Merge pull request #5 from choderalab/travis

Add support for continuous integration via travis

.travis.yml

@@ -0,0 +1,47 @@
+language: c
+sudo: false
+
+branches:
+  only:
+    - master
+
+install:
+  - source devtools/travis-ci/install.sh
+  - export PYTHONUNBUFFERED=true
+  # Add org channel
+  - conda config --add channels ${ORGNAME}
+
+script:
+  # Create a test environment
+  - conda create --yes -n test python=$python
+  # Activate the test environment
+  - source activate test
+  # Add channels
+  - conda config --add channels conda-forge
+  - conda config --add channels omnia
+  - conda config --add channels https://conda.anaconda.org/omnia/label/dev
+  # Install extras for OpenEye and testing
+  - conda install --yes --quiet pip nose nose-timer
+  # Build the recipe
+  - conda build devtools/conda-recipe
+  # Install the package
+  - conda install --yes --use-local ${PACKAGENAME}-dev
+  # Test the package
+  #- cd devtools && nosetests $PACKAGENAME --nocapture --verbosity=2 --with-timer -a '!slow' && cd ..
+  - nosetests $PACKAGENAME --nocapture --verbosity=2 --with-timer
+  # Test the examples
+  - python benchmark/experiments/baoab_vs_vvvr.py
+
+os:
+  - osx
+  - linux
+
+env:
+  matrix:
+    - python=2.7  CONDA_PY=2.7
+    - python=3.5  CONDA_PY=3.5
+    - python=3.5  CONDA_PY=3.6
+
+  global:
+    - ORGNAME="omnia"
+    - PACKAGENAME="benchmark"

README.md

@@ -1,2 +1,5 @@
+[![Build Status](https://travis-ci.org/choderalab/integrator-benchmark.svg?branch=master)](https://travis-ci.org/choderalab/integrator-benchmark?branch=master)
+
 # integrator-benchmark
+
 Enumerating and evaluating numerical integrators of Langevin dynamics

devtools/README.md

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+Developer Notes / Tools
+=======================
+
+Assorted "Ho-To's" for developers
+
+How to contribute changes
+-------------------------
+- Clone the repository if you have write access to the main repo, fork the repositiory if you are a collaborator.
+- Make a new branch with `git checkout -b {your branch name}`
+- Make changes and test your code
+- Push the branch to the repo (either the main or your fork) with `git push -u origin {your branch name}`
+  * Note that `origin` is the default name assigned to the remote, yours may be different
+- Make a PR on GitHub with your changes
+- We'll review the changes and get your code into the repo after lively discussion!
+
+
+Checklist for all Updates
+-------------------------
+- [ ] Update `setup.py` version number (see specific update type for details)
+- [ ] Make sure there is an/are issue(s) opened for your specific update
+- [ ] Create the PR, referencing the issue
+- [ ] Debug the PR as needed until tests pass
+- [ ] Tag the final, debugged version as the one in `setup.py`
+   *  `git tag -a X.Y.Z [latest pushed commit] && git push --follow-tags`
+- [ ] Get the PR merged in
+
+
+Checklist for Major Revisions (`integrator-benchmark` X.Y+1.0)
+--------------------------------------------------------------
+- [ ] Make sure all issues related to the milestone will be closed by this commit or moved to future releases
+- [ ] Update `docs/whatsnew.rst`
+- [ ] Update `setup.py` with version number and `ISRELEASED` to `True`
+- [ ] Do the steps for All Upates
+- [ ] Create a new release on GitHub, reference the tag and copy the changes in `docs/whatsnew.rst`
+- [ ] Update the `omnia-md/conda-recipies` repo by creating a new PR with updated versions
+  * Be sure to pin dependencies to fixed version
+
+Checklist for Minor Revisions (`integrator-benchmark` X.Y.Z+1)
+--------------------------------------------
+- [ ] Update `setup.py` with the correct Z version number in X.Y.Z
+- [ ] In `setup.py`, set `ISRELEASED` to `False`
+- [ ] Do all the steps for All Updates
+  * If this is a critical bugfix (i.e. `integrator-benchmark` X.Y.0 is broken and/or flat out wrong without the fix):
+- [ ] Update `docs/whatsnew.rst`
+- [ ] Update the released version on the site to this version, adjusting the tag and note that this is a critical bugfix which corrects the X.Y release
+- [ ] Update the `omnia-md/conda-recipies` repo to point at the corrected version

devtools/conda-recipe/README.md

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+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 yank-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.

devtools/conda-recipe/build.sh

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+#!/bin/bash
+
+#export CC=${PREFIX}/bin/gcc
+#export CXX=${PREFIX}/bin/g++
+
+# conda provides default values of these on Mac OS X,
+# but we don't want them when building with gcc
+#export CFLAGS=""
+#export CXXFLAGS=""
+#export LDFLAGS=""
+
+# Build the python package
+$PYTHON setup.py install

devtools/conda-recipe/meta.yaml

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+package:
+  name: benchmark-dev
+  version: 0.0.0
+
+source:
+  path: ../..
+
+build:
+  preserve_egg_dir: True
+  number: 0
+
+requirements:
+  build:
+    - python
+    - cython
+    - numpy
+    - scipy
+    - setuptools
+    - netcdf4
+    - openmm >=7.1
+    - mdtraj >=1.7.2
+    - openmmtools
+    - pymbar
+    - seaborn
+    - tqdm
+    - scikit-learn
+    - numba
+
+  run:
+    - python
+    - pandas
+    - numpy
+    - scipy
+    - cython
+    - netcdf4
+    - openmm >=7.1
+    - mdtraj >=1.7.2
+    - openmmtools
+    - pymbar
+    - seaborn
+    - tqdm
+    - scikit-learn
+    - numba
+
+test:
+  requires:
+    - nose
+    - nose-timer
+  imports:
+    - benchmark
+
+about:
+  home: https://github.com/choderalab/integrator-benchmark
+  license: MIT License

devtools/travis-ci/install.sh

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+# Temporarily change directory to $HOME to install software
+pushd .
+cd $HOME
+
+if [[ "$TRAVIS_OS_NAME" == "osx" ]];   then MINICONDA=Miniconda3-latest-MacOSX-x86_64.sh; fi
+if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then MINICONDA=Miniconda3-latest-Linux-x86_64.sh;  fi
+
+MINICONDA_MD5=$(curl -s https://repo.continuum.io/miniconda/ | grep -A3 $MINICONDA | sed -n '4p' | sed -n 's/ *<td>\(.*\)<\/td> */\1/p')
+wget https://repo.continuum.io/miniconda/$MINICONDA
+bash $MINICONDA -b
+rm -f $MINICONDA
+
+export PATH=$HOME/miniconda3/bin:$PATH
+
+conda update -yq conda
+conda install -yq conda-build jinja2 anaconda-client pip
+
+# Restore original directory
+popd