.. currentmodule:: py4cytoscape
Release date: 21 Jul 2023
- Allowed load_table_data() to handle lists containing float, int and bool instead of just str
- Fixed base_url= not recognized for update_style_defaults() and set_visual_property_default()
- Update python-igraph name to igraph
- Clean up property value warnings for set_node_property_bypass() and set_edge_property_bypass()
Release date: 12 Mar 2023
- Updated annotations.ungroup() to call Cytoscape via GET instead of POST, per document
- Fixed networks.create_network_from_data_frames() 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
Release date: 12 Jan 2023
- 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 get_table_columns()
- For failed connections to Cytoscape, use exponential backoff retry
- Updated support for Python's improved comparison semantics and treatment of NANs (e.g., style_auto_mappings(), create_column_filter())
- 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 PY4CYTOSCAPE_DETAIL_LOGGER environment variable
- Allow execution delays to be set via environment variable (PY4CYTOSCAPE_CATCHUP_FILTER_SECS, PY4CYTOSCAPE_MODEL_PROPAGATION_SECS, PY4CYTOSCAPE_CATCHUP_NETWORK_SECS, PY4CYTOSCAPE_CATCHUP_NETWORK_TIMEOUT_SECS)
- Disallow string as value when setting opacity properties
- Added value syntax checks for map_visual_property(), set_node_property_bypass(), set_edge_property_bypass(), set_network_property_bypass(), set_visual_property_default(), update_style_defaults() & set_visual_property_default()
- Added ability to use old property names in all property functions
- Fixed occasional status 404 in cytoscape_api_versions()
- Fixed apps functions to support Cytoscape 3.10 (get_app_information())
- Added set_catchup_network_merge_secs() and PY4CYTOSCAPE_CATCHUP_NETWORK_MERGE_SECS environment variable to control post-merge delay
- Eliminated futures warning for load_table_data() for use of .iteritems()
- Added select_edges_adjacent_to_nodes()
Release date: 28 Jun 2022
- Removed dependence on Enum package due to build errors
Release date: 28 Jun 2022
- Supported Metascape migration from py2cytoscape to py4cytoscape
- Added names= to get_network_list
- Added create_cytoscapejs_from_network and create_network_from_cytoscapejs
- Added get_visual_style_JSON
- Added delete_all_visual_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
Release date: 22 May 2022
- Added import_file_from_url() function to improve cloud file download
- Added Gang Su basic protocol 1 & 2 Jupyter Notebook demonstrations
- Added network enrichment demonstration in local & remote Gang Su basic protocol 1
- Moved tutorials to https://github.com/cytoscape/cytoscape-automation/wiki
Release date: 30 Apr 2022
- Added annotation functions (mirroring new Cytoscape Annotation features)
- When running Notebook on Cytoscape workstation, files now resolved to local file system (instead of automatic sandbox)
- Added create_view and select_all functions, updated get_network_view_suid() and get_network_views() to coordinate
- Sped up select_all_nodes, select_all_edges
Release date: 11 Oct 2021
- 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
Cancelled
Release date: 3 Jun 2021
- 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 delete_duplicate_edges to ignore edge direction
- Added support for discrete and continuous value generators (as gen* functions in new style_auto_mappers module)
Release date: 26 Mar 2021
- 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
Release date: 08 Jan 2021
- Compatibility of node, edge and group parameter with RCy3 formats
- Improved verify_supported_versions parsing for Cytoscape 3.10 and beyond
Release date: 30 Oct 2020
- Made default directory for standalone Python the same as the Python kernel directory
- Shortened delays that wait for Cytoscape to stabilize, removed NDEx function delays
- Began docker support
- Improved sandboxing and Jupyter Notebook documentation
- Added shorter test (test_sanity) for quick installation verification
Release date: 15 Oct 2020
- Referenced Concepts:Sandboxing from documentation for sandbox functions
- Updated installation and logging documentation
- Updated test to detect Colab shell
Release date: 05 Oct 2020
- Corrected a build problem that stopped 0.0.3 from initializing
Release date: 05 Oct 2020
- Conform to Cytoscape Automation API Definition
- Change CyError logger to write exceptions to stderr
- Add Sandboxing interface and functions
- Add merge_network() and analyze_network()
- Add Jupyter-bridge, Cytoscape Automation API, py4cytoscape versions to cytoscape_version_info
- Add support for Jupyter-bridge
- Add Concepts section to documentation
Release date: 21 Aug 2020
Initial release, matches API signatures for RCy3