topicexplorer 1.0b233
InPhO Topic Explorer
License: MIT License
Keywords: topic modeling, lda, visualization

InPhO Topic Explorer and Hypershelf
===================================

|GitHub license| |PyPI|

The InPhO Topic Explorer provides an integrated system for text modeling
making it simple to go from a set of documents to an interactive
visualization of LDA topic models generated using the `InPhO VSM
module <http://github.com/inpho/vsm/>`__. More advanced analysis is made
possible by a built-in pipeline to Jupyter (iPython) notebooks.

Live demos trained on the Stanford Encyclopedia of Philosophy, a
selection of books from the HathiTrust Digital Library, and the original
LDA training set of Associated Press articles are available at
`https://www.hypershelf.org <https://www.hypershelf.org/>`__.

The Hypershelf provides an interactive, document-centered visualization
of the topic models. Each document is represented by a multi-colored,
horizontal bar representing the overall topic distribution for the
document, with different colors representing the topics. The relative
lengths of each segment of the bar indicates the weight of the topic in
that document. The total width of each row indicates similarity to the
focal topic or document, measured by the quantity sim(doc) = 1 –
JSD(doc, focus entity), where JSD is the Jensen-Shannon distance between
the word probability distributions of each item. Each topic’s label and
color is arbitrarily assigned, but is consistent across articles in the
browser.

Display options include topic normalization, alphabetical sort and topic
sort. By normalizing topics, the combined width of each bar expands so
that topic weights per document can be compared. By clicking a topic,
the documents will reorder acoording to that topic’s weight and topic
bars will reorder according to the topic weights in the highest weighted
document. When a topic is selected, clicking “Top Documents for [Topic]”
will take you to a new page showing the most similar documents to that
topic’s word distribution. The original sort order can be restored with
the “Reset Topic Sort” button.

Installation
------------

There are two types of install: Default and Developer. Currently we are
debugging the Windows Default installation. Before installing, Mac users
should install `XCode from
Apple <https://developer.apple.com/xcode/downloads/>`__ and Windows
users should install a Python compiler such as `Microsoft Visual C_\_
Compiler <https://www.microsoft.com/en-us/download/details.aspx?id=44266>`__

**Note:** If you attempt to install this while connected to the Internet
by way of a restricted network (such as eduroam) you may experience
difficulty. Our pypi server requires port 8080 to be accessible, and
this is sometimes blocked on public networks.

**Note:** This package is currently tested with Python 3.12. The most
recent build working with Python 2.7 is 1.0b227.

Default Install (Windows users should use Developer Install until further notice)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

1. Go to the `Anaconda website <http://continuum.io/downloads>`__ and
   choose the Python 3.7 Distribution. (Windows users: during
   installation, during “Advanced Options” choose “Add Anaconda to my
   PATH environment variable” and don’t worry about the warning.)

2. Open a Terminal (Mac and Linux) or PowerShell (Windows).

3. Run ``pip install --pre topicexplorer``.

   **Note:** ``--pre`` has *two* ``-`` characters. When the ``1.0``
   release happens, ``--pre`` will no longer be necessary.

4. Test installation by typing ``topicexplorer -h`` to print usage
   instructions.

Developer Install
~~~~~~~~~~~~~~~~~

1. `Set up Git <https://help.github.com/articles/set-up-git/>`__
2. Install the `Anaconda Python 3.7
   Distribution <https://www.anaconda.com/distribution/#download-section>`__.
3. Open a terminal and run
   ``pip install --src . -e git+https://github.com/inpho/topic-explorer#egg=topicexplorer``
4. Test installation by typing ``topicexplorer -h`` to print usage
   instructions.

Usage
-----

.. figure:: http://inphodata.cogs.indiana.edu/img/workflow.png
   :alt: Workflow

   Workflow

1. Initialize the Topic Explorer on a file, folder of text files, or
   folder of folders:

   ::

      topicexplorer init PATH

   This will generate a configuration file called *CONFIG*.

2. Train LDA models using the on-screen instructions:

   ::

      topicexplorer train CONFIG

3. Launch the topic explorer:

   ::

      topicexplorer launch CONFIG

4. Press Ctrl+C to quit all servers.

See the sample configuration files in the ``config`` directory for
examples of how to extend the topic explorer.

Bug Reports
-----------

Please report issues on the `issue
tracker <http://github.com/inpho/topic-explorer/issues>`__ or contact
Jaimie directly (contact info at bottom of README).

In your report, please include the error message, the command you ran,
your operating system, and the output of the command
``topicexplorer version``. This will ensure that we can quickly diagnose
your issue.

**Note:** When using a developer install ``topicexplorer version`` will
print in the following format: ``1.0b39-1-g7c834bf-dirty``. \* The first
part is the most recent release tag. (``1.0b39``) \* The second part is
the number of commits since the tag. (``1``) \* The next is the hash of
the most recent commit. (``g7c834bf``) \* The optional ``-dirty`` flag
indicates that the local repository has uncommitted changes.

Alternate Installs
------------------

We highly recommend using the Anaconda Python 3.7 Distribution using the
straightforward instructions provided above. While we continue to
support Python 2.7 installations for the time being, this will not
continue indefinitely.

Below we offer guidance for installing the Python 2.7 version alongside
Python 3 using Anaconda, and for installing without Anaconda, with notes
on dependencies.

Python 2 alongside Python 3
~~~~~~~~~~~~~~~~~~~~~~~~~~~

The InPhO Topic Explorer is compatible with Python 2.7. Anaconda for
Python 3.6 makes it possible to set up a side-by-side install of Python
2.7 so you can use both Python 3.7 and Python 2.7.

1. Install the `Anaconda Python 3.7
   Distribution <https://www.anaconda.com/distribution/#download-section>`__.
2. Open a terminal and run ``conda create -n py27 python=2.7 anaconda``.
   This will create a Python 2.7 Anaconda environment.
3. Run ``source activate py27`` to activate the Python 2.7 bindings. You
   should see ``(py27)`` before your prompt.
4. Use either the Default or Developer `install
   instructions <#installation>`__, skipping the step to install
   Anaconda Python 2.7.
5. Run ``source deactivate`` to deactivate Python 2.7 bindings and
   reactivate Python 3.7 bindings. Note that the ``topicexplorer``
   command will only work when the Python 2.7 bindings are activated.

Non-Anaconda Install
~~~~~~~~~~~~~~~~~~~~

-  **Miniconda**

   1. If using Miniconda (a small version of Anaconda), the necessary
      packages are:
      ``conda install numpy scipy scikit-learn nltk matplotplib ipython unidecode wget decorator chardet ujson requests notebook``

-  **Debian/Ubuntu**

   1. ``sudo apt-get-install build-essential python-dev python-pip python-numpy python-matplotlib python-scipy python-ipython``

   2. `IPython Notebooks <http://ipython.org/install.html>`__

-  **Windows**

   1. Install `Microsoft Visual C++ Compiler for Python
      2.7 <http://www.microsoft.com/en-us/download/details.aspx?id=44266>`__

   2. Install the Python packages below:

      -  `Numpy <http://sourceforge.net/projects/numpy/files/NumPy/>`__
      -  `Scipy <http://sourceforge.net/projects/scipy/files/scipy/>`__
      -  `matplotlib <http://matplotlib.org/downloads.html>`__
      -  `IPython Notebooks <http://ipython.org/install.html>`__

Deployment
----------

The Topic Explorer includes a simple HTTP server through the Bottle Web
Framework. This simple server is what the ``topicexplorer launch`` and
``topicexplorer serve`` commands use.

If you wish to host a high-traffic version of InPhO-TE, we recommend
using the Apache Web Server and the mod_wsgi module. This infrastructure
powers the demos at [http://inphodata.cogs.indiana.edu/] and is readily
available on cloud compute platforms. Details for that configuration are
below.

If you have deployed InPhO-TE using another infrastructure, please
submit a pull request with the documentation. The function
``topicexplorer.server.create_app`` will make a WSGI-compliant
application for use with any WSGI-compliant server.

mod_wsgi
~~~~~~~~

1.  Install apache2 with mod_wsgi:
    ``apt-get install apache2 libapache2-mod-wsgi``

2.  Create ``/etc/apache2/sites-available/topicexplorer.conf`` [you will
    need to fill in your local paths where specified]:

    ::

       <VirtualHost *:80>
           ServerName localhost
           ServerAdmin admin@localhost

           ErrorLog /var/www/topicexplorer/log/error.log
           CustomLog /var/www/topicexplorer/log/access.log combined

           WSGIDaemonProcess topicexplorer user=www-data group=www-data \
             python-path=[fill in; e.g. /home/jaimie/anaconda3/lib/python3.7/site-packages/]
           WSGIScriptAlias /ap /var/www/topicexplorer/app.wsgi

           <Directory /var/www/topicexplorer>
               WSGIProcessGroup topicexplorer
               WSGIApplicationGroup %{GLOBAL}
               Options All
               AllowOverride All
               Require all granted
           </Directory>
       </VirtualHost>

3.  Create the application directory:
    ``sudo mkdir -p /var/www/topicexplorer/``

4.  Create the log directory:
    ``sudo mkdir -p /var/www/topicexplorer/log``

5.  Create the www directory:
    ``sudo mkdir -p /var/www/topicexplorer/www``

6.  Create the config directory:
    ``sudo mkdir -p /var/www/topicexplorer/config``

7.  Add a symlink from ``/var/www/topicexplorer/`` to your local
    installation of ``app.wsgi``. For example:
    ``ln -s /home/jaimie/workspace/topic-explorer/app.wsgi /var/www/topicexplorer/app.wsgi``

8.  Add a symlink to your ``.ini`` files in the
    ``/var/www/topicexplorer/config`` directory. For example, if working
    with the AP corpus trained in my home directory:
    ``ln -s /home/jaimie/ap.ini /var/www/topicexplorer/config/ap.ini``

9.  Enable the site: ``sudo a2ensite topicexplorer``

10. Restart apache: ``sudo apache2ctl restart``

11. Test the site at [http://localhost/]. If an HTTP 500 Internal Server
    Error is returned, check the log in
    ``/var/www/topicexplorer/log/error.log``.

Caching
^^^^^^^

Credit to `Digital
Ocean <https://www.digitalocean.com/community/tutorials/how-to-configure-apache-content-caching-on-ubuntu-14-04>`__
for a very helpful guide.

To enable caching: 1. Modify
``/etc/apache2/sites-available/topicexplorer.conf`` to add Cache
directives before the closing ``</VirtualHost>`` tag:

::

   <VirtualHost *:80>
       # ...

       CacheQuickHandler off

       CacheLock on
       CacheLockPath /tmp/mod_cache-lock
       CacheLockMaxAge 5

       CacheIgnoreHeaders Set-Cookie

       <Location />
           CacheEnable disk
           CacheHeader on

           CacheDefaultExpire 600
           CacheMaxExpire 86400
           CacheLastModifiedFactor 0.5
       </Location>
   </VirtualHost>

2. Enable caching modules:
   ``sudo a2enmod cache && sudo a2enmod cache_disk``
3. Restart apache: ``sudo apache2ctl restart``

Server Status
^^^^^^^^^^^^^

The following snippet may help debug issues, enabling you to visit
[http://localhost/server-status] to find more details. Remove these
lines for production environments.

::

   <VirtualHost *:80>
       # ...

       <Location /server-status>
           SetHandler server-status
           
           Order Deny,Allow
           Allow from all
       </Location>
   </VirtualHost>

Licensing and Attribution
-------------------------

The project is released under an `Open-Source Initiative-approved MIT
License <http://opensource.org/licenses/MIT>`__.

The InPhO Topic Explorer may be cited as:

-  Jaimie Murdock and Colin Allen. (2015) *Visualization Techniques for
   Topic Model Checking* in Proceedings of the 29th AAAI Conference on
   Artificial Intelligence (AAAI-15). Austin, Texas, USA, January 25-29,
   2015. http://inphoproject.org/papers/

A `BibTeX
file <https://github.com/inpho/topic-explorer/blob/master/citation.bib>`__
is included in the repository for easier attribution.

Collaboration and Maintenance
-----------------------------

The InPhO Topic Explorer is maintained by `Jaimie
Murdock <http://jamram.net/>`__:

-  E-mail: jaimie.murdock@gmail.com
-  Twitter: `@JaimieMurdock <http://twitter.com/JaimieMurdock>`__
-  GitHub: `@JaimieMurdock <http://github.com/JaimieMurdock>`__
-  Homepage: http://jamram.net/

Please report issues on the `issue
tracker <http://github.com/inpho/topic-explorer/issues>`__ or contact
Jaimie directly.

We are open to collaboration! If there’s a feature you’d like to see
implemented, please contact us and we can lend advice and technical
assistance.

.. |GitHub license| image:: https://img.shields.io/badge/license-MIT-blue.svg
   :target: https://github.com/inpho/topic-explorer/blob/master/LICENSE.txt
.. |PyPI| image:: https://img.shields.io/pypi/v/topicexplorer.svg
   :target: https://pypi.python.org/pypi/topicexplorer