Update tests

bhelsel · Feb 29, 2024 · 0568e85 · 0568e85
1 parent c47daef
commit 0568e85
Show file tree

Hide file tree

Showing 5 changed files with 14 additions and 28 deletions.
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master, development]
+    branches: [main, master]
   pull_request:
-    branches: [main, master, development]
+    branches: [main, master]
 
 name: test-coverage
 
@@ -23,22 +23,9 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr remotes
+          extra-packages: any::covr
           needs: coverage
 
-      - uses: actions/setup-python@4
-        with:
-          Python-version: '3.11'
-
-      - name: setup r-reticulate venv
-        shell: Rscript {0}
-        run: |
-          remotes::install_local()
-          reticulate::virtualenv_create("agcounts", Sys.which("python"))
-          reticulate::virtualenv_install("agcounts", c("numpy", "pandas", "pygt3x"))
-          python <- reticulate::virtualenv_python("agcounts")
-          writeLines(sprintf("RETICULATE_PYTHON=%s", python), Sys.getenv("GITHUB_ENV"))
-
       - name: Test coverage
         run: |
           covr::codecov(

diff --git a/tests/testthat/test_actilife_counts.R b/tests/testthat/test_actilife_counts.R
@@ -2,7 +2,7 @@
 
 testthat::test_that("agcounts and Actilife counts are the same",{
 
-  #skip_if(!py_module_available("pygt3x"))
+  skip_if(!py_module_available("pygt3x"))
   gt3xPath <- system.file("extdata/example.gt3x", package = "agcounts")
   agdPath <- system.file("extdata/example5sec.agd", package = "agcounts")
 

diff --git a/tests/testthat/test_agread.R b/tests/testthat/test_agread.R
@@ -1,16 +1,17 @@
 # Copyright © 2022 University of Kansas. All rights reserved.
 
-testthat::test_that("Check that data can be read into agcounts using each agread method", {
-
-  #skip_if(!py_module_available("pygt3x"))
-
+testthat::test_that("Check that data can be read into agcounts using pygt3x", {
+  skip_if(!py_module_available("pygt3x"))
   file <- system.file("extdata/example.gt3x", package = "agcounts")
-
-  expect_error(agread(path = file, parser = "no parser"))
-
   pygt3x <- agread(path = file, parser = "pygt3x", verbose = FALSE)
   expect_equal(nrow(pygt3x), 18000)
   expect_equal(ncol(pygt3x), 4)
+})
+
+
+testthat::test_that("Check that data can be read into agcounts using each agread method", {
+  file <- system.file("extdata/example.gt3x", package = "agcounts")
+  expect_error(agread(path = file, parser = "no parser"))
 
   invisible(capture.output(ggir <- agread(path = file, parser = "GGIR", verbose = FALSE)))
   expect_equal(nrow(ggir), 18000)

diff --git a/tests/testthat/test_shinyReactable.R b/tests/testthat/test_shinyReactable.R
@@ -1,7 +1,6 @@
 # Copyright © 2022 University of Kansas. All rights reserved.
 
 testthat::test_that("Test raw module reactable table output", {
-  #skip_if(!py_module_available("pygt3x"))
   app <- shinytest2::AppDriver$new(agShinyDeployApp())
   app$upload_file(`rawDataModule-gt3xFile` = system.file("extdata/example.gt3x", package = "agcounts"))
   app$set_inputs(`rawDataModule-parser` = "read.gt3x")

diff --git a/tests/testthat/test_shinyServer.R b/tests/testthat/test_shinyServer.R
@@ -1,7 +1,7 @@
 # Copyright © 2022 University of Kansas. All rights reserved.
 
 testthat::test_that("Shiny app rawDataModuleServer loads raw acceleration data", {
-  #skip_if(!py_module_available("pygt3x"))
+  skip_if(!py_module_available("pygt3x"))
   shiny::testServer(rawDataModuleServer, {
     path = system.file("extdata/example.gt3x", package = "agcounts")
     session$setInputs(gt3xFile = list(datapath = path), parser = "pygt3x",
@@ -31,7 +31,7 @@ testthat::test_that("Shiny app rawDataModuleServer loads raw acceleration data",
 })
 
 testthat::test_that("Shiny app rawDataModuleServer loads dynamic UI", {
-  #skip_if(!py_module_available("pygt3x"))
+
   app <- shinytest2::AppDriver$new(agShinyDeployApp())
   app$upload_file(`rawDataModule-gt3xFile` = system.file("extdata/example.gt3x", package = "agcounts"))
   app$set_inputs(`rawDataModule-parser` = "read.gt3x")
@@ -52,7 +52,6 @@ testthat::test_that("Shiny app rawDataModuleServer loads dynamic UI", {
 
 testthat::test_that("Shiny app compareCountsModule loads agd data", {
 
-  #skip_if(!py_module_available("pygt3x"))
   shiny::testServer(compareCountsModuleServer, {
     path = system.file("extdata/calibration1sec.agd", package = "agcounts")
     data <- .read_agd(path)