From 7f33a24550bbde5101742ec4be3c39a68394ead4 Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Wed, 3 Jun 2020 11:51:07 -0400 Subject: [PATCH 1/4] more details in the package description --- DESCRIPTION | 10 +++++++--- NEWS.md | 6 ++++++ 2 files changed, 13 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index e9f7076..5c9a6e4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,12 +1,16 @@ Package: pepr Type: Package Title: Reading Portable Encapsulated Projects -Version: 0.3.1 -Date: 2020-05-27 +Version: 0.3.2 +Date: 2020-06-03 Authors@R: c(person("Nathan", "Sheffield", email = "nathan@code.databio.org", role = c("aut", "cph")),person("Michal","Stolarczyk",email="michal@virginia.edu",role=c("aut","cre"))) Maintainer: Michal Stolarczyk -Description: Reads standardized project configuration files into R. +Description: A PEP, or Portable Encapsulated Project, is a dataset that + subscribes to the PEP structure for organizing metadata. It is written using + a simple yaml + csv format, it is your one-stop solution to metadata + management across data analysis environments. This package reads this + standardized project configuration structure into R. Imports: yaml, stringr, diff --git a/NEWS.md b/NEWS.md index f73a93e..cadbc8b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,9 @@ +# pepr 0.3.2 - 2020-06-03 + +## Changed + +* package description + # pepr 0.3.1 - 2020-05-27 ## Fixed From 3249804d320dda3cda4e77f342b24cd9ea9d55dd Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Wed, 3 Jun 2020 13:20:31 -0400 Subject: [PATCH 2/4] correct check breaking acronyms --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 5c9a6e4..db921f5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -8,7 +8,7 @@ Authors@R: c(person("Nathan", "Sheffield", email = "nathan@code.databio.org", Maintainer: Michal Stolarczyk Description: A PEP, or Portable Encapsulated Project, is a dataset that subscribes to the PEP structure for organizing metadata. It is written using - a simple yaml + csv format, it is your one-stop solution to metadata + a simple YAML + CSV format, it is your one-stop solution to metadata management across data analysis environments. This package reads this standardized project configuration structure into R. Imports: From 869b6acc673869b276f84734580560e12476c207 Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Thu, 4 Jun 2020 09:42:11 -0400 Subject: [PATCH 3/4] updates after CRAN release --- README.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index e27d0ce..72f603a 100644 --- a/README.md +++ b/README.md @@ -1,27 +1,27 @@ - +[![Downloads](http://cranlogs.r-pkg.org/badges/grand-total/pepr)](http://cranlogs.r-pkg.org/badges/grand-total/pepr) +[![CRAN](http://www.r-pkg.org/badges/version-last-release/pepr)](http://www.r-pkg.org/badges/version-last-release/pepr) [![Build Status](https://travis-ci.org/pepkit/pepr.svg?branch=master)](https://travis-ci.org/pepkit/pepr) [![Coverage Status](https://coveralls.io/repos/github/pepkit/pepr/badge.svg?branch=dev)](https://coveralls.io/github/pepkit/pepr?branch=dev&service=github) [![PEP compatible](http://pepkit.github.io/img/PEP-compatible-green.svg)](http://pepkit.github.io) -`pepr` is not yet released, but has been submitted to CRAN and should be available for a standard installation shortly. Complete documentation and API for the `pepr` R package is at [code.databio.org/pepr](http://code.databio.org/pepr/). - # The `pepr` package: Portable Encapsulated Projects in R `pepr` is an R package for reading [Portable Encapsulated Projects](http://pep.databio.org/en/2.0.0/), or **PEP**s, in R. If you describe your project (configuration and samples) according to this format, you can load all project metadata into R using the `pepr` package. To test `pepr`, you can try loading one of the [example PEPs](https://github.com/pepkit/example_peps). +Complete documentation and API for the `pepr` R package is at [code.databio.org/pepr](http://code.databio.org/pepr/). ## Quick start: -Install from GitHub: +Install from [CRAN](https://cran.rstudio.com/web/packages/pepr/index.html): ```R -devtools::install_github("pepkit/pepr") +install.packages("pepr") ``` Load a project and explore metadata like this: ```R -library("pepr"") +library("pepr") cfgPath = system.file( "extdata", paste0("example_peps-master"), From 68c3c6b7945c93e9ef1ed8bc557d071c9925fb0b Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Thu, 4 Jun 2020 09:42:58 -0400 Subject: [PATCH 4/4] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 72f603a..3acaf6a 100644 --- a/README.md +++ b/README.md @@ -7,6 +7,7 @@ # The `pepr` package: Portable Encapsulated Projects in R `pepr` is an R package for reading [Portable Encapsulated Projects](http://pep.databio.org/en/2.0.0/), or **PEP**s, in R. If you describe your project (configuration and samples) according to this format, you can load all project metadata into R using the `pepr` package. To test `pepr`, you can try loading one of the [example PEPs](https://github.com/pepkit/example_peps). + Complete documentation and API for the `pepr` R package is at [code.databio.org/pepr](http://code.databio.org/pepr/).