Merge pull request #621 from remlapmot/devel

Allow toggling of tests that require OpenGWAS access

Author: remlapmot

.github/workflows/check-full.yaml

@@ -25,7 +25,7 @@ jobs:
 
     strategy:
       fail-fast: false
-      max-parallel: 2
+      # max-parallel: 2
       matrix:
         config:
           - {os: macos-latest,   r: 'release'}

.github/workflows/test-coverage.yaml

@@ -3,8 +3,8 @@
 on:
   push:
     branches: [main, master]
-  pull_request:
-    branches: [main, master]
+  # pull_request:
+  #   branches: [main, master]
   workflow_dispatch:
 
 name: test-coverage
@@ -18,6 +18,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       OPENGWAS_X_TEST_MODE_KEY: ${{ secrets.OPENGWAS_X_TEST_MODE_KEY }}
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS: TRUE
 
     steps:
       - uses: actions/checkout@v4
@@ -34,6 +35,7 @@ jobs:
       - name: Create and populate .Renviron file
         run: |
           echo OPENGWAS_X_TEST_MODE_KEY="$OPENGWAS_X_TEST_MODE_KEY" >> ~/.Renviron
+          echo TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS="$TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS" >> ~/.Renviron
         shell: bash
 
       - name: Test coverage

TwoSampleMR.Rproj

@@ -14,6 +14,7 @@ RnwWeave: Sweave
 LaTeX: pdfLaTeX
 
 AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
 
 BuildType: Package
 PackageUseDevtools: Yes

tests/testthat/test_add_metadata.r

@@ -1,5 +1,6 @@
 context("add metadata")
 
+skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
 skip_if_offline()
 skip_if_offline(host = "api.opengwas.io")
 skip_on_cran()

tests/testthat/test_create_test_data.r

@@ -1,4 +1,5 @@
 test_that("Create local data", {
+  skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
 skip("Skip local data creation unless you have good access to the API.")
 
 exp_dat <- extract_instruments("ieu-a-2")

tests/testthat/test_instruments.R

@@ -1,5 +1,6 @@
 context("Instruments")
 
+skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
 skip_if_offline()
 skip_if_offline(host = "api.opengwas.io")
 skip_on_cran()

tests/testthat/test_ld.R

@@ -1,5 +1,6 @@
 context("ld")
 
+skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
 skip_if_offline()
 skip_if_offline(host = "api.opengwas.io")
 skip_on_cran()

tests/testthat/test_ldsc.R

@@ -1,7 +1,7 @@
 context("LDSC")
 
-
 test_that("get afl2", {
+  skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
 	skip("Very slow")
 	hm3info <- ieugwasr::afl2_list("hapmap3")
 	if(inherits(hm3info, "response")) skip("Server issues")

tests/testthat/test_mvmr.R

@@ -1,5 +1,6 @@
 context("mvmr")
 
+skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
 skip_on_cran()
 skip_if_offline()
 skip_if_offline(host = "api.opengwas.io")

tests/testthat/test_mvmr_local.R

@@ -10,6 +10,7 @@ context("mvmr local")
 load(system.file("extdata", "test_add_mvmr_local.RData", package="TwoSampleMR"))
 
 test_that("mv exposure local", {
+  skip_if(Sys.getenv('TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS') != TRUE, "Tests requiring OpenGWAS")
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
 	skip_on_cran()