Merge pull request #42 from KristinaGomoryova/correct-tests

Failing tests corrected
RECETOX · Jul 25, 2024 · b545949 · b545949
2 parents 5265322 + 11f9fbc
commit b545949
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Showing 11 changed files with 15 additions and 7 deletions.
diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml
@@ -28,10 +28,10 @@ jobs:
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Create conda environment
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: mfassignr-dev
           auto-update-conda: true

diff --git a/tests/testthat/test-MFAssignCHO.R b/tests/testthat/test-MFAssignCHO.R
@@ -1,10 +1,20 @@
+make_path <- function(mode, identifier) {
+  file.path("test-data", paste0(mode, "_cho_", identifier, ".rds"))
+}
+
 load_expected <- function(mode) {
-  unambig <- readRDS(file.path("test-data", paste0(mode, "_cho_unambig.rds")))
-  ambig <- readRDS(file.path("test-data", paste0(mode, "_cho_ambig.rds")))
-  none <- readRDS(file.path("test-data", paste0(mode, "_cho_none.rds")))
+  unambig <- readRDS(make_path(mode, "unambig"))
+  ambig <- readRDS(make_path(mode, "ambig"))
+  none <- readRDS(make_path(mode, "none"))
   return(list(Unambig = unambig, Ambig = ambig, None = none))
 }
 
+update_expected <- function(actual, mode) {
+  saveRDS(actual$Ambig, file = make_path(mode, "ambig"))
+  saveRDS(actual$Unambig, file = make_path(mode, "unambig"))
+  saveRDS(actual$None, file = make_path(mode, "none"))
+}
+
 patrick::with_parameters_test_that("MFAssignCHO works",
   {
     peaks <- readRDS(file.path("test-data", paste0(mode, "_iso.rds")))
@@ -15,8 +25,6 @@ patrick::with_parameters_test_that("MFAssignCHO works",
     )
 
     expected <- load_expected(mode)
-    # keys <- c("Ambig", "Unambig", "None")
-    # expect_equal(actual[keys], expected)
 
     expect_equal(actual$Ambig, expected$Ambig)
     expect_equal(actual$Unambig, expected$Unambig)

diff --git a/tests/testthat/test-data/neg_cho_ambig.rds b/tests/testthat/test-data/neg_cho_ambig.rds
diff --git a/tests/testthat/test-data/neg_cho_none.rds b/tests/testthat/test-data/neg_cho_none.rds
diff --git a/tests/testthat/test-data/neg_cho_unambig.rds b/tests/testthat/test-data/neg_cho_unambig.rds
diff --git a/tests/testthat/test-data/neg_recal_iso.rds b/tests/testthat/test-data/neg_recal_iso.rds
diff --git a/tests/testthat/test-data/neg_recal_mono.rds b/tests/testthat/test-data/neg_recal_mono.rds
diff --git a/tests/testthat/test-data/neg_recal_recallist.rds b/tests/testthat/test-data/neg_recal_recallist.rds
diff --git a/tests/testthat/test-data/pos_recal_iso.rds b/tests/testthat/test-data/pos_recal_iso.rds
diff --git a/tests/testthat/test-data/pos_recal_mono.rds b/tests/testthat/test-data/pos_recal_mono.rds
diff --git a/tests/testthat/test-data/pos_recal_recallist.rds b/tests/testthat/test-data/pos_recal_recallist.rds