regime 2 wip #150
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| --- | |
| 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 |