From e1dd7caed0eb5932c49ed55b7ebe96303d180d78 Mon Sep 17 00:00:00 2001
From: hyginn <boris.steipe@utoronto.ca>
Date: Thu, 23 Feb 2017 22:47:09 -0500
Subject: [PATCH] Update and move from "ekplektoR" to "rete"

---
 .gitignore                    | 39 ++++++++++++++++++++++++++++++++---
 DESCRIPTION                   |  4 ++--
 README                        |  4 ++--
 ekplektoR.Rproj => rete.Rproj |  1 +
 tests/testthat.R              |  4 ++--
 5 files changed, 43 insertions(+), 9 deletions(-)
 rename ekplektoR.Rproj => rete.Rproj (93%)

diff --git a/.gitignore b/.gitignore
index 5b6a065..73dda08 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,37 @@
-.Rproj.user
+# History files
 .Rhistory
-.RData
-.Ruserdata
+.Rapp.history
+
+# User profile
+.myProfile.R
+
+# Session Data files
+#.RData
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+/*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+.Rproj.user
diff --git a/DESCRIPTION b/DESCRIPTION
index b8d6ef6..8ce5b51 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,10 +1,10 @@
-Package: ekplektoR
+Package: rete
 Type: Package
 Title: Network Analysis for Cell- and Systems Biology
 Version: 0.1.0
 Author: Boris Steipe et al.
 Maintainer: Boris Steipe <boris.steipe@utoronto.ca>
-Description: ekplektor combines a workflow for affected-subnetwork discovery in
+Description: rete combines a workflow for affected-subnetwork discovery in
     cancer genome data and analysis tools.
 License: GPL-3
 Encoding: UTF-8
diff --git a/README b/README
index a3d06dc..1afded2 100644
--- a/README
+++ b/README
@@ -1,4 +1,4 @@
-ekplektoR
+rete
 
 Network topology analysis
 
@@ -32,6 +32,6 @@ DO NOT SUBMIT CODE that does not pass without error, warnings and notes.
 -----------------------------------------------
 
 Load the package (outside of this project) with:
-   devtools::install_github("hyginn/ekplektoR")
+   devtools::install_github("hyginn/rete")
 
 
diff --git a/ekplektoR.Rproj b/rete.Rproj
similarity index 93%
rename from ekplektoR.Rproj
rename to rete.Rproj
index 5b5852f..767608a 100644
--- a/ekplektoR.Rproj
+++ b/rete.Rproj
@@ -12,6 +12,7 @@ Encoding: UTF-8
 RnwWeave: knitr
 LaTeX: XeLaTeX
 
+AutoAppendNewline: Yes
 StripTrailingWhitespace: Yes
 
 BuildType: Package
diff --git a/tests/testthat.R b/tests/testthat.R
index a93fb67..41cdac3 100644
--- a/tests/testthat.R
+++ b/tests/testthat.R
@@ -1,4 +1,4 @@
 library(testthat)
-library(ekplektoR)
+library(rete)
 
-test_check("ekplektoR")
+test_check("rete")