ci.yaml

---
name: CI

# yamllint disable-line rule:truthy
on:
  push:
    branches:
      - develop

  workflow_dispatch:
  repository_dispatch:

concurrency:
  group: ci
  cancel-in-progress: true

jobs:
  lint:
    name: Apply lintr in all R and Rmd files
    runs-on: ubuntu-latest
    # runs-on: self-hosted
    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      RENV_PATHS_ROOT: ~/.local/share/renv
    steps:
      - name: Checking out shallow repository
        uses: actions/checkout@v2

      - run: git branch

      - name: Setting up R installation
        uses: r-lib/actions/setup-r@v2

      - name: Cache R packages
        uses: actions/cache@v2.1.4
        id: cache-packages
        with:
          path: ${{ env.RENV_PATHS_ROOT }}
          key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }}-targets-v2
          restore-keys: |
            ${{ runner.os }}-renv-

      - name: Query dependencies
        run: |
          install.packages('remotes')
          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: Install system dependencies
        if: runner.os == 'Linux'
        run: |
          while read -r cmd
          do
            eval sudo $cmd
          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')

      - name: Install other dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y libgit2-dev libharfbuzz-dev libcurl4-openssl-dev \
          libfribidi-dev libzmq3-dev libmagick++-dev

      - name: Install dependencies
        run: |
          if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv")
          Sys.unsetenv("GITHUB_PAT")
          renv::restore()
        shell: Rscript {0}

      - name: Lint
        run: |
          library(lintr)
          for (i in c("analysis", "R", "scripts", "review", "thesis", "output")) {
            print(lint_dir(i, linters = with_defaults(
              open_curly_linter = NULL, T_and_F_symbol_linter,
              assignment_linter, closed_curly_linter = NULL, commas_linter, commented_code_linter = NULL,
              cyclocomp_linter(50), object_name_linter(styles = "snake_case"), object_length_linter(30),
              equals_na_linter, function_left_parentheses_linter, infix_spaces_linter,
              line_length_linter(500), no_tab_linter, object_usage_linter = NULL, paren_brace_linter,
              absolute_path_linter(lax = TRUE), nonportable_path_linter = NULL, pipe_continuation_linter,
              semicolon_terminator_linter(semicolon = "trailing"), seq_linter, single_quotes_linter,
              spaces_inside_linter, spaces_left_parentheses_linter, trailing_blank_lines_linter,
              trailing_whitespace_linter, undesirable_function_linter, undesirable_operator_linter,
              unneeded_concatenation_linter
            ), exclusions = list("R/RcppExports.R")))
          }
        shell: Rscript {0}

  targets:
    name: Run targets pipeline
    needs: lint
    runs-on: ubuntu-latest
    # runs-on: self-hosted
    if: "contains(github.event.head_commit.message, 'targets')"
    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      RENV_PATHS_ROOT: ~/.local/share/renv
    steps:
      - name: Checking out shallow repository
        uses: actions/checkout@v2

      - run: git branch

      - name: Setting up R installation
        uses: r-lib/actions/setup-r@v2

      - name: Setting up pandoc and pandoc-citeproc
        uses: r-lib/actions/setup-pandoc@v2

      - name: Cache R packages
        uses: actions/cache@v2.1.4
        id: cache-packages
        with:
          path: ${{ env.RENV_PATHS_ROOT }}
          key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }}-targets-v2
          restore-keys: |
            ${{ runner.os }}-renv-

      - name: Query dependencies
        run: |
          install.packages('remotes')
          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: Install system dependencies
        if: runner.os == 'Linux'
        run: |
          while read -r cmd
          do
            eval sudo $cmd
          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')

      - name: Install other dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y libgit2-dev libharfbuzz-dev libcurl4-openssl-dev \
          libfribidi-dev libzmq3-dev libmagick++-dev

      - name: Install dependencies
        run: |
          if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv")
          Sys.unsetenv("GITHUB_PAT")
          renv::install(".")
          renv::restore()
        shell: Rscript {0}

      - name: Check if previous runs exist
        id: runs-exist
        run: git ls-remote --exit-code --heads origin targets-runs
        continue-on-error: true

      - name: Checking out shallow previous run
        if: steps.runs-exist.outcome == 'success'
        uses: actions/checkout@v2
        with:
          ref: targets-runs
          path: .targets-runs

      - name: Restore output files from the previous run
        if: steps.runs-exist.outcome == 'success'
        run: |
          for (dest in scan(".targets-runs/.targets-files", what = character())) {
            source <- file.path(".targets-runs", dest)
            if (!file.exists(dirname(dest))) dir.create(dirname(dest), recursive = TRUE)
            if (file.exists(source)) file.rename(source, dest)
          }
        shell: Rscript {0}

      - name: Run targets pipeline
        run: renv::run('run.R')
        shell: Rscript {0}
        continue-on-error: true # if the pipeline fails, the workspace is saved for inspection.

      - name: Identify files that the targets pipeline produced
        id: check-new-files
        run: |
          git ls-files -mo -x renv -x inst -x src > .targets-files
          ([ -s .targets-files ] && echo "New files produced" && cat .targets-files && echo "::set-output name=newfiles::true") || (echo "Nothing to do" && echo "::set-output name=newfiles::false")

      - name: Update the current repository without the objects
        if: steps.check-new-files.outputs.newfiles == 'true'
        run: |
          git config --local user.name "GitHub Actions"
          git config --local user.email "actions@github.com"
          git add --all -- ':!renv'
          git commit -am "Update current branch"
          git push --quiet
        continue-on-error: true

      - name: Create the runs branch if it does not already exist
        if: steps.check-new-files.outputs.newfiles == 'true' && steps.runs-exist.outcome != 'success'
        run: git checkout --orphan targets-runs
        continue-on-error: true # if the pipeline fails, the workspace is saved for inspection.

      - name: Put the worktree in the runs branch if the latter already exists
        if: steps.check-new-files.outputs.newfiles == 'true' && steps.runs-exist.outcome == 'success'
        run: |
          rm -r .git
          mv .targets-runs/.git .
          rm -r .targets-runs
        continue-on-error: true # if the pipeline fails, the workspace is saved for inspection.

      - name: Upload latest run to the runs branch
        if: steps.check-new-files.outputs.newfiles == 'true'
        run: |
          git config --local user.name "GitHub Actions"
          git config --local user.email "actions@github.com"
          rm -r .github/workflows
          git add --all -- ':!renv'
          git add -f .targets-files
          git add -f _targets
          git commit -am "Run pipeline"
          git push origin targets-runs
        continue-on-error: true # if the pipeline fails, the workspace is saved for inspection.

      - name: Prepare failure artifact
        if: failure()
        run: rm -rf .git .github .targets-files .targets-runs

      - name: Post failure artifact
        if: failure()
        uses: actions/upload-artifact@main
        with:
          name: ${{ runner.os }}-r-targets-results
          path: .

  workflowr:
    name: Runs Workflowr versioning
    runs-on: ubuntu-latest
    # runs-on: self-hosted
    if: "contains(github.event.head_commit.message, 'workflowr')"
    needs:
      - lint
    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      RENV_PATHS_ROOT: ~/.local/share/renv
    steps:
      - name: Checking out deep repository
        uses: actions/checkout@v2
        with:
          fetch-depth: 0 ## all history
          ref: ${{ github.event.workflow_run.head_branch }}

      - run: git branch

      - run: echo ${{ github.event.head_commit.message }}

      - name: Setting up R installation
        uses: r-lib/actions/setup-r@v2

      - name: Setting up pandoc and pandoc-citeproc
        uses: r-lib/actions/setup-pandoc@v2

      - name: Setting up tinytex
        uses: r-lib/actions/setup-tinytex@v2

      - name: Install additional LaTeX packages
        run: |
          tlmgr --version
          tlmgr install svg subfig
          tlmgr list --only-installed

      - name: Cache R packages
        uses: actions/cache@v2.1.4
        id: cache-packages
        with:
          path: ${{ env.RENV_PATHS_ROOT }}
          key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }}-targets-v2
          restore-keys: |
            ${{ runner.os }}-renv-

      - name: Query dependencies
        run: |
          install.packages('remotes')
          install.packages('yaml')
          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: Install system dependencies
        if: runner.os == 'Linux'
        run: |
          while read -r cmd
          do
            eval sudo $cmd
          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')

      - name: Install other dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y libgit2-dev libharfbuzz-dev libcurl4-openssl-dev \
          libfribidi-dev libzmq3-dev libmagick++-dev

      - name: Install dependencies
        run: |
          if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv")
          Sys.unsetenv("GITHUB_PAT")
          renv::restore()
        shell: Rscript {0}

      # - name: pull database
      #   run: |
      #     chmod 755 run.R && ./run.R -r FALSE
      #   shell: bash

      - name: Knit thesisdown
        run: |
          bookdown::render_book("thesis", output_format="all")
        shell: Rscript {0}

      - name: Configure git and stage changes
        run: |
          git config --local user.name "GitHub Actions"
          git config --local user.email "actions@github.com"
          git add --all -- ':!renv'
          git commit -am "Update thesisdown"

      - name: Build workflowr that creates the commit
        run: workflowr::wflow_publish(all = TRUE, update = TRUE, verbose = TRUE)
        shell: Rscript {0}

      - name: Push changes
        run: |
          git push