change line 139 of cpp/gpp_python_common.cpp

.gitignore

@@ -8,9 +8,6 @@
 # Data files
 *.mat
 
-# Tox files
-.tox
-
 # OSX crap
 *.DS_Store
 
@@ -39,6 +36,9 @@ docs/latex/*
 docs/html/*
 docs/.doctrees/*
 docs/moe.*.rst
+docs/moe.rst
+docs/moe_examples.rst
+docs/moe_examples.*.rst
 docs/gpp_*.rst
 docs/cpp_tree.rst
 

.mailmap

@@ -0,0 +1,10 @@
+Scott Clark <[email protected]> <[email protected]>
+Scott Clark <[email protected]> <[email protected]>
+Eric Liu <[email protected]> <[email protected]>
+Deniz Oktay <[email protected]> <[email protected]>
+Deniz Oktay <[email protected]> <[email protected]>
+norases <[email protected]> <[email protected]>
+JiaLei Wang <[email protected]> <[email protected]>
+JiaLei Wang <[email protected]> <[email protected]>
+JiaLei Wang <[email protected]> <[email protected]>
+JiaLei Wang <[email protected]> <[email protected]>

.travis.yml

@@ -0,0 +1,25 @@
+language: python
+python:
+    - "2.7"
+cache:
+    - apt
+before_install:
+    - sudo apt-get update -qq
+    - sudo apt-get install -y build-essential libblas-dev liblapack-dev gfortran make libedit-dev
+    - sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test && sudo apt-get update -q && sudo apt-get install -y gcc-4.7 g++-4.7 && sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.7 20 && sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.7 20 && sudo update-alternatives --config gcc && sudo update-alternatives --config g++
+    - sudo add-apt-repository -y ppa:boost-latest/ppa && sudo apt-get update -q && sudo apt-get install -y boost1.55
+    - sudo add-apt-repository -y ppa:kalakris/cmake && sudo apt-get update -q && sudo apt-get install -y cmake
+    - sudo add-apt-repository -y ppa:chris-lea/python-numpy && sudo apt-get update -q && sudo apt-get install -y python-numpy
+    - wget http://ppa.launchpad.net/libreoffice/ppa/ubuntu/pool/main/d/doxygen/doxygen_1.8.7-2~precise1_amd64.deb -O doxygen.deb
+    - sudo dpkg -i doxygen.deb
+install:
+    - pip install -r requirements.txt
+    - pip install flake8 flake8-import-order pep8-naming flake8-docstrings
+    # Tell MOE to install the Python specified in Travis (b/c many are installed)
+    # The env-var may be "x.x_with_system_site_packages" so we need to extract just the front of the string
+    - export MOE_CMAKE_OPTS="-D MOE_PYTHON_ADDITIONAL_VERSIONS='`echo $TRAVIS_PYTHON_VERSION | cut -d '_' -f 1`'"
+    - python setup.py install
+script:
+    - make -B test
+    - make -B style-test
+    - make -B docs

AUTHORS.md

@@ -0,0 +1,25 @@
+MOE Authors
+===========
+
+MOE was developed at [Yelp Inc][0] and [Cornell University][1]. It spawned from [Scott Clark's PhD thesis][2] and original implementation.
+
+Co-Devlopers
+------------
+
+- Scott Clark ([email protected], [@DrScottClark][3], http://sigopt.com/about#scott)
+- Eric Liu ([email protected], [@ehliu][4])
+
+Contributors
+------------
+
+- Peter Frazier ([email protected], http://people.orie.cornell.edu/pfrazier/)
+- JiaLei Wang ([email protected], http://www.jialeiwang.net, [@garywang304][5])
+- Deniz Oktay ([email protected])
+- Norases Vesdapunt ([email protected], [@norasesv][6])
+[0]: http://www.yelp.com/careers
+[1]: http://www.orie.cornell.edu/
+[2]: https://github.com/sc932/Thesis
+[3]: https://twitter.com/drscottclark
+[4]: https://twitter.com/ehliu
+[5]: https://twitter.com/garywang304
+[6]: https://twitter.com/norasesv

CHANGELOG.md

@@ -0,0 +1,89 @@
+* Features
+
+* Changes
+
+* Bugs
+
+## v0.2.2 (2014-12-5)
+
+SHA: ``83a71512e6a4aa553866e4301ef11f172d485e23``
+
+* Features
+
+  * Added startup message to REST server including tips for OSX users (#400)
+  * Added GPU support to ``cpp_wrappers.expected_improvement.multistart_expected_improvement_optimization``; requires ``max_num_threads == 1`` until future multi-GPU support (#368)
+  * Added the COBYLA optimizer to the expected improvement optimization class. (#370)
+  * OptimizerParameter struct members now directly readable/writeable from Python; added EqualityComparisonMixin (#138)
+  * C++ GradientDescentParameters object now stores ``num_steps_averaged`` (but does not use it yet) (#391)
+  * conda build system for MOE (#417)
+
+* Changes
+
+  * Switched from `testify` to `py.test` - http://pytest.org/ (#36)
+  * [cleanup] Moved bandits into their own sub directories (#375)
+  * Supply PYTHON_LIBRARY and PYTHON_INCLUDE_DIR vars to cmake automatically in ``setup.py`` (#412)
+  * Added warning when colander version is out of date (#413)
+
+* Bugs
+
+  * Fixed UCB1 and UCB1-tuned algorithm confidence bound calculation (#432)
+
+## v0.2.1 (2014-09-22)
+
+SHA: ``ab6f959c11a0cacbed6dad618fe6ffed71092116``
+
+* Features
+
+  * Implemented BLA (Bayesian Learning Automaton). (#373)
+  * Connected GPU functions to multistart gradient descent optimizer. (#270)
+
+* Changes
+
+* Bugs
+
+  * variance in a sample arm was dropped in _make_bandit_historical_info_from_params. (#385)
+  * SampleArm's ``__add__`` and ``__str__`` were broken. (#387)
+  * Specifying ``max_num_threads`` on GPU compute paths caused a segfault (#394)
+
+## v0.2.0 (2014-08-15)
+
+SHA: ``8201917e3f9b47b8edd8039ea3278ef8631b0f2a``
+
+* Features
+
+  * Added multi-armed bandit endpoint. (#255)
+    * Implemented epsilon-greedy. (#255)
+    * Implemented epsilon-first. (#335)
+    * Implemented UCB1. (#354)
+    * Implemented UCB1-tuned. (#366)
+  * Added support for the L-BFGS-B optimizer. (#296)
+  * Added GPU implementation for q,p-EI and its gradient computation. (#219)
+    * Speed up GPU functions by redesign of memory allocation. (#297)
+
+* Changes
+
+  * Split up old ``schemas.py`` file into ``schemas/`` directory with several subfiles (#291)
+  * Improved Dockerfile, reducing Docker-based install times substantially, https://hub.docker.com/u/yelpmoe/ (#332)
+    * Created ``min_reqs`` docker container which is a snapshot of all MOE third-party requirements
+    * Created ``latest``, which tracks the latest MOE build
+    * Started releasing docker containers for each tagged MOE release (currently just ``v0.1.0``)
+  * ``GradientDescentOptimization`` (C++) no longer has a separate ``next_points`` output (#186)
+  * LogLikelihood evaluate at point list and latin hypercube search now return status dicts like every other optimizer (#189)
+    * status dicts also a little more informative/standardized now
+  * Update C++ autodoc tools to handle the new ``gpu`` directory (#353)
+  * Added ``__version__`` to ``moe/__init__.py`` (#353)
+
+* Bugs
+
+  * Throw exceptions (C++) if ``num_multistarts`` or ``num_random_samples`` is 0 (#345)
+  * ``combined_example`` endpoint was not passing ``kwargs`` through so users could not change the default server (#356)
+    * fix sometimes dropped general ``kwargs`` (#358)
+  * ``mean_var_of_gp_from_historic_data`` was also not passing ``kwargs`` (#359)
+
+## v0.1.0 (2014-07-29)
+
+SHA: ``5fef1d242cc8b6e0d6443522f8ba73ba743607de``
+
+* Features
+
+  * initial open source release

Dockerfile

@@ -1,20 +1,11 @@
-FROM ubuntu:14.04
+FROM yelpmoe/min_reqs
 MAINTAINER Scott Clark <[email protected]> and Eric Liu <[email protected]>
 
-# Create a non-privileged user named app to run MOE
-RUN addgroup --gid 9999 app &&\
-    adduser --uid 9999 --gid 9999 --disabled-password --gecos "Application" app &&\
-    usermod -L app
-
-# Install software from Ubuntu.
-RUN apt-get update
-RUN apt-get install -y build-essential gcc python python-dev python2.7 python2.7-dev cmake libboost-all-dev doxygen libblas-dev liblapack-dev gfortran git make flex bison libssl-dev libedit-dev
-
 # Install pip systemwide for Python.
-ADD https://raw.github.com/pypa/pip/master/contrib/get-pip.py /tmp/get-pip.py
+ADD https://bootstrap.pypa.io/get-pip.py /tmp/get-pip.py
 RUN python /tmp/get-pip.py
 
-# Install requirements (done here to allow for caching)
+# Install python requirements (these should be all in yelpmoe/min_reqs, but it is done again here to be safe)
 ADD requirements.txt /home/app/MOE/
 RUN cd /home/app/MOE/ && pip install -r requirements.txt
 
@@ -28,6 +19,7 @@ RUN python setup.py install
 
 # Build the C++
 WORKDIR /home/app/MOE/moe
+RUN rm -rf build
 RUN mkdir build
 WORKDIR /home/app/MOE/moe/build
 RUN cmake /home/app/MOE/moe/optimal_learning/cpp/
@@ -40,7 +32,7 @@ RUN chown -R app:app /home/app/MOE && chmod -R a+r /home/app/MOE
 WORKDIR /home/app/MOE
 
 # Run tests
-RUN testify -v moe.tests
+RUN make test
 
 # Configure docker container.
 EXPOSE 6543

Makefile

@@ -7,26 +7,21 @@ clean:
 production:
 		python setup.py install
 
-test-no-tox:
-		testify -v moe.tests
-
 test:
-		tox
-		tox -e pep8
-
-style-test-no-tox:
-		pip install flake8 flake8-import-order pep8-naming flake8-docstrings
-		flake8 --ignore=E501,E126,E123,I101,N806 moe
-		pep257 moe
+		py.test -v moe/tests moe_examples/tests
 
 style-test:
-		tox -e pep8
+		pip install flake8 flake8-import-order pep8-naming flake8-docstrings pyflakes
+		flake8 --ignore=E501,E126,E123,I101,I100,N806 moe
+		pep257 moe
+		pyflakes moe
+		flake8 --ignore=E501,E126,E123,I101,I100,N806 moe_examples
+		pep257 moe_examples
+		pyflakes moe_examples
 
-docs-no-tox:
+docs:
 		python docs/cpp_rst_maker.py
 		doxygen docs/doxygen_config
 		sphinx-apidoc -f -o docs moe
+		sphinx-apidoc -f -T -o docs moe_examples
 		sphinx-build -b html docs docs/_build/html
-
-docs:
-		tox -e docs