.. currentmodule:: py4cytoscape Release Log =========== .. include:: release/release_1.12.0.rst .. include:: release/release_1.11.0.rst .. include:: release/release_1.10.0.rst .. include:: release/release_1.9.0.rst py4cytoscape 1.8.0 ------------------- 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 notes ~~~~~~~~~~~~~ .. include:: release/release_1.8.0.rst py4cytoscape 1.7.0 ------------------- 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 notes ~~~~~~~~~~~~~ .. include:: release/release_1.7.0.rst py4cytoscape 1.6.0 ------------------- 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 notes ~~~~~~~~~~~~~ .. include:: release/release_1.6.0.rst py4cytoscape 1.5.0 ------------------- Release date: 28 Jun 2022 * Removed dependence on Enum package due to build errors Release notes ~~~~~~~~~~~~~ .. include:: release/release_1.5.0.rst py4cytoscape 1.4.0 ------------------- 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 notes ~~~~~~~~~~~~~ .. include:: release/release_1.4.0.rst py4cytoscape 1.3.0 ------------------- 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 notes ~~~~~~~~~~~~~ .. include:: release/release_1.3.0.rst py4cytoscape 1.2.0 ------------------- 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 notes ~~~~~~~~~~~~~ .. include:: release/release_1.2.0.rst py4cytoscape 0.0.11 ------------------- 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 Release notes ~~~~~~~~~~~~~ .. include:: release/release_0.0.11.rst py4cytoscape 0.0.10 ------------------- Cancelled py4cytoscape 0.0.9 ------------------ 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 notes ~~~~~~~~~~~~~ .. include:: release/release_0.0.9.rst py4cytoscape 0.0.8 ------------------ 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 notes ~~~~~~~~~~~~~ .. include:: release/release_0.0.8.rst py4cytoscape 0.0.7 ------------------ 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 notes ~~~~~~~~~~~~~ .. include:: release/release_0.0.7.rst py4cytoscape 0.0.6 ------------------ 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 notes ~~~~~~~~~~~~~ .. include:: release/release_0.0.6.rst py4cytoscape 0.0.5 ------------------ 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 notes ~~~~~~~~~~~~~ .. include:: release/release_0.0.5.rst py4cytoscape 0.0.4 ------------------ Release date: 05 Oct 2020 * Corrected a build problem that stopped 0.0.3 from initializing Release notes ~~~~~~~~~~~~~ .. include:: release/release_0.0.4.rst py4cytoscape 0.0.3 ------------------ 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 notes ~~~~~~~~~~~~~ .. include:: release/release_0.0.3.rst py4cytoscape 0.0.1 ------------------ Release date: 21 Aug 2020 Initial release, matches API signatures for RCy3 Release notes ~~~~~~~~~~~~~ .. include:: release/release_0.0.1.rst