Merge branch 'transform-R-notebooks-to-Rmd' of https://github.com/Cau… #18
Workflow file for this run
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| name: Convert and Lint R Notebooks | |
| on: | |
| push | |
| concurrency: | |
| group: convert-lint-notebooks | |
| cancel-in-progress: true | |
| jobs: | |
| convert-lint-notebooks: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.8' # Specify your Python version here | |
| - name: Install nbstripout | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install nbstripout | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Install rmarkdown, knitr, and lintr packages | |
| run: | | |
| R -e 'install.packages(c("rmarkdown", "knitr", "lintr", "xfun"), repos="https://cloud.r-project.org")' | |
| - name: Strip outputs from .irnb files | |
| run: | | |
| for notebook in PM1/*.irnb; do | |
| ipynb_notebook="${notebook%.irnb}.ipynb" | |
| mv "$notebook" "$ipynb_notebook" | |
| nbstripout "$ipynb_notebook" | |
| mv "$ipynb_notebook" "$notebook" | |
| done | |
| - name: Convert .irnb to .Rmd and .R | |
| run: | | |
| R -e ' | |
| files <- list.files(path = "PM1", pattern = "\\.irnb$", full.names = TRUE, recursive = FALSE) | |
| lapply(files, function(input) { | |
| rmarkdown::convert_ipynb(input) | |
| rmd_file <- xfun::with_ext(input, "Rmd") | |
| knitr::purl(rmd_file, output = xfun::with_ext(input, "R")) | |
| }) | |
| ' | |
| - name: Lint .Rmd files | |
| id: lint | |
| run: | | |
| R -e ' | |
| library(lintr) | |
| linters <- with_defaults(line_length_linter = line_length_linter(120)) | |
| rmd_files <- list.files(path = "PM1", pattern = "\\.Rmd$", full.names = TRUE) | |
| results <- lapply(rmd_files, function(file) { | |
| lints <- lint(file, linters) | |
| if (length(lints) > 0) { | |
| cat("Warnings found during linting:\n") | |
| print(lints) | |
| # stop("Linting failed with warnings") | |
| } | |
| }) | |
| ' | |
| - name: Execute R scripts | |
| id: execute | |
| run: | | |
| R -e ' | |
| files <- list.files(path = "PM1", pattern = "\\.R$", full.names = TRUE, recursive = FALSE) | |
| for (file in files) { | |
| tryCatch( | |
| { | |
| source(file) | |
| }, | |
| error = function(e) { | |
| cat("Error found in file:", file, "\n") | |
| cat("Error message:", e$message, "\n") | |
| # stop("Execution failed due to an error in ", file) | |
| } | |
| ) | |
| } | |
| ' | |
| - name: Zip .R files | |
| run: | | |
| mkdir r_scripts | |
| mv PM1/*.R r_scripts/ | |
| zip -r r_scripts.zip r_scripts | |
| - name: Upload artifact | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: r-scripts | |
| path: r_scripts.zip | |
| - name: Delete .R files and zip | |
| run: | | |
| rm -rf r_scripts | |
| rm r_scripts.zip | |
| - name: Commit and push stripped .irnb and .Rmd files | |
| run: | | |
| git config --global user.name 'github-actions[bot]' | |
| git config --global user.email 'github-actions[bot]@users.noreply.github.com' | |
| git add PM1/*.irnb PM1/*.Rmd | |
| git commit -m 'Strip outputs from .irnb, convert to .Rmd, lint .Rmd files, and execute .R files' | |
| git push | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} |