cytoscape-scripts

News

• 30/04/2021 Reorganized Notebook location and improved documentation.
• 1/30/2019 Updated with Jupyter Notebook walkthrough
• 11/15/2016 Updated for Cytoscape 3.5.0 release.
• 10/10/2014 Version 1.3.0 - Updated for Cytoscape 3.2.0 release.
• 9/11/2013 Version 1.2.0 - This version supports read-only repository for non-core developers.

Introduction

This repository contains scripts and instructions for managing the Cytoscape Release process, system requirements checking, and other core Cytoscape organization tools.

Primary build scripts

These are the primary scripts used for building installable versions of Cytoscape. These, or their eventual replacements, should always be able to produce a Cytoscape build and the accompanying Install4j installers.

• release-generator/build-nightly-release.sh

  • A fully automated build that can be run via a cron job. This build generates installers and puts them in a www accessible directory. This script DOES NOT sign the Mac installer, as nightly builds are not intended for public consumption.

• release-generator/jupyter-notebooks/Cytoscape SNAPSHOT Release Builder.ipynb

  • A step by step Jupyter notebook that generates a release from the develop branch. This script generates installers and puts them in a www accessible directory. This script signs Mac installers and is a public consumable SNAPSHOT.

Older build scripts

These build scripts are kept as reference and as potentially useful components for enhancing the current build.

• /release-generator/jupyter-notebooks/previous-releases/*

  • Archived Jupyter notebooks from previous public releases. These notebooks contain records of the build process and are useful in generating new public releases. A full public release can be generated by copying these scripts and replacing the appropriate parameters (STARTING_BRANCH, OLD_VERSION, NEW_VERSION ... ).

• /release-generator

  • Old scripts to generate new Cytoscape release. As the build process for Cytoscape changes due to updates in Maven, Install4j and Mac signing, these may have drifted, but can still contain useful functionality.

System checker script

• /system-checker
  • These are OS specific scripts intended for Cytoscape users to run to evaluate if their system can run Cytoscape. These script files are linked to from cytoscape.org help pages, and should not be moved or renamed without changing the relevant pages in cytoscape.org.

Information below is outdated and refers to the older build scripts.

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Scripts for Developers

cy

Git Repository management utility command for Cytoscape developers

Documentation is available here.

Scripts for Managers

release.sh

(Under construction... Not fully automated.)

deploy_installers.sh

This is a script to build, sign DMG, and upload the installers to specified location.

To run this script, you need:

• a Mac with certificate to sign Mac disk image (DMG).
• Entire Cytoscape repository cloned by cy script (cy init)
• SSH key to access the target server without password

How to Run

1. cd CYTOSCAPE_TOP_DIR
2. mkdir .cy3
3. cd .cy3
4. Copy the script to this directory.
5. Edit the script: USER_NAME should be your account
6. Run ./deplstallers.sh -au BRANCH_NAME where BRANCH_NAME is the name of branch you want to deploy.
7. Once it's done, it opens the browser and displays the uploaded files.