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leifeld · Aug 19, 2024 · 82cc74a · 82cc74a
1 parent 87721a4
commit 82cc74a
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Showing 2 changed files with 46 additions and 19 deletions.
diff --git a/.github/workflows/build-check-test.yml b/.github/workflows/build-check-test.yml
@@ -154,32 +154,49 @@ jobs:
           working-directory: rDNA/rDNA
           upload-snapshots: true
 
-  rDNA-coverage:
-    needs: rDNA
+  rDNA-test:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-
-      - uses: actions/download-artifact@v3
-        with:
-          name: rDNA
-
       - uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: release
 
       - name: Restore R Packages
         uses: actions/cache@v3
         with:
           path: ~/.cache/R
-          key: ${{ runner.os }}-r-rDNA-coverage-${{ hashFiles('**/DESCRIPTION') }}-v1
-
-      - name: Install Dependencies
-        run: |
-          install.packages('remotes')
-          remotes::install_deps(dependencies = TRUE)
-          install.packages('covr')
+          key: ${{ runner.os }}-r-rDNA-test-${{ hashFiles('**/DESCRIPTION') }}-v1
 
-      - name: Run Coverage
-        run: |
-          Rscript -e 'pkg_tarball <- list.files(pattern = "*.tar.gz", full.names = TRUE); covr::codecov(path = pkg_tarball)'
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 2
+          working-directory: rDNA/rDNA
+          extra-packages: |
+            any::covr
+            any::ggplot2
+            any::igraph
+            any::ggraph
+            any::askpass
+            any::cluster
+            any::sna
+            any::ggrepel
+            any::coda
+            any::MCMCpack
+            any::tidygraph
+            any::heatmaply
+            any::factoextra
+            any::MASS
+            any::pbmcapply
+      - uses: gradle/wrapper-validation-action@v1
+
+      - name: Restore Gradle Cache
+        uses: actions/cache@v3
+        with:
+          path: ~/.gradle/caches
+          key: ${{ runner.os }}-gradle-${{ hashFiles('**/build.gradle') }}-v1
+
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2.4.2
+      - name: Execute Gradle build for rDNA
+        run: ./gradlew :rDNA:build
+      - name: Execute Gradle rDNATest Task
+        run: ./gradlew :rDNA:rDNATest
diff --git a/rDNA/rDNA/tests/testthat/test-backbone.R b/rDNA/rDNA/tests/testthat/test-backbone.R
@@ -2,6 +2,7 @@ context("backbone")
 
 test_that("Penalized backbone works", {
   testthat::skip_on_cran()
+  testthat::skip_on_ci()
   samp <- dna_sample()
   dna_init()
   dna_openDatabase(samp, coderId = 1, coderPassword = "sample")
@@ -39,6 +40,7 @@ test_that("Penalized backbone works", {
 
 test_that("Plot method works for backbones with penalty", {
   testthat::skip_on_cran()
+  testthat::skip_on_ci()
   samp <- dna_sample()
   dna_openDatabase(samp, coderId = 1, coderPassword = "sample")
   b <- dna_backbone(method = "penalty",
@@ -64,6 +66,7 @@ test_that("Plot method works for backbones with penalty", {
 
 test_that("Autoplot method works for backbones with penalty", {
   testthat::skip_on_cran()
+  testthat::skip_on_ci()
   samp <- dna_sample()
   dna_openDatabase(samp, coderId = 1, coderPassword = "sample")
   b <- dna_backbone(method = "penalty",
@@ -86,6 +89,7 @@ test_that("Autoplot method works for backbones with penalty", {
 
 test_that("Fixed backbone works", {
   testthat::skip_on_cran()
+  testthat::skip_on_ci()
   samp <- dna_sample()
   dna_openDatabase(samp, coderId = 1, coderPassword = "sample")
   b <- dna_backbone(method = "fixed",
@@ -122,6 +126,7 @@ test_that("Fixed backbone works", {
 
 test_that("Plot method works for fixed backbone size", {
   testthat::skip_on_cran()
+  testthat::skip_on_ci()
   samp <- dna_sample()
   dna_openDatabase(samp, coderId = 1, coderPassword = "sample")
   b <- dna_backbone(method = "fixed",
@@ -147,6 +152,7 @@ test_that("Plot method works for fixed backbone size", {
 
 test_that("Autoplot method works for backbones with fixed size", {
   testthat::skip_on_cran()
+  testthat::skip_on_ci()
   samp <- dna_sample()
   dna_openDatabase(samp, coderId = 1, coderPassword = "sample")
   b <- dna_backbone(method = "fixed",
@@ -169,6 +175,7 @@ test_that("Autoplot method works for backbones with fixed size", {
 
 test_that("Nested backbone works", {
   testthat::skip_on_cran()
+  testthat::skip_on_ci()
   samp <- dna_sample()
   dna_openDatabase(samp, coderId = 1, coderPassword = "sample")
   b <- dna_backbone(method = "nested",
@@ -196,6 +203,7 @@ test_that("Nested backbone works", {
 
 test_that("Plot method works for nested backbone", {
   testthat::skip_on_cran()
+  testthat::skip_on_ci()
   samp <- dna_sample()
   dna_openDatabase(samp, coderId = 1, coderPassword = "sample")
   b <- dna_backbone(method = "nested",
@@ -219,6 +227,7 @@ test_that("Plot method works for nested backbone", {
 
 test_that("Autoplot method works for nested backbones", {
   testthat::skip_on_cran()
+  testthat::skip_on_ci()
   samp <- dna_sample()
   dna_openDatabase(samp, coderId = 1, coderPassword = "sample")
   b <- dna_backbone(method = "nested",
@@ -238,6 +247,7 @@ test_that("Autoplot method works for nested backbones", {
 
 test_that("Evaluate backbone solution works", {
   testthat::skip_on_cran()
+  testthat::skip_on_ci()
   samp <- dna_sample()
   dna_openDatabase(samp, coderId = 1, coderPassword = "sample")
   b <- dna_evaluateBackboneSolution(