Again, successfully execute all tests by using the tests/runalltests.bat file, Gang Su workflows and the Sanity Test.be sure you updated the version number in build.bat first Execute GangSu workflows (e.g., Workflow1 and Workflow2) on Google Colab.Execute liveness test (e.g., Sanity Test) on Google Colab.Successfully execute all tests by using the tests/runalltests.bat file.Check all sources (including documents and tests) into Github, merge them into the Master branch, and make Master the current branch.Verify that the requirements.txt file in the docs directory correctly identifies all external dependencies.rst file in the References section of the document. If any functions were added, be sure to add them to the appropriate.If any API changes were made, be sure to update the Automation API Definition and change the Automation API version in py4cytoscape/_version.py.Update the version number in both py4cytoscape/_version.py and build.bat.Update the theme list in doc/release_log.rst and reference the release file you just created.Create a new release file in doc/release to match the version number (e.g., release_0.0.1.rst).Py4cytoscape logging is based on the Python logging package, which is based on the Java logging framework.įor an explanation of log configuration and use, see the LOGGING.rst file. You can try py4cytoscape with a web browser only, without installing anything in your local environment. How to run a simple workflowįor a quick tutorial on how to build a workflow in Python and using py4cytoscape, see. How to install and testįor an explanation of py4cytoscape installation and testing, see the INSTALL.rst file. To understand the API structure and see calling examples, see the py4cytoscape documentation. Pay close attention to columns E and F, which show how much of RC圓 is reflected in py4cytoscape. The API is versioned, and you can see which API version RC圓 or py4cytoscape implements by executing the cytoscape_version_info() or cytoscapeVersionInfo() function.Īn overall scorecard comparing Py2Cytoscape, RC圓 and py4cytoscape can be found here. The official Automation API definition met by both RC圓 and py4cytoscape is here. Once that occurs, novel Py2Cytoscape functions will be added to both as appropriate. Over time, py4cytoscape functionality should match RC圓 functionality. This project uses P圜harm because of its excellent code management and debugging features. The previous Cytoscape Python interface ( Py2Cytoscape) has different features than the Cytoscape R library, and is therefore deprecated.Īdditionally, this project attempts to maintain the same function signatures, return values, function implementation and module structure as the RC圓, thereby enabling smooth maintenance and evolution of both RC圓 and py4cytoscape. The idea is to allow a Cytoscape workflow to be written in one language (R or Python) and translated to another language (Python or R) without having to learn different Cytoscape interfaces. This project recreates the R-based RC圓 Cytoscape Automation library as a Python package.
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