updating troublesome unit tests

Author: ncborcherding

.github/workflows/R-CMD-check.yaml

@@ -61,8 +61,8 @@ jobs:
           ), "configure")
           Sys.chmod("configure", mode = "0755")
           writeLines(c(
-            '@echo off',
-            '"%R_HOME%/bin/Rscript" -e "basilisk::configureBasiliskEnv()"'
+            '#!/bin/sh',
+            '"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "basilisk::configureBasiliskEnv()"'
           ), "configure.win")
         shell: Rscript {0}
 

tests/testthat/helper-immLynx.R

@@ -68,3 +68,37 @@ skip_if_no_python <- function() {
 skip_if_no_transformers <- function() {
   skip_if_no_python()
 }
+
+# Cache for module import checks (avoids repeated basiliskRun calls)
+.module_check_cache <- new.env(parent = emptyenv())
+
+# Check if a Python module can actually be imported (catches shared lib issues)
+can_import_module <- function(module_name) {
+  if (!is.null(.module_check_cache[[module_name]])) {
+    return(.module_check_cache[[module_name]])
+  }
+  result <- tryCatch({
+    basilisk::basiliskRun(env = immLynx:::immLynxEnv, fun = function(mod) {
+      reticulate::import(mod)
+      TRUE
+    }, mod = module_name)
+  }, error = function(e) FALSE)
+  .module_check_cache[[module_name]] <- result
+  result
+}
+
+# Skip if tcrdist (parasail shared library) can't be loaded
+skip_if_no_tcrdist <- function() {
+  skip_if_no_python()
+  if (!can_import_module("tcrdist.repertoire")) {
+    testthat::skip("tcrdist/parasail shared library not loadable")
+  }
+}
+
+# Skip if metaclonotypist can't be loaded
+skip_if_no_metaclonotypist <- function() {
+  skip_if_no_python()
+  if (!can_import_module("metaclonotypist")) {
+    testthat::skip("metaclonotypist shared library not loadable")
+  }
+}

tests/testthat/test-calculate_helpers.R

@@ -131,7 +131,7 @@ test_that("calculate.tcrDist function has correct default parameters", {
 })
 
 test_that("calculate.tcrDist returns distance results for beta chain", {
-  skip_if_no_python()
+  skip_if_no_tcrdist()
 
   df <- data.frame(
     count = rep(1L, 5),

tests/testthat/test-runMetaclonotypist.R

@@ -96,7 +96,7 @@ test_that("runMetaclonotypist rejects data.frame with all NA sequences", {
 test_that("runMetaclonotypist adds metaclone column to Seurat object", {
   skip_if_not_installed("Seurat")
   skip_if_not_installed("immApex")
-  skip_if_no_python()
+  skip_if_no_metaclonotypist()
 
   data("immLynx_example", package = "immLynx")
 
@@ -110,7 +110,7 @@ test_that("runMetaclonotypist adds metaclone column to Seurat object", {
 test_that("runMetaclonotypist returns data.frame when return_seurat=FALSE", {
   skip_if_not_installed("Seurat")
   skip_if_not_installed("immApex")
-  skip_if_no_python()
+  skip_if_no_metaclonotypist()
 
   data("immLynx_example", package = "immLynx")
 
@@ -127,7 +127,7 @@ test_that("runMetaclonotypist returns data.frame when return_seurat=FALSE", {
 test_that("runMetaclonotypist handles custom column name", {
   skip_if_not_installed("Seurat")
   skip_if_not_installed("immApex")
-  skip_if_no_python()
+  skip_if_no_metaclonotypist()
 
   data("immLynx_example", package = "immLynx")
 
@@ -139,7 +139,7 @@ test_that("runMetaclonotypist handles custom column name", {
 })
 
 test_that("runMetaclonotypist accepts data.frame input", {
-  skip_if_no_python()
+  skip_if_no_metaclonotypist()
   skip("metaclonotypist Python library IndexError with small datasets")
 
   tcr_data <- data.frame(
@@ -159,7 +159,7 @@ test_that("runMetaclonotypist accepts data.frame input", {
 test_that("runMetaclonotypist produces messages during execution", {
   skip_if_not_installed("Seurat")
   skip_if_not_installed("immApex")
-  skip_if_no_python()
+  skip_if_no_metaclonotypist()
 
   data("immLynx_example", package = "immLynx")
 

tests/testthat/test-runTCRdist.R

@@ -99,7 +99,7 @@ test_that("runTCRdist .add_allele handles vector input", {
 test_that("runTCRdist returns correct structure", {
   skip_if_not_installed("Seurat")
   skip_if_not_installed("immApex")
-  skip_if_no_python()
+  skip_if_no_tcrdist()
 
   data("immLynx_example", package = "immLynx")
 
@@ -114,7 +114,7 @@ test_that("runTCRdist returns correct structure", {
 test_that("runTCRdist returns distance matrix of correct dimensions", {
   skip_if_not_installed("Seurat")
   skip_if_not_installed("immApex")
-  skip_if_no_python()
+  skip_if_no_tcrdist()
 
   data("immLynx_example", package = "immLynx")
 
@@ -128,7 +128,7 @@ test_that("runTCRdist returns distance matrix of correct dimensions", {
 test_that("runTCRdist handles add_to_object parameter for Seurat", {
   skip_if_not_installed("Seurat")
   skip_if_not_installed("immApex")
-  skip_if_no_python()
+  skip_if_no_tcrdist()
 
   data("immLynx_example", package = "immLynx")
 
@@ -142,7 +142,7 @@ test_that("runTCRdist handles add_to_object parameter for Seurat", {
 test_that("runTCRdist handles both chains", {
   skip_if_not_installed("Seurat")
   skip_if_not_installed("immApex")
-  skip_if_no_python()
+  skip_if_no_tcrdist()
 
   data("immLynx_example", package = "immLynx")
 
@@ -155,7 +155,7 @@ test_that("runTCRdist handles both chains", {
 test_that("runTCRdist tcr_data has correct format", {
   skip_if_not_installed("Seurat")
   skip_if_not_installed("immApex")
-  skip_if_no_python()
+  skip_if_no_tcrdist()
 
   data("immLynx_example", package = "immLynx")
 
@@ -174,7 +174,7 @@ test_that("runTCRdist tcr_data has correct format", {
 test_that("runTCRdist produces messages during execution", {
   skip_if_not_installed("Seurat")
   skip_if_not_installed("immApex")
-  skip_if_no_python()
+  skip_if_no_tcrdist()
 
   data("immLynx_example", package = "immLynx")