NEWS

Changes in version 2.26.0
+ Added documentation & checks for super-long commands
 - suggest users to use commandsPost() when URI too long
+ Bug fixes:
 - check for Inf and -Inf in double columns during loadTableData, #224
 - fix missing base.url in some functions
+ Add test functions
Changes in version 2.24.0
+ Use stringi to replace uchardet
+ Add test functions
+ Doc fixes:
 - add "c" to anchor choices
+ Bug fixes:
 - fix setNodePositionBypass to support network and base.url
 - use viridis color palette for continuous mapping, #210
Changes in version 2.22.0
+ New functions:
 - setNodePositionBypass
 - getNodeLabelPosition
 - setNodeLabelPositionBypass
 - setNodeLabelPositionDefault
 - getNodeLabelPositionDefault
 - rotateLayout
 - scaleLayout
+ Update .verifySupportedVersions to support x.y.z
+ Bug fixes:
 - sync node/edge_name_to_suid utility functions to include new unique_list=False parameter, #139
 - getCurrentStyle and getNetworkName don't work with base.url specified, #208
 - styleBypasses.lockNodeDimensions calls don't propagate base.url, #209
 - no return value comes from the cytoscapePing function with the changed base.url parameter, #212
Changes in version 2.20.0
+ Add a delay in mergeNetworks method
 - Wait for Cytoscape to finish adding annotations column to Network table
+ Bug fixes:
 - ellipsis args in createNetworkFromDataFrames, #195
 - setNodeColorBypass: List of hex colors, #188
Changes in version 2.18.0
+ New functions:
 - exportPNG
 - exportJPG
 - exportPDF
 - exportPS
 - exportSVG
 - importFileFromUrl
 - selectEdgesAdjacentToNodes
Changes in version 2.16.0
+ Faster selectAll* functions
+ Add a new vignette about cloud notebooks with RCy3
+ Doc fixes:
  - Conflicting Brightness/Contrast documentation, #172
  - Conflicting Opacity documentation, #173
  - updateAnnotationText cleanup, #177
+ New functions:
  - createView
  - selectAll
+ Bug fixes:
  - addAnnotationShape customShape can only add rectangle, #160
  - setEdgeLineWidthMapping issue, #164
  - openAppStore function opens the Cytoscape App Store 404 web page, #169
  - groupAnnotation cleanup, #175
Changes in version 2.14.0
+ Cleaned up dependencies, dramatically reducing RCy3 package installation time
+ New functions:
  - add and update Annotations
  - uniqueList parameter added to edgeNameToEdgeSUID and nodeNameToNodeSUID, #139
+ Bug fixes:
  - loadTableData now works with tibbles, #143
  - sandboxSendTo now works with cys and png, #138
  - .verifySupportedVersions fixed comparisons, #152
Changes in version 2.12.x
+ Doc fixes
  - note about metabolite databases, #146
+ Bug fixes
  - createVisualStyle for notebooks, #145
  - regression bug for relative paths, #141
  - filepath handling in export functions, #122
  - Sys.sleep added to setVisualStyle, #137
Changes in version 2.12.0
+ New support for cloud-hosted Jupyter notebooks!
  - Jyputer notebooks running RCy3 in the cloud can communicate with local Cytoscape instances
  - Includes a Sandbox mechanism to manage file transfers between cloud and local dir
+ New functions:
  - addAnnotationText
  - getAnnotationList
  - deleteAnnotation
  - setters for Filter, Model Propagation and Catchup delays
  - many sandbox-related functions
  - getStyleMapping
  - getAllStyleMappings
  - paletteColorRandom
  - paletteColorBrewer* (33 in total!)
  - internal mapping value generators for color, opacity, dimension, line styles, arrows and shapes
+ New parameters:
  - overwrite_file added to export functions
  - apply added to create_*_filter functions
  - ndex.url and ndex.version added to CyNDEx functions
+ Consistent interchangeable handling of node|edge|network names and SUIDs
+ createNetworkFromDataframes plays nice with tibbles
+ Bug fixes:
  - .edgeNameToEdgeSUID revamped to better handle duplicate edge names
Changes in version 2.10.0
+ New functions:
  - getCurrentStyle, #15
+ Added Sys.sleep to buggy CyREST steps in...
  - createNetworkFromDataFrames, #98
  - importNetworkFromFile
  - importNetworkFromNDEx
  - exportNetworkToNDEx
  - updateNetworkInNDEx
  - importFilters
  - create***Filter
  - applyFilter
  - updateStyleMapping
  - setVisualPropertyDefault
+ Refactored getNetworkViewSuid
+ Handled special 404 cases in .cyError
+ Bug fix #94: added base.url param
+ Overhauled error handling and messaging
Changes in version 2.8.0
+ New functions:
  - mergeNetworks
  - analyzeNetwork
+ Better messaging for...
  - App-related functions, like installApp
  - When style changes are applied to "default" style
Changes in version 2.6.x
+ Doc Fixes
  - Roxygen update and man pages
  - Fixes to unitTests
+ Bug Fixes
  - getSelectedNodes/Edges -- #82 fixed missing param in usage
  - added missing base.url args -- #88
Changes in version 2.6.0
+ New functions: 
  - createGroupByColumn
  - clearEdgeBends
  - getNodePosition
+ New parameter to return SUIDs for
  - getSelectedNodes
  - getSelectedEdges
+ Node and edge property values returned as named lists
+ Faster results for getting all node and edge property values, #78
+ More robust handling of file type in export functions
+ More robust handling of dataframes in createNetworkFromDataFrames
+ New support for loading list data
+ Doc Fixes
  - added Filters to Overview vignette
  - improved file type handling descriptions
Changes in version 2.4.4
+ Bug Fixes
  - filter functions -- #73 wrong params
Changes in version 2.4.3
+ Bug Fixes
  - import functions -- #62 fixed default directory
Changes in version 2.4.2
+ Bug Fixes
  - getEdgeInfo -- #61 missing function
Changes in version 2.4.1
+ Bug Fixes
  - getLayoutPropertyNames -- #59 fixed returned values
  - createNetworkFromIgraph -- #58 flatten list attributes to strings
Changes in version 2.4.0
+ New style setting functions
  - setEdgeFontFaceDefault
  - setEdgeFontFaceMapping
  - setEdgeFontSizeMapping
  - setEdgeLabelDefault
  - setEdgeLabelColorDefault
  - setEdgeLabelColorMapping
  - setEdgeLabelOpacityDefault
  - setEdgeLabelOpacityMapping
  - setEdgeOpacityDefault
  - setEdgeSourceArrowShapeMapping
  - setEdgeTargetArrowShapeMapping
  - setEdgeTooltipDefault
  - setNodeBorderOpacityDefault
  - setNodeBorderOpacityMapping
  - setNodeFillOpacityDefault
  - setNodeFillOpacityMapping
  - setNodeFontFaceDefault
  - setNodeFontFaceBypass
  - setNodeFontFaceMapping
  - setNodeFontSizeMapping
  - setNodeHeightDefault
  - setNodeHeightMapping
  - setNodeLabelDefault
  - setNodeLabelColorMapping
  - setNodeLabelOpacityDefault
  - setNodeLabelOpactiyMapping
  - setNodeTooltipDefault
  - setNodeTooltipBypass
  - setNodeWidthDefault
  - setNodeWidthMapping
+ Bug Fixes
  - createSubnetwork -- #43 network suids i/o names
  - openSession works with current working directory -- #50
+ Doc Fixes
  - improved visual.prop handling in mapVisualProperty -- #49,#53 user report
  - added file overwrite warnings to all export and save functions
Changes in version 2.2.7
+ Doc Fixes
  - vignette for phylogenetic trees
Changes in version 2.2.6
+ Bug Fixes
  - saveSession, exportXXX -- #39 default to working directory
  - createNetworkFromDataFrame and .edgeNameToSuids -- #41 multigraph support
  - BiocCheck errors and warnings -- #42
+ Doc Fixes
  - added tests for multigraphs
Changes in version 2.2.5
+ Bug Fixes
  - createXXXFilter and applyFilter -- #40 network arg 
+ Doc Fixes
  - new filters vignette
Changes in version 2.2.4
+ Doc Fixes
   - vignettes
Changes in version 2.2.3
+ Doc Fixes
  - vignettes
Changes in version 2.2.2
+ Doc Fixes
  - new custom graphics vignette
Changes in version 2.2.1
+ Doc Fixes
  - vignettes, readme and test
Changes in version 2.2.0
+ New functions to remove duplicate edges
  - deleteDuplicateEdges
  - deleteSelfLoops
+ New node selection function
  - selectNodesConnectedBySelectedEdges
+ New visual style management functions
  - importVisualStyles
  - deleteVisualStyle
  - deleteStyleMapping
+ New edge bundling function
  - bundleEdges
+ New custom graphics options for nodes
  - setNodeCustomBarChart
  - setNodeCustomBoxChart
  - setNodeCustomHeatMapChart
  - setNodeCustomLineChart
  - setNodeCustomPieChart
  - setNodeCustomRingChart
  - setNodeCustomLinearGradient
  - setNodeCustomRadialGradient
  - setNodeCustomPosition
  - removeNodeCustomGraphics
+ New filter functions
  - applyFilter
  - createColumnFilter
  - createCompositeFilter
  - createDegreeFilter
  - getFilterList
  - exportFilters
  - importFilters
+ Improved speed on bulk node and edge property bypasses
+ Bug Fixes
  - selectEdgesConnectingSelectedNodes -- set default by.col = 'name'
  - setEdgeLineWidthMapping -- fixes input type
  - getGroupInfo -- works without collapsing first
  - getTableColumns -- work with List type columns
+ For Developers
  - Updated many functions to properly pass the base.url parameter to functions like getNetworkSuid. Please be aware and vigilent about this with future development.
  - Adopted use of seq_len(). Please be aware and vigilent.
  - Replaced all but one case of sapply() with vapply().
+ Deprecated
  - Nothing
+ Defunct
  - Previously deprecated functions in v2.0 from older 1.x version of the package

Changes in version 2.0.0
+ New converter functions between Cytoscape and iGraph
  - createIgraphFromNetwork
  - createNetworkFromIgraph
+ New converter functions between Cytoscape and R data.frames
  - createNetworkFromDataFrames
+ New converter functions between Cytoscape and Bioconductor GraphNEL
  - createNetworkFromGraph
  - createGraphFromNetwork
  - addGraphToNetwork
+ Fixed visual style "Direct" functions to set persistent bypass values
  - setNodePropertyBypass
  - setEdgePropertyBypass
  - see all setNode***Bypass and setEdge***Bypass functions
+ Streamlined interfaces to CyREST and Commands API
  - cyrestGET
  - cyrestPUT
  - cyrestPOST
  - cyrestDELETE
  - cyrestAPI
  - commandsGET
  - commandsPOST
  - commandsAPI
  - commandsHelp
+ Optional network parameter supports calls to "current" or specified Cytoscape network by name or SUID
+ New functions for importing/exporting tabular data into/out of Cytoscape
  - getTableColumns
  - loadTableData
+ New function for batch setting visual style property mappings
  - mapVisualProperty
+ Access to Cytoscape System information
  - cytoscapeVersionInfo
  - cytoscapeApiVersions
  - cytoscapeNumberOfCores
  - cytoscapeMemoryStatus
  - cytoscapeFreeMemory
+ Updated layoutCopyCat feature
+ Update network management functions
  - createSubnetwork
  - cloneNetwork
  - renameNetwork
  - importNetworkFromFile
+ Updated selection features
  - selectFirstNeighbors
  - selectEdgesConnectingSelectedNodes
  - selectEdgesAdjacentToSelectedNodes
+ New Cytoscape session functions
  - openSession
  - closeSession
+ Overhauled visual style settings to match Cytoscape's Defaults, Mappings, and Bypasses
+ Added style dependency functions, in addition to lockNodeDimensions
  - matchArrowColorToEdge
  - syncNodeCustomGraphicsSize
+ New set of functions for retrieving current visual property Values for nodes, edges and networks.
+ New functions for network-level Visual Property Defaults, Bypasses and Values.
+ Streamlined data table loading and retrieval
+ New functions for installing and managing Cytoscape Apps, e.g.,
  - installApp
  - uninstallApp
  - udpateApp
  - getInstalledApps
  - getAvailableApps
  - getAppUpdates
  - getAppStatus
+ New functions for network Collections
  - getCollectionList
  - getCollectionName
  - getCollectionSuid
  - getCollectionNetworks
+ New functions for accessing NDEx via CyNDEx2
  - importNetworkFromNDEx
  - exportNetworkToNDEx
  - updateNetworkInNDEx
  - getNetworkNDExId
+ For Developers
  - Reorganized functions into files corresponding to CyREST API, e.g., Collections, CytoscapeSystem, Layouts, Networks, etc.
+ Normalized all documentation using roxygen2
+ Streamlined interfaces to CyREST and Commands API (see above), greatly facilitating the implementation of any new functions matching CyREST or Command API additions
+ Reverted all single-instance methods to simple functions, replacing class-based signatures with simple default values
+ Established handy functions for validating network and view SUIDs
  - getNetworkName
  - getNetworkSuid
  - getNetworkViewSuid
+ Deprecated
  - Outdated function names
+ Defunct
  - CytoscapeConnection and CytoscapeWindow classes, functions and parameters