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Updating installation instructions, removing Auto-Encoder section for now.
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docs/guide_installation.rst

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You have multiple options to get up and running, though using ``pip`` is by far the easiest and most reliable.
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A) Download Latest Release [Recommended]
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Downloading Package
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-------------------
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**Recommended.** To download and setup the last officially released package, you can do so from PYPI directly::
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If you want to use the latest official release, you can do so from PYPI directly::
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> pip install scikit-neuralnetwork
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This contains its own packaged version of ``pylearn2`` from the date of the release (and tag) but will use any globally installed version if available.
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If you want to install the very latest from source, please visit the `Project Page <http://github.com/aigamedev/scikit-neuralnetwork>`_ on GitHub for details.
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This will install the latest official ``Lasagne`` and ``Theano`` as well as other minor packages too as a dependency. We strongly suggest you use a `virtualenv <https://virtualenv.pypa.io/en/latest/>`_ for Python.
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B) Pulling Repositories [Optional]
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Pulling Repositories
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--------------------
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If you want to use the more advanced features like convolution, pooling or upscaling, these depend on the latest code from ``Lasagne`` and ``Theano`` master branches. You can install them manually as follows::
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**Optional.** To setup a developer version of the project, you'll need to first install some dependencies manually. Unfortunately, ``pylearn2`` isn't yet installable via PyPI and recommends an editable (``pip -e``) installation::
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> pip install numpy scipy theano
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> pip install -e git+https://github.com/lisa-lab/pylearn2.git#egg=Package
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> pip install -r https://github.com/aigamedev/scikit-neuralnetwork/master/requirements.txt
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Once that's done, you can grab this repository and install from ``setup.py`` in the exact same way::
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> git clone https://github.com/aigamedev/scikit-neuralnetwork.git
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> cd scikit-neuralnetwork
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> python setup.py develop
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> cd scikit-neuralnetwork; python setup.py develop
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This will make the ``sknn`` package globally available within Python as a reference to the current directory.
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.. image:: console_tests.png
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We strive to maintain 100% test coverage for all code-paths, to ensure that rapid changes in the underlying ``pylearn2`` library are caught automatically.
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We strive to maintain 100% test coverage for all code-paths, to ensure that rapid changes in the underlying ``Lasagne`` and ``Theano`` libraries are caught automatically.

docs/index.rst

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:maxdepth: 2
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module_mlp
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module_ae
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User Guide

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