Merge pull request #3 from Sage-Bionetworks/dockerization

fix gh workflow and update testthat version
Sage-Bionetworks · Apr 8, 2023 · 3d7e999 · 3d7e999
2 parents 86c5477 + 952e950
commit 3d7e999
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Showing 5 changed files with 11 additions and 9 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -21,10 +21,10 @@ jobs:
           - {os: macOS-latest,   r: 'devel'}
           - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-16.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,   r: '3.6',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,   r: '3.5',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,   r: '3.4',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-18.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-18.04,   r: '3.6',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-18.04,   r: '3.5',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-18.04,   r: '3.4',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -37,7 +37,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 

diff --git a/.github/workflows/Release_Docker_build.yml b/.github/workflows/Release_Docker_build.yml
@@ -16,6 +16,8 @@ env:
 jobs:
   tagging:
     runs-on: ubuntu-latest
+    outputs:
+      tag: ${{steps.tag_version.outputs.new_tag}}
     steps:
       - uses: actions/checkout@v3
         with:

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -15,7 +15,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
 
       - uses: r-lib/actions/setup-pandoc@master
 

diff --git a/Dockerfile b/Dockerfile
@@ -5,7 +5,7 @@ COPY --chown=shiny ./ ./
 
 # Set up Python and install the Synapse Python client
 RUN Rscript -e "install.packages('reticulate', repos='http://cran.rstudio.com/', verbose=FALSE)"
-RUN Rscript -e "library(reticulate); py_install(c('synapseclient', 'pandas'), pip = TRUE, pip_ignore_installed=TRUE)"
+RUN Rscript -e "library(reticulate); install_miniconda(); py_discover_config(); py_install(c('synapseclient', 'pandas'), pip = TRUE, pip_ignore_installed=TRUE)"
 
 # By default the log level is TRACE.  We bump up one level to DEBUG to make the logs a bit less verbose
 ENV SHINY_LOG_LEVEL=DEBUG

diff --git a/renv.lock b/renv.lock
@@ -837,10 +837,10 @@
     },
     "testthat": {
       "Package": "testthat",
-      "Version": "3.0.0",
+      "Version": "3.0.4",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "13298cedd051cb7b8a8972d380b559a6"
+      "Hash": "575216c9946ca70016c3ffb9c31709ba"
     },
     "textshaping": {
       "Package": "textshaping",