Merge branch 'master' of https://github.com/bmabey/pyLDAvis

* 'master' of https://github.com/bmabey/pyLDAvis: (84 commits)
  fixes other typo in gl notebook
  fix typo
  use the graphlab API for it's prepare, 3x+ speed improvement!
  updates notebook with models from LDAvis package
  replaces use of map with list comprehension to help with bmabey#8
  pass kargs to prepare fn in gensim and graphlab helpers. Closes bmabey#6, bmabey#7.
  releases v1.2.0
  adds link to the R vignette that explains the visualization
  prevents prepare from blowing up when used with a vocab smaller than R
  make the gensim extraction more explicit... trying to find bug in logic
  updates gensim adapter to get topic term dists directly /ht @cscorley
  fixes Makefile to run on osx
  releases v1.1.0
  change how web assets are served from github.. using detatched branch
  fixes graphlab viz
  fixes bug in graphlab model prepare causing bogus visualizations!
  doc fixes
  fix pypi badge
  release v1.0.0
  prep for v1.0.0 release
  ...

.gitignore

@@ -5,6 +5,7 @@
 
 # Packages
 *.egg
+.eggs
 *.egg-info
 dist
 build

.travis.yml

@@ -6,10 +6,35 @@ python:
   - "3.4"
   - "3.3"
   - "2.7"
-  - "2.6"
 
-# command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors
-install: pip install -r requirements.txt
+env:
+  - DEPS="numpy=1.9.2 pandas=0.16.0 jinja2=2.7.2 scikit-bio=0.2.3 joblib=0.8.4 numexpr pytest"
+
+before_install:
+  # conda instructions from http://conda.pydata.org/docs/travis.html
+  - sudo apt-get update
+  # We do this conditionally because it saves us some downloading if the
+  # version is the same.
+  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
+      wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
+    else
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+    fi
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+  # Useful for debugging any issues with conda
+  - conda info -a 
+install:
+  - conda create -n testenv --yes python=$TRAVIS_PYTHON_VERSION
+  - source activate testenv
+  - conda install --yes $DEPS
+  - python setup.py install
+  # download JSON data from github since travis does not have git-lfs rolled out yet
+  - (cd tests/data; curl -L -O https://github.com/bmabey/pyLDAvis/raw/master/tests/data/movie_reviews_input.json && curl -L -O https://github.com/bmabey/pyLDAvis/raw/master/tests/data/movie_reviews_output.json)
+  - ls -la tests/data/
 
 # command to run tests, e.g. python setup.py test
 script: python setup.py test

AUTHORS.rst

@@ -10,4 +10,4 @@ Development Lead
 Contributors
 ------------
 
-None yet. Why not be the first?
+* Paul English <[email protected]> - JS and CSS fixes and improvements.

CONTRIBUTING.rst

@@ -102,10 +102,3 @@ Before you submit a pull request, check that it meets these guidelines:
 3. The pull request should work for Python 2.6, 2.7, 3.3, and 3.4, and for PyPy. Check
    https://travis-ci.org/bmabey/pyLDAvis/pull_requests
    and make sure that the tests pass for all supported Python versions.
-
-Tips
-----
-
-To run a subset of tests::
-
-    $ python -m unittest tests.test_pyLDAvis

HISTORY.rst

@@ -3,7 +3,17 @@
 History
 -------
 
-0.1.0 (2015-04-06)
+1.2.0 (2015-06-13)
 ---------------------
 
-* First release on PyPI.
+* Updates gensim logic to be clearer and work with Python 3.x.
+
+1.1.0 (2015-06-02)
+---------------------
+
+* Fixes bug with GraphLab function that was producing bogus visualizations.
+
+1.0.0 (2015-05-29)
+---------------------
+
+* First release on PyPI. Faithful port of R version with IPython support and helper functions for GraphLab & gensim.

MANIFEST.in

@@ -4,8 +4,12 @@ include HISTORY.rst
 include LICENSE
 include README.rst
 
-recursive-include tests *
+recursive-include tests *.py
+recursive-include notebooks *.ipynb
+recursive-exclude notebooks/.ipynb_checkpoints *
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
+include tests/data/movie_reviews_input.json tests/data/movie_reviews_output.json tests/data/export_data.R
 
 recursive-include docs *.rst conf.py Makefile make.bat
+recursive-include pyLDAvis *.py *.js *.css

Makefile

@@ -6,7 +6,6 @@ help:
 	@echo "clean-pyc - remove Python file artifacts"
 	@echo "clean-test - remove test and coverage artifacts"
 	@echo "lint - check style with flake8"
-	@echo "fetch_R_data - download needed data files and computes expected outputs for tests"
 	@echo "test - run tests quickly with the default Python"
 	@echo "test-all - run tests on every Python version with tox"
 	@echo "coverage - check code coverage quickly with the default Python"
@@ -18,33 +17,30 @@ help:
 clean: clean-build clean-pyc clean-test
 
 clean-build:
-	rm -fr build/
-	rm -fr dist/
-	rm -fr .eggs/
-	find . -name '*.egg-info' -exec rm -fr {} +
-	find . -name '*.egg' -exec rm -f {} +
+	rm -rf build/
+	rm -rf dist/
+	rm -rf .eggs/
+	find . -name '*.egg-info' -exec rm -rf {} +
+	find . -name '*.egg' -exec rm -rf {} +
 
 clean-pyc:
 	find . -name '*.pyc' -exec rm -f {} +
 	find . -name '*.pyo' -exec rm -f {} +
 	find . -name '*~' -exec rm -f {} +
-	find . -name '__pycache__' -exec rm -fr {} +
+	find . -name '__pycache__' -exec rm -rf {} +
 
 clean-test:
-	rm -fr .tox/
+	rm -rf .tox/
 	rm -f .coverage
-	rm -fr htmlcov/
+	rm -rf htmlcov/
 
 lint:
 	flake8 pyLDAvis tests
 
-fetch_R_data:
-	(cd tests/data && ./export_data.R)
-
-test: fetch_R_data
+test:
 	python setup.py test
 
-test-all: fetch_R_data
+test-all:
 	tox
 
 coverage:
@@ -63,11 +59,11 @@ docs:
 
 release: clean
 	python setup.py sdist upload
-	python setup.py bdist_wheel upload
+	#python setup.py bdist_wheel upload
 
 dist: clean
 	python setup.py sdist
-	python setup.py bdist_wheel
+	#python setup.py bdist_wheel
 	ls -l dist
 
 install: clean

README.rst

@@ -0,0 +1,64 @@
+pyLDAvis
+========
+
+Python library for interactive topic model visualization.
+This is a port of the fabulous `R package <https://github.com/cpsievert/LDAvis>`__ by Carson Sievert and Kenny Shirley.
+
+.. figure:: http://www2.research.att.com/~kshirley/figures/ldavis-pic.png
+   :alt: LDAvis icon
+
+**pyLDAvis** is designed to help users interpret the topics in a topic model that has been fit to a corpus of text data. The package extracts information from a fitted LDA topic model to inform an interactive web-based visualization.
+
+The visualization is intended to be used within an IPython notebook but can also be saved to a stand-alone HTML file for easy sharing.
+
+|version status| |build status| |docs|
+
+Installation
+~~~~~~~~~~~~~~~~~~~~~~
+
+-  Stable version using pip:
+
+::
+
+    pip install pyldavis
+
+-  Development version on GitHub
+
+Clone the repository and run ``python setup.py``
+
+Usage
+~~~~~~~~~~~~~~~~~~~~~~
+
+The best way to learn how to use **pyLDAvis** is to see it in action.
+Check out this `notebook for an overview <http://nbviewer.ipython.org/github/bmabey/pyLDAvis/blob/master/notebooks/pyLDAvis_overview.ipynb>`__.
+Refer to the `documentation <https://pyLDAvis.readthedocs.org>`__ for details.
+
+For a concise explanation of the visualization see this
+`vignette <http://cran.r-project.org/web/packages/LDAvis/vignettes/details.pdf>`__ from the LDAvis R package.
+
+Video demos
+~~~~~~~~~~~
+
+Carson Sievert created a video demoing the R package. The visualization is the same and so it applies equally to pyLDAvis:
+
+-  `Visualizing & Exploring the Twenty Newsgroup Data <http://stat-graphics.org/movies/ldavis.html>`__
+
+More documentation
+~~~~~~~~~~~~~~~~~~
+
+To read about the methodology behind pyLDAvis, see `the original
+paper <http://nlp.stanford.edu/events/illvi2014/papers/sievert-illvi2014.pdf>`__,
+which was presented at the `2014 ACL Workshop on Interactive Language
+Learning, Visualization, and
+Interfaces <http://nlp.stanford.edu/events/illvi2014/>`__ in Baltimore
+on June 27, 2014.
+
+
+
+
+.. |version status| image:: https://img.shields.io/pypi/v/pyLDAvis.svg
+   :target: https://pypi.python.org/pypi/pyLDAvis
+.. |build status| image:: https://travis-ci.org/bmabey/pyLDAvis.png?branch=master
+   :target: https://travis-ci.org/bmabey/pyLDAvis
+.. |docs| image:: https://readthedocs.org/projects/pyldavis/badge/?version=latest
+   :target: https://pyLDAvis.readthedocs.org

docs/conf.py

@@ -16,10 +16,11 @@
 import sys
 import os
 
-# If extensions (or modules to document with autodoc) are in another
-# directory, add these directories to sys.path here. If the directory is
-# relative to the documentation root, use os.path.abspath to make it
-# absolute, like shown here.
+import mock
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
 #sys.path.insert(0, os.path.abspath('.'))
 
 # Get the project root dir, which is the parent dir of this
@@ -31,16 +32,30 @@
 # version is used.
 sys.path.insert(0, project_root)
 
+MOCK_MODULES = ['numpy','joblib', 'funcy', 'scipy', 'scipy.stats', 'scipy.spatial',
+                'scipy.spatial.distance', 'pandas', 'skbio', 'skbio.stats',
+                'skbio.stats.distance', 'skbio.stats.ordination']
+for mod_name in MOCK_MODULES:
+    sys.modules[mod_name] = mock.Mock()
+
 import pyLDAvis
 
+
+
 # -- General configuration ---------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
 #needs_sphinx = '1.0'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode']
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.doctest',
+    'sphinx.ext.coverage',
+    'sphinx.ext.viewcode',
+    'numpydoc']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

docs/modules/API.rst

@@ -0,0 +1,17 @@
+API documentation
+=================
+
+.. automodule:: pyLDAvis
+   :members:
+
+.. automodule:: pyLDAvis.gensim
+   :members:
+
+.. automodule:: pyLDAvis.graphlab
+   :members:
+
+.. automodule:: pyLDAvis.utils
+   :members:
+
+.. automodule:: pyLDAvis.urls
+   :members: