move to new template, add code repo, add build

root = true

[*]

charset = utf-8

insert_final_newline = true

trim_trailing_whitespace = true

[*.md]

indent_size = 2

indent_style = space

max_line_length = 100  # Please keep this in sync with bin/lesson_check.py!

trim_trailing_whitespace = false  # keep trailing spaces in markdown - 2+ spaces are translated to a hard break (<br/>)

[*.r]

max_line_length = 80

[*.py]

indent_size = 4

indent_style = space

max_line_length = 79

[*.sh]

end_of_line = lf

[Makefile]

indent_style = tab

<details>

<summary><strong>Instructions</strong></summary>

Thanks for contributing! :heart:

If this contribution is for instructor training, please email the link to this contribution to

checkout@carpentries.org so we can record your progress. You've completed your contribution

step for instructor checkout by submitting this contribution!

If this issue is about a specific episode within a lesson, please provide its link or filename.

Keep in mind that **lesson maintainers are volunteers** and it may take them some time to

respond to your contribution. Although not all contributions can be incorporated into the lesson

materials, we appreciate your time and effort to improve the curriculum. If you have any questions

about the lesson maintenance process or would like to volunteer your time as a contribution

reviewer, please contact The Carpentries Team at team@carpentries.org.

You may delete these instructions from your comment.

\- The Carpentries

</details>

<details>

<summary><strong>Instructions</strong></summary>

Thanks for contributing! :heart:

If this contribution is for instructor training, please email the link to this contribution to

instructor.training@carpentries.org so we can record your progress. You've completed your contribution

step for instructor checkout by submitting this contribution!

Keep in mind that **lesson maintainers are volunteers** and it may take them some time to

respond to your contribution. Although not all contributions can be incorporated into the lesson

materials, we appreciate your time and effort to improve the curriculum. If you have any questions

about the lesson maintenance process or would like to volunteer your time as a contribution

reviewer, please contact The Carpentries Team at team@carpentries.org.

You may delete these instructions from your comment.

\- The Carpentries

</details>

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: '3.0'

          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 "team@carpentries.org"

          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

name: Weekly Styles Update

on:

  workflow_dispatch:

    inputs:

      name:

        description: 'Person who triggered the workflow'

        required: true

        default: 'scheduled run'

  schedule:

    # Run every Wednesday

    - cron: '0 0 * * 3'

jobs:

  check-token:

    name: "Check STYLES_WORKFLOW token"

    runs-on: ubuntu-latest

    if: ${{ github.repository == 'carpentries/lesson-example' }}

    outputs:

      wf: ${{ steps.validate.outputs.wf }}

      repo: ${{ steps.validate.outputs.repo }}

    steps:

      - name: "validate token"

        id: validate

        uses: carpentries/actions/check-valid-credentials@main

        with:

          token: ${{ secrets.STYLES_WORKFLOW }}

  bad-token:

    name: "Invalid/Missing Token"

    runs-on: ubuntu-latest

    needs: check-token

    if: ${{ needs.check-token.outputs.wf != 'true' && github.repository == 'carpentries/lesson-example' }}

    steps:

      - name: "Instructions to create a new token"

        run: |

          printf "::warning::The STYLES_WORKFLOW secret is missing, invalid, "\

          "or does not have the right scope to update workflows.\n"\

          "If you want to have automated pull request updates to your workflows, "\

          "you will need to generate a new token by visiting "\

          "https://github.com/settings/tokens/new?scopes=repo,workflow&description=Styles%%20Token\n"\

          "Once you have created the token, go to "\

          "https://github.com/${{ github.repository }}/settings/secrets/actions/STYLES_WORKFLOW "\

          "to update it."

  update-styles:

    runs-on: ubuntu-latest

    name: Styles Update

    needs: check-token

    if: ${{ needs.check-token.outputs.wf == 'true' && github.repository == 'carpentries/lesson-example' }}

    steps:

      - uses: actions/checkout@v2

        with:

          fetch-depth: 0

      - name: Record Date

        id: today

        run: |

          echo "::set-output name=date::$(date -I)"

          echo "::set-output name=min::$(date +%Y-%m-%d-%H-%M)"

      - name: Sync lesson with carpentries/styles

        id: update

        uses: carpentries/actions/update-styles@main

        env:

          LESSON: "Lesson Example"

          REF: ${{ github.ref }}

        with:

          commit: true

      - name: Create Pull Request

        id: cpr

        if: ${{ steps.update.outputs.update == 'true' }}

        uses: peter-evans/create-pull-request@v3.10.0

        with:

          token: ${{ secrets.STYLES_WORKFLOW}}

          commit-message: "[actions] Sync lesson with carpentries/styles"

          branch: "update-styles-${{ steps.today.outputs.min }}"

          delete-branch: true

          title: "Update Styles (${{ steps.today.outputs.date }} via ${{ github.event.inputs.name }})"

          body: |

            Update styles repository. Please inspect the changes to make sure there are no conflicts with your lesson.

            - Auto-generated by [create-pull-request][1]

            [1]: https://github.com/peter-evans/create-pull-request

          labels: "type:template and tools"

          # NOTE: This tag is repository-specific

          team-reviewers: core-team-curriculum

          draft: false