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README.md
# Welcome to RCy3: 2.0 and Beyond [![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 ecosystem. We are beginning with a major refactor of RCy3 that includes: * independence from the graphNEL object model * 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 * 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., * [py4cytoscape](https://github.com/cytoscape/py4cytoscape) * [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)** ``` 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)** ``` install.packages("devtools") library(devtools) 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) ``` #### 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 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 This is a public, open source project. Come on in! You can contribute at multiple levels: * Report an issue or feature request * Fork and make pull requests * Contact current Cytoscape developers and inquire about joining the team ### Development ``` install.packages("devtools") install.packages("roxygen2") library(devtools,roxygen2) devtools::install_github("AlexanderPico/docthis") library(docthis) #shift+cmd+D BiocManager::install("BiocStyle") library(BiocStyle) BiocManager::install("BiocCheck") library(BiocCheck) install.packages("RUnit") library(RUnit) setwd("/git/cytoscape/RCy3") #customize to your setup devtools::document() devtools::check(args = "--no-examples", vignettes = F) 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 (requires RUnit): ``` source(system.file("unitTests", "test_RCy3.R", package="RCy3")) 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(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. ``` 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/ 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_13 upstream/RELEASE_3_13 git push origin RELEASE_3_13 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: ``` 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_13 # double check changes, and then... git push upstream RELEASE_3_13 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/ ### 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_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. ### 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 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.```