added extra tests, checking covr, issue #2

Author: agusinac

tests/testthat.R

@@ -9,5 +9,6 @@
 library(testthat)
 library(ggplot2)
 library(OmicFlow)
+library(patchwork)
 
 test_check("OmicFlow")

tests/testthat/_snaps/autoflow/report.html

@@ -1,17 +1,17 @@
-# test_that("Testing autoFlow while ignoring dynamic date", {
-#   taxa <- metagenomics$new(
-#     biomData = "input/metagenomics/biom_with_taxonomy_hdf5.biom",
-#     metaData = "input/metagenomics/metadata.tsv",
-#     treeData = "input/metagenomics/rooted_tree.newick"
-#   )
+test_that("Testing autoFlow while ignoring dynamic date", {
+  taxa <- metagenomics$new(
+    biomData = "input/metagenomics/biom_with_taxonomy_hdf5.biom",
+    metaData = "input/metagenomics/metadata.tsv",
+    treeData = "input/metagenomics/rooted_tree.newick"
+  )
 
-#   taxa$autoFlow(filename = paste0(getwd(), "/report.html"))
+  taxa$autoFlow(filename = paste0(getwd(), "/report.html"))
 
-#   # Define a transform function to replace dates (e.g., YYYY-MM-DD) with a placeholder
-#   transform_fn <- function(x) {
-#     gsub("\\d{4}-\\d{2}-\\d{2}", "<DATE>", x)
-#   }
+  # Define a transform function to replace dates (e.g., YYYY-MM-DD) with a placeholder
+  transform_fn <- function(x) {
+    gsub("\\d{4}-\\d{2}-\\d{2}", "<DATE>", x)
+  }
 
-#   expect_snapshot_file("report.html", transform = transform_fn)
-#   file.remove("report.html")
-# })
+  expect_snapshot_file("report.html", transform = transform_fn)
+  file.remove("report.html")
+})

tests/testthat/_snaps/metagenomics/test.biom

@@ -12,10 +12,10 @@ test_that("Testing Metagenomics reading and writing of BIOM files", {
     featureData = taxa_hdf5$featureData
   )
 
-  # taxa_ref$write_biom(filename = "test.biom")
+  taxa_ref$write_biom(filename = "test.biom")
 
-  # expect_snapshot_file("test.biom")
-  # file.remove("test.biom") # Cant create an existing file
+  expect_snapshot_file("test.biom")
+  file.remove("test.biom") # Cant create an existing file
   expect_snapshot(taxa_hdf5)
   expect_snapshot(taxa_ref)
 })