diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml index 3d71631..9b40bf2 100644 --- 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 index f8e5d5d..698240e 100644 --- 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 index bfef821..5decfa5 100644 --- 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)
[![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)

@@ -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)