cytoscape-cola/README.md

The Cola.js physics simulation layout for Cytoscape.js

cytoscape-cola
================================================================================

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## Description

The Cola.js physics simulation layout for Cytoscape.js ([demo](https://cytoscape.github.io/cytoscape.js-cola), [non-animated demo](https://cytoscape.github.io/cytoscape.js-cola/demo-non-animated.html), [compound demo](https://cytoscape.github.io/cytoscape.js-cola/demo-compound.html), [constraint demo](https://cytoscape.github.io/cytoscape.js-cola/demo-constraints.html))


The `cola` layout uses a [force-directed](http://en.wikipedia.org/wiki/Force-directed_graph_drawing) physics simulation with several sophisticated constraints, written by [Tim Dwyer](http://www.csse.monash.edu.au/~tdwyer/).  For more information about Cola and its parameters, refer to [its documentation](http://marvl.infotech.monash.edu/webcola/).

It supports noncompound and compound graphs well.

## Dependencies

* Cytoscape.js ^3.2.0
* Cola.js ^3.1.2


## Usage instructions

Download the library:
 * via npm: `npm install cytoscape-cola`,
 * via bower: `bower install cytoscape-cola`, or
 * via direct download in the repository (probably from a tag).

Import the library as appropriate for your project:

ES import:

```js
import cytoscape from 'cytoscape';
import cola from 'cytoscape-cola';

cytoscape.use( cola );
```

CommonJS require:

```js
let cytoscape = require('cytoscape');
let cola = require('cytoscape-cola');

cytoscape.use( cola ); // register extension
```

AMD:

```js
require(['cytoscape', 'cytoscape-cola'], function( cytoscape, cola ){
  cola( cytoscape ); // register extension
});
```

Plain HTML/JS has the extension registered for you automatically, because no `require()` is needed.



## API

Call the layout, e.g. `cy.layout({ name: 'cola', ... })`, with options:

```js
// default layout options
var defaults = {
  animate: true, // whether to show the layout as it's running
  refresh: 1, // number of ticks per frame; higher is faster but more jerky
  maxSimulationTime: 4000, // max length in ms to run the layout
  ungrabifyWhileSimulating: false, // so you can't drag nodes during layout
  fit: true, // on every layout reposition of nodes, fit the viewport
  padding: 30, // padding around the simulation
  boundingBox: undefined, // constrain layout bounds; { x1, y1, x2, y2 } or { x1, y1, w, h }
  nodeDimensionsIncludeLabels: false, // whether labels should be included in determining the space used by a node

  // layout event callbacks
  ready: function(){}, // on layoutready
  stop: function(){}, // on layoutstop

  // positioning options
  randomize: false, // use random node positions at beginning of layout
  avoidOverlap: true, // if true, prevents overlap of node bounding boxes
  handleDisconnected: true, // if true, avoids disconnected components from overlapping
  convergenceThreshold: 0.01, // when the alpha value (system energy) falls below this value, the layout stops
  nodeSpacing: function( node ){ return 10; }, // extra spacing around nodes
  flow: undefined, // use DAG/tree flow layout if specified, e.g. { axis: 'y', minSeparation: 30 }
  alignment: undefined, // relative alignment constraints on nodes, e.g. {vertical: [[{node: node1, offset: 0}, {node: node2, offset: 5}]], horizontal: [[{node: node3}, {node: node4}], [{node: node5}, {node: node6}]]}
  gapInequalities: undefined, // list of inequality constraints for the gap between the nodes, e.g. [{"axis":"y", "left":node1, "right":node2, "gap":25}]
  centerGraph: true, // adjusts the node positions initially to center the graph (pass false if you want to start the layout from the current position)

  // different methods of specifying edge length
  // each can be a constant numerical value or a function like `function( edge ){ return 2; }`
  edgeLength: undefined, // sets edge length directly in simulation
  edgeSymDiffLength: undefined, // symmetric diff edge length in simulation
  edgeJaccardLength: undefined, // jaccard edge length in simulation

  // iterations of cola algorithm; uses default values on undefined
  unconstrIter: undefined, // unconstrained initial layout iterations
  userConstIter: undefined, // initial layout iterations with user-specified constraints
  allConstIter: undefined, // initial layout iterations with all constraints including non-overlap
};
```


## Notes

- The `alignment` option isn't as flexible as the raw Cola option.  Here, only integers can be used to specify relative positioning, so it's a bit limited.  If you'd like to see a more sophisticated implementation, please send a pull request.



## Build targets

* `npm run test` : Run Mocha tests in `./test`
* `npm run build` : Build `./src/**` into `cytoscape-cola.js`
* `npm run watch` : Automatically build on changes with live reloading (N.b. you must already have an HTTP server running)
* `npm run dev` : Automatically build on changes with live reloading with webpack dev server
* `npm run lint` : Run eslint on the source

N.b. all builds use babel, so modern ES features can be used in the `src`.


## Publishing instructions

This project is set up to automatically be published to npm and bower.  To publish:

1. Build the extension : `npm run build:release`
1. Commit the build : `git commit -am "Build for release"`
1. Bump the version number and tag: `npm version major|minor|patch`
1. Push to origin: `git push && git push --tags`
1. Publish to npm: `npm publish .`
1. If publishing to bower for the first time, you'll need to run `bower register cytoscape-cola https://github.com/cytoscape/cytoscape.js-cola.git`
1. [Make a new release](https://github.com/cytoscape/cytoscape.js-cola/releases/new) for Zenodo.