test_change

Author: pfeiferl

.cache/R/renv/cache/v5/linux-ubuntu-noble/R-4.5/x86_64-pc-linux-gnu/.renvignore

@@ -0,0 +1 @@
+*

.cache/R/renv/index/linux-ubuntu-noble/R-4.5/x86_64-pc-linux-gnu/available-packages/data-1542fe3856c.rds

@@ -0,0 +1,6 @@
+{
+  "da5f745551bd38dd9bb0785f3e169675": {
+    "time": 1756144225,
+    "data": "data-1542fe3856c.rds"
+  }
+}

.cache/R/renv/index/linux-ubuntu-noble/R-4.5/x86_64-pc-linux-gnu/available-packages/index.json

@@ -18,40 +18,43 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-
       - name: Get scdrake package version from DESCRIPTION
         run: |
           pkg_version=$(grep -P '^Version: \d+\.\d+\.\d+$' DESCRIPTION | cut -d' ' -f2)
           echo "pkg_version=$pkg_version" >> $GITHUB_ENV
           echo "scdrake package version: $pkg_version"
-
       - name: Check that tag matches package version in DESCRIPTION
         if: github.event_name == 'release'
         run: |
           echo "pkg_version: $pkg_version"
           test -n "$pkg_version" || (echo "'Version:' not found in DESCRIPTION" && false)
           test "v$pkg_version" == "${{ github.event.release.tag_name }}" \
             || (echo "'Version: $pkg_version' in DESCRIPTION does not match current git tag ('${{ github.event.release.tag_name }}')" && false)
-
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v3
-
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
-
       - name: Login to Docker Hub
         uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
-
       - name: Free disk space
         run: |
           sudo rm -rf \
             /usr/share/dotnet /usr/local/lib/android /opt/ghc \
             /usr/local/share/powershell /usr/share/swift /usr/local/.ghcup \
             /usr/lib/jvm || true
-
+      # - name: Free Disk Space (Ubuntu)
+      #   uses: jlumbroso/free-disk-space@main
+      #   with:
+      #     tool-cache: false
+      #     android: true
+      #     dotnet: true
+      #     haskell: true
+      #     large-packages: false
+      #     docker-images: false
+      #     swap-storage: true
       - name: Build and export test image
         uses: docker/build-push-action@v5
         with:
@@ -62,7 +65,6 @@ jobs:
           tags: ${{ env.IMAGE }}:${{ env.TEST_TAG }}
           cache-from: type=gha
           cache-to: type=gha,mode=min
-
       - name: Run test image
         run: |
           docker run -d \
@@ -71,7 +73,6 @@ jobs:
             -e USERID=$(id -u) \
             -e GROUPID=$(id -g) \
             ${{ env.IMAGE }}:${{ env.TEST_TAG }}
-
       - name: Render README.md
         run: |
           docker exec -w /home/rstudio/scdrake_source scdrake_test \
@@ -80,31 +81,23 @@ jobs:
           git diff --exit-code README.md
           exit_code=$?
           set -e
+          # If exit code is > 0, then there are changes and README.md was not commited
           test $exit_code -eq 0 || (echo "README.Rmd has changed, but an updated version of README.md was not included in this commit" && false)
-
-      - name: Test image (skip all pipeline tests)
+      - name: Test image
         run: |
-          docker exec -w /home/rstudio/scdrake_source \
-            -e SCDRAKE_TEST_RUN_PIPELINE=FALSE \
-            -e SCDRAKE_TEST_RUN_PIPELINE_SINGLE_SAMPLE_FULL=FALSE \
-            -e SCDRAKE_TEST_RUN_PIPELINE_SINGLE_SAMPLE_FULL_SCT=FALSE \
-            -e SCDRAKE_TEST_RUN_PIPELINE_INTEGRATION=FALSE \
-            scdrake_test \
-            r --interactive -L /usr/local/lib/R/site-library -t dev/run_tests.R \
+          docker exec -w /home/rstudio/scdrake_source scdrake_test \
+            r --interactive -L /usr/local/lib/R/site-library -t dev/run_tests.R --no-test-pipeline \
             --output-dir /home/rstudio/scdrake_test_summary
-
       - name: Copy test results
         if: always()
         run: |
           sudo docker cp scdrake_test:/home/rstudio/scdrake_test_summary /
-
       - name: Upload test results
         if: always()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v3
         with:
           name: scdrake_test_summary
           path: /scdrake_test_summary/
-
       - name: Docker meta
         id: meta
         uses: docker/metadata-action@v5
@@ -113,7 +106,6 @@ jobs:
           tags: |
             type=raw,value=latest,enable=${{ github.ref == format('refs/heads/{0}', 'main') }}
             type=semver,pattern={{version}}
-
       - name: Build and push image to Docker Hub
         uses: docker/build-push-action@v5
         with:
@@ -126,26 +118,22 @@ jobs:
           labels: ${{ steps.meta.outputs.labels }}
           cache-from: type=gha
           cache-to: type=gha,mode=min
-
       - name: Remove devel mode from _pkgdown.yml
         if: github.event_name == 'release'
         run: |
           docker exec -w /home/rstudio/scdrake_source scdrake_test \
             bash -c 'sed -i "/development:/d" _pkgdown.yml; sed -i "/mode: devel/d" _pkgdown.yml'
-
       - name: Build pkgdown site
         run: |
           docker exec -w /home/rstudio/scdrake_source scdrake_test \
             Rscript -e "pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)"
-
       - name: Deploy to GitHub pages (stable docs)
         if: github.event_name == 'release'
         uses: JamesIves/github-pages-deploy-action@v4.4.1
         with:
           clean: false
           branch: gh-pages
           folder: docs
-
       - name: Deploy to GitHub pages (devel docs)
         if: github.event_name == 'push'
         uses: JamesIves/github-pages-deploy-action@v4.4.1
@@ -154,7 +142,6 @@ jobs:
           branch: gh-pages
           folder: docs/dev
           target-folder: dev
-
       - name: Rollback release
         if: github.event_name == 'release' && failure()
         uses: author/action-rollback@stable

.github/workflows/docker-ci.yml

@@ -11,3 +11,8 @@
 1756137218223:yq_version <- system2(yq_binary, "-V", stdout = TRUE)
 1756137236043:scdrake::check_yq()
 1756139940929:scdrake::init_project(set_active_project = F,download_example_data = T)
+1756144128936:install.packages("scrapper")
+1756144163257:BiocManager::install("scrapper")
+1756144192448:renv::snapshot()
+1756144215558:renv::snapshot()
+1756145529754:testthat::snapshot_accept('project')

.local/share/rstudio/history_database

@@ -1,15 +1,15 @@
-~/dev/run_check.R
-~/dev/run_tests.R
+~/DESCRIPTION
+~/tests/testthat/test-run_pipeline.R
 ~/tests/testthat/setup.R
 ~/tests/testthat.R
+~/dev/run_tests.R
+~/renv.lock
+~/tests/testthat/test-run_pipeline_vignettes.R
+~/dev/run_check.R
 ~/.github/workflows/update-docs.yaml.disabled
 ~/tests/testthat/run_pipeline_config_patches/integration/01_integration.default.yaml
 ~/tests/testthat/run_pipeline_config_patches/single_sample_pbmc3k/01_input_qc.default.yaml
 ~/tests/testthat/run_pipeline_config_patches/single_sample_pbmc1k_full_sct/01_input_qc.default.yaml
 ~/tests/testthat/run_pipeline_config_patches/single_sample_pbmc1k_full/02_norm_clustering.default.yaml
 ~/tests/testthat/run_pipeline_config_patches/single_sample_pbmc1k_full/01_input_qc.default.yaml
 ~/tests/testthat/run_pipeline_config_patches/single_sample_pbmc1k/01_input_qc.default.yaml
-~/.github/workflows/docker-ci.yml
-~/_pkgdown.yml
-~/tests/testthat/test-run_pipeline.R
-~/tests/testthat/test-plans.R

.local/share/rstudio/monitored/lists/file_mru

@@ -2,6 +2,7 @@
 /home/rstudio/.github/workflows/update-docs.yaml.disabled="9608941D"
 /home/rstudio/.gitignore="EB0E8E64"
 /home/rstudio/.renvignore="E0757FBB"
+/home/rstudio/DESCRIPTION="1BE3B9CA"
 /home/rstudio/Dockerfile="5F49DAE4"
 /home/rstudio/R/plans_single_sample.R="84CF5DF0"
 /home/rstudio/R/scdrake-package.R="A8949BB5"
@@ -39,6 +40,7 @@
 /home/rstudio/tests/testthat/test-plans.R="FDC7F0AD"
 /home/rstudio/tests/testthat/test-project.R="97A17A8A"
 /home/rstudio/tests/testthat/test-run_pipeline.R="89E36FE0"
+/home/rstudio/tests/testthat/test-run_pipeline_vignettes.R="2FFA5AFE"
 /home/rstudio/tests/testthat/yq_test_files/dest.yaml="8D09F3ED"
 /home/rstudio/vignettes/_drake_parallelism.Rmd="25F9EA33"
 /home/rstudio/vignettes/_version.Rmd="B971AEF9"

.local/share/rstudio/notebooks/paths

@@ -1,9 +1,13 @@
 {
     "sortOrder": [
+        {
+            "columnIndex": 4,
+            "ascending": false
+        },
         {
             "columnIndex": 2,
             "ascending": true
         }
     ],
-    "path": "~"
+    "path": "~/tests/testthat"
 }

.local/share/rstudio/pcs/files-pane.pper

@@ -1,3 +1,3 @@
 {
-    "activeTab": 1
+    "activeTab": 0
 }

.local/share/rstudio/pcs/source-pane.pper

@@ -1,6 +1,6 @@
 {
     "source_window_id": "",
     "Source": "Source",
-    "cursorPosition": "163,51",
-    "scrollLine": "150"
+    "cursorPosition": "86,14",
+    "scrollLine": "82"
 }