # Remove "deleted by us, unmerged" files from the staging area. | |
| # these are the files that were removed from the lesson | |
| # but are still present in the carpentries/styles repo | |
| echo "Removing previously deleted files" | |
| git rm $(git diff --name-only --diff-filter=DU) | |
| # If there are still "unmerged" files, | |
| # let's raise an error and look into this more closely | |
| if [[ -n $(git diff --name-only --diff-filter=U) ]] | |
| then | |
| echo "There were unmerged files in ${{ matrix.lesson-name }}:" | |
| echo "$(git diff --compact-summary --diff-filter=U)" | |
| exit 1 | |
| fi | |
| fi | |
| echo "Committing changes" | |
| git commit -m "Sync lesson with carpentries/styles" | |
| fi | |
| echo "::endgroup::" | |
| - name: Look for R-markdown files | |
| id: check-rmd | |
| working-directory: lesson | |
| run: | | |
| echo "count=$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})" >> $GITHUB_OUTPUT | |
| - name: Set up R | |
| if: steps.check-rmd.outputs.count != 0 | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| install-r: false | |
| - name: Install needed packages | |
| if: steps.check-rmd.outputs.count != 0 | |
| working-directory: lesson | |
| run: | | |
| source('bin/dependencies.R') | |
| install_required_packages(.libPaths()[1]) | |
| shell: Rscript {0} | |
| - name: Query dependencies | |
| if: steps.check-rmd.outputs.count != 0 | |
| working-directory: lesson | |
| run: | | |
| source('bin/dependencies.R') | |
| deps <- identify_dependencies() | |
| create_description(deps) | |
| use_bioc_repos() | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | |
| shell: Rscript {0} | |
| - name: Restore Package Cache | |
| if: runner.os != 'Windows' && steps.check-rmd.outputs.count != 0 | |
| uses: actions/cache@v2 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- | |
| - name: Install stringi from source | |
| if: runner.os == 'Linux' && steps.check-rmd.outputs.count != 0 | |
| run: install.packages('stringi', repos='https://cloud.r-project.org') | |
| shell: Rscript {0} | |
| - name: Install system dependencies for R packages | |
| if: runner.os == 'Linux' && steps.check-rmd.outputs.count != 0 | |
| working-directory: lesson | |
| run: | | |
| while read -r cmd | |
| do | |
| eval sudo $cmd || echo "Nothing to update" | |
| done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")') | |
| - run: make site | |
| working-directory: lesson | |
| - run: make lesson-check-all | |
| working-directory: lesson |