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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -8,14 +8,16 @@ jobs: | |
| name: ${{ matrix.lesson-name }} (${{ matrix.os-name }}) | ||
| if: github.repository == 'carpentries/styles' | ||
| runs-on: ${{ matrix.os }} | ||
| continue-on-error: ${{ matrix.experimental }} | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| lesson: [swcarpentry/shell-novice, datacarpentry/r-intro-geospatial, librarycarpentry/lc-git] | ||
| os: [ubuntu-20.04, macos-latest, windows-latest] | ||
| experimental: [false] | ||
| include: | ||
| - os: ubuntu-20.04 | ||
| os-name: Ubuntu | ||
| os-name: Linux | ||
| - os: macos-latest | ||
| os-name: macOS | ||
| - os: windows-latest | ||
|
|
@@ -26,16 +28,27 @@ jobs: | |
| lesson-name: (DC) R Intro Geospatial | ||
| - lesson: librarycarpentry/lc-git | ||
| lesson-name: (LC) Intro to Git | ||
| - lesson: datacarpentry/astronomy-python | ||
| lesson-name: (DC) Foundations of Astronomical Data Science | ||
| experimental: true | ||
| os: ubuntu-20.04 | ||
| os-name: Linux | ||
| - lesson: carpentries/lesson-example | ||
| lesson-name: (CP) Lesson Example | ||
| experimental: false | ||
| os: ubuntu-20.04 | ||
| os-name: Linux | ||
| defaults: | ||
| run: | ||
| shell: bash # forces 'Git for Windows' on Windows | ||
| env: | ||
| RSPM: 'https://packagemanager.rstudio.com/cran/__linux__/focal/latest' | ||
| steps: | ||
| - name: Set up Ruby | ||
| uses: actions/setup-ruby@v1 | ||
| uses: ruby/setup-ruby@v1 | ||
| with: | ||
| ruby-version: '2.7' | ||
| bundler-cache: true | ||
|
|
||
| - name: Set up Python | ||
| uses: actions/setup-python@v2 | ||
|
|
@@ -61,42 +74,74 @@ jobs: | |
| path: lesson | ||
| fetch-depth: 0 | ||
|
|
||
| - name: Determine the proper reference to use | ||
| id: styles-ref | ||
| - name: Sync lesson with carpentries/styles | ||
| working-directory: lesson | ||
| run: | | ||
| if [[ -n "${{ github.event.pull_request.number }}" ]]; then | ||
| echo "::set-output name=ref::refs/pull/${{ github.event.pull_request.number }}/head" | ||
| echo "::group::Fetch Styles" | ||
| if [[ -n "${{ github.event.pull_request.number }}" ]] | ||
| then | ||
| ref="refs/pull/${{ github.event.pull_request.number }}/head" | ||
| else | ||
| echo "::set-output name=ref::gh-pages" | ||
| ref="gh-pages" | ||
| fi | ||
| - name: Sync lesson with carpentries/styles | ||
| working-directory: lesson | ||
| run: | | ||
| 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 config --local remote.styles.tagOpt --no-tags | ||
| git fetch styles ${{ steps.styles-ref.outputs.ref }}:styles-ref | ||
| git merge -s recursive -Xtheirs --no-commit styles-ref | ||
| git commit -m "Sync lesson with carpentries/styles" | ||
| 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 ${#files[@]})" | ||
| echo "count=$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})" >> $GITHUB_OUTPUT | ||
| - name: Set up R | ||
| if: steps.check-rmd.outputs.count != 0 | ||
| uses: r-lib/actions/setup-r@master | ||
| uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| r-version: 'release' | ||
| use-public-rspm: true | ||
| install-r: false | ||
|
|
||
| - name: Install needed packages | ||
| if: steps.check-rmd.outputs.count != 0 | ||
| working-directory: lesson | ||
| run: | | ||
| install.packages(setdiff(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'), rownames(installed.packages()))) | ||
| source('bin/dependencies.R') | ||
| install_required_packages(.libPaths()[1]) | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Query dependencies | ||
|
|
@@ -106,13 +151,14 @@ jobs: | |
| source('bin/dependencies.R') | ||
| deps <- identify_dependencies() | ||
| create_description(deps) | ||
| use_bioc_repos() | ||
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | ||
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Cache R packages | ||
| - name: Restore Package Cache | ||
| if: runner.os != 'Windows' && steps.check-rmd.outputs.count != 0 | ||
| uses: actions/cache@v1 | ||
| uses: actions/cache@v2 | ||
| with: | ||
| path: ${{ env.R_LIBS_USER }} | ||
| key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} | ||
|
|
@@ -129,8 +175,11 @@ jobs: | |
| run: | | ||
| while read -r cmd | ||
| do | ||
| eval sudo $cmd | ||
| 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 | ||
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