[Bioc-devel] Big Changes for RCy3 v2.0.0

[Alex Pico]

Dear maintainers,

The RCy3 package will be undergoing a major transformation in this upcoming version bump to 2.0. The details are itemized in our NEWS and we even made a wiki page to help folks through the upgrade process for existing scripts.

https://www.bioconductor.org/packages/3.7/bioc/news/RCy3/NEWS <https://www.bioconductor.org/packages/3.7/bioc/news/RCy3/NEWS>

https://github.com/cytoscape/RCy3/wiki/Upgrading-Existing-Scripts <https://github.com/cytoscape/RCy3/wiki/Upgrading-Existing-Scripts> 

The fundamental change is that CytoscapeConnection and CytoscapeWindow classes are no longer used. These were pervasive arguments throughout the package in prior versions, so practically every function signature has changed. However, this change simplifies functions and in 99% of cases the old arg can simply be deleted.

Some summary stats regarding the changes:
 * 54 new functions (244 total)
 * Other than function signatures, 
 	* 44 functions are otherwise unchanged
	* 37 functions have been annotated as deprecated
	* 69 functions have been renamed to match updated docs
        * 38 functions have been annotated as defunct

Going forward, this realignment will help us maintain the package in sync with changes to critical upstream resources such as Cytoscape’s CyREST API. It will also greatly simply script writing for users.

If you have functions and vignettes that depend on RCy3, please don’t hesitate to contact me for help with upgrading to 2.0.
 - Alex

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Alexander Pico, PhD
NRNB Executive Director
Bioinformatics Assoc. Director
Gladstone Institutes
http://nrnb.org
http://gladstoneinstitutes.org
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