tests: add additional conditions for extra tests

ethanbass · Oct 10, 2023 · b1e3e3f · b1e3e3f
1 parent 2cd2ea0
commit b1e3e3f
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Showing 4 changed files with 9 additions and 10 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -37,7 +37,7 @@ Suggests:
     testthat (>= 3.0.0),
     mzR,
     chromConverterExtraTests
-Config/reticulate: list( packages = list( list(package = "scipy"),
+Config/reticulate: list( packages = list(list(package = "scipy"),
                                     list(package="numpy"),
                                     list(package = "pandas"),
                                     list(package="aston", pip = TRUE),

diff --git a/inst/shell/path_to_openchrom_commandline.txt b/inst/shell/path_to_openchrom_commandline.txt
@@ -1 +1 @@
-NULL
+/Applications/Eclipse.app/Contents/MacOS/openchrom
diff --git a/tests/testthat/helpers.R b/tests/testthat/helpers.R
@@ -3,8 +3,7 @@
 elementwise.all.equal <- Vectorize(function(x, y, ...) {isTRUE(all.equal(x, y, ...))})
 
 # helper function to skip tests if we don't have the right python dependencies
-skip_if_missing_dependecies <- function() {
-  reqs <- c("scipy","numpy", "aston", "pandas")
+skip_if_missing_dependecies <- function(reqs = c("scipy","numpy", "aston", "pandas", "olefile")) {
   have_reqs <- sapply(reqs, reticulate::py_module_available)
   if (mean(have_reqs) < 1)
     skip(paste("required packages", reqs[!have_reqs],
@@ -21,15 +20,13 @@ skip_if_missing_thermorawfileparser <- function() {
   }
   have_reqs <- fs::file_exists(path)
   if (mean(have_reqs) < 1)
-    skip(paste("required packages", reqs[!have_reqs],
-               "not available for testing"))
+    skip("ThermoRawFileParser could not be found.")
 }
 
 skip_if_missing_openchrom <- function() {
   have_openchrom_cli <- switch(configure_openchrom(cli="status"), true = TRUE,
          false = FALSE)
   if (!have_openchrom_cli){
-    skip(paste("required packages", reqs[!have_reqs],
-               "not available for testing"))
+    skip("OpenChrom could not be found.")
   }
 }
diff --git a/tests/testthat/test-extra.R b/tests/testthat/test-extra.R
@@ -181,8 +181,8 @@ test_that("read_chroms can read 'Chromeleon' period-separated files", {
 
 test_that("read_peaklist can read `Shimadzu` PDA files", {
   skip_on_cran()
+  skip_if_missing_dependecies()
   skip_if_not_installed("chromConverterExtraTests")
-
   path <- system.file("shimadzuDAD_Anthocyanin.txt",
                       package = "chromConverterExtraTests")
 
@@ -238,6 +238,7 @@ test_that("read_chroms can read 'Agilent' dx files", {
 
 test_that("read_chroms can read 'Thermo' RAW files", {
   skip_on_cran()
+  skip_on_ci()
   skip_if_not_installed("chromConverterExtraTests")
   skip_if_missing_thermorawfileparser()
 
@@ -259,6 +260,7 @@ test_that("read_chroms can read 'Thermo' RAW files", {
 
 test_that("read_chroms can use 'OpenChrom' parsers", {
   skip_on_cran()
+  skip_on_ci()
   skip_if_not_installed("chromConverterExtraTests")
   skip_if_missing_openchrom()
 
@@ -286,8 +288,8 @@ test_that("read_varian_peaklist function works", {
 
 test_that("read_cdf function can read peak tables", {
   skip_on_cran()
+  skip_if_not_installed("ncdf4")
   skip_if_not_installed("chromConverterExtraTests")
-
   path <- system.file("VARIAN1.CDF", package = "chromConverterExtraTests")
   x <- read_cdf(path, what = "peak_table")
   expect_s3_class(x, "data.frame")