Merge branch 'docs_mock'

LICENSE

@@ -1,21 +1,27 @@
-MIT License
+Copyright (c) 2016, Helsinki Institute for Information Technology
+All rights reserved.
 
-Copyright (c) 2016 Helsinki Institute for Information Technology
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
 
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
+1. Redistributions of source code must retain the above copyright notice, this list
+of conditions and the following disclaimer.
 
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
+2. Redistributions in binary form must reproduce the above copyright notice, this
+list of conditions and the following disclaimer in the documentation and/or other
+materials provided with the distribution.
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+3. Neither the name of the copyright holder nor the names of its contributors may
+be used to endorse or promote products derived from this software without specific
+prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
+EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -15,6 +15,7 @@ ELFI - Engine for Likelihood-Free Inference
  -->
 
 [![Build Status](https://travis-ci.com/HIIT/elfi.svg?token=xAu1DN2J4WjCapVWLinn&branch=dev)](https://travis-ci.com/HIIT/elfi)
+[![Documentation Status](https://readthedocs.org/projects/elfi/badge/?version=latest)](http://elfi.readthedocs.io/en/latest/?badge=latest)
 
 <img src="https://cloud.githubusercontent.com/assets/1233418/20178983/6e22ee44-a75c-11e6-8345-5934b55b9dc6.png" width="15%" align="right"></img>
 
@@ -27,7 +28,7 @@ Currently implemented ABC methods:
 - Sequential Monte Carlo sampler
 - [Bayesian Optimization for Likelihood-Free Inference (BOLFI) framework](https://arxiv.org/abs/1501.03291)
 
-See examples under [notebooks](notebooks) to get started.
+See examples under [notebooks](notebooks) to get started. Full documentation can be found at http://elfi.readthedocs.io/.
 
 <!-- ..
    Installation

docs/conf.py

@@ -16,6 +16,28 @@
 import sys
 import os
 
+# http://docs.readthedocs.io/en/latest/faq.html#i-get-import-errors-on-libraries-that-depend-on-c-modules
+from unittest.mock import MagicMock
+
+class Mock(MagicMock):
+    @classmethod
+    def __getattr__(cls, name):
+            return MagicMock()
+
+on_RTD = os.environ.get('READTHEDOCS', None) == 'True'
+if on_RTD:
+    MOCK_MODULES = ['pygtk', 'gtk', 'gobject', 'argparse', 'numpy', 'pandas', 'scipy', 'unqlite',
+                    'dask', 'distributed', 'graphviz', 'matplotlib', 'sobol_seq', 'GPy', 'dask.delayed',
+                    'scipy.optimize', 'scipy.stats', 'matplotlib.pyplot', 'numpy.random', 'distributed.client']
+                    # 'scipy.optimize', 'scipy.stats', 'matplotlib', 'matplotlib.pyplot', 'GPy']
+    sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
+
+    html_theme = 'default'
+
+else:
+    html_theme = 'sphinx_rtd_theme'
+
+
 # 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
@@ -142,7 +164,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+# html_theme = 'alabaster'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the

docs/installation.rst

@@ -5,22 +5,22 @@ Installation
 ============
 
 
-Stable release
---------------
+.. Stable release
+.. --------------
 
-To install ELFI, run this command in your terminal:
+.. To install ELFI, run this command in your terminal:
 
-.. code-block:: console
+.. .. code-block:: console
 
-    $ pip install elfi
+..     $ pip install elfi
 
-This is the preferred method to install ELFI, as it will always install the most recent stable release. 
+.. This is the preferred method to install ELFI, as it will always install the most recent stable release.
 
-If you don't have `pip`_ installed, this `Python installation guide`_ can guide
-you through the process.
+.. If you don't have `pip`_ installed, this `Python installation guide`_ can guide
+.. you through the process.
 
-.. _pip: https://pip.pypa.io
-.. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/
+.. .. _pip: https://pip.pypa.io
+.. .. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/
 
 
 From sources
@@ -32,7 +32,7 @@ You can either clone the public repository:
 
 .. code-block:: console
 
-    $ git clone git://github.com/HIIT/elfi
+    $ git clone https://github.com/HIIT/elfi.git
 
 Or download the `tarball`_:
 

docs/readme.rst

@@ -10,6 +10,7 @@ The probabilistic inference model is defined as a directed acyclic graph, which
 .. _Dask: https://dask.pydata.org
 
 Currently implemented ABC methods:
+
 - rejection sampler
 - Sequential Monte Carlo sampler
 - Bayesian Optimization for Likelihood-Free Inference (BOLFI_) framework

docs/source/elfi.bo.rst

@@ -0,0 +1,38 @@
+elfi.bo package
+===============
+
+Submodules
+----------
+
+elfi.bo.acquisition module
+--------------------------
+
+.. automodule:: elfi.bo.acquisition
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+elfi.bo.gpy_model module
+------------------------
+
+.. automodule:: elfi.bo.gpy_model
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+elfi.bo.utils module
+--------------------
+
+.. automodule:: elfi.bo.utils
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: elfi.bo
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/source/elfi.rst

@@ -0,0 +1,109 @@
+elfi package
+============
+
+Subpackages
+-----------
+
+.. toctree::
+
+    elfi.bo
+
+Submodules
+----------
+
+elfi.async module
+-----------------
+
+.. automodule:: elfi.async
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+elfi.core module
+----------------
+
+.. automodule:: elfi.core
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+elfi.decorators module
+----------------------
+
+.. automodule:: elfi.decorators
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+elfi.distributions module
+-------------------------
+
+.. automodule:: elfi.distributions
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+elfi.env module
+---------------
+
+.. automodule:: elfi.env
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+elfi.methods module
+-------------------
+
+.. automodule:: elfi.methods
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+elfi.posteriors module
+----------------------
+
+.. automodule:: elfi.posteriors
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+elfi.storage module
+-------------------
+
+.. automodule:: elfi.storage
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+elfi.utils module
+-----------------
+
+.. automodule:: elfi.utils
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+elfi.visualization module
+-------------------------
+
+.. automodule:: elfi.visualization
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+elfi.wrapper module
+-------------------
+
+.. automodule:: elfi.wrapper
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: elfi
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/source/modules.rst

@@ -0,0 +1,7 @@
+elfi
+====
+
+.. toctree::
+   :maxdepth: 4
+
+   elfi

docs/usage.rst

@@ -5,3 +5,7 @@ Usage
 To use ELFI in a project::
 
     import elfi
+
+For tutorials, please see the Jupyter Notebooks under the `notebooks directory`_.
+
+.. _notebooks directory: https://github.com/HIIT/elfi/tree/master/notebooks

elfi/__init__.py

@@ -7,4 +7,4 @@
 
 __author__ = 'ELFI authors'
 __email__ = 'aki.vehtari@aalto.fi'
-__version__ = '0.1.0'
+__version__ = '0.2.0'

setup.py

@@ -1,31 +1,34 @@
+import os
 from setuptools import setup
 from io import open
 
 with open('README.md', 'r', encoding='utf-8') as f:
     long_description = f.read()
 
+requirements = [
+                'toolz>=0.8',
+                'distributed>=1.13.3',
+                'graphviz>=0.5',
+                'cairocffi>=0.7',
+                'dask>=0.11.1',
+                'sobol_seq>=0.1.2',
+                'numpy>=1.8',
+                'scipy>=0.16.1',
+                'Cython>=0.25.1',
+                'matplotlib>=1.1',
+                'GPy>=1.0.9',
+                'unqlite>=0.6.0'
+                ]
+
 setup(
     name='elfi',
     packages=['elfi'],
-    version='0.1',
+    version='0.3',
     author='HIIT',
     author_email='aki.vehtari@aalto.fi',
     url='https://github.com/HIIT/elfi',
 
-    install_requires=[
-        'numpy>=1.8',
-        'scipy>=0.16.1',
-        'toolz>=0.8',
-        'distributed>=1.13.3',
-        'graphviz>=0.5',
-        'cairocffi>=0.7',
-        'dask>=0.11.1',
-        'matplotlib>=1.1',
-        'sobol_seq>=0.1.2',
-        'GPy>=1.0.9',
-        'Cython>=0.25.1',
-        'unqlite>=0.6.0'
-    ],
+    install_requires=requirements,
 
     extras_require={
         'doc': ['Sphinx'],
@@ -34,7 +37,7 @@
     description='Modular ABC inference framework for python',
     long_description=long_description,
 
-    license='MIT',
+    license='BSD3',
 
     classifiers=['Programming Language :: Python',
                  'Topic :: Scientific/Engineering',
@@ -43,4 +46,4 @@
                  'Operating System :: OS Independent',
                  'Development Status :: 2 - Pre-Alpha',
                  'Intended Audience :: Science/Research',
-                 'License :: OSI Approved :: MIT License'])
+                 'License :: OSI Approved :: BSD3 License'])