Use Quarto and Typst

insightsengineering · May 13, 2024 · ccf9abd · ccf9abd
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Showing 8 changed files with 152 additions and 258 deletions.
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     name: ${{ matrix.package.name }}
     container:
-      image: rocker/verse:4.1.2
+      image: rocker/verse:4.4.0
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     strategy:
@@ -21,14 +21,10 @@ jobs:
         package:
           - name: aragog
             report_pkg_dir: ./tests/packages/aragog
-            report_template_path: ./template.Rmd
-            report_rmarkdown_format: pdf_document
-            additional_tlmgr_packages: "courier ec fancyhdr"
+            report_template_path: ./template.qmd
           - name: buckbeak
             report_pkg_dir: ./tests/packages/buckbeak
-            report_template_path: ./tests/packages/buckbeak/validation-template.Rmd
-            report_rmarkdown_format: html_document
-            additional_tlmgr_packages: "courier ec"
+            report_template_path: ./tests/packages/buckbeak/validation-template.qmd
 
     steps:
       - name: Checkout ${{ matrix.package.name }}
@@ -40,14 +36,11 @@ jobs:
         with:
           report_pkg_dir: ${{ matrix.package.report_pkg_dir }}
           report_template_path: ${{ matrix.package.report_template_path }}
-          report_output_prefix: validation_report
-          report_rmarkdown_format: ${{ matrix.package.report_rmarkdown_format }}
-          additional_tlmgr_packages: ${{ matrix.package.additional_tlmgr_packages }}
 
       - name: Upload ${{ matrix.package.name }} validation report
         uses: actions/upload-artifact@v4
         if: success()
         with:
           name: ${{ matrix.package.name }} validation report
-          path: ${{ steps.validation.outputs.report_output_filename }}
+          path: validation_report.pdf
           if-no-files-found: error
diff --git a/.github/workflows/test_no_cache.yaml b/.github/workflows/test_no_cache.yaml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     name: ${{ matrix.package.name }}
     container:
-      image: rocker/verse:4.1.2
+      image: rocker/verse:4.4.0
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     strategy:
@@ -21,8 +21,7 @@ jobs:
         package:
           - name: buckbeak
             report_pkg_dir: ./tests/packages/buckbeak
-            report_template_path: ./tests/packages/buckbeak/validation-template.Rmd
-            report_rmarkdown_format: html_document
+            report_template_path: ./tests/packages/buckbeak/validation-template.qmd
 
     steps:
       - name: Checkout ${{ matrix.package.name }}
@@ -34,14 +33,12 @@ jobs:
         with:
           report_pkg_dir: ${{ matrix.package.report_pkg_dir }}
           report_template_path: ${{ matrix.package.report_template_path }}
-          report_output_prefix: validation_report
-          report_rmarkdown_format: ${{ matrix.package.report_rmarkdown_format }}
           no_cache: true
 
       - name: Upload ${{ matrix.package.name }} validation report
         uses: actions/upload-artifact@v4
         if: success()
         with:
           name: ${{ matrix.package.name }} validation report
-          path: ${{ steps.validation.outputs.report_output_filename }}
+          path: validation_report.pdf
           if-no-files-found: error
diff --git a/README.md b/README.md
@@ -6,6 +6,7 @@
 [![SuperLinter](https://github.com/insightsengineering/thevalidatoR/actions/workflows/lint.yaml/badge.svg)](https://github.com/insightsengineering/thevalidatoR/actions/workflows/lint.yaml)
 [![Test This Action](https://github.com/insightsengineering/thevalidatoR/actions/workflows/test.yaml/badge.svg)](https://github.com/insightsengineering/thevalidatoR/actions/workflows/test.yaml)
 
+- [thevalidatoR](#thevalidator)
 - [An R Package Validation Report](#an-r-package-validation-report)
     - [Description](#description)
     - [Action Type](#action-type)
@@ -19,99 +20,70 @@
       - [admiral](#admiral)
 
 <!-- BEGIN_ACTION_DOC -->
-# An R Package Validation Report
+# R Package Validation Report
 
 ### Description
-
-A Github Action that generates a validation report for an R package. The four main steps are:
-
+A Github Action that generates a validation report for an R package.
+The four main steps are:
 - Run `R CMD check` (check installation)
 - Run `covr::package_coverage()` (check unit test coverage)
 - Run `covtracer` (link documentation to unit tests)
 - Place results into report
-- _If valtools present - run valtools and also publish report?_ (to discuss)
 - Attach report as object to release
 
 ### Action Type
-
 Composite
 
 ### Author
-
 Roche
 
 ### Inputs
+* `report_pkg_dir`:
 
-- `report_pkg_dir`:
-
-  _Description_: Path to package's root
+  _Description_: Path to package's root.
 
   _Required_: `false`
 
   _Default_: `.`
 
-- `report_template_path`:
-
-  _Description_: File path of the R markdown template to use for the report. The default template is available [here.](./template.Rmd)
+* `report_template_path`:
 
-  _Required_: `false`
-
-  _Default_: `template.Rmd`
-
-- `report_rmarkdown_format`:
+  _Description_: File path of the R markdown template to use for the report.
+The default template is available [here.](./template.qmd)
 
-  _Description_: The output format to use when rendering the report. Value is used by `rmarkdown::render`'s `output_format` parameter.
 
   _Required_: `false`
 
-  _Default_: `pdf_document`
+  _Default_: `./template.qmd`
 
-- `report_output_prefix`:
+* `no_cache`:
 
-  _Description_: The output filename prefix for the validation report. If left blank, it defaults to the following convention: `<package name>-<package version>-validation-report`.
-
-  _Required_: `false`
-
-  _Default_: `""`
-
-- `additional_tlmgr_packages`:
-
-  _Description_: Additional tex packages to install with tlmgr.
-
-  _Required_: `false`
-
-  _Default_: `courier ec`
-
-- `no_cache`:
-
-  _Description_: Disable github action R dependency caching.
+  _Description_: Disable github action R dependency caching
 
   _Required_: `false`
 
   _Default_: `false`
 
-- `cache_version`:
+* `cache_version`:
 
   _Description_: Version of the cache. To clean cache bump this version.
 
   _Required_: `false`
 
   _Default_: `v1`
 
-- `disable_install_dev_deps`:
+* `disable_install_dev_deps`:
+
+  _Description_: Disable installation of dev dependencies while
+building the report.
 
-  _Description_: Disable installation of dev dependencies while building the report.
 
   _Required_: `false`
 
   _Default_: `false`
 
 ### Outputs
-
-- `report_output_filename`:
-
-  _Description_: Filename of the generated report.
-
+None
 <!-- END_ACTION_DOC -->
 
 ## How to use

diff --git a/action.yml b/action.yml
@@ -1,6 +1,7 @@
 name: R Package Validation Report
 author: Roche
-description: A Github Action that generates a validation report for an R package.
+description: |
+  A Github Action that generates a validation report for an R package.
 
 inputs:
   report_pkg_dir:
@@ -10,27 +11,9 @@ inputs:
   report_template_path:
     description: |
       File path of the R markdown template to use for the report.
-      The default template is available [here.](./template.Rmd)
+      The default template is available [here.](./template.qmd)
     required: false
-    default: "./template.Rmd"
-  report_rmarkdown_format:
-    description: |
-      The file format of the validation report. See `rmarkdown::render`'s
-      `output_format` parameter for accepted values.
-    required: false
-    default: "all"
-  report_output_prefix:
-    description: >
-      The output filename prefix for the validation report. If left blank,
-      it defaults to the following convention:
-      `<package name>-<package version>-validation-report`.
-    required: false
-    default: ""
-  additional_tlmgr_packages:
-    description: |
-      Additional tex packages to install with tlmgr.
-    required: false
-    default: "courier ec"
+    default: "./template.qmd"
   no_cache:
     description: "Disable github action R dependency caching"
     required: false
@@ -45,10 +28,6 @@ inputs:
       building the report.
     required: false
     default: "false"
-outputs:
-  report_output_filename:
-    description: Filename of the generated report.
-    value: ${{ steps.report-generator.outputs.output-filename }}
 branding: # https://feathericons.com/
   icon: "award"
   color: "blue"
@@ -68,13 +47,6 @@ runs:
         cat ~/.Rprofile
       shell: bash
 
-    - name: Set tlmgr cache folder
-      if: "contains(inputs.no_cache, 'false')"
-      id: texlive_version
-      run: |
-        echo "TEX_LIVE_VERSION=$(tlmgr --version |tail -1 |awk '{print $NF}')" >> $GITHUB_OUTPUT
-      shell: bash
-
     - name: Cache R packages
       if: "contains(inputs.no_cache, 'false')"
       uses: actions/cache@v4
@@ -83,40 +55,34 @@ runs:
         key: ${{ inputs.cache_version }}-${{ runner.os }}-${{ steps.r_version.outputs.R_VERSION }}-${{ hashFiles('DESCRIPTION') }}
         restore-keys: ${{ inputs.cache_version }}-${{ runner.os }}-${{ steps.r_version.outputs.R_VERSION }}
 
-    - name: Cache Tex packages
-      if: "contains(inputs.no_cache, 'false')"
-      uses: actions/cache@v4
-      with:
-        path: /home/runner/work/_temp/TinyTeX
-        key: ${{ inputs.cache_version }}-${{ runner.os }}-${{ steps.texlive_version.outputs.TEX_LIVE_VERSION }}-${{ hashFiles(inputs.report_template_path) }}
-        restore-keys: ${{ inputs.cache_version }}-${{ runner.os }}-${{ steps.texlive_version.outputs.TEX_LIVE_VERSION }}
-
     - name: Install dependencies
       run: |
         ${GITHUB_ACTION_PATH}/dependencies.R
-        export PATH=${RUNNER_TEMP}/TinyTeX/bin/x86_64-linux:${PATH}
-        echo "PATH=${PATH}" >> $GITHUB_ENV
-        tlmgr path add
-        tlmgr update --self
-        [ ! -f "./template.Rmd" ] && cp ${GITHUB_ACTION_PATH}/template.Rmd . || echo "./template.Rmd Already exists"
-      shell: bash
-
-    - name: Install additional tex packages
-      run: tlmgr install ${{ inputs.additional_tlmgr_packages }}
+        [ ! -f "./template.qmd" ] && cp ${GITHUB_ACTION_PATH}/template.qmd . || echo "./template.qmd already exists"
+        if [[ "$(echo -e "$(quarto --version)\n1.4.0" | sort -V | head -1)" == "1.4.0" ]]; then
+          echo "✅ Quarto CLI version sufficient (>= 1.4.0)"
+          echo "Quarto CLI version: $(quarto --version)"
+        else
+          echo "❌ Quarto CLI version insufficient (< 1.4.0)"
+          echo "Downloading Quarto CLI..."
+          # Install newer version of Quarto CLI.
+          export QUARTO_VERSION="1.4.554"
+          apt-get update
+          apt-get install -qy wget
+          wget https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-amd64.deb
+          dpkg -i quarto-${QUARTO_VERSION}-linux-amd64.deb
+          echo "New Quarto CLI version: $(quarto --version)"
+        fi
       shell: bash
 
     - name: Run report generator
       id: report-generator
       run: |
         ${GITHUB_ACTION_PATH}/report-generator.R
-        filename=$(basename $(cat /tmp/report_file_path.txt))
-        echo "output-filename=${filename}" >> $GITHUB_OUTPUT
       shell: bash
       env:
         # Composite action doesn't set inputs as env vars.
         # We need to do this manually...
         INPUT_REPORT_PKG_DIR: ${{ inputs.report_pkg_dir }}
         INPUT_REPORT_TEMPLATE_PATH: ${{ inputs.report_template_path }}
-        INPUT_REPORT_RMARKDOWN_FORMAT: ${{ inputs.report_rmarkdown_format }}
-        INPUT_REPORT_OUTPUT_PREFIX: ${{ inputs.report_output_prefix }}
         DISABLE_INSTALL_DEV_DEPS: ${{ inputs.disable_install_dev_deps }}
diff --git a/dependencies.R b/dependencies.R
@@ -14,29 +14,5 @@ lapply(github_packages, remotes::install_github)
 options(repos = c("https://cloud.r-project.org/"))
 ncores <- parallel::detectCores(all.tests = FALSE, logical = TRUE)
 if (!require("git2r")) install.packages("git2r", upgrade = "never", Ncpus = ncores)
-if (!require("kableExtra")) install.packages("kableExtra", upgrade = "never", Ncpus = ncores)
-if (!require("tinytex")) install.packages("tinytex", upgrade = "never", Ncpus = ncores)
-
-# Conditionally install TinyTex
-if(!dir.exists(paste(Sys.getenv("RUNNER_TEMP"), "TinyTeX", sep="/"))) {
-# nolint start
-  tinytex_installer <- '
-export TINYTEX_DIR=${RUNNER_TEMP}/TinyTeX
-wget -qO- "https://raw.githubusercontent.com/yihui/tinytex/master/tools/install-unx.sh" | sh -s - --admin --no-path
-mkdir -p ${RUNNER_TEMP}/TinyTeX
-cp -r ~/.TinyTeX/. ${RUNNER_TEMP}/TinyTeX
-rm -rf ~/.TinyTeX
-${RUNNER_TEMP}/TinyTeX/bin/*/tlmgr path add
-tlmgr update --self
-tlmgr install latex-bin luatex xetex ae bibtex context inconsolata listings makeindex metafont mfware parskip pdfcrop tex tools url xkeyval
-'
-  # nolint end
-  system(tinytex_installer)
-  tinytex::r_texmf()
-  permission_update <- '
-chown -R root:staff ${RUNNER_TEMP}/TinyTeX
-chmod -R g+w ${RUNNER_TEMP}/TinyTeX
-chmod -R g+wx ${RUNNER_TEMP}/TinyTeX/bin
-'
-  system(permission_update)
-}
+if (!require("quarto")) install.packages("quarto", upgrade = "never", Ncpus = ncores)
+if (!require("tinytable")) install.packages("tinytable", upgrade = "never", Ncpus = ncores)
diff --git a/report-generator.R b/report-generator.R
@@ -8,11 +8,11 @@ git_safe_dir <- system(
   sprintf("git config --global --add safe.directory '%s'", getwd())
 )
 
+cat(paste0("INPUT_REPORT_PKG_DIR = ", Sys.getenv("INPUT_REPORT_PKG_DIR", ".")))
+
 # Get the action inputs from preset env vars
 pkg_dir <- normalizePath(Sys.getenv("INPUT_REPORT_PKG_DIR", "."))
-template_path <- Sys.getenv("INPUT_REPORT_TEMPLATE_PATH", "/template.Rmd")
-report_format <- Sys.getenv("INPUT_REPORT_RMARKDOWN_FORMAT", "all")
-report_output_prefix <- Sys.getenv("INPUT_REPORT_OUTPUT_PREFIX", "")
+template_path <- Sys.getenv("INPUT_REPORT_TEMPLATE_PATH", "./template.qmd")
 disable_install_dev_deps <- tolower(
   Sys.getenv("DISABLE_INSTALL_DEV_DEPS")
 ) %in% c("yes", "y", "t", "true")
@@ -41,26 +41,6 @@ if (!disable_install_dev_deps) {
     devtools::install_dev_deps(pkg_dir, upgrade = "never")
 }
 
-# Set the output file name
-if (report_output_prefix == "") {
-  desc <- read.dcf(desc_file)
-  pkg_name <- toString(desc[, "Package"])
-  pkg_version <- toString(desc[, "Version"])
-  report_output_prefix <- paste0(
-    pkg_name, "-", pkg_version, "-validation-report"
-  )
-}
-
-# allow rmarkdown to choose appropriate file extension for output format
-report_file_path <- rmarkdown::render(
-  template_path,
-  output_dir = getwd(),  # create report wherever R script was called
-  output_file = report_output_prefix,
-  output_format = report_format,
-  params = list(pkg_dir = pkg_dir)
-)
-
-# Create a tmp file which contains the final report filename
-writeLines(report_file_path, "/tmp/report_file_path.txt")
-
-cat(sprintf("Created report at: '%s'\n\n", report_file_path))
+library(quarto)
+cat(paste0("Running Quarto render for template: ", template_path))
+quarto_render(template_path, output_file = "validation_report.pdf")