Release Log

py4cytoscape 1.11.0

Release date: 29 Sep 2024

We’re happy to announce the release of py4cytoscape 1.11.0!

py4cytoscape is a Python package that communicates with Cytoscape via its REST API, providing access to a set over 250 functions that enable control of Cytoscape from within standalone and Notebook Python programming environments. It provides nearly identical functionality to RCy3, an R package in Bioconductor available to R programmers.

The themes for this release are:

  • Minor bug fixes

Release notes

  • Fixed py4cytoscape_utils node_name_to_node_suid() to allow nodes named by integers instead of alphanumerics

API Changes

Added:

None

Deprecations

None

Contributors to this release

  • Barry Demchak

  • Harsh Sharma

Pull requests merged in this release

  • #143 by Harsh Sharma

Issues closed in this release

  • #142 by Barry Demchak

py4cytoscape 1.10.0

Release date: 24 Sep 2024

We’re happy to announce the release of py4cytoscape 1.10.0!

py4cytoscape is a Python package that communicates with Cytoscape via its REST API, providing access to a set over 250 functions that enable control of Cytoscape from within standalone and Notebook Python programming environments. It provides nearly identical functionality to RCy3, an R package in Bioconductor available to R programmers.

The themes for this release are:

  • Add missing parameters to enable non-default base_url

  • Add documentation & checks for large commands

  • Speed improvement on many functions that convert node or edge names to SUIDs

Release notes

  • Added base_url parameter propagation in filters, networks and tables functions

  • Add documentation & check for outsize commands_run and commands_get requests

  • Speed improvement on functions that convert node or edge names to SUIDs

    Edges:

    edge_name_to_edge_suid

    convert_edge_name_to_edge_info

    create_network_from_data_frames

    clear_edge_property_bypass

    set_edge_property_bypass

    get_edge_property

    get_table_value

    Nodes:

    node_name_to_name_suid

    add_cy_edges

    get_first_neighbors

    clear_node_property_bypass

    set_node_property_bypass

    get_node_property

    get_table_value

API Changes

Added:

None

Deprecations

None

Contributors to this release

  • Barry Demchak

  • Harsh Sharma

Pull requests merged in this release

  • #139 by Harsh Sharma

  • #140 by Barry Demchak

  • #141 by Harsh Sharma

Issues closed in this release

  • #137 by Harsh Sharma

  • #135 by Minghao Gong

  • #127 by Athina Gavriilidou

  • #94 by Harsh Sharma

py4cytoscape 1.9.0

Release date: 26 Dec 2023

We’re happy to announce the release of py4cytoscape 1.9.0!

py4cytoscape is a Python package that communicates with Cytoscape via its REST API, providing access to a set over 250 functions that enable control of Cytoscape from within standalone and Notebook Python programming environments. It provides nearly identical functionality to RCy3, an R package in Bioconductor available to R programmers.

The themes for this release are:

  • General bug fixes

  • New Style functions for node label position and node position

  • Improved Cytoscape version check

  • Added scale and rotate functions

Release notes

  • Removed value validation warning from set_visual_property_default()

  • Fixed missing URL parameter in create_network_from_data_frames() and create_network_from_networkx()

  • Added style functions for node_position and node_label_position

  • Allowed Cytoscape version check to include patch level (e.g., x.y.patch)

  • Added layout functions scale_layout() and rotate_layout() to match Cytoscape’s Layout Tools

API Changes

Added:

set_node_position_bypass(node_names, new_x_locations=None, new_y_locations=None, network=None, base_url=DEFAULT_BASE_URL)

set_node_label_position_bypass(node_names, new_positions, network=None, base_url=DEFAULT_BASE_URL)

get_node_label_position_default(style_name=None, base_url=DEFAULT_BASE_URL)

set_node_label_position_default(new_node_anchor, new_graphic_anchor, new_justification, new_xoffset, new_yoffset, style_name=None, base_url=DEFAULT_BASE_URL)

get_node_label_position(node_names=None, network=None, base_url=DEFAULT_BASE_URL)

scale_layout(axis, scale_factor, network=None, selected_only=False, base_url=DEFAULT_BASE_URL)

rotate_layout(angle, network=None, selected_only=False, base_url=DEFAULT_BASE_URL)

Deprecations

Contributors to this release

  • Barry Demchak

  • Yihang Xin

Pull requests merged in this release

Issues closed in this release

  • #125 by Barry Demchak

  • #124 by Barry Demchak

  • #123 by Barry Demchak

  • #122 by Barry Demchak

  • #121 by Minghao Gong

  • #119 by Minghao Gong

  • #118 by Minghao Gong

  • #117 by Minghao Gong

  • #116 by Minghao Gong

  • #115 by Minghao Gong

  • #113 by Jack Hart

  • #111 by Minghao Gong

  • #110 by Minghao Gong

  • #109 by Minghao Gong

  • #108 by Minghao Gong

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

Announcement: py4cytoscape 1.8.0

We’re happy to announce the release of py4cytoscape 1.8.0!

py4cytoscape is a Python package that communicates with Cytoscape via its REST API, providing access to a set over 250 functions that enable control of Cytoscape from within standalone and Notebook Python programming environments. It provides nearly identical functionality to RCy3, an R package in Bioconductor available to R programmers.

Highlights

The themes for this release are:

  • Bug fixes in tables.py and style_defaults.py

  • Update python-igraph name to igraph

  • Cleaned up warnings when setting style bypass properties

API Changes

Deprecations

Contributors to this release

  • Barry Demchak

  • Nils Oberg

Pull requests merged in this release

  • #112 by Szabolcs Horvat

Issues closed in this release

  • #105 by Nils Oberg

  • #107 by ObT1337

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

Announcement: py4cytoscape 1.7.0

We’re happy to announce the release of py4cytoscape 1.7.0!

py4cytoscape is a Python package that communicates with Cytoscape via its REST API, providing access to a set over 250 functions that enable control of Cytoscape from within standalone and Notebook Python programming environments. It provides nearly identical functionality to RCy3, an R package in Bioconductor available to R programmers.

Highlights

The themes for this release are:

  • Minor fixes and documentation updates

API Changes

Deprecations

Contributors to this release

  • Barry Demchak

Pull requests merged in this release

Issues closed in this release

  • #99 by Carissa Bleker

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

Announcement: py4cytoscape 1.6.0

We’re happy to announce the release of py4cytoscape 1.6.0!

py4cytoscape is a Python package that communicates with Cytoscape via its REST API, providing access to a set over 250 functions that enable control of Cytoscape from within standalone and Notebook Python programming environments. It provides nearly identical functionality to RCy3, an R package in Bioconductor available to R programmers.

Highlights

The themes for this release are:

  • Bug fixes and API additions to support Novartis’ Metascape

  • Enable use of color names wherever hex colors are allowed

  • Support updated Python and Pandas libraries (for comparisons)

  • Added environment variables for easier runtime configuration

  • Better syntax checking for visual style properties and values

  • Upgraded to support Cytoscape 3.10

API Changes

  • 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 parameters in export_image() to support Cytoscape 3.10 export functions

  • Added set_catchup_network_merge_secs() and PY4CYTOSCAPE_CATCHUP_NETWORK_MERGE_SECS environment variable to control post-merge delay

  • Added select_edges_adjacent_to_nodes()

Deprecations

  • export_image() parameters (resolution=, units=, height=, width=) when calling Cytoscape 3.10 or later

Contributors to this release

  • Barry Demchak

  • Alex Pico

  • Kozo Nishida

  • Yingyao Zhou

  • Yihang Xin

Pull requests merged in this release

  • #87 by Kozo Nashida

Issues closed in this release

  • #83 by Barry Demchak

  • #84 by Barry Demchak

  • #86 by Barry Demchak

  • #87 by Yihang Xin

  • #96 by Barry Demchak

  • #97 by Kozo Nashida

py4cytoscape 1.5.0

Release date: 28 Jun 2022

  • Removed dependence on Enum package due to build errors

Release notes

Announcement: py4cytoscape 1.5.0

We’re happy to announce the release of py4cytoscape 1.5.0!

py4cytoscape is a Python package that communicates with Cytoscape via its REST API, providing access to a set over 250 functions that enable control of Cytoscape from within standalone and Notebook Python programming environments. It provides nearly identical functionality to RCy3, an R package in Bioconductor available to R programmers.

Highlights

The themes for this release are:

  • Removed dependence on Enum package due to build errors

API Changes

None

Deprecations

None

Contributors to this release

  • Barry Demchak

Pull requests merged in this release

Issues closed in this release

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

Announcement: py4cytoscape 1.4.0

We’re happy to announce the release of py4cytoscape 1.4.0!

py4cytoscape is a Python package that communicates with Cytoscape via its REST API, providing access to a set over 250 functions that enable control of Cytoscape from within standalone and Notebook Python programming environments. It provides nearly identical functionality to RCy3, an R package in Bioconductor available to R programmers.

Highlights

The themes for this release are:

  • 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

API Changes

  • 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

Deprecations

None

Contributors to this release

  • Barry Demchak

  • Alex Pico

  • Kozo Nishida

  • Yingyao Zhou

  • Yihang Xin

Pull requests merged in this release

  • #87 by Kozo Nashida

Issues closed in this release

  • #83 by Barry Demchak

  • #84 by Barry Demchak

  • #86 by Barry Demchak

  • #87 by Yihang Xin

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

Announcement: py4cytoscape 1.3.0

We’re happy to announce the release of py4cytoscape 1.3.0!

py4cytoscape is a Python package that communicates with Cytoscape via its REST API, providing access to a set over 250 functions that enable control of Cytoscape from within standalone and Notebook Python programming environments. It provides nearly identical functionality to RCy3, an R package in Bioconductor available to R programmers.

Highlights

The themes for this release are:

  • Improved cloud file download

  • Improved support for local Jupyter Notebook execution

  • Demonstration of enrichment functionality

  • Rationalized tutorials

API Changes

  • Added import_file_from_url() function

Deprecations

None

Contributors to this release

  • Barry Demchak

  • Alex Pico

  • Kozo Nishida

Pull requests merged in this release

  • #82 by Kozo Nashida

Issues closed in this release

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

Announcement: py4cytoscape 1.2.0

We’re happy to announce the release of py4cytoscape 1.2.0!

py4cytoscape is a Python package that communicates with Cytoscape via its REST API, providing access to a set over 250 functions that enable control of Cytoscape from within standalone and Notebook Python programming environments. It provides nearly identical functionality to RCy3, an R package in Bioconductor available to R programmers.

Highlights

The themes for this release are:

  • Addition of annotation functions (per new Cytoscape features)

  • Changed default for sandboxing when running Notebook on local Workstation

  • Add new functions: create_view, select_all

  • Sped up select_all_nodes, select_all_edges

API Changes

  • Added annotation functions

  • Added create_view in network_views

  • Added select_all in network_selection

  • Changed get_network_view_suid to return None instead of exception when network has no view

  • Changed get_network_views to return [] instead of exception when network has no view

Deprecations

None

Contributors to this release

  • Barry Demchak

  • Yihang Xin

  • Alex Pico

  • Kozo Nishida

  • Nilsoberg2

Pull requests merged in this release

  • #72 by Nilsoberg2

Issues closed in this release

  • #40 by kyxhik

  • #54 by pkzerel

  • #67 by Kozo Nishida

  • #71 by Nilsoberg2

  • #73 by Barry Demchak

  • #75 by Barry Demchak

  • #76 by Yihang Xin

  • #77 by Eirinland

  • #80 by Alex Pico

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

Announcement: py4cytoscape 0.0.11

We’re happy to announce the release of py4cytoscape 0.0.11!

py4cytoscape is a Python package that communicates with Cytoscape via its REST API, providing access to a set over 250 functions that enable control of Cytoscape from within standalone and Notebook Python programming environments. It provides nearly identical functionality to RCy3, an R package in Bioconductor available to R programmers.

Highlights

The themes for this release are:

  • Improved documentation and tutorials

  • Improved Automatic value generators support for style mapping (consistent with RCy3)

  • Improved support for Notebook initialization and image display

Many of these themes support the definition and execution of the GangSu workflows.

API Changes

  • Added reverse= parameter for Value Generators

  • Automatically reverse color sequence for divergent palettes

  • Added notebook_show_image(), notebook_export_show_image() functions for Notebook execution

Deprecations

None

Contributors to this release

  • Barry Demchak

  • Yihang Xin

  • Alex Pico

  • Kozo Nishida

Pull requests merged in this release

  • #51 by Kozo Nishida

  • #53 by Kozo Nishida

  • #55 by Kozo Nishida

  • #58 by Kozo Nishida

  • #59 by Kozo Nishida

  • #60 by Kozo Nishida

  • #61 by Kozo Nishida

  • #63 by Kozo Nishida

  • #64 by Kozo Nishida

  • #65 by Kozo Nishida

  • #66 by Kozo Nishida

  • #68 by Kozo Nishida

Issues closed in this release

  • #52 by StefanR-github

  • #56 by Kozo Nishida

  • #57 by Rafael Diaz

  • #62 by Alex Pico

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

Announcement: py4cytoscape 0.0.9

We’re happy to announce the release of py4cytoscape 0.0.9!

py4cytoscape is a Python package that communicates with Cytoscape via its REST API, providing access to a set over 250 functions that enable control of Cytoscape from within standalone and Notebook Python programming environments. It provides nearly identical functionality to RCy3, an R package in Bioconductor available to R programmers.

Highlights

The themes for this release are:

  • Improved documentation and tutorials

  • Improved iGraph support (consistent with RCy3)

  • Allow edge direction to be ignored when deleting duplicate edges

  • Automatic value generators (including Brewer colors) for style mappings

Many of these themes support the definition and execution of the GangSu workflows.

API Changes

  • Added style_auto_mappers.py module to support automatic value generators

  • Added ignore_direction=False parameter for delete_duplicate_edges

  • Added unique_list=True to node/edge_name_to_suid utility functions

  • Added Value Generators section in Concepts documentation

  • Added iGraph support for Graph, DiGraph, MultiGraph, MultiDiGraph in create_network_from_networkx

Deprecations

None

Contributors to this release

  • Barry Demchak

  • Yihang Xin

  • Alex Pico

  • Kozo Nishida

Pull requests merged in this release

  • #46 by Kozo Nishida

  • #47 by Kozo Nishida

  • #48 by Kozo Nishida

  • #50 by Kozo Nishida

  • #51 by Kozo Nishida

Issues closed in this release

  • #41 by Alex Pico

  • #43 by Barry Demchak

  • #45 by Kozo Nishida

  • #49 by Jiafi

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

Announcement: py4cytoscape 0.0.8

We’re happy to announce the release of py4cytoscape 0.0.8!

py4cytoscape is a Python package that communicates with Cytoscape via its REST API, providing access to a set over 250 functions that enable control of Cytoscape from within standalone and Notebook Python programming environments. It provides nearly identical functionality to RCy3, an R package in Bioconductor available to R programmers.

Highlights

The themes for this release are:

  • Enable access to NDEx subdomains

  • Support Cytoscape v3.9 separation of filter definition from execution

  • Enable export functions to avoid popping a confirmation dialog

  • Enable cloud files to be downloaded directly to Sandbox

  • Fixes that allow commands_help to work

Many of these themes support the definition and execution of the GangSu workflows.

API Changes

  • 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

Deprecations

None

Contributors to this release

  • Barry Demchak

  • Yihang Xin

  • Alex Pico

Pull requests merged in this release

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

Announcement: py4cytoscape 0.0.7

We’re happy to announce the release of py4cytoscape 0.0.7!

py4cytoscape is a Python package that communicates with Cytoscape via its REST API, providing access to a set over 250 functions that enable control of Cytoscape from within standalone and Notebook Python programming environments. It provides nearly identical functionality to RCy3, an R package in Bioconductor available to R programmers.

Highlights

The themes for this release are:

  • Compatibility of node, edge and group parameter with RCy3 formats

  • Improved verify_supported_versions parsing for Cytoscape 3.10 and beyond

API Changes

None

Deprecations

None

Contributors to this release

  • Barry Demchak

  • Jorge Boucas

  • Kozo Nishida

Pull requests merged in this release

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

Announcement: py4cytoscape 0.0.6

We’re happy to announce the release of py4cytoscape 0.0.6!

py4cytoscape is a Python package that communicates with Cytoscape via its REST API, providing access to a set over 250 functions that enable control of Cytoscape from within standalone and Notebook Python programming environments. It provides nearly identical functionality to RCy3, an R package in Bioconductor available to R programmers.

Highlights

The themes for this release are:

  • Improved sandboxing and Jupyter Notebook documentation

  • Shortened execution delays

  • Docker support

  • More rational default directory for standalone Python execution

API Changes

None

Deprecations

None

Contributors to this release

  • Barry Demchak

  • Jorge Boucas

  • Kozo Nishida

Pull requests merged in this release

  • #17 Jorge Boucas

  • #18 Jorge Boucas

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

Announcement: py4cytoscape 0.0.5

We’re happy to announce the release of py4cytoscape 0.0.5!

py4cytoscape is a Python package that communicates with Cytoscape via its REST API, providing access to a set over 250 functions that enable control of Cytoscape from within standalone and Notebook Python programming environments. It provides nearly identical functionality to RCy3, an R package in Bioconductor available to R programmers.

Highlights

The themes for this release are:

  • Improved sandboxing documentation

  • Updated test for Colab shell to track Colab internal evolution

API Changes

None

Deprecations

None

Contributors to this release

  • Barry Demchak

Pull requests merged in this release

None

py4cytoscape 0.0.4

Release date: 05 Oct 2020

  • Corrected a build problem that stopped 0.0.3 from initializing

Release notes

Announcement: py4cytoscape 0.0.4

We’re happy to announce the release of py4cytoscape 0.0.4!

py4cytoscape is a Python package that communicates with Cytoscape via its REST API, providing access to a set over 250 functions that enable control of Cytoscape from within standalone and Notebook Python programming environments. It provides nearly identical functionality to RCy3, an R package in Bioconductor available to R programmers.

Highlights

The themes for this release are:

  • Correct a build problem that left 0.0.3 unable to initialize

API Changes

None

Deprecations

None

Contributors to this release

  • Barry Demchak

Pull requests merged in this release

None

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

Announcement: py4cytoscape 0.0.3

We’re happy to announce the release of py4cytoscape 0.0.3!

py4cytoscape is a Python package that communicates with Cytoscape via its REST API, providing access to a set over 250 functions that enable control of Cytoscape from within standalone and Notebook Python programming environments. It provides nearly identical functionality to RCy3, an R package in Bioconductor available to R programmers.

Highlights

The themes for this release are:

  • Add support for remote Notebook execution (via Jupyter-Bridge)

  • Sync with changes made to RCy3 since Jan 1, 2020

Remote Notebook execution involves a round trip between the Python kernel running on a remote server and Cytoscape running on a private workstation. The main component is Jupyter-Bridge, which routes py4cytoscape requests through the user’s browser and on to Cytoscape, and then returns the result in the reverse direction. Requests and responses are routed through the Jupyter-Bridge server, which is an independent entity on the web.

For most Cytoscape operations, it’s necessary to transfer files from the Notebook server so that Cytoscape can load them, or to transfer files created by Cytoscape to the Notebook server so Python can analyze them. Sandboxing was implemented to enable these transfers, and to enable portability of workflows across different Cytoscape workstations.

Finally, py4cytoscape functions and definitions were sync’d with RCy3 changes since 1/1/20, and a reference interface spec was created independent of py4cytoscape and RCy3: Conform to Cytoscape Automation API Definition.

API Changes

  • Add tools.merge_networks() and tools.analyze_network()

  • Add sandbox.* functions

  • Added a number of maintenance functions in commands and py4cytoscape_sandbox modules

Deprecations

None

Contributors to this release

  • Barry Demchak

  • Alex Pico

  • Kozo Nashida

  • Chris Churas

  • Yasir Demirtaş

Pull requests merged in this release

None

py4cytoscape 0.0.1

Release date: 21 Aug 2020

Initial release, matches API signatures for RCy3

Release notes

Announcement: py4cytoscape 0.0.1

We’re happy to announce the release of py4cytoscape 0.0.1!

py4cytoscape is a Python package that communicates with Cytoscape via its REST API, providing access to a set over 250 functions that enable control of Cytoscape from within standalone and Notebook Python programming environments. It provides nearly identical functionality to RCy3, an R package in Bioconductor available to R programmers.

Highlights

The themes for this release are:

  • Reproduce RCy3 functions

  • Create a testing system for all functions

  • Create the py4cytoscape user documentation

API Changes

None

Deprecations

None

Contributors to this release

  • Barry Demchak

  • Alex Pico

  • Kozo Nashida

  • Jorge Bouças

  • Stevan Georg

  • Chris Churas

Pull requests merged in this release

  • Set dependencies #10

  • Fixed broken link to the tutorials page on readthedocs #9

  • In the Verify Cytoscape connection code fragment made file path platform agnostic #8

  • Add how to try tutorial without installation (by using Binder) #6

  • Add a tutorial ipynb file to the Sphinx source #5

  • Move python-igraph from extras_require to install_requires #4

  • Rename the package name #3

  • Add How to install and use #2