WIP: correct Data Cleaning code #368
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| 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@v5 | |
| 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 "::set-output name=count::$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})" | |
| - name: Set up R | |
| if: steps.check-rmd.outputs.count != 0 | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 'release' | |
| - name: Install needed packages | |
| if: steps.check-rmd.outputs.count != 0 | |
| working-directory: lesson | |
| run: | | |
| source('bin/dependencies.R') | |
| install_required_packages(.libPaths()[1]) | |
| shell: Rscript {0} | |
| - name: Query dependencies | |
| if: steps.check-rmd.outputs.count != 0 | |
| working-directory: lesson | |
| run: | | |
| source('bin/dependencies.R') | |
| deps <- identify_dependencies() | |
| create_description(deps) | |
| use_bioc_repos() | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| writeLines(sprintf("R-%i.%i", getRversion()$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@v4 | |
| 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 |