Merge pull request #218 from jchodera/master

Update pymbar-dev builds with newer devtools framework

.travis.yml

@@ -4,19 +4,11 @@ addons:
   apt:
     sources:
     - ubuntu-toolchain-r-test
-    packages:
-      - g++
-      - gfortran
-      - valgrind
-      - csh
-      - g++-multilib
-      - gcc-multilib
 
 install:
-  - source devtools/travis-ci/install.sh
+  - bash -x devtools/travis-ci/install.sh
   - export PYTHONUNBUFFERED=true
-  - export CC=gcc
-  - export CXX=g++
+  - export PATH=$HOME/miniconda/bin:$PATH
 
 script:
   - conda config --add channels ${ORGNAME}
@@ -38,4 +30,4 @@ env:
 
 after_success:
   - echo "after_success"
-  - ./devtools/travis-ci/after_success.sh
+  - if [ "$TRAVIS_SECURE_ENV_VARS" == true ]; then source devtools/travis-ci/after_success.sh; fi

devtools/travis-ci/after_success.sh

@@ -16,13 +16,20 @@ fi
 
 # Deploy to binstar
 conda install --yes anaconda-client jinja2
-binstar -t $BINSTAR_TOKEN upload --force -u ${ORGNAME} -p ${PACKAGENAME}-dev $HOME/miniconda/conda-bld/*/${PACKAGENAME}-dev-*.tar.bz2
+pushd .
+cd $HOME/miniconda/conda-bld
+FILES=*/${PACKAGENAME}-dev-*.tar.bz2
+for filename in $FILES; do
+    anaconda -t $BINSTAR_TOKEN remove --force ${ORGNAME}/${PACKAGENAME}-dev/${filename}
+    anaconda -t $BINSTAR_TOKEN upload --force -u ${ORGNAME} -p ${PACKAGENAME}-dev ${filename}
+done
+popd
 
 if [ $PUSH_DOCS_TO_S3 = true ]; then
    # Create the docs and push them to S3
    # -----------------------------------
     conda install --yes pip
-    conda config --add channels http://conda.binstar.org/omnia
+    conda config --add channels $ORGNAME
     conda install --yes `conda build devtools/conda-recipe --output`
     pip install numpydoc s3cmd msmb_theme
     conda install --yes `cat docs/requirements.txt | xargs`

devtools/travis-ci/install.sh

@@ -1,20 +1,23 @@
-#!/bin/bash
+# Temporarily change directory to $HOME to install software
 pushd .
+cd $HOME
 
 # Install Miniconda
-cd $HOME
 MINICONDA=Miniconda-latest-Linux-x86_64.sh
+MINICONDA_HOME=$HOME/miniconda
 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/$MINICONDA
+wget -q http://repo.continuum.io/miniconda/$MINICONDA
 if [[ $MINICONDA_MD5 != $(md5sum $MINICONDA | cut -d ' ' -f 1) ]]; then
     echo "Miniconda MD5 mismatch"
     exit 1
 fi
-bash $MINICONDA -b -p miniconda
+bash $MINICONDA -b -p $MINICONDA_HOME
 
 # Configure miniconda
-export PATH=$HOME/miniconda/bin:$PATH
+export PIP_ARGS="-U"
+export PATH=$MINICONDA_HOME/bin:$PATH
+conda update --yes conda
 conda install --yes conda-build jinja2 anaconda-client pip
-conda config --add channels omnia
 
-popd
+# Restore original directory
+popd

devtools/travis-ci/push-docs-to-s3.py

@@ -1,15 +1,24 @@
+#!/usr/bin/env python
+
+"""
+Must have the vollowing environment variables defined:
+* BUCKET_NAME : AWS bucket name
+* PREFIX : 'latest' or other version number
+
+"""
+
 import os
 import pip
 import tempfile
 import subprocess
-import pymbar.version
+import thermopyl.version
 
 
-BUCKET_NAME = 'pymbar.org'
-if not pymbar.version.release:
+BUCKET_NAME = 'thermopyl.org'
+if not thermopyl.version.release:
     PREFIX = 'latest'
 else:
-    PREFIX = pymbar.version.short_version
+    PREFIX = thermopyl.version.short_version
 
 if not any(d.project_name == 's3cmd' for d in pip.get_installed_distributions()):
     raise ImportError('The s3cmd pacakge is required. try $ pip install s3cmd')