Release Log¶
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