Merge remote-tracking branch 'origin/master' into feature-dirichlet-distribution

Author: ihincks

.travis.yml

@@ -2,9 +2,9 @@ sudo: false
 language: python
 python:
   - "2.7"
-  - "3.3"
   - "3.4"
   - "3.5"
+  - "3.6"
 
 addons:
   apt:
@@ -18,6 +18,7 @@ addons:
       - texlive
       - texlive-latex-extra
       - texlive-fonts-extra
+      - latexmk
 
 # Explicitly add doctest support as separate parts of the build matrix,
 # since these tests require additional packages that should be optional.
@@ -79,7 +80,7 @@ script:
   - if [[ "${DOCTEST}" == "1" ]]; then
       cd $TRAVIS_BUILD_DIR/doc;
       make doctest;
-      make latexpdf;
+      make latexpdf LATEXOPTS="--interaction=nonstopmode";
     fi
 
 after_success:

COPYING.txt

@@ -26,7 +26,7 @@ help:
 	@echo "  devhelp    to make HTML files and a Devhelp project"
 	@echo "  epub       to make an epub"
 	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
-	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  latexpdf   to make LaTeX files and run them through latexmk"
 	@echo "  text       to make text files"
 	@echo "  man        to make manual pages"
 	@echo "  changes    to make an overview of all changed/added/deprecated items"
@@ -99,9 +99,9 @@ latex:
 
 latexpdf:
 	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
-	@echo "Running LaTeX files through pdflatex..."
+	@echo "Running LaTeX files through latexmk..."
 	$(MAKE) -C $(BUILDDIR)/latex all-pdf
-	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+	@echo "latexmk finished; the PDF files are in $(BUILDDIR)/latex."
 
 text:
 	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text

doc/Makefile

@@ -4,9 +4,9 @@
     license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a
     letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View,
     California, 94041, USA.
-    
+
 .. _derived_models:
-    
+
 .. currentmodule:: qinfer
 
 Derived Models
@@ -30,6 +30,12 @@ additional functionality or changing the behaviors of underlying models.
 .. autoclass:: BinomialModel
     :members:
 
+:class:`GaussianHyperparameterizedModel` - Model over Gaussian outcomes conditioned on two-outcome experiments
+--------------------------------------------------------------------------------------------------------------
+
+.. autoclass:: GaussianHyperparameterizedModel
+    :members:
+
 :class:`MultinomialModel` - Model over batches of D-outcome experiments
 ----------------------------------------------------------------------
 
@@ -41,13 +47,13 @@ additional functionality or changing the behaviors of underlying models.
 
 .. autoclass:: MLEModel
     :members:
-    
+
 :class:`RandomWalkModel` - Model for adding fixed random walk to parameters
 ---------------------------------------------------------------------------
 
 .. autoclass:: RandomWalkModel
     :members:
-    
+
 :class:`GaussianRandomWalkModel` - Model for adding gaussian random walk to parameters
 --------------------------------------------------------------------------------------
 

doc/source/apiref/derived_models.rst

@@ -28,22 +28,28 @@ built on top of QInfer.
 .. autoclass:: SimplePrecessionModel
     :members:
 
+:class:`UnknownT2Model` - Model of a single qubit undergoing Larmor precession with finite decoherence
+------------------------------------------------------------------------------------------------------
+
+.. autoclass:: UnknownT2Model
+    :members:
+
 :class:`NoisyCoinModel` - Classical coin flip model corrupted by a noisy process
 --------------------------------------------------------------------------------
 
 .. autoclass:: NoisyCoinModel
     :members:
-    
-:class:`NDieModel` 
+
+:class:`NDieModel`
 ------------------
 
 .. autoclass:: NDieModel
     :members:
-    
+
 Custom Models
 -------------
 
-Writing custom models is standard practice for QInfer users. 
+Writing custom models is standard practice for QInfer users.
 See :ref:`CustomModels`.
 
 .. currentmodule:: qinfer.tests.base_test

doc/source/apiref/test_models.rst

@@ -66,19 +66,17 @@
     \let\footnotesize\small
     \let\footnoterule\relax
     \rule{\textwidth}{1pt}%
-    \ifsphinxpdfoutput
-      \begingroup
-      % These \defs are required to deal with multi-line authors; it
-      % changes \\ to ', ' (comma-space), making it pass muster for
-      % generating document info in the PDF file.
-      \def\\{, }
-      \def\and{and }
-      \pdfinfo{
-        /Author (\@author)
-        /Title (\@title)
-      }
-      \endgroup
-    \fi
+    \begingroup
+    % These \defs are required to deal with multi-line authors; it
+    % changes \\ to ', ' (comma-space), making it pass muster for
+    % generating document info in the PDF file.
+    \def\\{, }
+    \def\and{and }
+    \pdfinfo{
+    /Author (\@author)
+    /Title (\@title)
+    }
+    \endgroup
     \begin{flushright}%
       \sphinxlogo%
       {\rm\Huge\py@HeaderFamily \@title \par}%
@@ -298,6 +296,11 @@
 
 # Additional stuff for the LaTeX preamble.
 latex_preamble = preamble
+# In Sphinx 1.5, this now appears as latex_elements, so we pack the
+# preamble that way, too.
+latex_elements = {
+    'preamble': preamble
+}
 
 # Documents to append as an appendix to all manuals.
 #latex_appendices = []

doc/source/conf.py

@@ -63,16 +63,17 @@ def write_version(filename=VERSION_TARGET):
         'Bayesian particle filtering for parameter estimation in quantum '
         'information applications.',
     long_description=long_description,
-    license='http://www.gnu.org/licenses/agpl-3.0.en.html',
+    license='https://opensource.org/licenses/BSD-3-Clause',
     classifiers=[
         'Development Status :: 4 - Beta',
         'Intended Audience :: Science/Research',
-        'License :: OSI Approved :: GNU Affero General Public License v3',
+        'License :: OSI Approved :: BSD License',
         'Natural Language :: English',
         'Operating System :: OS Independent',
         'Programming Language :: Python :: 2.7',
-        'Programming Language :: Python :: 3.3',
         'Programming Language :: Python :: 3.4',
+        'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: Implementation :: CPython',
         'Topic :: Scientific/Engineering :: Physics',
     ],

setup.py

@@ -1,26 +1,36 @@
 #!/usr/bin/python
 # -*- coding: utf-8 -*-
 ##
-# __init__.py: Root of Qinfer package.
+# __init__.py: Root of QInfer package.
 ##
-# © 2012 Chris Ferrie (csferrie@gmail.com) and
-#        Christopher E. Granade (cgranade@gmail.com)
-#     
-# This file is a part of the Qinfer project.
-# Licensed under the AGPL version 3.
-##
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU Affero General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
+# © 2017, Chris Ferrie (csferrie@gmail.com) and
+#         Christopher Granade (cgranade@cgranade.com).
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+#     1. Redistributions of source code must retain the above copyright
+#        notice, this list of conditions and the following disclaimer.
+#
+#     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.
 #
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU Affero General Public License for more details.
+#     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.
 #
-# You should have received a copy of the GNU Affero General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# 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.
 ##
 
 from __future__ import absolute_import

src/qinfer/__init__.py

@@ -1,26 +1,36 @@
 #!/usr/bin/python
 # -*- coding: utf-8 -*-
 ##
-# _exceptions.py: Derived classes for Errors and Warnings specific to Qinfer.
+# _exceptions.py: Derived classes for Errors and Warnings specific to QInfer.
 ##
-# © 2012 Chris Ferrie (csferrie@gmail.com) and
-#        Christopher E. Granade (cgranade@gmail.com)
-#     
-# This file is a part of the Qinfer project.
-# Licensed under the AGPL version 3.
-##
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU Affero General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
+# © 2017, Chris Ferrie (csferrie@gmail.com) and
+#         Christopher Granade (cgranade@cgranade.com).
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+#     1. Redistributions of source code must retain the above copyright
+#        notice, this list of conditions and the following disclaimer.
+#
+#     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.
 #
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU Affero General Public License for more details.
+#     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.
 #
-# You should have received a copy of the GNU Affero General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# 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.
 ##
 
 ## FEATURES ###################################################################

src/qinfer/_exceptions.py

@@ -6,23 +6,32 @@
 #        licensed as described within each file, or by the corresponding
 #        LICENSE and/or COPYING files.
 ##
-# © 2012 Chris Ferrie (csferrie@gmail.com) and
-#        Christopher E. Granade (cgranade@gmail.com)
-#     
-# This file is a part of the Qinfer project.
-# Licensed under the AGPL version 3.
-##
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU Affero General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
+# © 2017, Chris Ferrie (csferrie@gmail.com) and
+#         Christopher Granade (cgranade@cgranade.com).
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+#     1. Redistributions of source code must retain the above copyright
+#        notice, this list of conditions and the following disclaimer.
+#
+#     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.
 #
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU Affero General Public License for more details.
+#     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.
 #
-# You should have received a copy of the GNU Affero General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# 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.
 ##
-