Merge pull request #12 from zsigmas/separate_steps_qc_pr

include qc report in a separate step

.github/workflows/check.yml

@@ -16,15 +16,17 @@ on:
   workflow_call:
 
 concurrency:
-  group: check-test-${{ github.event.pull_request.number || github.ref }}
+  group: check-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
 jobs:
-  check-test:
+  check:
     name: ${{ vars.CI_IMAGE }}
     runs-on: ubuntu-latest
     container:
       image: ${{ vars.CI_IMAGE }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - name: Checkout project ⬇️
@@ -36,7 +38,7 @@ jobs:
       - name: Check 📦
         run: |
           options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(error_on = "error")
+          rcmdcheck::rcmdcheck(error_on = "error", args = "--no-tests")
         shell: Rscript {0}
 
 

.github/workflows/lintr.yml

@@ -31,6 +31,8 @@ jobs:
     runs-on: ubuntu-latest
     container:
       image: ${{ vars.CI_IMAGE }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - name: Checkout project ⬇️
@@ -41,7 +43,7 @@ jobs:
 
       - name: Import .lintr
         run: |
-          wget -O .lintr https://raw.githubusercontent.com/Boehringer-Ingelheim/dv.templates/main/.lintr
+          wget -O .lintr https://raw.githubusercontent.com/boehringer-ingelheim/dv.templates/main/.lintr
 
       - name: Lintr 🔍
         run: lintr::lint_package()

.github/workflows/pkgdown.yml

@@ -25,13 +25,21 @@ jobs:
     runs-on: ubuntu-latest
     container:
       image: ${{ vars.CI_IMAGE }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - name: Checkout project ⬇️
         uses: actions/checkout@v4
 
       - name: Install package dependencies 📄
-        uses: boehringer-ingelheim/dv.templates/.github/actions/dependencies@main           
+        uses: boehringer-ingelheim/dv.templates/.github/actions/dependencies@main        
+
+      - name: Get validation results
+        uses: actions/download-artifact@v4
+        with:
+          name: val_results
+          path: inst/validation/results
 
       - name: Build site 🔧
         run: pkgdown::build_site()

.github/workflows/roxygen.yml

@@ -25,6 +25,8 @@ jobs:
     runs-on: ubuntu-latest
     container:
       image: ${{ vars.CI_IMAGE }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - name: Checkout project ⬇️

.github/workflows/shared_ci.yml

@@ -5,10 +5,14 @@ on:
   workflow_call:
 
 jobs:
-  check-test:
+  check:
     name: Check 📦
     uses: boehringer-ingelheim/dv.templates/.github/workflows/check.yml@main
 
+  test:
+    name: Test 📦
+    uses: boehringer-ingelheim/dv.templates/.github/workflows/test.yml@main
+
   lintr:
     name: Lintr 🔍
     uses: boehringer-ingelheim/dv.templates/.github/workflows/lintr.yml@main
@@ -26,6 +30,7 @@ jobs:
   pkgdown:
     name: Pkgdown 📖
     uses: boehringer-ingelheim/dv.templates/.github/workflows/pkgdown.yml@main
+    needs: test
 
   styler:
     name: Styler 🌐

.github/workflows/styler.yml

@@ -25,6 +25,8 @@ jobs:
     runs-on: ubuntu-latest
     container:
       image: ${{ vars.CI_IMAGE }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - name: Checkout project ⬇️

.github/workflows/test.yml

@@ -0,0 +1,52 @@
+---
+name: Test 📦
+
+on:
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
+    branches:
+      - main
+  push:
+    branches:
+      - main
+  workflow_call:
+
+concurrency:
+  group: test-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: ${{ vars.CI_IMAGE }}
+    runs-on: ubuntu-latest
+    container:
+      image: ${{ vars.CI_IMAGE }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - name: Checkout project ⬇️
+        uses: actions/checkout@v4
+
+      - name: Checkout Repo Templates      
+        uses: actions/checkout@v4
+        with:
+          ref: include_qc_separate_steps
+          repository: boehringer-ingelheim/dv.templates
+          path: templates
+
+      - name: Install package dependencies 📄
+        uses: boehringer-ingelheim/dv.templates/.github/actions/dependencies@main     
+
+      - name: Test 📦
+        run: Rscript templates/scripts/test.R
+
+      - name: Archive validation results
+        uses: actions/upload-artifact@v4
+        with:
+          name: val_results
+          path: inst/validation/results

scripts/test.R

@@ -0,0 +1,126 @@
+#! /usr/local/bin/Rscript
+
+success <- c(
+  test = FALSE,
+  valdoc = FALSE
+)
+
+# Getting package information ----
+pkg_name <- read.dcf("DESCRIPTION")[1, "Package"]
+pkg_version <- read.dcf("DESCRIPTION")[1, "Version"]
+
+# Building ----
+
+message("############################")
+message("###### INSTALLING (S) ######")
+message("############################")
+
+devtools::install(upgrade = FALSE, args = "--install-tests")
+
+message("############################")
+message("###### INSTALLING (F) ######")
+message("############################")
+
+# Testing ----
+
+message("##########################")
+message("###### TESTING  (S) ######")
+message("##########################")
+
+reporter <- testthat::MultiReporter$new(
+  list(
+    testthat::ProgressReporter$new(),
+    testthat::SummaryReporter$new(file = file.path(getwd(), "tests", "test-out.xml"))
+  )
+)
+
+test_results <- tibble::as_tibble(
+  withr::with_envvar(
+    new = list(CI = TRUE, no_proxy = "127.0.0.1", NOT_CRAN = TRUE, TESTTHAT_CPUS = 1),
+    code = {
+      testthat::test_package(pkg_name, reporter, stop_on_failure = FALSE)
+    }
+  )
+)
+
+success[["test"]] <- sum(test_results[["failed"]]) == 0
+
+message("##########################")
+message("###### TESTING  (F) ######")
+message("##########################")
+
+# Validation ----
+
+message("#######################################")
+message("###### RENDERING VALIDATION  (S) ######")
+message("#######################################")
+
+success[["valdoc"]] <- local({
+  # This is evaluated inside a local because, otherwise, all the variables created in the chunks of the rendered
+  # document leak into the environment
+
+  validation_root <- "./inst/validation"
+  validation_report_rmd <- file.path(validation_root, "val_report.Rmd")
+  validation_report_html <- "val_report.html"
+  validation_results <- file.path(validation_root, "results")
+  val_param_rds <- file.path(validation_results, "val_param.rds")
+
+  stopifnot(dir.exists(validation_root))
+  stopifnot(file.exists(validation_report_rmd))
+
+  stopifnot(dir.exists(validation_results))
+  unlink(list.files(validation_results))
+
+  saveRDS(
+    list(
+      package = pkg_name,
+      tests = test_results,
+      version = pkg_version
+    ),
+    val_param_rds
+  )
+
+  rmarkdown::render(
+    input = validation_report_rmd,
+    params = list(
+      package = pkg_name,
+      tests = test_results,
+      version = pkg_version
+    ),
+    output_dir = validation_results,
+    output_file = validation_report_html
+  )
+
+  # We use one of the leaked variables, created inside the validation report to asses if the validation is succesful or not
+  VALIDATION_PASSED
+})
+
+
+message("#######################################")
+message("###### RENDERING VALIDATION  (F) ######")
+message("#######################################")
+
+# Exit ----
+message("##############################")
+message("###### BUILD RESULT (S) ######")
+message("##############################")
+
+message(paste("Was", names(success), "successful?\t", success, collapse = "\n"))
+
+# Write GITHUB ACTIONS summary
+github_summary_file <- Sys.getenv("GITHUB_STEP_SUMMARY")
+summary <- "# Test Summary"
+summary <- c(
+  summary,
+  purrr::imap_chr(success, ~ paste(" - ", if (.x) "\U02705" else "\U274C", "\t", .y))
+)
+
+CON <- file(github_summary_file, "a")
+on.exit(close(CON))
+writeLines(summary, CON)
+
+stopifnot(all(success))
+
+message("##############################")
+message("###### BUILD RESULT (F) ######")
+message("##############################")