Improve test coverage (#136)

* Add secrets to codecov workflow
* Add more tests

.github/workflows/test-coverage.yaml

@@ -26,6 +26,12 @@ jobs:
           extra-packages: any::covr
           needs: coverage
 
+      - name: Populate .Renviron with GitHub Secrets
+        run: |
+          echo AWS_ACCESS_KEY_ID="${{ secrets.AWS_ACCESS_KEY_ID }}" >> ~/.Renviron
+          echo AWS_SECRET_ACCESS_KEY="${{ secrets.AWS_SECRET_ACCESS_KEY }}" >> ~/.Renviron
+        shell: bash
+
       - name: Test coverage
         run: |
           covr::codecov(

tests/testthat/test-as_OpenSpecy.R

@@ -1,14 +1,42 @@
 library(data.table)
 
+data("raman_hdpe")
 df <- read_extdata("raman_hdpe.csv") |> read.csv()
 
+test_that("as_OpenSpecy() handles errors correctly", {
+  as_OpenSpecy(df$wavenumber, as.data.frame(df$intensity)) |> expect_silent()
+  as_OpenSpecy(df$wavenumber, df$intensity) |> expect_error()
+  as_OpenSpecy(df$wavenumber) |> expect_error()
+  as_OpenSpecy(df$wavenumber, as.data.frame(df$intensity[-1])) |> expect_error()
+  as_OpenSpecy(df$wavenumber, data.table(intensity = df$intensity,
+                                         intensity = df$intensity)) |>
+    expect_error()
+
+  as_OpenSpecy(data.frame(x = df$wavenumber, abs = df$intensity)) |>
+    expect_warning()
+  as_OpenSpecy(data.frame(wav = df$wavenumber, y = df$intensity)) |>
+    expect_warning()
+
+  amb <- df
+  names(amb) <- c("a", "b")
+  as_OpenSpecy(amb) |> expect_warning() |> expect_warning()
+
+  as_OpenSpecy(df$wavenumber, as.data.frame(df$intensity), coords = "") |>
+    expect_error()
+  as_OpenSpecy(df$wavenumber, as.data.frame(df$intensity), coords = df) |>
+    expect_error()
+  as_OpenSpecy(df$wavenumber, as.data.frame(df$intensity), metadata = "") |>
+    expect_error()
+})
+
 test_that("as_OpenSpecy() generates OpenSpecy objects", {
-  expect_silent(as_OpenSpecy(df))
+  as_OpenSpecy(df) |> expect_silent()
+  as_OpenSpecy(raman_hdpe, session_id = T) |> expect_silent()
 
-  expect_silent(osf <- as_OpenSpecy(df))
-  expect_silent(ost <- data.table(df) |> as_OpenSpecy())
-  expect_silent(osl <- list(df$wavenumber, df[2]) |> as_OpenSpecy())
-  expect_silent(OpenSpecy(osf))
+  osf <- as_OpenSpecy(df) |> expect_silent()
+  ost <- data.table(df) |> as_OpenSpecy() |> expect_silent()
+  osl <- list(df$wavenumber, df[2]) |> as_OpenSpecy() |> expect_silent()
+  OpenSpecy(osf) |> expect_silent()
 
   expect_s3_class(osf, "OpenSpecy")
   expect_s3_class(ost, "OpenSpecy")
@@ -29,32 +57,9 @@ test_that("as_OpenSpecy() generates OpenSpecy objects", {
   expect_false(is_OpenSpecy(df))
 })
 
-test_that("as_OpenSpecy() handles errors correctly", {
-  expect_silent(as_OpenSpecy(df$wavenumber, as.data.frame(df$intensity)))
-  expect_error(as_OpenSpecy(df$wavenumber, df$intensity))
-  expect_error(as_OpenSpecy(df$wavenumber))
-  expect_error(as_OpenSpecy(df$wavenumber, as.data.frame(df$intensity[-1])))
-  expect_error(as_OpenSpecy(df$wavenumber,
-                            data.table(intensity = df$intensity,
-                                       intensity = df$intensity)))
-
-  expect_warning(as_OpenSpecy(data.frame(x = df$wavenumber,
-                                         abs = df$intensity)))
-  expect_warning(as_OpenSpecy(data.frame(wav = df$wavenumber,
-                                         y = df$intensity)))
-
-  expect_error(as_OpenSpecy(df$wavenumber, as.data.frame(df$intensity),
-                            coords = ""))
-  expect_error(as_OpenSpecy(df$wavenumber, as.data.frame(df$intensity),
-                            coords = df))
-  expect_error(as_OpenSpecy(df$wavenumber, as.data.frame(df$intensity),
-                            metadata = ""))
-})
-
 test_that("check_OpenSpecy() work as expected", {
   os <- as_OpenSpecy(df)
   check_OpenSpecy(os) |> expect_true()
-
   check_OpenSpecy(df) |> expect_error()
 
   osv <- osn <- oss <- ost <- osl <- os

tests/testthat/test-manage_spec.R

@@ -1,7 +1,20 @@
 library(data.table)
 data("raman_hdpe")
 
-test_that("merging identical files without range specification", {
+specs <- lapply(c(read_extdata("raman_hdpe.yml"),
+                  read_extdata("ftir_ldpe_soil.asp")), read_any)
+no_overlap <- specs
+no_overlap[[1]] <- restrict_range(no_overlap[[1]], 300, 500)
+no_overlap[[2]] <- restrict_range(no_overlap[[2]], 700, 1000)
+
+test_that("c_spec() handles input errors correctly", {
+  c_spec(1:1000) |> expect_error()
+  c_spec(list(1:1000, 1000:2000)) |> expect_error()
+  c_spec(raman_hdpe) |> expect_warning()
+  c_spec(no_overlap) |> expect_error()
+})
+
+test_that("c_spec() merges identical files without range specification", {
   specs <- lapply(c(read_extdata("raman_hdpe.yml"),
                     read_extdata("raman_hdpe.yml")), read_spec)
   same <- c_spec(specs) |> expect_silent()
@@ -10,10 +23,7 @@ test_that("merging identical files without range specification", {
   expect_equal(same$spectra$intensity, raman_hdpe$spectra$intensity)
 })
 
-specs <- lapply(c(read_extdata("raman_hdpe.yml"),
-                  read_extdata("ftir_ldpe_soil.asp")), read_any)
-
-test_that("merging different files with common range", {
+test_that("c_spec() merges different files with common range", {
   diff <- c_spec(specs, range = "common", res = 5) |>
     expect_silent()
 
@@ -22,7 +32,7 @@ test_that("merging different files with common range", {
   diff$spectra$intensity.1[1:2] |> round(2) |> expect_equal(c(0.03, 0.03))
 })
 
-test_that("merging different files with specified range", {
+test_that("c_spec() merges different files with specified range", {
   spec <- c_spec(specs, range = c(1000, 2000), res = 5) |>
     expect_silent()
 

tests/testthat/test-process_spec.R

@@ -1,23 +1,32 @@
+data("raman_hdpe")
+tiny_map <- read_extdata("CA_tiny_map.zip") |> read_any()
+
+test_that("process_spec() handles input errors corretly", {
+  process_spec(1:1000) |> expect_error()
+})
+
 test_that("process_spec() returns expected values", {
-  tiny_map <- read_extdata("CA_tiny_map.zip") |> read_any()
+  process_spec(raman_hdpe, adj_intens = T, conform_spec = T, restrict_range = T,
+               flatten_range = T, subtr_baseline = T, smooth_intens = T) |>
+    expect_silent()
 
   conf <- process_spec(tiny_map) |> expect_silent()
+
   expect_equal(conf, conform_spec(tiny_map, range = NULL, res = 5) |>
                  smooth_intens(polynomial = 3,
                                window = 11,
                                derivative = 1,
                                abs = T,
                                make_rel = T))
 
-
   proc <- process_spec(raman_hdpe,
                        smooth_intens = TRUE,
                        smooth_intens_args = list(
                          polynomial = 3,
                          window = 11,
                          derivative = 1
-                       )
-  ) |> expect_silent()
+                       )) |>
+    expect_silent()
 
   expect_equal(proc, conform_spec(raman_hdpe) |>
                  smooth_intens(derivative = 1, make_rel = T))

tests/testthat/test-sig_noise.R

@@ -1,7 +1,12 @@
-# Load your OpenSpecy object
 data("raman_hdpe")
 
-test_that("sig_noise returns correct values", {
+test_that("sig_noise() handles input errors corretly", {
+  sig_noise(1:1000) |> expect_error()
+  restrict_range(raman_hdpe, 300, 320) |> sig_noise() |>
+    expect_warning()
+})
+
+test_that("sig_noise() returns correct values", {
   sig_noise(raman_hdpe, metric = "sig") |> round(2) |> unname() |>
     expect_equal(101.17)