Merge pull request #509 from jchodera/conda-dev-travis-ci

Automated conda packaging of openmm-dev [ready to merge]

.travis.yml

-language: cpp
-compiler:
-  - clang
+language: c
 
-before_install:
-  - sudo apt-get update -qq
-  - sudo apt-get install -qq libpcre3 libpcre3-dev gromacs
-  - sudo apt-get install -qq swig doxygen llvm-3.3
-  - sudo apt-get install -qq python-numpy python-scipy python-pip
-  - sudo pip install nose
-  - export ASAN_SYMBOLIZER_PATH=/usr/bin/llvm-symbolizer-3.3
+install:
+  - source tools/ci/install.sh
+  - export PYTHONUNBUFFERED=true
 
 script:
-  - cmake -DCMAKE_INSTALL_PREFIX=$HOME/OpenMM .
-  - make -j2
-  - make -j2 install
-  - sudo make PythonInstall
-  - # run all of the tests
-  - ctest -j2 -V
-  - # get a list of all of the failed tests into this stupid ctest format
-  - python -c 'fn = "Testing/Temporary/LastTestsFailed.log"; import os; os.path.exists(fn) or exit(0); l = [line.split(":")[0] for line in open(fn)]; triplets = zip(l, l, [","]*len(l)); print "".join(",".join(t) for t in triplets)' > FailedTests.log
-  - # rerun all of the failed tests
-  - if [ -s FailedTests.log ]; then ctest -V -I FailedTests.log; fi;
-  - # run the python tests too
-  - cd python/tests
+  - export CC="clang++"
+  - source deactivate
+  - conda install --yes conda-build
+  - # Build the conda package, testing build before packaging.
+  - conda build tools/conda-recipe
+  - # Install the conda package locally.
+  - source activate $python
+  - conda install $HOME/miniconda/conda-bld/linux-64/openmm-dev-*
+  - conda list -e
+  - # Run the Python tests.
+  - pushd .
+  - cd wrappers/python/tests
   - nosetests -vv --processes=-1 --process-timeout=200
+  - popd
+
+env:
+  global:
+    # encrypted BINSTAR_TOKEN for push of dev package to binstar
+    - secure: Qz3pEYXXFnNQ/WK+15ad4cdbLJvzgCIZRwKD9fLiS3CDO2ldAQWxzaz8RQOwqbFtZUWu7lQpr+GukNJz5p0w18QEto+BxLYG9aW5mjoc+F2vCjyWFjkwnJ/Z/3uBKTcr5x9Y7HKaPGivaJ4BNACifjt7cCpeVJzV6u2+bBgSoHc=
+
+  matrix:
+    - python=2.7  CONDA_PY=27
+    #- python=3.3  CONDA_PY=33
+
+after_success:
+  - echo "after_success"
+  - source tools/ci/after_success.sh
+
+

tools/ci/after_success.sh

+echo $TRAVIS_PULL_REQUEST $TRAVIS_BRANCH
+
+if [[ "$TRAVIS_PULL_REQUEST" == "true" ]]; then
+    echo "This is a pull request. No deployment will be done."; exit 0
+fi
+
+
+if [[ "$TRAVIS_BRANCH" != "master" ]]; then
+    echo "No deployment on BRANCH='$TRAVIS_BRANCH'"; exit 0
+fi
+
+
+if [[ "2.7 3.3" =~ "$python" ]]; then
+    conda install --yes binstar
+    binstar -t $BINSTAR_TOKEN upload --force -u omnia -p openmm-dev $HOME/miniconda/conda-bld/linux-64/openmm-dev-*
+fi
+
+if [[ "$python" != "2.7" ]]; then
+    echo "No deploy on PYTHON_VERSION=${python}"; exit 0
+fi
+

tools/ci/install.sh

+# Original OpenMM .travis.yml requirements.
+sudo apt-get update -qq
+sudo apt-get install -qq libpcre3 libpcre3-dev gromacs
+sudo apt-get install -qq swig doxygen llvm-3.3
+sudo apt-get install -qq libgl1-mesa-dev opencl-headers fglrx=2:8.960-0ubuntu1 # for opencl support
+export ASAN_SYMBOLIZER_PATH=/usr/bin/llvm-symbolizer-3.3
+
+# New requirements.
+sudo apt-get install -qq -y g++ gfortran csh
+sudo apt-get install -qq -y g++-multilib gcc-multilib
+wget http://repo.continuum.io/miniconda/Miniconda-3.0.5-Linux-x86_64.sh
+bash Miniconda-3.0.5-Linux-x86_64.sh -b
+PIP_ARGS="-U"
+
+export PATH=$HOME/miniconda/bin:$PATH
+
+conda update --yes conda
+conda config --add channels http://conda.binstar.org/omnia
+conda create --yes -n ${python} python=${python} --file tools/ci/requirements-conda.txt
+source activate $python
+$HOME/miniconda/envs/${python}/bin/pip install $PIP_ARGS nose-exclude

tools/ci/requirements-conda.txt

+numpy
+cython
+pip
+nose
+

tools/conda-recipe/README.md

+This is a recipe for building the current development package into a conda binary.
+
+The installation on travis-ci is done by building the conda package, installing
+it, running the tests, and then if successful pushing the package to binstar
+(and the docs to AWS S3). The binstar auth token is an encrypted environment
+variable generated using:
+
+binstar auth -n openmm-travis -o omnia --max-age 22896000 -c --scopes api:write
+
+and then saved in the environment variable BINSTAR_TOKEN.
+
+You can set up travis to store an encrypted token via
+
+gem install travis travis encrypt BINSTAR_TOKEN=xx
+
+where xx is the token output by binstar. The final command should print a line (containing 'secure') for inclusion in your .travis.yml file.

tools/conda-recipe/build.sh

+#!/bin/bash
+
+CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=$PREFIX"
+
+if [[ "$OSTYPE" == "linux-gnu" ]]; then
+    # setting the rpath so that libOpenMMPME.so finds the right libfftw3
+    CMAKE_FLAGS+=" -DCMAKE_INSTALL_RPATH=.."
+    CMAKE_FLAGS+=" -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++"
+    #CMAKE_FLAGS+=" -DOPENCL_LIBRARY=/opt/AMDAPP/lib/x86_64/libOpenCL.so" # TEST
+
+elif [[ "$OSTYPE" == "darwin"* ]]; then
+    export MACOSX_DEPLOYMENT_TARGET="10.7"
+    CMAKE_FLAGS+=" -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++"
+fi
+
+# Set location for FFTW3 on both linux and mac
+CMAKE_FLAGS+=" -DFFTW_INCLUDES=$PREFIX/include"
+if [[ "$OSTYPE" == "linux-gnu" ]]; then
+    CMAKE_FLAGS+=" -DFFTW_LIBRARY=$PREFIX/lib/libfftw3f.so"
+    CMAKE_FLAGS+=" -DFFTW_THREADS_LIBRARY=$PREFIX/lib/libfftw3f_threads.so"
+elif [[ "$OSTYPE" == "darwin"* ]]; then
+    CMAKE_FLAGS+=" -DFFTW_LIBRARY=$PREFIX/lib/libfftw3f.dylib"
+    CMAKE_FLAGS+=" -DFFTW_THREADS_LIBRARY=$PREFIX/lib/libfftw3f_threads.dylib"
+fi
+
+# Copy source to current directory.
+cp -r $RECIPE_DIR/../.. .
+
+# Build in subdirectory.
+mkdir build
+cd build
+cmake .. $CMAKE_FLAGS
+make -j4
+make install
+
+# Run C tests.
+# Exclude OpenCL tests because @peastman suspects mesa on travis implementation is broken.
+# @jchodera and @pgrinaway suspect travis is working, but AMD OpenCL tests are actually failing due to a bug.
+ctest -j2 -V -E "[A-Za-z]+OpenCL[A-Za-z]+"
+
+# Install Python wrappers.
+export OPENMM_INCLUDE_PATH=$PREFIX/include
+export OPENMM_LIB_PATH=$PREFIX/lib
+cd python
+$PYTHON setup.py install
+cd ..
+
+# Remove one random file
+#rm $PREFIX/bin/TestReferenceHarmonicBondForce
+
+# Copy all tests to bin directory so they will be distributed with install package.
+cp `find . -name "Test*" -type f -maxdepth 1` $PREFIX/bin
+

tools/conda-recipe/meta.yaml

+package:
+  name: openmm
+  version: !!str dev
+
+requirements:
+  build:
+    - cmake
+    - python
+    - fftw3f
+
+  run:
+    - python
+    - fftw3f
+    - numpy
+
+about:
+  home: https://simtk.org/home/openmm
+  license: GPL

tools/conda-recipe/plugin-dir.patch

+diff --git wrappers/python/simtk/openmm/__init__.py wrappers/python/simtk/openmm/__init__.py
+index 7e47b11..0ef290a 100644
+--- wrappers/python/simtk/openmm/__init__.py
++++ wrappers/python/simtk/openmm/__init__.py
+@@ -13,6 +13,10 @@ import os, os.path
+ from simtk.openmm.openmm import *
+ from simtk.openmm.vec3 import Vec3
+ from simtk.openmm import version
+-if os.getenv('OPENMM_PLUGIN_DIR') is None and os.path.isdir(version.openmm_library_path):
++_plugin_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.abspath(__file__)), '..', '..', '..', '..', 'plugins'))
++if os.path.isdir(_plugin_dir):
++    pluginLoadedLibNames = Platform.loadPluginsFromDirectory(_plugin_dir)
++    del _plugin_dir
++elif os.getenv('OPENMM_PLUGIN_DIR') is None and os.path.isdir(version.openmm_library_path):
+     pluginLoadedLibNames = Platform.loadPluginsFromDirectory(os.path.join(version.openmm_library_path, 'plugins'))
+ else:
+     pluginLoadedLibNames = Platform.loadPluginsFromDirectory(Platform.getDefaultPluginsDirectory())
\ No newline at end of file

wrappers/python/tests/TestBytes.py

@@ -8,7 +8,8 @@ class TestBytes(unittest.TestCase):
         system.addParticle(1.0)
         refPositions = [(0,0,0)]
 
-        context = mm.Context(system, mm.VerletIntegrator(0))
+        platform = mm.Platform.getPlatformByName('Reference')
+        context = mm.Context(system, mm.VerletIntegrator(0), platform)
         context.setPositions(refPositions)
         chk = context.createCheckpoint()
         # check that the return value of createCheckpoint is of type bytes (non-unicode)