update readme

.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 }}

README.Rmd

@@ -1,12 +1,6 @@
 ---
 title: ""  
-author: "<img src='https://github.com/RajLabMSSM/`r read.dcf('DESCRIPTION', fields = 'Package')[1]`/raw/main/inst/hex/hex.png' height='300'><br><br>
-        `r badger::badge_github_version(color = 'black')` 
-        `r badger::badge_github_actions(action = 'rworkflows')`
-        `r badger::badge_last_commit(branch = 'main')`
-        `r badger::badge_codecov(branch = 'main')` 
-        `r badger::badge_license()` 
-        <h5>Author: <i>Brian M. Schilder</i></h5>" 
+author: "`r rworkflows::use_badges(branch='main')`" 
 date: "<h5>README updated: <i>`r format( Sys.Date(), '%b-%d-%Y')`</i></h5>"
 output:
   github_document

README.md

@@ -1,13 +1,20 @@
-<img src='https://github.com/RajLabMSSM/echoannot/raw/main/inst/hex/hex.png' height='300'><br><br>
-[![](https://img.shields.io/badge/devel%20version-0.99.10-black.svg)](https://github.com/RajLabMSSM/echoannot)
-[![R build
-status](https://github.com/RajLabMSSM/echoannot/workflows/rworkflows/badge.svg)](https://github.com/RajLabMSSM/echoannot/actions)
-[![](https://img.shields.io/github/last-commit/RajLabMSSM/echoannot.svg)](https://github.com/RajLabMSSM/echoannot/commits/main)
-[![](https://app.codecov.io/gh/RajLabMSSM/echoannot/branch/main/graph/badge.svg)](https://app.codecov.io/gh/RajLabMSSM/echoannot)
+<img src='https://github.com/RajLabMSSM/echoannot/raw/main/inst/hex/hex.png' title='Hex sticker for echoannot' height='300'><br>
 [![License:
 GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://cran.r-project.org/web/licenses/GPL-3)
-¶ <h5> ¶ Author: <i>Brian M. Schilder</i> ¶ </h5>
-<h5> ¶ README updated: <i>Dec-22-2022</i> ¶ </h5>
+[![](https://img.shields.io/badge/devel%20version-0.99.11-black.svg)](https://github.com/RajLabMSSM/echoannot)
+[![](https://img.shields.io/github/languages/code-size/RajLabMSSM/echoannot.svg)](https://github.com/RajLabMSSM/echoannot)
+[![](https://img.shields.io/github/last-commit/RajLabMSSM/echoannot.svg)](https://github.com/RajLabMSSM/echoannot/commits/main)
+<br> [![R build
+status](https://github.com/RajLabMSSM/echoannot/workflows/rworkflows/badge.svg)](https://github.com/RajLabMSSM/echoannot/actions)
+[![](https://codecov.io/gh/RajLabMSSM/echoannot/branch/main/graph/badge.svg)](https://app.codecov.io/gh/RajLabMSSM/echoannot)
+<br>
+<a href='https://app.codecov.io/gh/RajLabMSSM/echoannot/tree/main' target='_blank'><img src='https://codecov.io/gh/RajLabMSSM/echoannot/branch/main/graphs/icicle.svg' title='Codecov icicle graph' width='200' height='50' style='vertical-align: top;'></a>  
+<h4>  
+Authors: <i>Brian Schilder, Jack Humphrey, Towfique Raj</i>  
+</h4>
+<h5>  
+README updated: <i>Oct-20-2023</i>  
+</h5>
 
 ## `echoannot`: Functions for annotating genomic data