https://github.com/cytoscape/py4cytoscape - 1.11.0

Fixed py4cytoscapeutils nodenametonode_suid() to allow nodes named by integers instead of alphanumerics

- Python
Published by bdemchak over 1 year ago

https://github.com/cytoscape/py4cytoscape - 1.10.0

• Added base_url parameter propagation in filters, networks and tables functions
• Add documentation & check for outsize commandsrun and commandsget requests
• Speed improvement on functions that convert node or edge names to SUIDs

- Python
Published by bdemchak over 1 year ago

https://github.com/cytoscape/py4cytoscape - 1.9.0

• Removed value validation warning from setvisualproperty_default()
• Fixed missing URL parameter in createnetworkfromdataframes() and createnetworkfrom_networkx()
• Added style functions for nodeposition and nodelabel_position
• Allowed Cytoscape version check to include patch level (e.g., x.y.patch)
• Added layout functions scalelayout() and rotatelayout() to match Cytoscape's Layout Tools

- Python
Published by bdemchak about 2 years ago

https://github.com/cytoscape/py4cytoscape - 1.8.0

• Allowed loadtabledata() to handle lists containing float, int and bool instead of just str
• Fixed baseurl= not recognized for updatestyledefaults() and setvisualpropertydefault()
• Update python-igraph name to igraph
• Clean up property value warnings for setnodepropertybypass() and setedgepropertybypass()

- Python
Published by bdemchak over 2 years ago

https://github.com/cytoscape/py4cytoscape - 1.7.0

• Updated annotations.ungroup() to call Cytoscape via GET instead of POST, per document
• Fixed networks.createnetworkfromdataframes() to allow key column different than 'id'
• Documented how to include a comma in a node name
• Fixed timing issue in merge_networks() where network wasn't stable before returning

- Python
Published by bdemchak almost 3 years ago

https://github.com/cytoscape/py4cytoscape - 1.6.0

• Now supporting Metascape migration from py2cytoscape to py4cytoscape
• Added sandbox support when Cytoscape is at URL different than 127.0.0.1
• Fixed bugs for calling Cytoscape at URL different than 127.0.0.1
• Removed slow n^2 algorithm from gettablecolumns()
• For failed connections to Cytoscape, use exponential backoff retry
• Updated support for Python's improved comparison semantics and treatment of NANs (e.g., styleautomappings(), createcolumnfilter())
• Added Alternate IP Address section to Concepts.rst
• Allow text colors (e.g., "red") in addition to hex colors when setting color properties
• Allow log directory to be set via PY4CYTOSCAPEDETAILLOGGER environment variable
• Allow execution delays to be set via environment variable (PY4CYTOSCAPECATCHUPFILTERSECS, PY4CYTOSCAPEMODELPROPAGATIONSECS, PY4CYTOSCAPECATCHUPNETWORKSECS, PY4CYTOSCAPECATCHUPNETWORKTIMEOUT_SECS)
• Disallow string as value when setting opacity properties
• Added value syntax checks for mapvisualproperty(), setnodepropertybypass(), setedgepropertybypass(), setnetworkpropertybypass(), setvisualpropertydefault(), updatestyledefaults() & setvisualproperty_default()
• Added ability to use old property names in all property functions
• Fixed occasional status 404 in cytoscapeapiversions()
• Fixed apps functions to support Cytoscape 3.10 (getappinformation())
• Added setcatchupnetworkmergesecs() and PY4CYTOSCAPECATCHUPNETWORKMERGESECS environment variable to control post-merge delay
• Eliminated futures warning for loadtabledata() for use of .iteritems()
• Added selectedgesadjacenttonodes()

- Python
Published by bdemchak about 3 years ago

https://github.com/cytoscape/py4cytoscape - 1.5.0

• Removed dependence on Enum package due to build errors

- Python
Published by bdemchak over 3 years ago

https://github.com/cytoscape/py4cytoscape - 1.4.0

• Supported Metascape migration from py2cytoscape to py4cytoscape
• Added names= to getnetworklist
• Added createcytoscapejsfromnetwork and createnetworkfromcytoscapejs
• Added getvisualstyle_JSON
• Added deleteallvisual_styles
• Added sandbox support when Cytoscape is at URL different than 127.0.0.1
• Fixed bugs for calling Cytoscape at URL different than 127.0.0.1

- Python
Published by bdemchak over 3 years ago

https://github.com/cytoscape/py4cytoscape - 1.3.0

• Improved cloud file download
• Improved support for local Jupyter Notebook execution
• Demonstration of enrichment functionality
• Rationalized tutorials

- Python
Published by bdemchak almost 4 years ago

https://github.com/cytoscape/py4cytoscape - New annotation and selection functions, local notebook file system access

• Addition of annotation functions (per new Cytoscape features)
• Changed default for sandboxing when running Notebook on local Workstation
• Add new functions: createview, selectall
• Sped up selectallnodes, selectalledges

- Python
Published by bdemchak almost 4 years ago

https://github.com/cytoscape/py4cytoscape - 0.0.11

• Updated documentation and tutorials
  

• Made set_*_property_bypass more resilient to null node/edge lists
  

• For Notebook support, improved startup code and added notebook_show_image(), notebook_export_show_image() functions
  

• For color generators, added reverse= parameter and made divergent palettes automatically reversed
  

• Fixed filter and style bypass functions to not crash when there are no selected nodes
  

- Python
Published by bdemchak over 4 years ago

https://github.com/cytoscape/py4cytoscape - 0.0.9

• Updated documentation and tutorials
• Reworked iGraph support to track RCy3 implementation
• Added iGraph support for Graph, DiGraph, MultiGraph, MultiDiGraph
• Updated node/edge-to-suid functions to allow detection of multiple copies of a node/edge
• Enabled deleteduplicateedges to ignore edge direction
• Added support for discrete and continuous value generators (as gen* functions in new styleautomappers module)

- Python
Published by kozo2 over 4 years ago

https://github.com/cytoscape/py4cytoscape - 0.0.8

• Added parameters in CyNDEX functions to support subdomains
• Added apply= parameter in filter definition functions to support Cytoscape v3.9.0 separating apply from definition
• Added overwrite_file parameter to export functions
• Added Sandbox direct download from URL
• Added functions for import network from tabular file & get current style, etc
• Fixes that allow commands_help to work

- Python
Published by bdemchak almost 5 years ago

https://github.com/cytoscape/py4cytoscape - 0.0.7

• Compatibility of node, edge and group parameter with RCy3 formats
• Improved verifysupportedversions parsing for Cytoscape 3.10 and beyond

- Python
Published by bdemchak about 5 years ago

https://github.com/cytoscape/py4cytoscape -

• Improved sandboxing and Jupyter Notebook documentation
• Shortened execution delays
• Docker support
• More rational default directory for standalone Python execution

- Python
Published by bdemchak over 5 years ago

https://github.com/cytoscape/py4cytoscape -

• Referenced Concepts:Sandboxing from documentation for sandbox functions
• Updated installation and logging documentation
• Updated test to detect Colab shell

- Python
Published by bdemchak over 5 years ago

https://github.com/cytoscape/py4cytoscape - 0.0.4

Includes everything in 0.0.3 (defective release):

• Conform to Cytoscape Automation API Definition <https://docs.google.com/spreadsheets/d/1XLWsKxGLqcBWLzoW2y6HyAUU2jMXaEaWw7QLn3NE5nY/edit?usp=sharing>_
• Change CyError logger to write exceptions to stderr
• Add Sandboxing interface and functions
• Add mergenetwork() and analyzenetwork()
• Add Jupyter-bridge, Cytoscape Automation API, py4cytoscape versions to cytoscapeversioninfo
• Add support for Jupyter-bridge
• Add Concepts section to documentation

- Python
Published by bdemchak over 5 years ago

https://github.com/cytoscape/py4cytoscape -

- Python
Published by bdemchak over 5 years ago