ci: add basic tests for main.R

Author: kelly-sovacool

.github/workflows/tests.yml

@@ -0,0 +1,29 @@
+name: tests
+
+on:
+  push:
+    branches: [ main, dev ]
+  pull_request:
+    branches: [ main, dev ]
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Parse environment.json and set Docker image
+        id: docker_image
+        run: |
+          IMAGE=$(jq -r '.base_image' .codeocean/environment.json)
+          IMAGE=${IMAGE//codeocean/nciccbr}
+          echo "image=$IMAGE" >> $GITHUB_OUTPUT
+          echo "Using Docker image: $IMAGE"
+
+      - name: Run tests in Docker
+        run: |
+          docker run --rm \
+            -v ${{ github.workspace }}:/workspace \
+            -w /workspace \
+            ${{ steps.docker_image.outputs.image }} \
+            Rscript tests/testthat.R

tests/test-setup.R

@@ -0,0 +1,35 @@
+#!/usr/bin/env Rscript
+
+cat("Testing basic test setup...\n")
+
+cwd <- getwd()
+cat("Current directory:", cwd, "\n")
+
+repo_root_script <- normalizePath(dirname(cwd))
+cat("Calculated repo_root:", repo_root_script, "\n")
+
+fixture_file <- file.path(
+  repo_root_script,
+  "..",
+  "code",
+  "MOSuite",
+  "tests",
+  "testthat",
+  "data",
+  "moo.rds"
+)
+cat("\nLooking for fixture data at:", fixture_file, "\n")
+cat("Fixture data exists:", file.exists(fixture_file), "\n")
+
+code_main <- file.path(repo_root_script, "..", "code", "main.R")
+code_run <- file.path(repo_root_script, "..", "code", "run")
+cat("code/main.R exists:", file.exists(code_main), "\n")
+cat("code/run exists:", file.exists(code_run), "\n")
+
+if (file.exists(fixture_file)) {
+  cat("\nTrying to load fixture MOO object...\n")
+  library(readr)
+  moo <- readr::read_rds(fixture_file)
+  cat("Fixture MOO loaded successfully!\n")
+  cat("MOO class:", class(moo), "\n")
+}

tests/testthat.R

@@ -0,0 +1,2 @@
+library(testthat)
+test_dir(here::here('tests/testthat/'))

tests/testthat/helper-cli.R

@@ -0,0 +1,75 @@
+setup_cli_workspace <- function(prefix = "mosuite_plot_expr_heatmap_test_") {
+  workspace <- tempfile(prefix)
+  dir.create(workspace)
+
+  code_dir <- file.path(workspace, "code")
+  data_dir <- file.path(workspace, "data")
+  results_dir <- file.path(workspace, "results")
+  dir.create(code_dir, recursive = TRUE)
+  dir.create(data_dir, recursive = TRUE)
+  dir.create(file.path(results_dir, "figures"), recursive = TRUE)
+  dir.create(file.path(results_dir, "moo"), recursive = TRUE)
+
+  repo_root <- normalizePath(
+    file.path(testthat::test_path(), "..", ".."),
+    mustWork = TRUE
+  )
+
+  test_data_file <- file.path(
+    repo_root,
+    "code",
+    "MOSuite",
+    "tests",
+    "testthat",
+    "data",
+    "moo.rds"
+  )
+
+  expect_true(
+    file.exists(test_data_file),
+    info = paste("Test data file should exist at", test_data_file)
+  )
+  file.copy(test_data_file, file.path(data_dir, "moo.rds"), overwrite = TRUE)
+
+  file.copy(
+    file.path(repo_root, "code", "main.R"),
+    file.path(code_dir, "main.R"),
+    overwrite = TRUE
+  )
+
+  # Keep main.R behavior the same while pointing to this checkout's MOSuite package.
+  main_copy <- file.path(code_dir, "main.R")
+  main_lines <- readLines(main_copy)
+  main_lines <- gsub(
+    'devtools::load_all("/code/MOSuite")',
+    sprintf(
+      'devtools::load_all("%s")',
+      file.path(repo_root, "code", "MOSuite")
+    ),
+    main_lines,
+    fixed = TRUE
+  )
+  writeLines(main_lines, main_copy)
+
+  list(
+    workspace = workspace,
+    code_dir = code_dir,
+    results_dir = results_dir,
+    repo_root = repo_root
+  )
+}
+
+expect_plot_created <- function(results_dir) {
+  plot_path <- file.path(results_dir, "figures", "heatmap", "expr_heatmap.png")
+  expect_true(file.exists(plot_path), info = "Heatmap plot should be created")
+  expect_true(
+    file.info(plot_path)$size > 0,
+    info = "Heatmap plot should be non-empty"
+  )
+}
+
+common_cli_args <- c(
+  "--count_type=clean",
+  "--display_gene_names=FALSE",
+  "--display_sample_names=TRUE"
+)

tests/testthat/test-main.R

@@ -0,0 +1,33 @@
+test_that("main.R CLI creates expression heatmap plot", {
+  setup <- setup_cli_workspace("mosuite_plot_expr_heatmap_test_")
+  on.exit(unlink(setup$workspace, recursive = TRUE), add = TRUE)
+
+  old_wd <- getwd()
+  setwd(setup$code_dir)
+  on.exit(setwd(old_wd), add = TRUE)
+
+  exit_code <- system2("Rscript", args = c("main.R", common_cli_args))
+  expect_equal(exit_code, 0, info = "main.R should execute without error")
+
+  expect_plot_created(setup$results_dir)
+})
+
+test_that("run wrapper executes and creates expression heatmap plot", {
+  setup <- setup_cli_workspace("mosuite_plot_expr_heatmap_run_test_")
+  on.exit(unlink(setup$workspace, recursive = TRUE), add = TRUE)
+
+  file.copy(
+    file.path(setup$repo_root, "code", "run"),
+    file.path(setup$code_dir, "run"),
+    overwrite = TRUE
+  )
+
+  old_wd <- getwd()
+  setwd(setup$code_dir)
+  on.exit(setwd(old_wd), add = TRUE)
+
+  exit_code <- system2("bash", args = c("run", common_cli_args))
+  expect_equal(exit_code, 0, info = "run script should execute without error")
+
+  expect_plot_created(setup$results_dir)
+})