biocore · ElDeveloper · Jul 14, 2016 · Jul 15, 2016 · Jul 15, 2016 · Jul 15, 2016
diff --git a/.gitignore b/.gitignore
@@ -44,3 +44,9 @@ pip-log.txt
 # autogenerated documentation
 doc/source/scripts/
 doc/source/generated/
+
+# unwanted files
+examples/new-emperor.html
+new-emperor.html
+.ipynb_checkpoints
+doc/jsdoc/
diff --git a/.travis.yml b/.travis.yml
@@ -1,28 +1,55 @@
 language: python
 python:
-  - "2.7"
+  - 3.5
+  - 3.6
+  # also includes 3.7 (see below)
 env:
-  - NUMPY_VERSION=""  WITH_COVERAGE=1 # environment to test with the latest version of NumPy
-  - NUMPY_VERSION="=1.8"
-  - NUMPY_VERSION="=1.7"
+  - NUMPY_VERSION=""  # environment to test with the latest version of NumPy
+  - NUMPY_VERSION="<1.13"
+
+matrix:
+  # support for python 3.7 is rather awkward via Travis CI
+  # https://github.com/travis-ci/travis-ci/issues/9815
+  include:
+    - python: 3.7
+      dist: xenial
+      sudo: true
+      env: NUMPY_VERSION=""
+    - python: 3.7
+      dist: xenial
+      sudo: true
+      env: NUMPY_VERSION="<1.13"
+  exclude:
+      - python: 3.5
+        env: NUMPY_VERSION="<1.13"
+
 before_install:
-  - wget http://repo.continuum.io/miniconda/Miniconda-2.2.2-Linux-x86_64.sh -O miniconda.sh
-  - chmod +x 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:
-  - conda create --yes -n env_name python=$TRAVIS_PYTHON_VERSION pip numpy${NUMPY_VERSION} scipy matplotlib openpyxl=1.8.2 pandas nose flake8 pep8
-  - source activate env_name
-  - pip install sphinx sphinx-bootstrap-theme coverage coveralls
-  - pip install -e '.[all]'
+  # gjslint only runs in py27
+  - conda create --yes -n gjslint python=2.7 pip six
+  - conda run -n gjslint pip install https://github.com/google/closure-linter/archive/master.zip
+
+  # install requests using conda to avoid a distutils error in certifi
+  - conda create --yes -n travis python=$TRAVIS_PYTHON_VERSION pip numpy${NUMPY_VERSION} 'scipy>=0.17.0' matplotlib pandas flake8 pep8 jupyter coverage cython scikit-learn requests
+  - source activate travis
+  - conda install -c conda-forge phantomjs --yes
+  - pip install 'sphinx<1.6' sphinx-bootstrap-theme coveralls
+  - pip install -e '.[all]' --verbose
+  - npm install -g jsdoc
+
 script:
   - flake8 emperor/*.py tests/*.py scripts/*.py setup.py
-  # execute the full test suite
-  - python tests/all_tests.py --emperor_scripts_dir scripts
   # we just check coverage in the latest version of NumPy
-  - if [ ${WITH_COVERAGE} ]; then nosetests emperor --with-coverage --cover-package=emperor --cover-inclusive tests; fi
+  - coverage run tests/all_tests.py && coverage report
   - make -C doc html
+
+  # we can only run gjslint using py27
+  - conda run -n gjslint gjslint --custom_jsdoc_tags 'module,function,constructs,alias,default' 'emperor/support_files/js/*.js' 'tests/javascript_tests/*.js'
 after_success:
   - coveralls
diff --git a/CONTRIBUTING.md b/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.
 

diff --git a/ChangeLog.md b/ChangeLog.md
@@ -1,8 +1,13 @@
 Emperor ChangeLog
 =================
 
-Emperor 0.9.51-dev (changes since Emperor 0.9.5 go here)
---------------------------------------------------------
+# Emperor 1.0
+
+Introducing Emperor 1.0, an improved and new version of Emperor. Including
+a stable Python API and JavaScript API.
+
+Emperor 0.9.51-dev
+------------------
 
 ### Bug Fixes
 * Fix problem where the taxonomic vectors weren't scaled properly when the scale coordinates button was toggled  ([#386](https://github.com/biocore/emperor/issues/373).

diff --git a/INSTALL.md b/INSTALL.md
@@ -1,31 +1,56 @@
 Emperor Installation Notes
 ==========================
 
-Emperor is a python package that relies in [QCLI](https://pypi.python.org/pypi/qcli) and [NumPy](http://www.numpy.org). These packages must be installed prior running the `setup.py` script.
+Emperor is a Python package that powers a JavaScript-based user interface. The
+Python library relies on several packages from the scientific Python stack.
 
-To download Emperor, use [this link](https://github.com/biocore/emperor/archive/master.zip) or use git to get the latest version of the repository:
+To install the latest release version of Emperor, you can use `pip` or
+`conda`:
 
-    git clone git://github.com/biocore/emperor.git
+```bash
+    # with pip
+    pip install emperor
 
-Installation
-============
+    # with conda
+    conda install -c bioconda emperor
+```
 
-By far the easiest way to install Emperor is running:
 
-    pip install emperor
+Pre-releases (not compatible with QIIME 1.x)
+============================================
 
-In other case, to perform a global installation of Emperor, execute the following command from a terminal session:
+If you are interested in using a pre-release version (for example `1.0.0beta`)
+you can use `pip` or `conda`:
 
-    python setup.py install
+```bash
+    # with pip
+    pip install emperor --pre
 
-If you do not want to do a global installation, you will have to add the Emperor scripts and libraries to the `PATH` and `PYTHONPATH` environment variables. To add these variables to your `.bash_profile` issue the following terminal commands:
-
-``` bash
-echo "export PATH=$HOME/emperor_bin/:$PATH" >> ~/.bash_profile
-echo "export PYTHONPATH=$HOME/emperor_lib/:$PYTHONPATH" >> ~/.bash_profile
-python setup.py install --install-scripts=~/emperor_bin/ --install-purelib=~/emperor_lib/ --install-lib=~/emperor_lib/
+    # with conda
+    conda install -c conda-forge emperor
 ```
 
-To test for a correct installation, open a new terminal window and issue the following command to see the help of `make_emperor.py`:
+Note that we will update these pre-releases as often as it makes sense.
+
+Developers
+==========
 
-    make_emperor.py -h
+If you are planning to do development, we recommend that you clone the git
+repository, create a new environment (using `conda` or `virtualenvs`) and then
+use `pip install -e` to work on the source code without having to reinstall
+when you make editions:
+
+```bash
+    # fork
+    git clone git://github.com/YOUR-USERNAME/emperor.git
+
+    # if you are using conda
+    conda create -n emperor-dev scipy numpy pandas matplotlib jupyter
+
+    # if you are using virtualenvs
+    mkvirtualenv emperor-dev && workon emperor-dev
+
+    # now install the repository
+    cd emperor
+    pip install -e '.[all]'
+```