cytoscape/py4cytoscape issues and pull requests

#147 - p4c.map_visual_properties(...) with argument "EDGE_TARGET_ARROW_SHAPE" ignores `base_url`.

Issue - State: open - Opened by stephanmg 11 days ago - 3 comments

#146 - How to export high dpi pictures with export_image and cytoscape v3.10?

Issue - State: closed - Opened by matthiaskoenig 27 days ago - 3 comments

#145 - set_node_position_bypass does not support z_locations

Issue - State: open - Opened by matthiaskoenig 27 days ago - 4 comments

#144 - How to set node x and y position?

Issue - State: open - Opened by matthiaskoenig 29 days ago - 12 comments
Labels: enhancement

#143 - Fix Key Type Conflict in `item_name_to_suid_list` Dictionary

Pull Request - State: closed - Opened by GeneCodeSavvy 2 months ago - 2 comments

#142 - node_name_to_node_suid() does not accept node name that is also a number

Issue - State: closed - Opened by bdemchak 2 months ago - 4 comments

#141 - py4cytoscape_utils changes

Pull Request - State: closed - Opened by GeneCodeSavvy 2 months ago - 2 comments

#140 - Revert "py4cytoscape_utils changes"

Pull Request - State: closed - Opened by bdemchak 2 months ago

#139 - py4cytoscape_utils changes

Pull Request - State: closed - Opened by GeneCodeSavvy 2 months ago - 4 comments

#138 - gen_node_color_map does not set the correct MAX value for a continuous mapping

Issue - State: open - Opened by rpillich 2 months ago - 6 comments
Labels: help wanted

#137 - string protein query gives errors when there are too many proteins

Issue - State: open - Opened by mehmetdirenc 4 months ago - 16 comments

#136 - include how to add py4cytoscape on msys2

Pull Request - State: closed - Opened by Kreijstal 4 months ago - 1 comment

#135 - Is there a way to even export the attribute (e.g., curveness)of the edge from a cytoscape console to a data frame

Issue - State: closed - Opened by gmhhope 5 months ago - 5 comments

#134 - 4.B.4 - powershell.exe adds a value under HKCU:\Software\Classes\ms-settings\shell\open\command via New-Item and New-ItemProperty

Issue - State: open - Opened by CHRISTENLYNN 6 months ago - 1 comment

#133 - 1.9.0 changes to merge into Master

Pull Request - State: closed - Opened by bdemchak 7 months ago

#132 - create_column_filter error with base_url handling

Issue - State: open - Opened by SebNik 7 months ago - 5 comments

#131 - add_image_annotation only works https

Issue - State: open - Opened by carissableker 8 months ago - 1 comment

#130 - Delay needed after layout_network in some cases

Issue - State: open - Opened by nilsoberg 10 months ago

#130 - Delay needed after layout_network in some cases

Issue - State: open - Opened by nilsoberg 10 months ago

#129 - Bump jinja2 from 3.0.3 to 3.1.3 in /doc

Pull Request - State: open - Opened by dependabot[bot] 11 months ago
Labels: dependencies

#128 - importing NNF files?

Issue - State: closed - Opened by AthinaGav 11 months ago - 2 comments

#127 - `create_network_from_data_frames` too long

Issue - State: open - Opened by cfz1998 11 months ago

#126 - Group attribute layout with certain ordering of the members?

Issue - State: open - Opened by gmhhope 11 months ago - 4 comments

#125 - Add set_node_label_position_default

Issue - State: closed - Opened by bdemchak about 1 year ago - 1 comment

#124 - Add rotation and scaling functions to layout.py

Issue - State: closed - Opened by bdemchak about 1 year ago - 1 comment

#123 - Implement rotation et al in layouts.py

Issue - State: closed - Opened by bdemchak about 1 year ago

#122 - In version check, remove "-SNAPSHOT" when comparing versions

Issue - State: closed - Opened by bdemchak about 1 year ago - 2 comments

#121 - Is it more pythonic way to provide an option to load JSON file instead of table to opt out `load_table_data`

Issue - State: closed - Opened by gmhhope about 1 year ago - 2 comments

#120 - Embed image in nodes automation by py4cytoscape

Issue - State: closed - Opened by gmhhope about 1 year ago - 14 comments

#119 - Run notebook container side-by-side with cytoscape in docker servers.

Issue - State: closed - Opened by gmhhope about 1 year ago - 18 comments

#118 - Options to automate Node layout tools

Issue - State: closed - Opened by gmhhope about 1 year ago - 4 comments

#117 - Clear the label rotation bypass

Issue - State: closed - Opened by gmhhope about 1 year ago - 1 comment

#116 - A general question, can cytoscape render markdown text format?

Issue - State: closed - Opened by gmhhope about 1 year ago - 5 comments

#115 - How to set what attribute to use for attribute-circle layout ?

Issue - State: closed - Opened by gmhhope about 1 year ago - 6 comments

#114 - style bypasses for node width and node height change current style to 'default'

Issue - State: open - Opened by carissableker over 1 year ago - 6 comments

#113 - Editing base_url leads to cyrest_get errors

Issue - State: closed - Opened by jackhart591 over 1 year ago - 3 comments

#112 - change python-igraph to igraph

Pull Request - State: closed - Opened by szhorvat over 1 year ago - 2 comments

#111 - How to set the label rotation bypass and if that can be copied to another network?

Issue - State: closed - Opened by gmhhope over 1 year ago - 13 comments

#110 - Figure export to PDF cannot fit the whole graph

Issue - State: closed - Opened by gmhhope over 1 year ago - 2 comments

#109 - How to apply the node positions back to a new graph?

Issue - State: closed - Opened by gmhhope over 1 year ago - 7 comments

#108 - Cannot handle list in `create_network_from_cytoscapejs`

Issue - State: closed - Opened by gmhhope over 1 year ago - 1 comment

#107 - List with float throws exception when sending pandas datatable

Issue - State: closed - Opened by ObT1337 over 1 year ago - 6 comments

#106 - Revert "Properly pass base_url when validating style values."

Pull Request - State: closed - Opened by bdemchak over 1 year ago

#105 - Properly pass base_url when validating style values.

Pull Request - State: closed - Opened by nilsoberg over 1 year ago

#104 - Set size of window/exported image

Issue - State: closed - Opened by nilsoberg over 1 year ago - 3 comments

#103 - Request py4cytoscape version of radial label automation from RCy3

Issue - State: closed - Opened by gmhhope over 1 year ago - 3 comments

#102 - Delay needed at end of add_to_group()

Issue - State: open - Opened by bdemchak over 1 year ago

#101 - Delay for commands_api and cyrest_api

Issue - State: open - Opened by bdemchak over 1 year ago

#100 - load_table_data changes the table

Issue - State: open - Opened by carissableker over 1 year ago - 1 comment

#99 - select_nodes fails with comma in node name

Issue - State: closed - Opened by carissableker over 1 year ago - 1 comment

#98 - get_table_columns does not get all columns

Issue - State: open - Opened by kozo2 almost 2 years ago - 9 comments

#97 - FutureWarning: in py4cytoscape\tables.py:502:

Issue - State: closed - Opened by kozo2 almost 2 years ago - 2 comments

#96 - Add selectEdgesAdjacentToNodes() per RCy3

Issue - State: closed - Opened by bdemchak about 2 years ago - 1 comment

#95 - Customize the path of the detailed log file

Issue - State: closed - Opened by agitter about 2 years ago - 6 comments

#94 - Remove n^2 loops

Issue - State: closed - Opened by bdemchak over 2 years ago - 14 comments

#93 - Bottleneck in `load_table_data`

Issue - State: closed - Opened by ConsueTerra over 2 years ago - 5 comments

#92 - Rendered image appears as a single dot for very large networks

Issue - State: open - Opened by nilsoberg over 2 years ago - 4 comments

#91 - Nodes not colored when using large network

Issue - State: open - Opened by nilsoberg over 2 years ago - 2 comments

#90 - Zoom parameter has no effect in export_image

Issue - State: closed - Opened by nilsoberg over 2 years ago - 4 comments

#89 - Take advantage of v10 CyREST export image functions and parameters

Issue - State: closed - Opened by bdemchak over 2 years ago

#88 - Connection to Cytoscape sometimes fails

Issue - State: closed - Opened by bdemchak over 2 years ago - 3 comments

#87 - .gitignore: build and dist

Pull Request - State: closed - Opened by kozo2 over 2 years ago

#86 - Allow full style definition to be fetched and created

Issue - State: closed - Opened by bdemchak over 2 years ago - 1 comment

#85 - get_edge_info throws some errors when having a large SUID list as the input

Issue - State: closed - Opened by kozo2 over 2 years ago - 1 comment

#84 - Add get_network_list()

Issue - State: closed - Opened by bdemchak over 2 years ago - 1 comment

#83 - Add delete_all_visual_styles()

Issue - State: closed - Opened by bdemchak over 2 years ago - 1 comment

#82 - Move all ipynbs in this repo to `cytoscape-automation` repo

Pull Request - State: closed - Opened by kozo2 over 2 years ago

#81 - Graphics details upon export

Issue - State: open - Opened by nilsoberg over 2 years ago - 14 comments

#80 - faster select_all_* functions

Issue - State: closed - Opened by AlexanderPico over 2 years ago - 1 comment
Labels: enhancement, RCy3 Sync

#79 - Nodes size specification error

Issue - State: closed - Opened by IlonaGA over 2 years ago - 5 comments

#78 - p4c.layout_network() ++

Issue - State: closed - Opened by eirinland almost 3 years ago - 15 comments

#77 - problem with p4c.set_node_boarder...

Issue - State: closed - Opened by eirinland almost 3 years ago - 2 comments

#76 - open_app_store function opens the Cytoscape App Store 404 web page

Issue - State: closed - Opened by yihangx almost 3 years ago - 1 comment
Labels: RCy3 Sync

#75 - Create AnnotationShape functions per RCy3

Issue - State: closed - Opened by bdemchak almost 3 years ago - 1 comment

#74 - Verify that substantial remote workflow executes simultaneously for multiple users

Issue - State: closed - Opened by bdemchak almost 3 years ago - 3 comments

#73 - Need option to allow local Jupyter to use local paths directly

Issue - State: closed - Opened by bdemchak almost 3 years ago - 1 comment

#72 - Added ability to create a network view.

Pull Request - State: closed - Opened by nilsoberg2 about 3 years ago - 13 comments

#71 - import_network_from_file fails on some XGMML

Issue - State: closed - Opened by nilsoberg2 about 3 years ago - 3 comments

#70 - import_network_from_file() fails if file name contains space followed by equal symbol

Issue - State: open - Opened by coleslaw481 about 3 years ago - 1 comment
Labels: bug

#69 - get_network_list() fails in local notebook

Issue - State: closed - Opened by kozo2 about 3 years ago - 3 comments

#68 - Update MCODE notebook

Pull Request - State: closed - Opened by kozo2 about 3 years ago

#67 - get_installed_apps() fails

Issue - State: closed - Opened by kozo2 about 3 years ago - 1 comment

#66 - Delete the part that was not merged well

Pull Request - State: closed - Opened by kozo2 about 3 years ago