@@ -4,7 +4,7 @@

 [![BioC Dev Build Status](http://bioconductor.org/shields/build/devel/bioc/RCy3.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/RCy3/) - Bioconductor Dev Build

-[![Travis-CI Build Status](https://travis-ci.org/cytoscape/RCy3.svg?branch=master)](https://travis-ci.org/cytoscape/RCy3) - GitHub Dev Build by Travis

+[![Travis-CI Build Status](https://travis-ci.org/cytoscape/RCy3.svg?branch=devel)](https://travis-ci.org/cytoscape/RCy3) - GitHub Dev Build by Travis

 Building upon the phenominal success of RCytoscape and RCy3, Cytoscape is adopting 

 this project to provide a robust R package for the rapidly evolving Cytoscape 

@@ -14,7 +14,7 @@ ecosystem. We are beginning with a major refactor of RCy3 that includes:

 * harmonized function and argument names

 * support for Cytoscape commands

 * better support for Cytoscape apps

-* see [NEWS](https://github.com/cytoscape/RCy3/blob/master/NEWS) for the complete release notes

+* see [NEWS](https://github.com/cytoscape/RCy3/blob/devel/NEWS) for the complete release notes

 * coordinated development with CyREST and the Cytoscape service model

   * [New API](https://github.com/cytoscape/cyREST/issues?utf8=✓&q=milestone%3A*+label%3A%22new+API%22+is%3A*)

 * coordinated development with other scripting libraries, e.g., 

@@ -97,31 +97,31 @@ pkgdown::build_site(examples=FALSE)

 ### Bioconductor

-While this is the primary development repository for the RCy3 project, we also make regular pushes to official bioconductor repository ([devel](http://bioconductor.org/packages/devel/bioc/html/RCy3.html) & [release](http://bioconductor.org/packages/release/bioc/html/RCy3.html)) from which the official releases are generated. This is the correct repo for all coding and bug reporting interests. The tagged releases here correspond to the bioconductor releases via a manual syncing process. The `master` branch here corresponds to the latest code in development and not yet released. 

+While this is the primary development repository for the RCy3 project, we also make regular pushes to official bioconductor repository ([devel](http://bioconductor.org/packages/devel/bioc/html/RCy3.html) & [release](http://bioconductor.org/packages/release/bioc/html/RCy3.html)) from which the official releases are generated. This is the correct repo for all coding and bug reporting interests. The tagged releases here correspond to the bioconductor releases via a manual syncing process. The `devel` branch here corresponds to the latest code in development and not yet released. 

 ```

 git commit -m "informative commit message"

-git push origin master

-git push upstream master

+git push origin devel

+git push upstream devel

 ```

 http://bioconductor.org/developers/how-to/git/push-to-github-bioc/

-Following each bioconductor release, a `RELEASE_#_#` branch is created. The new branch is fetched and master is updated:

+Following each bioconductor release, a `RELEASE_#_#` branch is created. The new branch is fetched and devel is updated:

 ```

 git fetch upstream

 git checkout -b RELEASE_3_13 upstream/RELEASE_3_13

 git push origin RELEASE_3_13

-git checkout master

-git pull upstream master

-git push origin master

+git checkout devel

+git pull upstream devel

+git push origin devel

 ```

-Only bug fixes and documentation updates can be pushed to the official bioconductor release branch. After committing and pushing fixes to `master`, then:

+Only bug fixes and documentation updates can be pushed to the official bioconductor release branch. After committing and pushing fixes to `devel`, then:

 ```

 git checkout RELEASE_3_13

-git cherry-pick master #for lastest commit

+git cherry-pick devel #for lastest commit

 # or git cherry-pick 1abc234 #for specific commit

 # or git cherry-pick 1abc234^..5def678 #for an inclusive range

 # bump release version in DESCRIPTION

@@ -129,11 +129,11 @@ git commit -am 'version bump'

 git push origin RELEASE_3_13

 # double check changes, and then...

 git push upstream RELEASE_3_13

-git checkout master

+git checkout devel

 # bump dev version in DESCRIPTION

 git commit -am 'version bump'

-git push origin master

-git push upstream master

+git push origin devel

+git push upstream devel

 ```

 https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/

@@ -37,7 +37,7 @@ BiocManager::install("RCy3")

 ```

 install.packages("devtools")

 library(devtools)

-install_github('cytoscape/RCy3', build_vignettes=TRUE)

+install_github('cytoscape/RCy3', build_vignettes=FALSE)

 #If installation fails due to package 'XXX' not found,

 # then run install.packages("XXX") and then try install_github('cytoscape/RCy3') again

 library(RCy3)

@@ -110,8 +110,8 @@ Following each bioconductor release, a `RELEASE_#_#` branch is created. The new

 ```

 git fetch upstream

-git checkout -b RELEASE_3_12 upstream/RELEASE_3_12

-git push origin RELEASE_3_12

+git checkout -b RELEASE_3_13 upstream/RELEASE_3_13

+git push origin RELEASE_3_13

 git checkout master

 git pull upstream master

 git push origin master

@@ -120,15 +120,15 @@ git push origin master

 Only bug fixes and documentation updates can be pushed to the official bioconductor release branch. After committing and pushing fixes to `master`, then:

 ```

-git checkout RELEASE_3_12

+git checkout RELEASE_3_13

 git cherry-pick master #for lastest commit

 # or git cherry-pick 1abc234 #for specific commit

 # or git cherry-pick 1abc234^..5def678 #for an inclusive range

 # bump release version in DESCRIPTION

 git commit -am 'version bump'

-git push origin RELEASE_3_12

+git push origin RELEASE_3_13

 # double check changes, and then...

-git push upstream RELEASE_3_12

+git push upstream RELEASE_3_13

 git checkout master

 # bump dev version in DESCRIPTION

 git commit -am 'version bump'

@@ -1,7 +1,10 @@

 # Welcome to RCy3: 2.0 and Beyond

-[![Travis-CI Build Status](https://travis-ci.org/cytoscape/RCy3.svg?branch=master)](https://travis-ci.org/cytoscape/RCy3)

-[![BioC Build Status](http://bioconductor.org/shields/build/devel/bioc/RCy3.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/RCy3/)

+[![BioC Release Build Status](http://bioconductor.org/shields/build/release/bioc/RCy3.svg)](http://bioconductor.org/checkResults/release/bioc-LATEST/RCy3/) - Bioconductor Release Build

+

+[![BioC Dev Build Status](http://bioconductor.org/shields/build/devel/bioc/RCy3.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/RCy3/) - Bioconductor Dev Build

+

+[![Travis-CI Build Status](https://travis-ci.org/cytoscape/RCy3.svg?branch=master)](https://travis-ci.org/cytoscape/RCy3) - GitHub Dev Build by Travis

 Building upon the phenominal success of RCytoscape and RCy3, Cytoscape is adopting 

 this project to provide a robust R package for the rapidly evolving Cytoscape 

@@ -1,6 +1,8 @@

 # Welcome to RCy3: 2.0 and Beyond

 [![Travis-CI Build Status](https://travis-ci.org/cytoscape/RCy3.svg?branch=master)](https://travis-ci.org/cytoscape/RCy3)

+[![BioC Build Status](http://bioconductor.org/shields/build/devel/bioc/RCy3.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/RCy3/)

+

 Building upon the phenominal success of RCytoscape and RCy3, Cytoscape is adopting 

 this project to provide a robust R package for the rapidly evolving Cytoscape 

 ecosystem. We are beginning with a major refactor of RCy3 that includes:

@@ -13,7 +13,7 @@ ecosystem. We are beginning with a major refactor of RCy3 that includes:

 * coordinated development with CyREST and the Cytoscape service model

   * [New API](https://github.com/cytoscape/cyREST/issues?utf8=✓&q=milestone%3A*+label%3A%22new+API%22+is%3A*)

 * coordinated development with other scripting libraries, e.g., 

-  * [py2cytoscape](https://github.com/cytoscape/py2cytoscape)

+  * [py4cytoscape](https://github.com/cytoscape/py4cytoscape)

   * [RCyjs](http://bioconductor.org/packages/release/bioc/html/RCyjs.html)

 ## Getting Started

@@ -109,6 +109,7 @@ git checkout -b RELEASE_3_12 upstream/RELEASE_3_12

 git push origin RELEASE_3_12

 git checkout master

 git pull upstream master

+git push origin master

 ```

 Only bug fixes and documentation updates can be pushed to the official bioconductor release branch. After committing and pushing fixes to `master`, then:

@@ -105,8 +105,8 @@ Following each bioconductor release, a `RELEASE_#_#` branch is created. The new

 ```

 git fetch upstream

-git checkout -b RELEASE_3_11 upstream/RELEASE_3_11

-git push origin RELEASE_3_11

+git checkout -b RELEASE_3_12 upstream/RELEASE_3_12

+git push origin RELEASE_3_12

 git checkout master

 git pull upstream master

 ```

@@ -114,15 +114,15 @@ git pull upstream master

 Only bug fixes and documentation updates can be pushed to the official bioconductor release branch. After committing and pushing fixes to `master`, then:

 ```

-git checkout RELEASE_3_11

+git checkout RELEASE_3_12

 git cherry-pick master #for lastest commit

 # or git cherry-pick 1abc234 #for specific commit

 # or git cherry-pick 1abc234^..5def678 #for an inclusive range

 # bump release version in DESCRIPTION

 git commit -am 'version bump'

-git push origin RELEASE_3_11

+git push origin RELEASE_3_12

 # double check changes, and then...

-git push upstream RELEASE_3_11

+git push upstream RELEASE_3_12

 git checkout master

 # bump dev version in DESCRIPTION

 git commit -am 'version bump'

@@ -66,7 +66,7 @@ install.packages("RUnit")

 library(RUnit)

 setwd("/git/cytoscape/RCy3") #customize to your setup

 devtools::document()

-devtools::check(args = "--no-examples")

+devtools::check(args = "--no-examples", vignettes = F)

 BiocCheck::BiocCheck('./')

 ```

@@ -66,7 +66,7 @@ install.packages("RUnit")

 library(RUnit)

 setwd("/git/cytoscape/RCy3") #customize to your setup

 devtools::document()

-devtools::check()

+devtools::check(args = "--no-examples")

 BiocCheck::BiocCheck('./')

 ```

@@ -26,8 +26,9 @@ ecosystem. We are beginning with a major refactor of RCy3 that includes:

 install.packages("BiocManager")

 BiocManager::install("RCy3")

 ```

+*Note: Be sure to use the [latest Bioconductor](https://www.bioconductor.org/install/) and recommended R version*  

-_Development version from this repo_ (at your own risk)

+**_Development version from this repo_ (at your own risk)**

 ```

 install.packages("devtools")

 library(devtools)

@@ -100,26 +101,28 @@ git push upstream master

 ```

 http://bioconductor.org/developers/how-to/git/push-to-github-bioc/

-Following each bioconductor release, a `RELEASE_#_#` branch is created here:

+Following each bioconductor release, a `RELEASE_#_#` branch is created. The new branch is fetched and master is updated:

 ```

 git fetch upstream

-git checkout -b RELEASE_3_10 upstream/RELEASE_3_10

-git push origin RELEASE_3_10

+git checkout -b RELEASE_3_11 upstream/RELEASE_3_11

+git push origin RELEASE_3_11

+git checkout master

+git pull upstream master

 ```

 Only bug fixes and documentation updates can be pushed to the official bioconductor release branch. After committing and pushing fixes to `master`, then:

 ```

-git checkout RELEASE_3_10

+git checkout RELEASE_3_11

 git cherry-pick master #for lastest commit

 # or git cherry-pick 1abc234 #for specific commit

 # or git cherry-pick 1abc234^..5def678 #for an inclusive range

 # bump release version in DESCRIPTION

 git commit -am 'version bump'

-git push origin RELEASE_3_10

+git push origin RELEASE_3_11

 # double check changes, and then...

-git push upstream RELEASE_3_10

+git push upstream RELEASE_3_11

 git checkout master

 # bump dev version in DESCRIPTION

 git commit -am 'version bump'

@@ -9,7 +9,7 @@ ecosystem. We are beginning with a major refactor of RCy3 that includes:

 * harmonized function and argument names

 * support for Cytoscape commands

 * better support for Cytoscape apps

-* see [NEWS](NEWS) for the complete release notes

+* see [NEWS](https://github.com/cytoscape/RCy3/blob/master/NEWS) for the complete release notes

 * coordinated development with CyREST and the Cytoscape service model

   * [New API](https://github.com/cytoscape/cyREST/issues?utf8=✓&q=milestone%3A*+label%3A%22new+API%22+is%3A*)

 * coordinated development with other scripting libraries, e.g., 

@@ -86,7 +86,7 @@ They take about 4 minutes to run.

 We use [pkgdown](https://pkgdown.r-lib.org/) to generate the [main site for RCy3](http://cytoscape.org/RCy3/index.html) based on this README, metadata, man pages and vignettes. If you make changes to any of these, please take a moment to regenerate the site:

 ```

 library(pkgdown)

-pkgdown::build_site()

+pkgdown::build_site(examples=FALSE)

 ```

@@ -16,6 +16,10 @@ ecosystem. We are beginning with a major refactor of RCy3 that includes:

   * [py2cytoscape](https://github.com/cytoscape/py2cytoscape)

   * [RCyjs](http://bioconductor.org/packages/release/bioc/html/RCyjs.html)

+## Getting Started

+ * [Documenation site](http://cytoscape.org/RCy3/index.html) 

+ * [Cytoscape Rmd noteboods](https://cytoscape.org/cytoscape-automation/for-scripters/R/notebooks/)

+ 

 ## How to install

 **_Official bioconductor releases_ (recommended)**

 ```

@@ -77,6 +81,15 @@ run.tests()

 They take about 4 minutes to run.

+

+### Updating site

+We use [pkgdown](https://pkgdown.r-lib.org/) to generate the [main site for RCy3](http://cytoscape.org/RCy3/index.html) based on this README, metadata, man pages and vignettes. If you make changes to any of these, please take a moment to regenerate the site:

+```

+library(pkgdown)

+pkgdown::build_site()

+```

+

+

 ### Bioconductor

 While this is the primary development repository for the RCy3 project, we also make regular pushes to official bioconductor repository ([devel](http://bioconductor.org/packages/devel/bioc/html/RCy3.html) & [release](http://bioconductor.org/packages/release/bioc/html/RCy3.html)) from which the official releases are generated. This is the correct repo for all coding and bug reporting interests. The tagged releases here correspond to the bioconductor releases via a manual syncing process. The `master` branch here corresponds to the latest code in development and not yet released. 

@@ -91,22 +91,22 @@ Following each bioconductor release, a `RELEASE_#_#` branch is created here:

 ```

 git fetch upstream

-git checkout -b RELEASE_3_9 upstream/RELEASE_3_9

-git push origin RELEASE_3_9

+git checkout -b RELEASE_3_10 upstream/RELEASE_3_10

+git push origin RELEASE_3_10

 ```

 Only bug fixes and documentation updates can be pushed to the official bioconductor release branch. After committing and pushing fixes to `master`, then:

 ```

-git checkout RELEASE_3_9

+git checkout RELEASE_3_10

 git cherry-pick master #for lastest commit

 # or git cherry-pick 1abc234 #for specific commit

 # or git cherry-pick 1abc234^..5def678 #for an inclusive range

 # bump release version in DESCRIPTION

 git commit -am 'version bump'

-git push origin RELEASE_3_9

+git push origin RELEASE_3_10

 # double check changes, and then...

-git push upstream RELEASE_3_9

+git push upstream RELEASE_3_10

 git checkout master

 # bump dev version in DESCRIPTION

 git commit -am 'version bump'

@@ -91,22 +91,22 @@ Following each bioconductor release, a `RELEASE_#_#` branch is created here:

 ```

 git fetch upstream

-git checkout -b RELEASE_3_8 upstream/RELEASE_3_8

-git push origin RELEASE_3_8

+git checkout -b RELEASE_3_9 upstream/RELEASE_3_9

+git push origin RELEASE_3_9

 ```

 Only bug fixes and documentation updates can be pushed to the official bioconductor release branch. After committing and pushing fixes to `master`, then:

 ```

-git checkout RELEASE_3_8

+git checkout RELEASE_3_9

 git cherry-pick master #for lastest commit

 # or git cherry-pick 1abc234 #for specific commit

 # or git cherry-pick 1abc234^..5def678 #for an inclusive range

 # bump release version in DESCRIPTION

 git commit -am 'version bump'

-git push origin RELEASE_3_8

+git push origin RELEASE_3_9

 # double check changes, and then...

-git push upstream RELEASE_3_8

+git push upstream RELEASE_3_9

 git checkout master

 # bump dev version in DESCRIPTION

 git commit -am 'version bump'

@@ -129,3 +129,5 @@ When adding or updating vignettes, consider the following tips for consistency:

 The entire commit history has been preserved during this transition, but you can find the repo for RCy3 v1.5.3 and earlier

 at https://github.com/tmuetze/Bioconductor_RCy3_the_new_RCytoscape and you can find the Bioconductor

 page for v1.8.0, including archives at https://www.bioconductor.org/packages/3.6/bioc/html/RCy3.html.

+

+```Note to repository maintainers: Please *DO NOT* move this page ... the Cytoscape Automation paper refers directly to it.```

@@ -59,7 +59,7 @@ BiocManager::install("BiocCheck")

 library(BiocCheck)

 install.packages("RUnit")

 library(RUnit)

-setwd("/git/cytoscape/RCy3")

+setwd("/git/cytoscape/RCy3") #customize to your setup

 devtools::document()

 devtools::check()

 BiocCheck::BiocCheck('./')

@@ -59,6 +59,7 @@ BiocManager::install("BiocCheck")

 library(BiocCheck)

 install.packages("RUnit")

 library(RUnit)

+setwd("/git/cytoscape/RCy3")

 devtools::document()

 devtools::check()

 BiocCheck::BiocCheck('./')

@@ -99,14 +99,18 @@ Only bug fixes and documentation updates can be pushed to the official bioconduc

 ```

 git checkout RELEASE_3_8

 git cherry-pick master #for lastest commit

-# or git cherry-pick <commit number> #for specific commit

-# bump version in DESCRIPTION

-git add DESCRIPTION

-git commit -m 'version bump'

+# or git cherry-pick 1abc234 #for specific commit

+# or git cherry-pick 1abc234^..5def678 #for an inclusive range

+# bump release version in DESCRIPTION

+git commit -am 'version bump'

 git push origin RELEASE_3_8

 # double check changes, and then...

 git push upstream RELEASE_3_8

 git checkout master

+# bump dev version in DESCRIPTION

+git commit -am 'version bump'

+git push origin master

+git push upstream master

 ```

 https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/

@@ -89,7 +89,9 @@ http://bioconductor.org/developers/how-to/git/push-to-github-bioc/

 Following each bioconductor release, a `RELEASE_#_#` branch is created here:

 ```

+git fetch upstream

 git checkout -b RELEASE_3_8 upstream/RELEASE_3_8

+git push origin RELEASE_3_8

 ```

 Only bug fixes and documentation updates can be pushed to the official bioconductor release branch. After committing and pushing fixes to `master`, then:

@@ -52,7 +52,7 @@ install.packages("devtools")

 install.packages("roxygen2") 

 library(devtools,roxygen2)

 devtools::install_github("AlexanderPico/docthis")

-library(docthis)

+library(docthis) #shift+cmd+D 

 BiocManager::install("BiocStyle")

 library(BiocStyle)

 BiocManager::install("BiocCheck")

@@ -89,21 +89,21 @@ http://bioconductor.org/developers/how-to/git/push-to-github-bioc/

 Following each bioconductor release, a `RELEASE_#_#` branch is created here:

 ```

-git checkout -b RELEASE_3_7 upstream/RELEASE_3_7

+git checkout -b RELEASE_3_8 upstream/RELEASE_3_8

 ```

 Only bug fixes and documentation updates can be pushed to the official bioconductor release branch. After committing and pushing fixes to `master`, then:

 ```

-git checkout RELEASE_3_7

+git checkout RELEASE_3_8

 git cherry-pick master #for lastest commit

 # or git cherry-pick <commit number> #for specific commit

 # bump version in DESCRIPTION

 git add DESCRIPTION

 git commit -m 'version bump'

-git push origin RELEASE_3_7

+git push origin RELEASE_3_8

 # double check changes, and then...

-git push upstream RELEASE_3_7

+git push upstream RELEASE_3_8

 git checkout master

 ```

@@ -69,8 +69,10 @@ Unit tests are a crucial tool in software development.

 In order to run them 'offline' (not on the Bioconductor build system),

 take these steps from within a running R session (requires RUnit):

-  1) source(system.file("unitTests", "test_RCy3.R", package="RCy3"))

-  2) run.tests()

+```

+source(system.file("unitTests", "test_RCy3.R", package="RCy3"))

+run.tests()

+```

 They take about 4 minutes to run.

@@ -19,11 +19,11 @@ ecosystem. We are beginning with a major refactor of RCy3 that includes:

 ## How to install

 **_Official bioconductor releases_ (recommended)**

 ```

-source("https://bioconductor.org/biocLite.R")

-biocLite("RCy3")

+install.packages("BiocManager")

+BiocManager::install("RCy3")

 ```

-_Unstable development code from this repo_ (at your own risk)

+_Development version from this repo_ (at your own risk)

 ```

 install.packages("devtools")

 library(devtools)

@@ -53,8 +53,10 @@ install.packages("roxygen2")

 library(devtools,roxygen2)

 devtools::install_github("AlexanderPico/docthis")

 library(docthis)

-BiocInstaller::biocLite('BiocStyle')

+BiocManager::install("BiocStyle")

 library(BiocStyle)

+BiocManager::install("BiocCheck")

+library(BiocCheck)

 install.packages("RUnit")

 library(RUnit)

 devtools::document()

@@ -48,12 +48,15 @@ This is a public, open source project. Come on in! You can contribute at multipl

 ### Development

 ```

 install.packages("devtools")

+

 install.packages("roxygen2") 

 library(devtools,roxygen2)

 devtools::install_github("AlexanderPico/docthis")

 library(docthis)

 BiocInstaller::biocLite('BiocStyle')

 library(BiocStyle)

+install.packages("RUnit")

+library(RUnit)

 devtools::document()

 devtools::check()

 BiocCheck::BiocCheck('./')

@@ -62,7 +65,7 @@ BiocCheck::BiocCheck('./')

 ### Testing

 Unit tests are a crucial tool in software development.

 In order to run them 'offline' (not on the Bioconductor build system),

-take these steps from within a running R session:

+take these steps from within a running R session (requires RUnit):

   1) source(system.file("unitTests", "test_RCy3.R", package="RCy3"))

   2) run.tests()

@@ -52,6 +52,8 @@ install.packages("roxygen2")

 library(devtools,roxygen2)

 devtools::install_github("AlexanderPico/docthis")

 library(docthis)

+BiocInstaller::biocLite('BiocStyle')

+library(BiocStyle)

 devtools::document()

 devtools::check()

 BiocCheck::BiocCheck('./')

@@ -105,7 +107,7 @@ When adding or updating vignettes, consider the following tips for consistency:

 * Copy/paste the header from an existing RCy3 vignette, including the global knitr options

 * Number the *VignetteIndexEntry* names w.r.t. other vignettes (this determines their presentation order)

 * Avoid spaces in Rmd filenames; causes CHECK errors

-* When ready, run **Knit to html_vignette_** and review the generated html

+* When ready, run **Knit to html_document** and review the generated html (requires BiocStyle)

 * Note: you don't need to save the html version; it will be generated anew at Bioconductor.

 * In the end, you should just have an Rmd version of each vignette in the repo.

@@ -86,16 +86,16 @@ git checkout -b RELEASE_3_7 upstream/RELEASE_3_7

 Only bug fixes and documentation updates can be pushed to the official bioconductor release branch. After committing and pushing fixes to `master`, then:

 ```

-git checkout origin RELEASE_3_7

+git checkout RELEASE_3_7

 git cherry-pick master #for lastest commit

-# or git cherry-pick <commit number>

+# or git cherry-pick <commit number> #for specific commit

 # bump version in DESCRIPTION

 git add DESCRIPTION

 git commit -m 'version bump'

 git push origin RELEASE_3_7

 # double check changes, and then...

 git push upstream RELEASE_3_7

-git checkout origin master

+git checkout master

 ```

 https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/

@@ -86,14 +86,16 @@ git checkout -b RELEASE_3_7 upstream/RELEASE_3_7

 Only bug fixes and documentation updates can be pushed to the official bioconductor release branch. After committing and pushing fixes to `master`, then:

 ```

-git checkout RELEASE_3_7

-git cherry-pick master

+git checkout origin RELEASE_3_7

+git cherry-pick master #for lastest commit

+# or git cherry-pick <commit number>

 # bump version in DESCRIPTION

 git add DESCRIPTION

 git commit -m 'version bump'

-git push

+git push origin RELEASE_3_7

+# double check changes, and then...

 git push upstream RELEASE_3_7

-git checkout master

+git checkout origin master

 ```

 https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/

@@ -35,7 +35,7 @@ library(RCy3)

 #### Troubleshooting

 1. If you see this error on a Mac: ```make: gfortran-4.8: No such file or directory```, then try reinstalling R via [homebrew](https://brew.sh/): ```brew update && brew reinstall r```

-   * warning: this make take ~30 minutes

+   * warning: this may take ~30 minutes

 2. If you see this error in RStudio: ```ERROR: dependency ‘XML’ is not available for package```, then try this command: ```install.packages("XML")``` and then try installing RCy3 again.

 ## How to contribute

@@ -83,7 +83,18 @@ Following each bioconductor release, a `RELEASE_#_#` branch is created here:

 git checkout -b RELEASE_3_7 upstream/RELEASE_3_7

 ```

-Only bug fixes and documentation updates can be pushed to the official bioconductor release branch.

+Only bug fixes and documentation updates can be pushed to the official bioconductor release branch. After committing and pushing fixes to `master`, then:

+

+```

+git checkout RELEASE_3_7

+git cherry-pick master

+# bump version in DESCRIPTION

+git add DESCRIPTION

+git commit -m 'version bump'

+git push

+git push upstream RELEASE_3_7

+git checkout master

+```

 https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/

@@ -77,14 +77,24 @@ git push upstream master

 ```

 http://bioconductor.org/developers/how-to/git/push-to-github-bioc/

-#### Vignettes

+Following each bioconductor release, a `RELEASE_#_#` branch is created here:

+

+```

+git checkout -b RELEASE_3_7 upstream/RELEASE_3_7

+```

+

+Only bug fixes and documentation updates can be pushed to the official bioconductor release branch.

+

+https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/

+

+### Vignettes

 When adding or updating vignettes, consider the following tips for consistency:

 * Copy/paste the header from an existing RCy3 vignette, including the global knitr options

 * Number the *VignetteIndexEntry* names w.r.t. other vignettes (this determines their presentation order)

 * Avoid spaces in Rmd filenames; causes CHECK errors

 * When ready, run **Knit to html_vignette_** and review the generated html

 * Note: you don't need to save the html version; it will be generated anew at Bioconductor.

-* In the end, you should just have an Rmd versionof each vignette in the repo.

+* In the end, you should just have an Rmd version of each vignette in the repo.

 ### Former Repo

 The entire commit history has been preserved during this transition, but you can find the repo for RCy3 v1.5.3 and earlier

@@ -50,6 +50,8 @@ This is a public, open source project. Come on in! You can contribute at multipl

 install.packages("devtools")

 install.packages("roxygen2") 

 library(devtools,roxygen2)

+devtools::install_github("AlexanderPico/docthis")

+library(docthis)

 devtools::document()

 devtools::check()

 BiocCheck::BiocCheck('./')

@@ -86,4 +86,5 @@ When adding or updating vignettes, consider the following tips for consistency:

 ### Former Repo

 The entire commit history has been preserved during this transition, but you can find the repo for RCy3 v1.5.3 and earlier

-at https://github.com/tmuetze/Bioconductor_RCy3_the_new_RCytoscape.

+at https://github.com/tmuetze/Bioconductor_RCy3_the_new_RCytoscape and you can find the Bioconductor

+page for v1.8.0, including archives at https://www.bioconductor.org/packages/3.6/bioc/html/RCy3.html.

@@ -79,15 +79,10 @@ http://bioconductor.org/developers/how-to/git/push-to-github-bioc/

 When adding or updating vignettes, consider the following tips for consistency:

 * Copy/paste the header from an existing RCy3 vignette, including the global knitr options

 * Number the *VignetteIndexEntry* names w.r.t. other vignettes (this determines their presentation order)

-* Avoid markdown encoded links; only exposed URLs will translate to the PDF version

 * Avoid spaces in Rmd filenames; causes CHECK errors

 * When ready, run **Knit to html_vignette_** and review the generated html

-* For PDF generation:

-  * Uncomment ```highlight=FALSE``` in global knitr options and generate a new html. Unfortunately, the code highlighting looks terrible in PDF.

-  * Pop the html out of the Viewer and into a browser

-  * Choose print, then Save as PDF. Click *Print Background Colors* to retain code backgrounds. Replace spaces with hyphens in filename.

-  * Review the generated PDF and comment out ```highlight=FALSE``` once again

-* In the end, you should have Rmd and PDf versions of each vignette.

+* Note: you don't need to save the html version; it will be generated anew at Bioconductor.

+* In the end, you should just have an Rmd versionof each vignette in the repo.

 ### Former Repo

 The entire commit history has been preserved during this transition, but you can find the repo for RCy3 v1.5.3 and earlier

@@ -52,6 +52,7 @@ install.packages("roxygen2")

 library(devtools,roxygen2)

 devtools::document()

 devtools::check()

+BiocCheck::BiocCheck('./')

 ```

 ### Testing

@@ -1,4 +1,6 @@

 # Welcome to RCy3: 2.0 and Beyond

+[![Travis-CI Build Status](https://travis-ci.org/cytoscape/RCy3.svg?branch=master)](https://travis-ci.org/cytoscape/RCy3)

+

 Building upon the phenominal success of RCytoscape and RCy3, Cytoscape is adopting 

 this project to provide a robust R package for the rapidly evolving Cytoscape 

 ecosystem. We are beginning with a major refactor of RCy3 that includes:

@@ -75,13 +75,14 @@ http://bioconductor.org/developers/how-to/git/push-to-github-bioc/

 #### Vignettes

 When adding or updating vignettes, consider the following tips for consistency:

 * Copy/paste the header from an existing RCy3 vignette, including the global knitr options

+* Number the *VignetteIndexEntry* names w.r.t. other vignettes (this determines their presentation order)

 * Avoid markdown encoded links; only exposed URLs will translate to the PDF version

 * Avoid spaces in Rmd filenames; causes CHECK errors

 * When ready, run **Knit to html_vignette_** and review the generated html

 * For PDF generation:

   * Uncomment ```highlight=FALSE``` in global knitr options and generate a new html. Unfortunately, the code highlighting looks terrible in PDF.

   * Pop the html out of the Viewer and into a browser

-  * Choose print, then Save as PDF. Click *Print Background Colors* to retain code backgrounds

+  * Choose print, then Save as PDF. Click *Print Background Colors* to retain code backgrounds. Replace spaces with hyphens in filename.

   * Review the generated PDF and comment out ```highlight=FALSE``` once again

 * In the end, you should have Rmd and PDf versions of each vignette.

@@ -25,7 +25,7 @@ _Unstable development code from this repo_ (at your own risk)

 ```

 install.packages("devtools")

 library(devtools)

-install_github('cytoscape/RCy3')

+install_github('cytoscape/RCy3', build_vignettes=TRUE)

 #If installation fails due to package 'XXX' not found,

 # then run install.packages("XXX") and then try install_github('cytoscape/RCy3') again

 library(RCy3)

@@ -26,6 +26,8 @@ _Unstable development code from this repo_ (at your own risk)

 install.packages("devtools")

 library(devtools)

 install_github('cytoscape/RCy3')

+#If installation fails due to package 'XXX' not found,

+# then run install.packages("XXX") and then try install_github('cytoscape/RCy3') again

 library(RCy3)

 ```

@@ -23,6 +23,8 @@ biocLite("RCy3")

 _Unstable development code from this repo_ (at your own risk)

 ```

+install.packages("devtools")

+library(devtools)

 install_github('cytoscape/RCy3')

 library(RCy3)

 ```

@@ -61,6 +61,13 @@ They take about 4 minutes to run.

 ### Bioconductor

 While this is the primary development repository for the RCy3 project, we also make regular pushes to official bioconductor repository ([devel](http://bioconductor.org/packages/devel/bioc/html/RCy3.html) & [release](http://bioconductor.org/packages/release/bioc/html/RCy3.html)) from which the official releases are generated. This is the correct repo for all coding and bug reporting interests. The tagged releases here correspond to the bioconductor releases via a manual syncing process. The `master` branch here corresponds to the latest code in development and not yet released. 

+```

+git commit -m "informative commit message"

+git push origin master

+git push upstream master

+```

+http://bioconductor.org/developers/how-to/git/push-to-github-bioc/

+

 #### Vignettes

 When adding or updating vignettes, consider the following tips for consistency:

 * Copy/paste the header from an existing RCy3 vignette, including the global knitr options

@@ -42,10 +42,10 @@ This is a public, open source project. Come on in! You can contribute at multipl

 ### Development

 ```

 install.packages("devtools")

-library(devtools)

+install.packages("roxygen2") 

+library(devtools,roxygen2)

 devtools::document()

 devtools::check()

-# may require 'brew install libxml2'

 ```

 ### Testing

@@ -65,6 +65,7 @@ While this is the primary development repository for the RCy3 project, we also m

 When adding or updating vignettes, consider the following tips for consistency:

 * Copy/paste the header from an existing RCy3 vignette, including the global knitr options

 * Avoid markdown encoded links; only exposed URLs will translate to the PDF version

+* Avoid spaces in Rmd filenames; causes CHECK errors

 * When ready, run **Knit to html_vignette_** and review the generated html

 * For PDF generation:

   * Uncomment ```highlight=FALSE``` in global knitr options and generate a new html. Unfortunately, the code highlighting looks terrible in PDF.

@@ -39,7 +39,16 @@ This is a public, open source project. Come on in! You can contribute at multipl

 * Fork and make pull requests

 * Contact current Cytoscape developers and inquire about joining the team

-## Testing

+### Development

+```

+install.packages("devtools")

+library(devtools)

+devtools::document()

+devtools::check()

+# may require 'brew install libxml2'

+```

+

+### Testing

 Unit tests are a crucial tool in software development.

 In order to run them 'offline' (not on the Bioconductor build system),

 take these steps from within a running R session:

@@ -49,9 +58,21 @@ take these steps from within a running R session:

 They take about 4 minutes to run.

-## Bioconductor

+### Bioconductor

 While this is the primary development repository for the RCy3 project, we also make regular pushes to official bioconductor repository ([devel](http://bioconductor.org/packages/devel/bioc/html/RCy3.html) & [release](http://bioconductor.org/packages/release/bioc/html/RCy3.html)) from which the official releases are generated. This is the correct repo for all coding and bug reporting interests. The tagged releases here correspond to the bioconductor releases via a manual syncing process. The `master` branch here corresponds to the latest code in development and not yet released. 

-## Former Repo

+#### Vignettes

+When adding or updating vignettes, consider the following tips for consistency:

+* Copy/paste the header from an existing RCy3 vignette, including the global knitr options

+* Avoid markdown encoded links; only exposed URLs will translate to the PDF version

+* When ready, run **Knit to html_vignette_** and review the generated html

+* For PDF generation:

+  * Uncomment ```highlight=FALSE``` in global knitr options and generate a new html. Unfortunately, the code highlighting looks terrible in PDF.

+  * Pop the html out of the Viewer and into a browser

+  * Choose print, then Save as PDF. Click *Print Background Colors* to retain code backgrounds

+  * Review the generated PDF and comment out ```highlight=FALSE``` once again

+* In the end, you should have Rmd and PDf versions of each vignette.

+

+### Former Repo