Merge pull request #95 from neurogenomics/dev

Upgrade to 0.99.14
neurogenomics · Oct 28, 2023 · c6cbf94 · c6cbf94
2 parents 0886fd7 + 488817c
commit c6cbf94
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Showing 71 changed files with 2,325 additions and 895 deletions.
diff --git a/.Rhistory b/.Rhistory
diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml
@@ -14,8 +14,7 @@ name: rworkflows
     - RELEASE_**
 jobs:
   rworkflows:
-    permissions:
-      contents: write
+    permissions: write-all
     runs-on: ${{ matrix.config.os }}
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
     container: ${{ matrix.config.cont }}
@@ -27,19 +26,21 @@ jobs:
           r: devel
           bioc: devel
           cont: bioconductor/bioconductor_docker:devel
-          rspm: https://packagemanager.rstudio.com/cran/__linux__/latest/release
+          python-version: 3.11
         - os: macOS-latest
           r: latest
           bioc: release
+          python-version: 3.11
         - os: windows-latest
           r: latest
           bioc: release
+          python-version: 3.11
     steps:
     - uses: neurogenomics/rworkflows@master
       with:
-        run_bioccheck: ${{ true }}
+        run_bioccheck: ${{ false }}
         run_rcmdcheck: ${{ true }}
-        as_cran: ${{ true }}
+        as_cran: ${{ false }}
         run_vignettes: ${{ true }}
         has_testthat: ${{ true }}
         run_covr: ${{ true }}
@@ -53,3 +54,4 @@ jobs:
         DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
         runner_os: ${{ runner.os }}
         cache_version: cache-v1
+        miniforge_variant: ""
diff --git a/.github/workflows/rworkflows_dev.yml b/.github/workflows/rworkflows_dev.yml
@@ -16,8 +16,7 @@ name: rworkflows_dev
     - dev
 jobs:
   rworkflows:
-    permissions:
-      contents: write
+    permissions: write-all
     runs-on: ${{ matrix.config.os }}
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
     container: ${{ matrix.config.cont }}
@@ -28,8 +27,7 @@ jobs:
         - os: ubuntu-latest
           r: devel
           bioc: devel
-          cont: bioconductor/bioconductor_docker:devel
-          rspm: https://packagemanager.rstudio.com/cran/__linux__/focal/release
+          cont: ghcr.io/bioconductor/bioconductor_docker:devel
         - os: macOS-latest
           r: latest
           bioc: release
@@ -39,19 +37,20 @@ jobs:
     steps:
     - uses: neurogenomics/rworkflows@dev
       with:
-        run_bioccheck: ${{ true }}
-        run_rcmdcheck: ${{ true }}
+        run_bioccheck: ${{ false }}
+        run_rcmdcheck: ${{ false }}
         as_cran: ${{ true }}
-        run_vignettes: ${{ true }}
-        has_testthat: ${{ true }}
-        run_covr: ${{ true }}
-        run_pkgdown: ${{ true }}
+        run_vignettes: ${{ false }}
+        has_testthat: ${{ false }}
+        run_covr: ${{ false }}
+        run_pkgdown: ${{ false }}
         has_runit: ${{ false }}
-        has_latex: ${{ true }}
+        has_latex: ${{ false }}
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run_docker: ${{ true }}
         docker_user: bschilder
         docker_org: neurogenomicslab
         DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
         runner_os: ${{ runner.os }}
         cache_version: cache-v1
+        free_diskspace: ${{ true }}