add string metadata to build.py

add scaling for non-numeric only

recolor non-numeric values

address comments

break out plottables and add tests

add vertical colorbar

fix slickgrid height issue

cleaner resize for svg

single pass numeric check

update tests

hide non-numeric color set if none exist

fix scale issues

fix slickgrid canvas size

fix load issue

fix resize issue

change percent height

add teste for fromJSON

change deepEqual to equal

add end tag for linearGradient

fixed bixel size resize

resize body manually before super call

address comments

replace removed line break

add splashscreen

update test string

remove extra css

Use alt text to show missing resources message. Fixes biocore#424

fix test string

only render orbitcontrol on change

re-render on resize

render only on decView changes as well

add clarifying comment. Fixes biocore#164

condense checks to sceneplotview3d

address comments

set re-render needed on per sceneview basis

render on per-scene basis

add tests for setting needsUpdate and checking needsUpdate

address comments

initial info visualization

remove logging. Fixes biocore#327

clean up

remove extra var instantiation

use on function

clean up code

make offset work for notebooks

remove fadein

make duration variable

automatic gjslint

BUG: Add missing _ dependency

Noticed this while trying to load a gist, it seems like "most times"
browsers load underscore.js.

MAINT: Remove emperor.js

It's been a good run! 💔

remove ui.js and tests for it

BLD/TST: Fix problems with miniconda in travis

update jquery, bootstrap, and add link to jsdocs

clean up menu a bit

install jsdoc in travis

update animate.js

add missing property docs

update docs for view-controller.js

pass gjslint tests

address comments

start on docs updates

finish update for gjslint

remove module declaration

add missing *

for update purposes

formatting

install and build jsdocs in travis

update settings for linting and doc creation

Fix @ElDeveloper's comments

change reference path to jsdoc config file

update docstrings and gjslint for util

fix gjslint issue

update contributing and readme for javascript info

add text about custom JSDoc tags for linter

formatting

add links to the linters

update sceneplotview3d for jsdoc and gjslint compliance

reorder for proper rendering

DOC: Add docs for color editor & formatter

DOC: Add documentation for model.js

DOC/STY: Adds necessary jsdoc and fixes gjslint

I've also renamed buildUI to _buildUI, because it shouldn't be a method
that's publicly used.

DOC: Add documentation for DecompositionView

update gjslint and jsdoc for visibility-controller.js

fix return value

upadate trajectory.js docs

address comments

update ddraw.js for gjslint and jsdoc

update draw.js for gjslint and jsdoc

address comment

update shape-controller.js to comply with gjslint and jsdocs

update surrounding files of shape controller for gjslint and jsdocs

move the stars

DOC: Address @squirrelo's comments

STY: Fix test_draw.js

STY: Fix test_plottable.js

STY: Fix test_sceneplotview3d.js

STY: Fix test_shape_controller.js

STY: Fix test_trajectory.js

STY: Fix test_util.js

STY: Fix test_view_controller.js

STY: Fix test_visibility_controller.js

STY: Fix test_decomposition_view.js

STY: Fix test_decomposition_model.js

add @see to colorviewcontroller

fix runner.js

fix test_animate

gjslint compliance

update shape-editor to render correctly in module

add @see to mroe files

squash last linter problems

clean up more

fix runner.js

fix for gjslint

.gitignore

@@ -48,3 +48,4 @@ doc/source/generated/
 # unwanted files
 examples/new-emperor.html
 .ipynb_checkpoints
+doc/jsdoc/

.travis.yml

@@ -7,10 +7,10 @@ env:
   - NUMPY_VERSION="<1.10"
   - NUMPY_VERSION="<1.11"
 before_install:
-  - wget http://repo.continuum.io/miniconda/Miniconda-2.2.2-Linux-x86_64.sh -O miniconda.sh
+  - wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh
   - chmod +x miniconda.sh
   - ./miniconda.sh -b
-  - export PATH=/home/travis/anaconda/bin:$PATH
+  - export PATH=/home/travis/miniconda2/bin:$PATH
   # Update conda itself
   - conda update --yes conda
 install:
@@ -19,9 +19,10 @@ install:
   - pip install https://github.com/google/closure-linter/archive/master.zip
   - pip install sphinx sphinx-bootstrap-theme coverage coveralls
   - pip install -e '.[all]' --no-use-wheel
+  - npm install -g jsdoc
 script:
   - flake8 emperor/*.py tests/*.py scripts/*.py setup.py
-  - gjslint emperor/support_files/js/*.js tests/javascript_tests/*.js
+  - gjslint --custom_jsdoc_tags module,function,constructs,alias,default emperor/support_files/js/*.js tests/javascript_tests/*.js
   # execute the full test suite
   - python tests/all_tests.py
   # we just check coverage in the latest version of NumPy

CONTRIBUTING.md

@@ -3,7 +3,7 @@ Contributing to Emperor
 
 [Emperor](http://biocore.github.io/emperor/) is an open source software package, and we welcome community contributions. You can find the source code and test code for Emperor under public revision control in the Emperor git repository on [GitHub](https://github.com/biocore/emperor). We very much welcome contributions.
 
-This document covers what you should do to get started with contributing to Emperor. You should read this whole document before considering submitting code to Emperor. This will save time for both you and the Emperor developers.  
+This document covers what you should do to get started with contributing to Emperor. You should read this whole document before considering submitting code to Emperor. This will save time for both you and the Emperor developers.
 
 Type of Submissions
 -------------------
@@ -94,16 +94,18 @@ git push origin my-topic-branch
 Coding Guidelines
 -----------------
 
-We adhere to the [PEP 8](http://www.python.org/dev/peps/pep-0008/) python coding guidelines for code and documentation standards. Before submitting any code to Emperor, you should read these carefully and apply the guidelines in your code.
+For **Python** code, we adhere to the [PEP 8](http://www.python.org/dev/peps/pep-0008/) python coding guidelines for code and documentation standards. For **JavaScript** code, we adhere to the [Google closure](https://google.github.io/styleguide/javascriptguide.xml) javascript coding standards, and use [JSDoc](http://usejsdoc.org/) to compile all javascript documentation. When using the closure linter, we allow the `module`, `function`, `constructs`, `alias`, and `default` custom JSDoc tags. For the most up to date version of the allowed JSDoc tags, see the [Travis configuration file](.travis.yml).
 
+Before submitting any code to Emperor, you should read these carefully and apply the guidelines in your code. As part of our automated testing, we make sure that all code passes linter standards and documentation compiles. We use the [gjslint](https://developers.google.com/closure/utilities/) linter to test javascript code with the `--custom_jsdoc_tags module,function,constructs,alias,default` modifier, and the [flake8](https://pypi.python.org/pypi/flake8) linter to test python code.
 
 Testing Guidelines
 ------------------
 
 All code that is added to Emperor must be unit tested, and the unit test code must be submitted in the same pull request as the library code that you are submitting. We will only merge code that is unit tested and that passes the [continuous integration build](https://github.com/biocore/emperor/blob/master/.travis.yml), this build verifies that the:
 
 - Full test suite executes without errors (including JavaScript and script usage tests).
-- All the code in Emperor is PEP8-compliant.
+- All python code in Emperor is PEP8-compliant.
+- All javascript code in Emperor is google closure compliant.
 - All code is valid in Python 2.7.x.
 - The documentation can be built correctly.
 

README.md

@@ -9,6 +9,8 @@ Emperor is a next-generation tool for the analysis and visualization of large mi
 
 To start using Emperor, please refer to the [installation notes](INSTALL.md).
 
+Before contributing code to Emperor, please familiarize yourself with the [contributing guidelines](CONTRIBUTING.md).
+
 ## Usage examples
 
 The main interface to create Emperor visualizations is the `make_emperor.py` script, inputing a mapping file and a PCoA data file, will generate an Emperor graphical user interface to analyze and visualize your data.

doc/Makefile

@@ -50,9 +50,11 @@ clean:
 	rm -rf $(BUILDDIR)/*
 	rm -rf source/scripts/*
 	rm -rf source/generated
+	rm -rf doc/build/jsdoc/*
 
 html:
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	jsdoc ../emperor/support_files/js/ -d $(BUILDDIR)/jsdoc -c jsdoc-config.json
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."