Merge pull request #417 from rmcgibbo/conda-recipe

Conda Installer recipe

conda-recipe/README.md

@@ -0,0 +1,49 @@
+conda-moe
+=========
+
+This repository provides the recipes for building binary packages of [MOE](https://github.com/yelp/moe), a global, black box optimization engine for real world metric optimization, to be used with the Anaconda Python distribution or other conda environments.
+
+The built binaries are available on binstar.org, and can be installed using the following command
+
+```
+conda config --add channels https://conda.binstar.org/rmcgibbo
+conda install moe
+```
+
+This package is available for linux-64, targetting Ubuntu 10.04 or later, CentOS 6.0+ or later, or similar.
+
+### Notes
+This repository obviously includes recipes for a number of packages other than MOE. These are all direct or indirect dependencies of MOE, which are not included with the `default` conda channels, and we therefore build and push to binstar to make things _just work_.
+
+### libstdc++
+
+MOE uses C++11 features, which requires a quite modern version of GCC (4.7.3+), and a similarly new version of the runtime c++ standard library, libstd++. The version of libstdc++ distributed with Ubuntu 10.04 and CentOS 6.0 is
+too old to support runtime C++11 code. Therefore, this conda build of MOE depends on an external libstdc++ conda package, which povides a more recent library. See [the recipe](https://github.com/rmcgibbo/conda-moe/blob/master/libstdcplusplus/build.sh) for the dirty, dirty hack.
+
+### building the binaries
+
+Our builds of these conda recipes were performed on a fresh Ubuntu 10.04 64-bit VM (vagrant) with the following provisioning:
+
+```
+sudo apt-get update
+sudo apt-get install python-software-properties
+sudo add-apt-repository ppa:ubuntu-toolchain-r/test
+sudo apt-get update
+sudo apt-get install libgcc-4.7-dev  cpp-4.7 gcc-4.7-base  g++-4.7 make libbz2-1.0 libbz2-dev git-core
+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
+
+wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
+bash Miniconda-latest-Linux-x86_64.sh -b
+export PATH=$HOME/miniconda/bin/:$PATH
+conda install conda-build
+
+# The conda recipes for the boost dependency are in a separate github
+# repository:
+# https://github.com/rmcgibbo/conda-cheminformatics/tree/master/boost
+conda config --add channels https://conda.binstar.org/rmcgibbo
+
+git clone https://github.com/rmcgibbo/conda-moe.git
+cd conda-moe
+conda build *
+```

conda-recipe/Vagrantfile

@@ -0,0 +1,48 @@
+# -*- mode: ruby -*-
+# vi: set ft=ruby :
+
+$script = <<SCRIPT
+set -e
+sudo apt-get update
+sudo apt-get install -y python-software-properties
+sudo add-apt-repository ppa:ubuntu-toolchain-r/test
+sudo apt-get update
+sudo apt-get install -y libgcc-4.7-dev  cpp-4.7 gcc-4.7-base  g++-4.7 make libbz2-1.0 libbz2-dev git-core
+sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.7 20
+sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.7 20
+
+wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
+bash Miniconda-latest-Linux-x86_64.sh -b
+export PATH=$HOME/miniconda/bin/:$PATH
+conda install --yes conda-build binstar jinja2
+
+git clone https://github.com/yelp/moe.git
+cd moe/conda-recipe
+
+conda build boost
+conda build certifi
+conda build colander
+conda build libstdcplusplus
+conda build mako
+conda build paste
+conda build pyramid_mako
+conda build simplejson
+conda build waitress
+conda build webtest
+conda build moe
+SCRIPT
+
+
+# Vagrantfile API/syntax version. Don't touch unless you know what you're doing!
+VAGRANTFILE_API_VERSION = "2"
+
+Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
+  config.vm.provision "shell", inline: $script, run: "always"
+
+  # Every Vagrant virtual environment requires a box to build off of.
+  config.vm.box = "lucid64"
+  config.vm.define :lucid64 do |t|
+  end
+
+
+end

conda-recipe/boost/6bb71fdd.patch

@@ -0,0 +1,48 @@
+From 6bb71fdd8f7cc346d90fb14beb38b7297fc1ffd9 Mon Sep 17 00:00:00 2001
+From: Andrey Semashev <andrey.semashev@gmail.com>
+Date: Sun, 26 Jan 2014 13:58:48 +0400
+Subject: [PATCH] Fixed incorrect initialization of 128-bit values, when no
+ native support for 128-bit integers is available.
+
+---
+ boost/atomic/detail/cas128strong.hpp | 10 +++++++---
+ 1 file changed, 7 insertions(+), 3 deletions(-)
+
+diff --git boost/atomic/detail/cas128strong.hpp boost/atomic/detail/cas128strong.hpp
+index 906c13e..dcb4d7d 100644
+--- boost/atomic/detail/cas128strong.hpp
++++ boost/atomic/detail/cas128strong.hpp
+@@ -196,15 +196,17 @@ class base_atomic<T, void, 16, Sign>
+
+ public:
+     BOOST_DEFAULTED_FUNCTION(base_atomic(void), {})
+-    explicit base_atomic(value_type const& v) BOOST_NOEXCEPT : v_(0)
++    explicit base_atomic(value_type const& v) BOOST_NOEXCEPT
+     {
++        memset(&v_, 0, sizeof(v_));
+         memcpy(&v_, &v, sizeof(value_type));
+     }
+
+     void
+     store(value_type const& value, memory_order order = memory_order_seq_cst) volatile BOOST_NOEXCEPT
+     {
+-        storage_type value_s = 0;
++        storage_type value_s;
++        memset(&value_s, 0, sizeof(value_s));
+         memcpy(&value_s, &value, sizeof(value_type));
+         platform_fence_before_store(order);
+         platform_store128(value_s, &v_);
+@@ -247,7 +249,9 @@ class base_atomic<T, void, 16, Sign>
+         memory_order success_order,
+         memory_order failure_order) volatile BOOST_NOEXCEPT
+     {
+-        storage_type expected_s = 0, desired_s = 0;
++        storage_type expected_s, desired_s;
++        memset(&expected_s, 0, sizeof(expected_s));
++        memset(&desired_s, 0, sizeof(desired_s));
+         memcpy(&expected_s, &expected, sizeof(value_type));
+         memcpy(&desired_s, &desired, sizeof(value_type));
+
+-- 
+1.9.1
+

conda-recipe/boost/build.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+
+# Hints:
+# http://boost.2283326.n4.nabble.com/how-to-build-boost-with-bzip2-in-non-standard-location-td2661155.html
+# http://www.gentoo.org/proj/en/base/amd64/howtos/?part=1&chap=3
+
+# Build dependencies:
+# - bzip2-devel
+
+export CFLAGS="-m64 -pipe -O2 -march=x86-64 -fPIC -shared"
+export CXXFLAGS="${CFLAGS}"
+
+mkdir -vp ${PREFIX}/bin;
+
+./bootstrap.sh --prefix="${PREFIX}/";
+
+sed -i'.bak' -e's/^using python.*;//' ./project-config.jam
+
+PY_INC=`$PYTHON -c "from distutils import sysconfig; print (sysconfig.get_python_inc(0, '$PREFIX'))"`
+
+echo "using python" >> ./project-config.jam
+echo "     : $PY_VER" >> ./project-config.jam
+echo "     : $PYTHON" >> ./project-config.jam
+echo "     : $PY_INC" >> ./project-config.jam
+echo "     : $PREFIX/lib" >> ./project-config.jam
+echo "     ;" >> ./project-config.jam
+
+./b2 -q install --debug-configuration;
+

conda-recipe/boost/e4bde20f.patch

@@ -0,0 +1,68 @@
+From e4bde20f2eec0a51be14533871d2123bd2ab9cf3 Mon Sep 17 00:00:00 2001
+From: Andrey Semashev <andrey.semashev@gmail.com>
+Date: Fri, 28 Feb 2014 12:43:11 +0400
+Subject: [PATCH] More compilation fixes for the case when 128-bit integers are
+ not supported.
+
+---
+ boost/atomic/detail/gcc-atomic.hpp | 17 ++++++++++++-----
+ 1 file changed, 12 insertions(+), 5 deletions(-)
+
+diff --git boost/atomic/detail/gcc-atomic.hpp boost/atomic/detail/gcc-atomic.hpp
+index a130590..4af99a1 100644
+--- boost/atomic/detail/gcc-atomic.hpp
++++ boost/atomic/detail/gcc-atomic.hpp
+@@ -958,14 +958,16 @@ class base_atomic<T, void, 16, Sign>
+
+ public:
+     BOOST_DEFAULTED_FUNCTION(base_atomic(void), {})
+-    explicit base_atomic(value_type const& v) BOOST_NOEXCEPT : v_(0)
++    explicit base_atomic(value_type const& v) BOOST_NOEXCEPT
+     {
++        memset(&v_, 0, sizeof(v_));
+         memcpy(&v_, &v, sizeof(value_type));
+     }
+
+     void store(value_type const& v, memory_order order = memory_order_seq_cst) volatile BOOST_NOEXCEPT
+     {
+-        storage_type tmp = 0;
++        storage_type tmp;
++        memset(&tmp, 0, sizeof(tmp));
+         memcpy(&tmp, &v, sizeof(value_type));
+         __atomic_store_n(&v_, tmp, atomics::detail::convert_memory_order_to_gcc(order));
+     }
+@@ -980,7 +982,8 @@ class base_atomic<T, void, 16, Sign>
+
+     value_type exchange(value_type const& v, memory_order order = memory_order_seq_cst) volatile BOOST_NOEXCEPT
+     {
+-        storage_type tmp = 0;
++        storage_type tmp;
++        memset(&tmp, 0, sizeof(tmp));
+         memcpy(&tmp, &v, sizeof(value_type));
+         tmp = __atomic_exchange_n(&v_, tmp, atomics::detail::convert_memory_order_to_gcc(order));
+         value_type res;
+@@ -994,7 +997,9 @@ class base_atomic<T, void, 16, Sign>
+         memory_order success_order,
+         memory_order failure_order) volatile BOOST_NOEXCEPT
+     {
+-        storage_type expected_s = 0, desired_s = 0;
++        storage_type expected_s, desired_s;
++        memset(&expected_s, 0, sizeof(expected_s));
++        memset(&desired_s, 0, sizeof(desired_s));
+         memcpy(&expected_s, &expected, sizeof(value_type));
+         memcpy(&desired_s, &desired, sizeof(value_type));
+         const bool success = __atomic_compare_exchange_n(&v_, &expected_s, desired_s, false,
+@@ -1010,7 +1015,9 @@ class base_atomic<T, void, 16, Sign>
+         memory_order success_order,
+         memory_order failure_order) volatile BOOST_NOEXCEPT
+     {
+-        storage_type expected_s = 0, desired_s = 0;
++        storage_type expected_s, desired_s;
++        memset(&expected_s, 0, sizeof(expected_s));
++        memset(&desired_s, 0, sizeof(desired_s));
+         memcpy(&expected_s, &expected, sizeof(value_type));
+         memcpy(&desired_s, &desired, sizeof(value_type));
+         const bool success = __atomic_compare_exchange_n(&v_, &expected_s, desired_s, true,
+-- 
+1.9.1
+

conda-recipe/boost/meta.yaml

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+
+package:
+    name: boost
+    version: 1.55.0
+
+source:
+    fn: boost_1_55_0.tar.bz2 [unix]
+    url: http://sourceforge.net/projects/boost/files/boost/1.55.0/boost_1_55_0.tar.bz2 [unix]
+    fn: boost_1_55_0-msvc-10.0-64.exe [win64]
+    url: http://downloads.sourceforge.net/project/boost/boost-binaries/1.55.0-build2/boost_1_55_0-msvc-10.0-64.exe [win64]
+    fn: boost_1_55_0-msvc-10.0-32.exe [win32]
+    url: http://download.sourceforge.net/project/boost/boost-binaries/1.55.0-build2/boost_1_55_0-msvc-10.0-32.exe [win32]
+    patches:
+      - e4bde20f.patch [osx]
+      - 6bb71fdd.patch [osx]
+
+build:
+    number: 3
+
+requirements:
+    build:
+      - zlib [unix]
+      - bzip2 [unix]
+      - python [unix]
+    run:	
+      - zlib [unix]
+      - bzip2 [unix]
+      - python [unix]
+
+about:
+    home: http://www.boost.org/
+    license: Boost-1.0
+

conda-recipe/certifi/build.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+$PYTHON setup.py install
+
+# Add more build steps here, if they are necessary.
+
+# See
+# http://docs.continuum.io/conda/build.html
+# for a list of environment variables that are set during the build process.

conda-recipe/certifi/meta.yaml

@@ -0,0 +1,60 @@
+package:
+  name: certifi
+  version: !!str 14.05.14
+
+source:
+  fn: certifi-14.05.14.tar.gz
+  url: https://pypi.python.org/packages/source/c/certifi/certifi-14.05.14.tar.gz
+  md5: 315ea4e50673a16ab047099f816fd32a
+#  patches:
+   # List any patch files here
+   # - fix.patch
+
+# build:
+  # preserve_egg_dir: True
+  # entry_points:
+    # Put any entry points (scripts to be generated automatically) here. The
+    # syntax is module:function.  For example
+    #
+    # - certifi = certifi:main
+    #
+    # Would create an entry point called certifi that calls certifi.main()
+
+
+  # If this is a new build for the same version, increment the build
+  # number. If you do not include this key, it defaults to 0.
+  # number: 1
+
+requirements:
+  build:
+    - python
+    - setuptools
+
+  run:
+    - python
+
+test:
+  # Python imports
+  imports:
+    - certifi
+
+  # commands:
+    # You can put test commands to be run here.  Use this to test that the
+    # entry points work.
+
+
+  # You can also put a file called run_test.py in the recipe that will be run
+  # at test time.
+
+  # requires:
+    # Put any additional test requirements here.  For example
+    # - nose
+
+about:
+  home: http://python-requests.org
+  license: ISC
+  summary: "Python package for providing Mozilla's CA Bundle."
+
+# See
+# http://docs.continuum.io/conda/build.html for
+# more information about meta.yaml

conda-recipe/colander/build.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+$PYTHON setup.py install
+
+# Add more build steps here, if they are necessary.
+
+# See
+# http://docs.continuum.io/conda/build.html
+# for a list of environment variables that are set during the build process.