code review

[pixelzoom]

Since this sim will be published without the Real Molecules screen (see #27), we can move forward with code review.

@ariel-phet please prioritize and assign.

I'd like to make one more pass through the code. So whoever is assigned, please wait for the go-ahead from me.

[ariel-phet]

@pixelzoom I am going to have @zepumph tackle this one with support from @jessegreenberg if needed. He has now done reviews of some simpler sims like RIAW and Ohm's Law so this will be a good learning experience for him.

Marking as medium priority since @zepumph has a fair number of things going on. Since we are wanting to publish this sim, it would be good to get out by the end of the summer, so lets plan on finishing up code review by July 21. Let me know if we see any issues with that tentative timeline.

[pixelzoom]

Please mark failed items with ❌

PhET code-review checklist

Build and Run Checks

• Does the sim build without warnings or errors?
• Does the sim start up? (requirejs and built versions)
• Does the sim experience any assertion failures? (run with query parameter ea)
• Does the sim pass a scenery fuzz test? (run with query parameter fuzzMouse&ea)

Internationalization

• Are there any strings that are not being internationalized? (run with query parameter stringTest=x, you should see nothing but 'x' strings)
• Does the sim layout gracefully handle internationalized strings that are twice as long as the English strings? (run with query parameter stringTest=double)
• Does the sim layout gracefully handle internationalized strings that are exceptionally long? (run with query parameter stringTest=long)
• Does the sim layout gracefully handle internationalized strings that are shorter than the English strings? (run with query parameter stringTest=X)
• Does the sim stay on the sim page (doesn't redirect to an external page) when running with the query parameter stringTest=xss? This test passes if sim does not redirect, OK if sim crashes or fails to fully start. Only test on one desktop platform.
• Use named placeholders (e.g. "{{value}} {{units}}") instead of numbered placeholders (e.g. "{0} {1}").
• Make sure the string keys are all perfect, they are difficult to change after 1.0.0 is published. Strings keys should generally match the values, such as {binaryProbability: "Binary Probability"}. Screen names should use camelcase, like so screen.screenName. For patterns that contain placeholders (e.g. "My name is {{first}} {{last}}") choose keys that are unlikely to conflict with strings that might be needed in the future. For example, for "{{price}}"consider using key "pricePattern" instead of "price", if you think there might be a future need for a "price" string.

Repository structure

• Are all required files and directories present?
  For a sim repository named “my-repo”, the general structure should look like this (where assets/, audio/ or images/ may be omitted if the sim doesn’t have those types of assets).

   my-repo/
      assets/
      audio/
         license.json
      doc/
         model.md
         implementation-notes.md
      images/
         license.json
      js/
         (see section below)
      dependencies.json
      .gitignore
      my-repo_en.html
      my-repo-strings_en.json
      Gruntfile.js
      LICENSE
      package.json
      README.md

For a common-code repository, the structure is similar, but some of the files and directories may not be present if the repo doesn’t have audio, images, strings, or a demo application.

• Is the js/ directory properly structured?
  All JavaScript source should be in the js/ directory. There should be a subdirectory for each screen (this also applies for single-screen sims, where the subdirectory matches the repo name). For a multi-screen sim, code shared by 2 or more screens should be in a js/common/ subdirectory. Model and view code should be in model/ and view/ subdirectories for each screen and common/. For example, for a sim with screens “Introduction” and “Lab”, the general directory structure should look like this:

   my-repo/
      js/
         common/
            model/
            view/
         introduction/
            model/
            view/
         lab/
            model/
            view/
         my-repo-config.js
         my-repo-main.js
         myRepo.js

• ❌Is there a file in assets/ for every resource file in audio/ and images/? Note that there is not necessarily a 1:1 correspondence between asset and resource files; for example, several images may be in the same .ai file.
• Was the README.md generated by grunt published-README or grunt unpublished-README?
• Does package.json refer to any dependencies that are not used by the sim?
• ❌Does sim-config.js refer to any dependencies that are not used by the sim?
• Does package.json contain phetLibs for all non-default entries in sim-config.json?
• Is the LICENSE file correct? (GPL v3 for sims, MIT for common code)
• ❌Does .gitignore match the one in simula-rasa?
• Does a GitHub issue exist for tracking credits, to ensure that they are correct before publication? (The issue is credits #28.)
• Are there git repository branches that are no longer used and should be pruned?
• Does model.md adequately describe the model, in terms appropriate for teachers?
• Does implementation-notes.md adequately describe the implementation, with an overview that will be useful to future maintainers?
• Are sim-specific query parameters (if any) identified and documented in one .js file in js/common/ or js/ (if there is no common/)? The .js file should be named {{REPO}}QueryParameters.js, for example ArithmeticQueryParameters.js for the aritmetic repository.

Coding Conventions

• Is the code formatted according to PhET conventions? See phet-idea-code-style.xml for IntelliJ IDEA code style.
• Are copyright headers present and up to date? Run grunt update-copyright-dates.
• Names (types, variables, properties, functions,...) should be sufficiently descriptive and specific, and should avoid non-standard abbreviations. For example:

var numPart            // incorrect
var numberOfParticles  // correct

var width              // incorrect
var beakerWidth        // correct

• Require statements should be organized into blocks, with the code modules first, followed by strings, images and audio (any order ok for strings/images/audio). For modules, the var name should match the file name. Example below.

// modules
var inherit = require( 'PHET_CORE/inherit' );
var Rectangle = require( 'SCENERY/nodes/Rectangle' );
var Line = require( 'SCENERY/nodes/Line' );

// strings
var kineticString = require( 'string!ENERGY/energy.kinetic' );
var potentialString = require( 'string!ENERGY/energy.potential' );
var thermalString = require( 'string!ENERGY/energy.thermal' );

// images
var energyImage = require( 'image!ENERGY/energy.png' );

// audio
var kineticAudio = require( 'audio!ENERGY/energy' );

• Do the @author annotations seem correct?

• For constructors, use parameters for things that don’t have a default. Use options for things that have a default value. This improves readability at the call site, especially when the number of parameters is large. It also eliminates order dependency that is required by using parameters.

For example, this constructor uses parameters for everything. At the call site, the semantics of the arguments are difficult to determine without consulting the constructor.

/**
 * @param {Ball} ball - model element
 * @param {Property.<boolean>} visibleProperty - is the ball visible?
 * @param {Color|string} fill - fill color
 * @param {Color|string} stroke - stroke color
 * @param {number} lineWidth - width of the stroke
 * @constructor
 */
function BallNode( ball, visibleProperty, fill, stroke, lineWidth ){
   ...
}

// Call site
var ballNode = new BallNode( ball, visibleProperty, 'blue', 'black', 2 );

Here’s the same constructor with an appropriate use of options. The call site is easier to read, and the order of options is flexible.

/**
 * @param {Ball} ball - model element
 * @param {Property.<boolean>} visibleProperty - is the ball visible?
 * @param {Object} [options]
 * @constructor
 */
function BallNode( ball, visibleProperty, options ) {

  options = _.extend( {
    fill: 'white',  // {Color|string} fill color
    stroke: 'black', // {Color|string} stroke color
    lineWidth: 1 // {number} width of the stroke
  }, options ); 

  // ...
}

// Call site
var ballNode = new BallNode( ball, visibleProperty, {
  fill: 'blue', 
  stroke: 'black', 
  lineWidth: 2 
} );

• Constructor and function documentation. Parameter types and names should be clearly specified for each function and constructor (if there are any parameters) using @param annotations. The description for each parameter should follow a hyphen. Primitive types should use lower case. Constructors should additionally include the @constructor annotation. For example:

/** 
 * The PhetDeveloper is responsible for creating code for simulations
 * and documenting their code thoroughly.
 * 
 * @param {string} name - full name
 * @param {number} age - age, in years
 * @param {boolean} isEmployee - whether this developer is an employee of CU
 * @param {function} callback - called immediate after coffee is consumed
 * @param {Property.<number>} hoursProperty - cumulative hours worked
 * @param {string[]} friendNames - names of friends
 * @param {Object} [options] - optional configuration, see constructor
 * @constructor
 */
function PhetDeveloper( name, age, isEmployee, callback, hoursProperty, friendNames, options ) {}

• For most functions, the same form as above should be used, with a @return annotation which identifies the return type and the meaning of the returned value. Functions should also document any side effects. For extremely simple functions that are just a few lines of simple code, an abbreviated line-comment can be used, for example: // Computes {Number} distance based on {Foo} foo.

• If references are needed to the enclosing object, such as for a closure, self should be defined, but it should only be used in closures. The self variable should not be defined unless it is needed in a closure. Example:

var self = this;
someProperty.link( function(){
  self.doSomething();
} );
this.doSomethingElse();

• Comments should not extend beyond 120 columns. Break long comments into multiple lines to optimize readability (use your judgement).

• Where inheritance is needed, use PHET_CORE/inherit. Add prototype and static functions via the appropriate arguments to inherit. Spaces should exist between the function names unless the functions are all short and closely related. Example:

  return inherit( Object, Line, {

   /**
    * Gets the slope of the line
    * @returns {number}
    */
    getSlope: function() {
      if ( this.undefinedSlope() ) {
        return Number.NaN;
      }
      else {
        return this.rise / this.run;
      }
    },

    /**
     * Given x, solve y = m(x - x1) + y1.  Returns NaN if the solution is not unique, or there is no solution (x can't 
     * possibly be on the line.)  This occurs when we have a vertical line, with no run.
     * @param {number} x - the x coordinate
     * @returns {number} the solution
     */
    solveY: function( x ) {
      if ( this.undefinedSlope() ) {
        return Number.NaN;
      }
      else {
        return ( this.getSlope() * ( x - this.x1 ) ) + this.y1;
      }
    }
  } );

• Functions should be invoked using the dot operator rather than the bracket operator. For more details, please see Style question: bracket notation vs dot notation gravity-and-orbits#9. For example:

// avoid
self[ isFaceSmile ? 'smile' : 'frown' ]();

// OK
isFaceSmile ? self.smile() : self.frown();

// OK
if ( isFaceSmile ) {
  self.smile();
}
else {
  self.frown();
}

• It is not uncommon to use conditional shorthand and short circuiting for invocation.

( expression ) && statement;
( expression ) ? statement1 : statement2;
( foo && bar ) ? fooBar() : fooCat();
( foo && bar ) && fooBar();
( foo && !(bar && fooBar)) && nowIAmConfused();
this.fill = ( foo && bar ) ? 'red' : 'blue'; 

If the expression is only one item, the parentheses can be omitted. This is the most common use case.

assert && assert( happy, ‘Why aren\’t you happy?’ );
happy && smile();
var thoughts = happy ? ‘I am happy’ : ‘I am not happy :(’;

• Naming for Property values: All AXON/Property instances should be declared with the suffix Property. For example, if a visible property is added, it should have the name visibleProperty instead of simply visible. This will help to avoid confusion with non-Property definitions.

• Line comments should be preceded by a blank line. For example:

// Randomly choose an existing crystal to possibly bond to
var crystal = this.crystals.get( _.random( this.crystals.length - 1 ) );

// Find a good configuration to have the particles move toward
var targetConfiguration = this.getTargetConfiguration( crystal );

• Line comments should have whitespace between the // and the first letter of the line comment. See the preceding example.

• Differentiate between Property and "property" in comments. They are different things. Property is a type in AXON; property is any value associated with a JavaScript object.

• Files should be named like CapitalizedCamelCasing.js when returning a constructor, or lower-case-style.js when returning a non-constructor function. When returning a constructor, the constructor name should match the filename.

• The HTML5/CSS3/JavaScript source code must be reasonably well documented. This is difficult to specify precisely, but the idea is that someone who is moderately experienced with HTML5/CSS5/JavaScript can quickly understand the general function of the source code as well as the overall flow of the code by reading through the comments. For an example of the type of documentation that is required, please see the example-sim repository.

• Because JavaScript lacks visibility modifiers (public, protected, private), PhET uses JSdoc visibility annotations to document the intent of the programmer, and define the public API. Visibility annotations are required for anything that JavaScript makes public. Information about these annotations can be found here. (Note that other documentation systems like the Google Closure Compiler use slightly different syntax in some cases. Where there are differences, JSDoc is authoritative. For example, use Array.<Object> or Object[] instead of Array<Object>). PhET guidelines for visibility annotations are as follows:

• Use @public for anything that is intended to be part of the public API.
• Use @protected for anything that is intended for use by subtypes.
• Use @private for anything that is NOT intended to be part of the public or protected API.
• Put qualifiers in parenthesis after the annotation, for example:
• To quality that something is read-only, use @public (read-only). This indicates that the given property (AND its value) should not be changed by outside code (e.g. a Property should not have its value changed)
• To qualify that something is public to a specific repository, use (for example) @public (scenery-internal)
• Separate multiple qualifiers with commas. For example: @public (scenery-internal, read-only)

For JSDoc-style comments, the annotation should appear in context like this:

/**
 * Creates the icon for the "Energy" screen, a cartoonish bar graph.
 * @returns {Node}
 * @public
 */

For Line comments, the annotation can appear like this:

// @public Adds a {function} listener
addListener: function( listener ) { /*...*/ }

Math Libraries

• Check that dot.Util.roundSymmetric is used instead of Math.round. Math.round does not treat positive and negative numbers symmetrically, see fix nearest-neighbor rounding in Util.toFixed dot#35 (comment).
• DOT/Util.toFixed or DOT/Util.toFixedNumber should be used instead of toFixed. JavaScript's toFixed is notoriously buggy. Behavior differs depending on browser, because the spec doesn't specify whether to round or floor.
• Check that random numbers are generated using phet.joist.random, and are doing so after modules are declared (non-statically). For example, the following methods (and perhaps others) should not be used:

• Math.random
• _.shuffle
• _.sample
• _.random
• new Random()

Organization, Readability, Maintainability

• Does the organization and structure of the code make sense? Do the model and view contain types that you would expect (or guess!) by looking at the sim? Do the names of things correspond to the names that you see in the user interface?
• Are appropriate design patterns used?
• Is inheritance used where appropriate? Does the type hierarchy make sense?
• Is there any unnecessary coupling? (e.g., by passing large objects to constructors, or exposing unnecessary properties/functions)
• Is there too much unnecessary decoupling? (e.g. by passing all of the properties of an object independently instead of passing the object itself)?
• Are the source files reasonable in size? Scrutinize large files with too many responsibilities - can responsibilities be broken into smaller delegates?
• Are any significant chunks of code duplicated? This will be checked manually as well as with https://github.com/danielstjules/jsinspect or grunt find-duplicates
• Is there anything that should be generalized and migrated to common code?
• Are there any TODO or FIXME comments in the code? They should be addressed or promoted to GitHub issues.
• Does the implementation rely on any specific constant values that are likely to change in the future? Identify constants that might be changed in the future. (Use your judgement about which constants are likely candidates.) Does changing the values of these constants break the sim? For example, see allow minimum rows to go to "1" and address dependency on current minimum of "5" plinko-probability#84.
• The simulation should use Property instead of PropertySet.
• Are all dependent properties modeled as DerivedProperty instead of Property?

Performance, Usability

• Does the sim perform as desired across the range of supported platforms? (eg, not too slow on slow platforms, not too fast on fast platforms)
• If the sim uses WebGL, does it have a fallback? Does the fallback perform reasonably well? (run with query parameter webgl=false)
• Are UI components sufficiently responsive? (especially continuous UI components, such as sliders)
• Are pointer areas optimized, especially for touch? (run with query parameter showPointerAreas)
• Do pointer areas overlap? (run with query parameter showPointerAreas)

Memory Leaks

• Does a heap comparison using Chrome Developer Tools indicate a memory leak? (Describing this process is beyond the scope of this document.)
• For each common-code component (sun, scenery-phet, vegas, …) that opaquely registers observers or listeners, is there a call to that component’s dispose function, or documentation about why dispose is unnecessary?
• Are there leaks due to registering observers or listeners? These guidelines should be followed, or documentation added about why following them is not necessary:
  • AXON: Property.link is accompanied by Property.unlink.
  • AXON: PropertySet.link is accompanied by PropertySet.unlink.
  • AXON: Creation of DerivedProperty is accompanied by dispose.
  • AXON: Creation of Multilink is accompanied by dispose.
  • AXON: Events.on is accompanied by Events.off.
  • AXON: Emitter.addListener is accompanied by Emitter.removeListener.
  • SCENERY: Node.on is accompanied by Node.off
  • TANDEM: tandem.addInstance is accompanied by tandem.removeInstance.
• Do all types that require a dispose function have one? This should expose a public dispose function that calls this.disposeMyType(), where disposeMyType is a private function declared in the constructor. MyType should exactly match the filename.

PhET-iO

• If the simulation is supposed to be instrumented for PhET-iO, please see How to Instrument a PhET Simulation for PhET-iO for the PhET-iO development process.

[pixelzoom]

@zepumph This sim is ready for your review.

Memory testing is close to wrapping up in #33. All memory leaks have been in common code, so I'm confident that there will be no significant sim changes required.

Please reference this issue in any related GitHub issues that you create.

[pixelzoom]

Memory testing #33 has been completed. No changes to sim code were required.

[zepumph]

Are there any strings that are not being internationalized? (run with query parameter stringTest=x, you should see nothing but 'x' strings)

Everything except the hyperlink on the real molecules page, which I think is desirable. Correct me if I am wrong.

[pixelzoom]

@zepumph I noticed that you marked this item with as failing:

• ❌Is there a file in assets/ for every resource file in audio/ and images/? Note that there is not necessarily a 1:1 correspondence between asset and resource files; for example, several images may be in the same .ai file.

This sim has 2 images and (for both of them) images/license.json indicates:

"notes": "created using a screenshot from Real Molecules screen"

So there is no assets/ directory because there are no images that were produced from a .ai file. The checklist should probably be modified to be a little clearer on this point.

[zepumph]

I've never seen that pattern before (using the screenshot as the source of an image file), but that sounds good to me. Would you mind updating the checklist?

[pixelzoom]

@zepumph Some things that I neglected to mention, but which you may have already figured out...

We decided to publish this sim without completing the "Real Molecules" screen, see #27. The implementation of that screen is complete, with the exception of the 3D molecule viewer. And I recommend reviewing the code for that screen. To see that screen in it's partially-completed state, run with ?realMolecules.

You can ignore JSmolViewerNode.js. As indicated in the TODO comment, we're keeping it around until the 3D molecule viewer has been implemented.

Sorry for not mentioning this in an earlier comment.

[zepumph]

I just finished going through the first screen completely. As expected, things are going smoothly. There isn't much to change, more for me to ask about and learn from. Thanks for bearing with me @pixelzoom. @ariel-phet I'm not sure if I will be done by the end of the week, but that is the goal, and I'll keep you posted as we get closer.

[ariel-phet]

@zepumph that was a target, but it is OK if it takes longer. And yes, a big point of this code review was we figured the sim was likely in pretty good shape and it would mostly be a learning experience for you and a chance to ask questions/dig deeper.

[pixelzoom]

@zepumph said:

There isn't much to change, more for me to ask about and learn from.

Au contraire, you've suggested some good changes. This sim was feature complete in March 2014, and there's been much progress since then, so there was definitely room for improvement here and there.

[zepumph]

I see 9 TODOs in the code. They are all related to #15 and #32, to me this seems fine to keep until the 3d viewer is implemented. I just wanted to note why we are keeping these.

[pixelzoom]

@zepumph said:

I see 9 TODOs in the code. ...

Thanks for the summary. I changed a couple of these to point to #32 rather than #15, since they deal with completing the Real Molecules screen vs implementing the 3D viewer. See above commit.

[zepumph]

The UnderDevelopmentPlane.js is a bit messy. I don't think it is a big deal because it is "temporary" (what ever that means by phet sim development standards). It could use some variable names and less nesting. @pixelzoom it's your call if you think that is worth your time for such a temporary and simple Node.

[zepumph]

Code review completed @pixelzoom, thanks for all the good work and help you gave me during the process. Back to you.

[pixelzoom]

Thanks for the thorough review @zepumph. All related issues are closed, so closing this issue.

[zepumph]

Thank you!