update rworkflows

RajLabMSSM · Oct 20, 2023 · f5a0db0 · f5a0db0
1 parent 5e0b07d
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Showing 3 changed files with 21 additions and 10 deletions.
diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml
@@ -4,14 +4,19 @@ name: rworkflows
     branches:
     - master
     - main
+    - devel
     - RELEASE_**
   pull_request:
     branches:
     - master
     - main
+    - devel
     - RELEASE_**
 jobs:
   rworkflows:
+    permissions:
+      contents: write
+      packages: write
     runs-on: ${{ matrix.config.os }}
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
     container: ${{ matrix.config.cont }}
@@ -20,16 +25,20 @@ jobs:
       matrix:
         config:
         - os: ubuntu-latest
-          r: devel
           bioc: devel
-          cont: bioconductor/bioconductor_docker:devel
-          rspm: https://packagemanager.rstudio.com/cran/__linux__/focal/release
+          r: auto
+          cont: ghcr.io/bioconductor/bioconductor_docker:devel
+          rspm: https://packagemanager.rstudio.com/cran/__linux__/latest/release
         - os: macOS-latest
-          r: latest
           bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
         - os: windows-latest
-          r: latest
           bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
     steps:
     - uses: neurogenomics/rworkflows@master
       with:
@@ -42,7 +51,7 @@ jobs:
         run_pkgdown: ${{ true }}
         has_runit: ${{ false }}
         has_latex: ${{ false }}
-        GITHUB_TOKEN: ${{ secrets.PAT_GITHUB }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run_docker: ${{ false }}
         DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
         runner_os: ${{ runner.os }}

diff --git a/README.Rmd b/README.Rmd
@@ -7,12 +7,14 @@ output:
 
 ```{r, echo=FALSE, include=FALSE}
 pkg <- read.dcf("DESCRIPTION", fields = "Package")[1]
-description <- read.dcf("DESCRIPTION", fields = "Description")[1]
+description <- read.dcf("DESCRIPTION", fields = "Description")[1] |> 
+    gsub(pattern="\n", replacement=" ")
 ```
 
 ## ``r pkg``: `r gsub("echoverse module: ","", description)`
 
-This R package is part of the *echoverse* suite that supports [`echolocatoR`](https://github.com/RajLabMSSM/echolocatoR):
+This R package is part of the *echoverse* suite that supports
+[`echolocatoR`](https://github.com/RajLabMSSM/echolocatoR):
 an automated genomic fine-mapping pipeline. 
 
 If you use ``r pkg``, please cite: 

diff --git a/README.md b/README.md
@@ -7,7 +7,7 @@ GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://cran.r-pro
 [![](https://img.shields.io/github/last-commit/RajLabMSSM/echoverseTemplate.svg)](https://github.com/RajLabMSSM/echoverseTemplate/commits/master)
 <br> [![R build
 status](https://github.com/RajLabMSSM/echoverseTemplate/workflows/rworkflows/badge.svg)](https://github.com/RajLabMSSM/echoverseTemplate/actions)
-[![](https://codecov.io/gh/RajLabMSSM/echoverseTemplate/branch/master/graph/badge.svg)](https://codecov.io/gh/RajLabMSSM/echoverseTemplate)
+[![](https://codecov.io/gh/RajLabMSSM/echoverseTemplate/branch/master/graph/badge.svg)](https://app.codecov.io/gh/RajLabMSSM/echoverseTemplate)
 <br>
 <a href='https://app.codecov.io/gh/RajLabMSSM/echoverseTemplate/tree/master' target='_blank'><img src='https://codecov.io/gh/RajLabMSSM/echoverseTemplate/branch/master/graphs/icicle.svg' title='Codecov icicle graph' width='200' height='50' style='vertical-align: top;'></a>  
 <h4>  
@@ -40,7 +40,7 @@ library(echoverseTemplate)
 
 ### [Website](https://rajlabmssm.github.io/echoverseTemplate)
 
-### [Getting started](https://rajlabmssm.github.io/echoverseTemplate/articles/echoverseTemplate)
+### [Get started](https://rajlabmssm.github.io/echoverseTemplate/articles/echoverseTemplate)
 
 <hr>