Merge pull request #77 from jchodera/pdbfixer-dev

Have travis build pdbfixer-dev conda package and push to binstar

.travis.yml

 language: c
 
 env:
-    matrix:
-        - CONDA_PY=2.7
-        - CONDA_PY=3.3
-        - CONDA_PY=3.4
+  matrix:
+    - CONDA_PY=2.7
+    - CONDA_PY=3.3
+    - CONDA_PY=3.4
+
+  global:
+    # BINSTAR_TOKEN
+    - secure: "cnxHeIjLZF279xukl4VXXr/wTcQALeOek9a//ngFahvRA/GA/ysFWZ5UdDrH9fSN9bom1Q5zAsnmV/53deVtbcJ4CzUVAsug3TJtRnPEs42LJP8AQrTxlF5tgonHxC1IKxpJ47wezTBebRVe6223BV1J5fATnrploZeHPVq4/Do="
 
 install:
-    - sudo apt-get update -qq
-    - sudo apt-get install -qq python-dev python-pip python-yaml g++ ftp
-    - sudo pip install conda eventlet
-    - sudo conda init
-    - conda config --add channels http://conda.binstar.org/omnia
-    - conda create --yes --name test nose setuptools numpy biopython pyflakes openmm-dev
-    - export PATH="$HOME/envs/test/bin/:$PATH"
-    
+  - source devtools/ci/install.sh
+  - export PYTHONUNBUFFERED=true
+
 script:
-    - python setup.py install
-    - cd tests
-    - nosetests --with-doctest
+  # Build the conda package, running tests as part of the build.
+  - conda build devtools/conda-recipe
 
 after_script:
-    - pyflakes pdbfixer/*.py
+  # Run pyflakes.
+  - pyflakes pdbfixer/*.py
+
+after_success:
+  - echo "after_success"
+  # Upload conda dev package to binstar if all tests pass.
+  - bash -x devtools/ci/after_sucess.sh
 

devtools/ci/README.md

+Creating binstar token:
+```
+binstar auth --create -o omnia --max-age -1 --name pdbfixer-travis -s "api:read api:write"
+```

devtools/ci/after_sucess.sh

+#!/bin/bash
+
+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 jinja2
+    binstar -t $BINSTAR_TOKEN upload --force -u omnia -p pdbfixer-dev $HOME/miniconda/conda-bld/*/pdbfixer-dev-*.tar.bz2
+fi
+
+if [[ "$python" != "2.7" ]]; then
+    echo "No deploy on PYTHON_VERSION=${python}"; exit 0
+fi

devtools/ci/install.sh

+
+MINICONDA=Miniconda-latest-Linux-x86_64.sh
+MINICONDA_MD5=$(curl -s http://repo.continuum.io/miniconda/ | grep -A3 $MINICONDA | sed -n '4p' | sed -n 's/ *<td>\(.*\)<\/td> */\1/p')
+wget http://repo.continuum.io/miniconda/$MINICONDA
+if [[ $MINICONDA_MD5 != $(md5sum $MINICONDA | cut -d ' ' -f 1) ]]; then
+    echo "Miniconda MD5 mismatch"
+    exit 1
+fi
+bash $MINICONDA -b
+PIP_ARGS="-U"
+
+export PATH=$HOME/miniconda/bin:$PATH
+
+sudo apt-get update
+#sudo apt-get install -qq -y g++ gfortran csh g++-multilib gcc-multilib openbabel
+
+conda update --yes conda
+conda config --add channels http://conda.binstar.org/omnia
+conda install --yes conda-build jinja2 binstar pip

devtools/conda-recipe/build.sh

+#!/bin/bash
+
+cp -r $RECIPE_DIR/../.. $SRC_DIR
+$PYTHON setup.py install

devtools/conda-recipe/meta.yaml

+package:
+  name: pdbfixer-dev
+  version: dev
+
+requirements:
+  build:
+    - python
+    - setuptools
+    - openmm-dev
+    - numpy
+
+  run:
+    - python
+    - openmm-dev
+    - numpy
+
+test:
+  requires:
+    - nose
+
+  commands:
+    - nosetests pdbfixer --nocapture --verbosity=2 --with-doctest
+
+about:
+  home: http://github.com/pandegroup/pdbfixer
+  license: free
+  summary: PDBFixer fixes problems in PDB files to prepare them for molecular simulation.

setup.cfg

+[nosetests]
+verbosity=2
+with-doctest=1