From 326f63c8ab45d89c6d10ad438f4a10abc5fdbdcf Mon Sep 17 00:00:00 2001
From: Bharath Air <bharath.ananthsub@gmail.com>
Date: Sun, 5 Mar 2023 16:19:33 +0100
Subject: [PATCH] 1. Updated README. 2. Removed Travis CI.

---
 .travis.yml | 43 -------------------------------------------
 README.Rmd  |  9 +++++----
 README.md   | 14 ++++++++------
 3 files changed, 13 insertions(+), 53 deletions(-)
 delete mode 100644 .travis.yml

diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 83a43a4..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,43 +0,0 @@
-# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
-
-language: r
-sudo: true
-cache: packages
-warnings_are_errors: false
-
-# environment variables set for all builds
-env:
-  global:
-    - BIOC_USE_DEVEL="FALSE"
-    - R_BUILD_ARGS="--no-build-vignettes --no-manual"
-    - R_BUILD_ARGS="--no-build-vignettes --no-manual --timings"
-    - _R_CHECK_TIMINGS_="0"
-r:
-  - release
-  - oldrel
-
-# do not build vignettes...takes too long and times out on travis
-r_build_args: --no-build-vignettes --no-manual
-r_check_args: --no-build-vignettes --no-manual --timings
-
-# for codecov
-r_packages:
-  - covr
-
-r_binary_packages:
-  - tidyverse
-  - statmod
-  - rmarkdown
-  - knitr
-  - testthat
-
-r_github_packages:
-  - cran/npsm
-  - cran/DODR
-
-# we need to install BiocInstaller for testing Bioconductor packages
-bioc_required: true
-
-# only report coverage for the release version
-after_success:
-  - test $TRAVIS_R_VERSION_STRING = 'release' && Rscript -e 'covr::codecov()'
diff --git a/README.Rmd b/README.Rmd
index 3164a4a..7630292 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -30,6 +30,7 @@ cat(
 	badge_doi("10.1111/febs.16095", "yellow")
 )
 ```
+[![DOI](https://zenodo.org/badge/314899899.svg)](https://zenodo.org/badge/latestdoi/314899899)
 <!-- badges: end -->
 
 
@@ -59,12 +60,12 @@ library(compareRhythms)
 vignette("UserGuide", package="compareRhythms")
 ```
 
-## Reference
+## Citation
 
-To cite *compareRhythms* in publications use:
+Please cite *compareRhythms* in publications as:
 
-  Venn diagram analysis overestimates the extent of circadian rhythm reprogramming. FEBS Journal, *In Press*. URL
-  https://febs.onlinelibrary.wiley.com/doi/10.1111/febs.16095
+-  Software v1.0.0  https://doi.org/10.5281/zenodo.7699722
+-  Venn diagram analysis overestimates the extent of circadian rhythm reprogramming. FEBS J, 289: 6605-6621. https://doi.org/10.1111/febs.16095
   
   The R code to perform all the analyses in this publication (using *compareRhythms*) can be found in the repository https://github.com/bharathananth/FEBSJ-VDA-overestimates
 
diff --git a/README.md b/README.md
index 542a2ed..687d5fe 100644
--- a/README.md
+++ b/README.md
@@ -8,9 +8,10 @@
 [![](https://img.shields.io/badge/devel%20version-1.0.1-green.svg)](https://github.com/compareRhythms)
 [![License:
 GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://cran.r-project.org/web/licenses/GPL-3)
-[![](https://app.codecov.io/gh/bharathananth/compareRhythms/branch/master/graph/badge.svg)](https://app.codecov.io/gh/bharathananth/compareRhythms)
+[![](https://codecov.io/gh/bharathananth/compareRhythms/branch/master/graph/badge.svg)](https://codecov.io/gh/bharathananth/compareRhythms)
 [![](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![](https://img.shields.io/badge/doi-10.1111/febs.16095-yellow.svg)](https://doi.org/10.1111/febs.16095)
+[![DOI](https://zenodo.org/badge/314899899.svg)](https://zenodo.org/badge/latestdoi/314899899)
 <!-- badges: end -->
 
 The goal of *compareRhythms* is to find features with altered circadian
@@ -53,13 +54,14 @@ library(compareRhythms)
 vignette("UserGuide", package="compareRhythms")
 ```
 
-## Reference
+## Citation
 
-To cite *compareRhythms* in publications use:
+Please cite *compareRhythms* in publications as:
 
-Venn diagram analysis overestimates the extent of circadian rhythm
-reprogramming. FEBS Journal, *In Press*. URL
-<https://febs.onlinelibrary.wiley.com/doi/10.1111/febs.16095>
+- Software v1.0.0 <https://doi.org/10.5281/zenodo.7699722>
+- Venn diagram analysis overestimates the extent of circadian rhythm
+  reprogramming. FEBS J, 289: 6605-6621.
+  <https://doi.org/10.1111/febs.16095>
 
 The R code to perform all the analyses in this publication (using
 *compareRhythms*) can be found in the repository