Spring of Rebirth

[drew-diamantoukos]

Organization

• Renamed scripts_1_6_dev -> src.
• Removed scripts_1_5_dev, and almost every mention of 1_5_dev !
• Moved vendor files to separate vendor directory to split up.
• Renamed springViewer_1_6_dev.html -> springViewer.html

Updates

• Updated d3 to version 5 - updated all API calls accordingly to use the new methods and take advantage of the performance optimizations.
• Updated Pixi.js from 4.5.1 to 4.8.1 for similar performance boosts and optimizations used by the existing LineSprite class.

JavaScript

• Using TypeScript to transpile newer JavaScript to ES6, mainly for async/await.
• Also using TSLint... to lint JS files! It's magic.
• Addressed a good chunk of things found by the above 2 tools - things like unused variables, shadowed variable names, using const/let, using arrow functions, etc.
• Converted most script files to singleton modules, to help connect where variables are coming from. For example, accessing all_nodes just needs to go through forceLayout.all_nodes.
• As part of the https://github.com/cBioCenter/chell-viz / BioBlocks work, added the beginnings of postMessage hooks which should not get in the way if the springViewer isn't is an iframe.

Python

• Ran through python files, updating lines my IDE said needed to be updated for Python 3, primarily parenthesis for print statements.

I do apologize for the sheer mass of this PR, I'm more than willing to help walk through any and all changes/issues/thoughts/etc !