NEWS

Changes in version 1.25.1
+ bug fix: downloadPathwayArchive scrapes "File Name" column
Changes in version 1.22.0
+ Reimplementation of every function, replacing web service with static JSON
+ getRecentChanges now returns data.frame of pathways per last-edit date 
+ findPathwaysByText has new param, "field" to optionally specify which fields to search
+ getPathwayHistory now opens pathway commit history in browser
+ getPathwayInfo now returns all pathways if param is left NULL
+ New functions: 
    - listCommunities
    - getPathwaysByCommunity
    - getPathwayXXXsByCommunity
    - getCounts
    - findPathwaysByOrcid
    - getCurationStatus
+ Deprecated functions:
    - getCurationTags
    - getCurationTagNames
    - getXXXByCurationTag
    - wikipathwaysAPI
    - wikipathwaysGET
Changes in version 1.17.1
+ doc fix: dplyr redundant, throws error
+ doc fix: specify rjson and lib packages in Rmd
+ README: removed Travis-CI badge (discontinued)
+ README: added latest WikiPathways paper
Changes in version 1.16.0
+ HTTPS updates
+ Update vignette to include new clusterProfiler functions
Changes in version 1.14.0
+ None
Changes in version 1.12.0
+ Removed getColoredPathway
+ New function: writeGMT
+ Updated URLs to BridgeDb datasources.tsv (again)
+ Bug fix: downloadPathwaysArchive works with redirected urls
Changes in version 1.11.4
+ Updated URLs to BridgeDb datasources.tsv
Changes in version 1.11.3
+ New features
    - new readGMT and readGMTnames methods
Changes in version 1.10.0
+ Defuncted getColoredPathway
+ Doc fix: examples fixed and sample gmt included
Changes in version 1.8.5
+ Doc fix: added reference to clusterProfiler 
Changes in version 1.8.4
+ Doc fix: fixed Pathway Analysis vignette 
Changes in version 1.8.3
+ Bug fix: GMT parsing #16
Changes in version 1.8.2
+ Doc fix: vignette with BridgeDbR
+ Bug fix: fixed rjson replacement
Changes in version 1.8.0
+ Replaced RJSONIO with rjson
+ Replaced all but one sapply() with vapply()
+ Deprecated getColoredPathway
+ New features
    - Upgraded findPathwaysByXXX, listPathways and getPathwayInfo functions to return dataframes
    - Upgraded findPathwaysByLiterature to present literature fields
+ Doc fixes
    - Updated tests and vignettes using dataframes
Changes in version 1.6.0
+ Minor updates to the Pathway Analysis vignette
Changes in version 1.4.1
+ Bug fixes
    - Updated the findPathwaysByLiterature test case (fixing a false positive fail)
    - Removed tests for unavailable service: getColoredPathway
Changes in version 1.4.0
+ Bug fixes
    - Added XML to Imports -- #4 missing import
+ Doc fixes
    - Fixed sign in subsetting function in vignette -- user issue on bioc forum
    - Added the missing References section to one of the vignettes
    - Added BioSchemas annotation to the vignettes
Changes in version 1.2.0
+ Bug fixes
    - Added method to retrieve GMT files -- #3 issue
+ Doc fixes
    - New vignette for pathway analysis
Changes in version 1.0.0
+ New features
    - Added derivative functions for both listPathways and getPathwaysByXref to allow specifying the return of simple lists of WPIDs, URLs or names.
    - Added support for PNG from getColoredPathway
    - Added functions for all remaining web service API methods
    - Added a download function for archived pathway sets in various formats
    - Added Overview and BridgeDbR vignettes
+ Significant changes under the hood
    - Updated all functions to use REST calls instead of Curl
    - Simplified function development by abstracting as dedicated wikipathwaysGET function
    - Added tests for all new functions
    - Added enumerated parameters in a number of places for better input validation
+Bug fixes
    - First official release. No bugs... yet!