Merge pull request #208 from animint/coverage

tdhock · web-flow · commit 33f5a809e362 · 2025-07-10T15:36:45.000-04:00
Implementing code coverage
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -19,3 +19,7 @@ test-compiler-gist.R
 ^docs$
 ^pkgdown$
 ^\.github$
+^package\.json$
+^package-lock\.json$
+^node_modules/
+^v8-to-istanbul\.js$
diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
@@ -19,6 +19,8 @@ jobs:
       TEST_SUITE: ${{ matrix.test-suite }}
       GITHUB_PAT: ${{ secrets.PAT_GITHUB }}
       GH_ACTION: "ENABLED"
+      COLLECT_COVERAGE: "TRUE"
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
     steps:
       - uses: actions/checkout@v3
       - name: install and update texlive
@@ -35,6 +37,49 @@ jobs:
 
       - name: git config user.email
         run: git config --global user.email toby.hocking@r-project.org
+
+      - name: Setup Node.js
+        if: matrix.test-suite == 'renderer'
+        uses: actions/setup-node@v3
+        with:
+          node-version: '18'
+        
+      - name: Install Node.js dependencies
+        if: matrix.test-suite == 'renderer'
+        run: |
+          npm install v8-to-istanbul
+          echo "Node modules installed"
       
       - name: run tests
-        run: if [ "$TEST_SUITE" == "CRAN" ];then bash build.sh;else Rscript -e "source('tests/testthat.R', chdir = TRUE)";fi
+        run: |
+          if [ "$TEST_SUITE" == "CRAN" ]; then
+            bash build.sh
+          elif [ "$TEST_SUITE" == "compiler" ]; then
+            Rscript -e "source('tests/testthat.R', chdir = TRUE)"
+            Rscript -e 'covr::codecov(quiet = TRUE)'
+          else
+            Rscript -e "source('tests/testthat.R', chdir = TRUE)"
+          fi
+
+      - name: Convert JS coverage to Istanbul format
+        if: matrix.test-suite == 'renderer'
+        run: |
+          if [ -f "tests/testthat/js-coverage.json" ]; then
+            echo "Converting JS coverage to LCOV format..."
+            node v8-to-istanbul.js
+          else
+            echo "No JS coverage file found"
+            exit 1
+          fi
+
+      - name: Upload JS coverage to Codecov
+        if: matrix.test-suite == 'renderer'
+        run: |
+          if [ -f "coverage-istanbul.json" ]; then
+            curl -Os https://uploader.codecov.io/latest/linux/codecov
+            chmod +x codecov
+            ./codecov -f coverage-istanbul.json -t ${{ secrets.CODECOV_TOKEN }} --flags javascript
+          else
+            echo "No coverage file found"
+            exit 1
+          fi
diff --git a/.gitignore b/.gitignore
@@ -10,4 +10,5 @@
 *ANIMINT_TEST_FOO
 *pids.txt
 *~
-.vscode/settings.json
+.vscode/settings.jsonnode_modules/
+node_modules/
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: animint2
 Title: Animated Interactive Grammar of Graphics
-Version: 2025.6.28
+Version: 2025.7.10
 URL: https://animint.github.io/animint2/
 BugReports: https://github.com/animint/animint2/issues
 Authors@R: c(
@@ -89,6 +89,7 @@ Suggests:
     sp,
     gistr (>= 0.2),
     shiny,
+    covr,
     RColorBrewer,
     htmltools,
     rmarkdown,
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# Changes in version 2025.7.10 (PR#208)
+
+- Added Codecov integration for both R and JavaScript tests; coverage reports now available at https://app.codecov.io/github/animint/animint2
+
 # Changes in version 2025.6.28 (PR#204) 
 
 - The geom_raster implementation has been removed.
diff --git a/README.md b/README.md
@@ -22,6 +22,8 @@ Play around with [this interactive data visualization of data from the World Ban
 
 To learn how to generate your own interactive data visualizations, go to the official [Animint2 Manual](https://rcdata.nau.edu/genomic-ml/animint2-manual/Ch00-preface.html). If you encounter problems, please see the [animint2 wiki](https://github.com/animint/animint2/wiki) or [report them](https://github.com/animint/animint2/issues).
 
+[![codecov](https://codecov.io/gh/animint/animint2/branch/main/graph/badge.svg)](https://codecov.io/gh/animint/animint2)
+
 ## Installation
 
 ``` r
diff --git a/build.sh b/build.sh
@@ -1,5 +1,6 @@
 #!/bin/bash
 set -o errexit
+set -o pipefail
 R -e 'devtools::document()'
 cd ..
 rm -rf animint2-release
@@ -30,4 +31,18 @@ EOF
 PKG_TGZ=$(R CMD build animint2-release|grep building|sed "s/.*\(animint2.*.tar.gz\).*/\1/")
 echo built $PKG_TGZ so now we INSTALL 
 R CMD INSTALL $PKG_TGZ
-R CMD check --as-cran $PKG_TGZ
+echo "Running R CMD check --as-cran $PKG_TGZ"
+check_output=$(R CMD check --as-cran $PKG_TGZ 2>&1)
+check_status=$?
+echo "$check_output"
+# Check for WARNINGs or NOTEs in the output
+if echo "$check_output" | grep -q -E "WARNING|NOTE"; then
+    echo "CRAN check generated WARNINGs or NOTEs:"
+    exit 1
+fi
+# Exit with original status if no WARNINGs/NOTEs but check failed
+if [ $check_status -ne 0 ]; then
+    echo "R CMD check failed with status $check_status"
+    exit $check_status
+fi
+echo "CRAN check completed successfully"
diff --git a/inst/htmljs/animint.js b/inst/htmljs/animint.js
@@ -1717,6 +1717,15 @@ var animint = function (to_select, json_file) {
       }
       return selected_values;
   };
+
+  // DEAD CODE FOR COVERAGE TESTING
+    function deadCodeForCoverage() {
+      // This function is never called and should show as uncovered in coverage reports.
+      var unused = 42;
+      if (unused === 43) {
+        console.log("This should never be printed.");
+      }
+    }
   
   // update scales for the plots that have update_axes option in
   // theme_animint
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -0,0 +1,28 @@
+{
+  "name": "animint2",
+  "version": "1.0.0",
+  "description": "<a href=\"https://github.com/tdhock/animint2/actions/workflows/tests.yaml\"> \t<img src=\"https://github.com/tdhock/animint2/actions/workflows/tests.yaml/badge.svg\"  \t     alt=\"A badge verifying if this package has passed all its tests.\"> </a> <!-- Feel free to change the HTML block above this comment into Markdown. It's just in HTML cuz I couldn't be arsed to figure out how to correctly combine an image and a link in Github-flavored Markdown. -->",
+  "main": "index.js",
+  "directories": {
+    "doc": "docs",
+    "man": "man",
+    "test": "tests"
+  },
+  "scripts": {
+    "test": "echo \"Error: no test specified\" && exit 1"
+  },
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/animint/animint2.git"
+  },
+  "keywords": [],
+  "author": "",
+  "license": "ISC",
+  "bugs": {
+    "url": "https://github.com/animint/animint2/issues"
+  },
+  "homepage": "https://github.com/animint/animint2#readme",
+  "dependencies": {
+    "v8-to-istanbul": "^9.3.0"
+  }
+}
diff --git a/tests/testthat.R b/tests/testthat.R
@@ -8,10 +8,30 @@ source("helper-plot-data.r")
 filter <- Sys.getenv("TEST_SUITE")
 gh.action <- Sys.getenv("GH_ACTION")
 use.browser <- grepl("renderer", filter)
+collect.coverage <- Sys.getenv("COLLECT_COVERAGE", "FALSE") == "TRUE"
 if(filter == ""){
   filter <- NULL
 }
 message(gh.action)
-if(use.browser)tests_init()
-tests_run(filter=filter)
-if(use.browser)tests_exit()
+
+if(use.browser) {
+  tests_init()
+  # Start coverage if enabled
+  coverage_active <- FALSE
+  if(collect.coverage) {
+    coverage_active <- start_js_coverage()
+    if(coverage_active) {
+      message("JS coverage collection started")
+    }
+  }
+  # Run tests
+  tests_run(filter=filter)
+  # Save coverage and cleanup
+  if(coverage_active) {
+    stop_js_coverage()
+  }
+  tests_exit()
+} else {
+  # Non-browser tests
+  tests_run(filter=filter)
+}
diff --git a/tests/testthat/helper-HTML.R b/tests/testthat/helper-HTML.R
@@ -43,6 +43,10 @@ tests_init <- function(dir = ".", ...) {
   unlink(testDir, recursive = TRUE)
   options(chromote.timeout = 120)
   chrome.session <- chromote::ChromoteSession$new()
+  # Enable required DevTools domains for coverage
+  chrome.session$Runtime$enable()
+  chrome.session$Profiler$enable()
+
   chrome.session$view()
   chrome.session$refresh <- function(){
     ## from https://github.com/rstudio/chromote?tab=readme-ov-file#loading-a-page-reliably
@@ -104,3 +108,36 @@ getClassBound <- function(geom.class, position){
   Sys.sleep(2)
   runtime_evaluate(script=script.txt)
 }
+
+# JS Coverage collection functions
+start_js_coverage <- function() {
+  tryCatch({
+    remDr$Profiler$enable()
+    remDr$Profiler$startPreciseCoverage(
+      callCount = TRUE,
+      detailed = TRUE
+    )
+    TRUE
+  }, error = function(e) {
+    warning("Failed to start JS coverage: ", e$message)
+    FALSE
+  })
+}
+
+stop_js_coverage <- function() {
+  tryCatch({
+    cov <- remDr$Profiler$takePreciseCoverage()
+    outfile <- "js-coverage.json"
+    # Ensure the format matches what v8-to-istanbul expects
+    coverage_data <- list(
+      result = cov$result,
+      url = "http://localhost:4848/animint-htmltest/animint.js"
+    )
+    jsonlite::write_json(coverage_data, outfile, auto_unbox = TRUE)
+    message("JS coverage saved to ", normalizePath(outfile))
+    TRUE
+  }, error = function(e) {
+    warning("Failed to save JS coverage: ", e$message)
+    FALSE
+  })
+}
diff --git a/tests/testthat/test-compiler-ghpages.R b/tests/testthat/test-compiler-ghpages.R
@@ -62,6 +62,7 @@ test_that("animint2pages() returns list of meta-data", {
 })
 
 test_that("animint2pages raises an error if no GitHub token is present", {
+  if (identical(Sys.getenv("R_COVR"), "true")) skip("Skip on covr: environment manipulation not supported")
   env.names <- c("GITHUB_PAT", "GITHUB_PAT_GITHUB_COM")
   env.old <- Sys.getenv(env.names)
   Sys.unsetenv(env.names)
diff --git a/tests/testthat/test-renderer2-PredictedPeaks.R b/tests/testthat/test-renderer2-PredictedPeaks.R
diff --git a/v8-to-istanbul.js b/v8-to-istanbul.js
