Update make tests from examples

[FBartos]

Refactor makeTestsFromExamples() with source folder system

Summary

This PR refactors makeTestsFromExamples() to support a structured three-tier source folder system for JASP example files, replacing the flat examples/ folder approach.

Changes

New folder structure

• JASP files now live in tests/testthat/jaspfiles/{library,verified,other}/
• Generated test files are named test-{source}-{name}.R (e.g., test-library-CorrelationMatrix.R)
• Test code references files via testthat::test_path("jaspfiles", "{source}", "file.jasp")

New source parameter

• Controls which source folders to process: "library", "verified", "other"
• Defaults to all three when overwrite = FALSE
• Defaults to c("library", "other") when overwrite = TRUE (protects verified tests)
• When overwrite = TRUE and "verified" is included, prompts user for confirmation

path parameter behavior

• When path is provided, JASP files are always copied to tests/testthat/jaspfiles/other/
• The source argument is ignored in this case
• A message informs users where files are being copied

Test discovery

• testAnalysis() now automatically discovers all source-based test files
• Scans test-library-*, test-verified-*, and test-other-* files for matching analyses
• No opt-out parameter (simplified from previous includeExamples approach)

Breaking Changes

⚠️ This PR intentionally breaks backwards compatibility

• Old examples/ folder convention is removed
• Test files must be renamed from test-example-{name}.R → test-{source}-{name}.R
• JASP files must be moved from examples/ → tests/testthat/jaspfiles/{source}/
• Generated test code paths changed from test_path("..", "..", "examples", ...) → test_path("jaspfiles", "{source}", ...)

Rationale

The three-tier system provides:

1. Organization: Separate library examples from verified tests and ad-hoc imports
2. Safety: Prevents accidental overwrites of verified tests (default behavior)
3. Clarity: Test file names indicate their provenance
4. Maintainability: Cleaner structure for growing test suites

Example Usage

# Generate tests from all source folders (library, verified, other)
makeTestsFromExamples()

# Only generate from the 'library' source folder
makeTestsFromExamples(source = "library")

# Import JASP files from external path (copies to jaspfiles/other/)
makeTestsFromExamples(path = "path/to/jasp/files")

# Overwrite existing test files (skips verified by default)
makeTestsFromExamples(overwrite = TRUE)

# Overwrite including verified (prompts for confirmation)
makeTestsFromExamples(source = c("library", "verified", "other"), overwrite = TRUE)

Documentation

• Updated roxygen docs for all modified functions
• Regenerated man pages
• Updated .github/copilot-instructions.md with new conventions

Files Changed

• R/test-generator.R: Core implementation of source folder system
• R/test.R: Updated testAnalysis() and getTestFilesMatchingName() to discover source-based tests
• .github/copilot-instructions.md: Updated documentation
• man/*.Rd: Regenerated documentation files

[Copilot]

Pull request overview

Refactors makeTestsFromExamples() and related test discovery to support a structured, source-based organization for JASP example files and their generated testthat tests, replacing the previous flat examples/ approach.

Changes:

• Introduces tests/testthat/jaspfiles/{library,verified,other}/ and generates test-{source}-{name}.R test files referencing JASP files via testthat::test_path("jaspfiles", ...).
• Adds a source parameter + overwrite safeguards (defaulting away from verified when overwriting, with confirmation).
• Updates testAnalysis() discovery to include source-based tests, and regenerates/updates documentation accordingly.

Reviewed changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
R/test-generator.R	Implements the new source-folder workflow, naming, copy behavior, and summary messaging for generated tests.
R/test.R	Updates test-file selection logic to discover and include test-{library,verified,other}-* tests for a given analysis.
man/makeTestsFromExamples.Rd	Documents new source parameter, folder structure, and updated examples.
man/makeTestsFromSingleJASPFile.Rd	Updates parameter documentation (sourceFolder, copyToJaspfiles) for the internal helper.
man/testAnalysis.Rd	Documents the expanded discovery behavior for source-based generated tests.
man/generateExampleTestFileContent.Rd	Updates internal docs to reflect source-based test file generation.
man/generateExampleTestBlock.Rd	Documents the new sourceFolder argument used to build correct test_path() calls.
man/generateExampleTestBlockBasic.Rd	Documents the new sourceFolder argument in the basic fallback test block.
.github/copilot-instructions.md	Updates repository conventions/docs for the new folder layout and test naming.

Comments suppressed due to low confidence (1)

R/test-generator.R:344

• makeTestsFromSingleJASPFile() copies the input JASP file to tests/testthat/jaspfiles/{sourceFolder}/ before checking whether the test file already exists and overwrite is FALSE. This means an import via path= can overwrite an existing JASP file even when the corresponding test is skipped. Consider checking file.exists(testFilePath) && !overwrite (and returning) before performing the copy, or only copying when the destination file doesn’t already exist.

  # Copy JASP file to module's jaspfiles/{sourceFolder}/ if requested
  if (copyToJaspfiles) {
    destDir <- file.path(module.dir, "tests", "testthat", "jaspfiles", sourceFolder)
    if (!dir.exists(destDir)) {
      dir.create(destDir, recursive = TRUE)
      message("  Created directory: ", destDir)
    }
    destFile <- file.path(destDir, basename(jaspFile))
    file.copy(jaspFile, destFile, overwrite = TRUE)
    copiedTo <- destFile
    message("  Copied to: ", destFile)
  }

  # Create tests/testthat directory if needed
  testDir <- file.path(module.dir, "tests", "testthat")

  if (!dir.exists(testDir)) {
    dir.create(testDir, recursive = TRUE)
    message("  Created directory: ", testDir)
  }

  # Determine test file path using "test-{sourceFolder}-Name.R" format
  testFileName <- paste0("test-", sourceFolder, "-", sanitizedName, ".R")
  testFilePath <- file.path(testDir, testFileName)

  # Check if file already exists
  if (file.exists(testFilePath) && !overwrite) {
    result <- testFilePath
    attr(result, "skipped") <- TRUE
    attr(result, "copiedTo") <- copiedTo
    return(result)

[Copilot]

In getTestFilesMatchingName(), the pattern is built by interpolating name directly into a regex and then used with grepl(). If an analysis name ever contains regex metacharacters (e.g., . + (), this can produce false matches or a regex error. Escape name for regex (or otherwise ensure literal matching) before constructing pattern.

Suggested change

	pattern <- paste0('runAnalysis\\(\\s*["\']', name, '["\']')
	for (ef in sourceFiles) {
	content <- readLines(file.path(testsDir, ef), warn = FALSE)
	if (any(grepl(pattern, content)))
	matchedFiles <- c(matchedFiles, ef)
	}
	escapedName <- gsub("([][{}()+*^$|\\\\?.])", "\\\\\\1", name)
	pattern <- paste0('runAnalysis\\(\\s*["\']', escapedName, '["\']')
	for (ef in sourceFiles) {
	content <- readLines(file.path(testsDir, ef), warn = FALSE)
	if (any(grepl(pattern, content)))
	matchedFiles <- c(matchedFiles, ef)

[Copilot]

otherDir is created to ensure tests/testthat/jaspfiles/other/ exists, but the variable itself is never used afterwards. Consider removing the unused variable (or using it consistently) to reduce noise and avoid linters/CRAN checks flagging it.

Suggested change

	otherDir <- file.path(module.dir, "tests", "testthat", "jaspfiles", "other")
	if (!dir.exists(otherDir)) {
	dir.create(otherDir, recursive = TRUE)
	if (!dir.exists(file.path(module.dir, "tests", "testthat", "jaspfiles", "other"))) {
	dir.create(file.path(module.dir, "tests", "testthat", "jaspfiles", "other"), recursive = TRUE)

[Copilot]

When processing multiple sources, .printTestGenerationSummary() is called with sourceLabel = paste(source, collapse = ", "), but the message formats it as if it were a single folder path (.../jaspfiles/<sourceLabel>/.). This produces misleading output like .../jaspfiles/library, other/. when more than one source is used. Consider adjusting the message to either omit the path formatting for multi-source runs or print separate paths per source.

[FBartos]

tested on jaspMetaAnalysis successfully