fix test workflow (#3)

* fix: add build * build: further fixes hopefully * build: further fixes * fix: run where the renv env be * test: update tests to work with workflow
sof202 · Sep 19, 2024 · 1c216ba · 1c216ba
1 parent 2fb2dc8
commit 1c216ba
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Showing 5 changed files with 38 additions and 16 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -7,11 +7,13 @@ on:
     branches: [ "main" ]
   workflow_dispatch:
 
-permissions:
-  contents: read
 jobs:
+  build:
     runs-on: ubuntu-latest
 
+    permissions:
+      contents: read
+
     steps:
       - name: Checkout code
         uses: actions/checkout@v4
@@ -20,12 +22,11 @@ jobs:
         uses: r-lib/actions/setup-r@v2
 
       - name: Install dependencies
-        uses: r-lib/actions/setup-r-dependencies@v2
-        working-directory: chrombinarize
+        uses: r-lib/actions/setup-renv@v2
 
       - name: Run tests
         run: |
           library(testthat)
           library(chrombinarize)
-          test_dir("tests/testthat")
-        working-directory: chrombinarize
+          test_dir("chrombinarize/tests/testthat")
+        shell: Rscript {0}
diff --git a/chrombinarize/tests/testthat/test-CPG_robustness_plots.R b/chrombinarize/tests/testthat/test-CPG_robustness_plots.R
@@ -5,7 +5,7 @@ test_that("Normal functionality is obtained for data creation", {
     "expected_bedmethyl_data.Rds"
   ))
   actual_cpg_robustness_data <-
-    create_cpg_robustness_data(methylation_data, 0, 1000)
+    chrombinarize:::create_cpg_robustness_data(methylation_data, 0, 1000)
   expected_cpg_robustness_data <- readRDS(test_path(
     "test_data",
     "cpg_robustness",
@@ -28,16 +28,34 @@ test_that("Edge cases are handled as expected", {
 
   # Filtering steps will always leave an empty data frame
   expect_no_error(
-    calculate_nearby_methylation(methylation_data, "chr1", 1000, 0, 0)
+    chrombinarize:::calculate_nearby_methylation(
+      methylation_data,
+      "chr1",
+      1000,
+      0,
+      0
+    )
   )
 
   # Chromosome doesn't exist
   expect_no_error(
-    calculate_nearby_methylation(methylation_data, "chrZ", 1000, 0, 0)
+    chrombinarize:::calculate_nearby_methylation(
+      methylation_data,
+      "chrZ",
+      1000,
+      0,
+      30
+    )
   )
 
   # Base pair position doesn't exist
   expect_no_error(
-    calculate_nearby_methylation(methylation_data, "chr1", -1, 0, 0)
+    chrombinarize:::calculate_nearby_methylation(
+      methylation_data,
+      "chr1",
+      -1,
+      0,
+      30
+    )
   )
 })
diff --git a/chrombinarize/tests/testthat/test-ONT_BS_comparison_plots.R b/chrombinarize/tests/testthat/test-ONT_BS_comparison_plots.R
@@ -4,7 +4,8 @@ test_that("New columns added are as expected", {
     "read_comparison_files",
     "expected_comparitive_bedmethyl.Rds"
   ))
-  actual_updated_columns <- add_absolute_change_columns(methylation_data)
+  actual_updated_columns <-
+    chrombinarize:::add_absolute_change_columns(methylation_data)
   expected_updated_columns <- readRDS(test_path(
     "test_data",
     "ONT_BS_comparison",

diff --git a/chrombinarize/tests/testthat/test-create_blank_bed_data.R b/chrombinarize/tests/testthat/test-create_blank_bed_data.R
@@ -1,17 +1,18 @@
 # Test data is a subset of hg19.txt that contains chromosomes 1-22, X and Y
 chromosome_sizes_test_file <-
-  testthat::test_path("test_data", "example_chromsizes.txt")
+  test_path("test_data", "example_chromsizes.txt")
 
 # This test bed data only includes chromosome 1 as it allows for a smaller
 # rds file
 expected_small_bed_data <-
-  readRDS(testthat::test_path("test_data", "expected_bed_data.Rds"))
+  readRDS(test_path("test_data", "expected_bed_data.Rds"))
 
 expected_chromosome_lengths <-
-  readRDS(testthat::test_path("test_data", "expected_chromosome_lengths.Rds"))
+  readRDS(test_path("test_data", "expected_chromosome_lengths.Rds"))
 
 testthat::test_that("Processing function returns correct vector", {
-  chromosome_lengths <- process_chromosome_sizes(chromosome_sizes_test_file)
+  chromosome_lengths <-
+    chrombinarize:::process_chromosome_sizes(chromosome_sizes_test_file)
 
   expect_true(is.integer(chromosome_lengths))
   expect_equal(

diff --git a/chrombinarize/tests/testthat/test-error_rate_plots.R b/chrombinarize/tests/testthat/test-error_rate_plots.R
@@ -4,7 +4,8 @@ test_that("Expected value is obtained", {
     "read_bedmethyl_files",
     "expected_bedmethyl_data.Rds"
   ))
-  actual_error_rate_data <- create_error_rate_data(methylation_data, 60, 5)
+  actual_error_rate_data <-
+    chrombinarize:::create_error_rate_data(methylation_data, 60, 5)
   expected_error_rate_data <- readRDS(test_path(
     "test_data",
     "error_rate_plot_data",