Release Log¶
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¶
This 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¶
This 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¶
This 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¶
This 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¶
This 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¶
This 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¶
This 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¶
This 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¶
This 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