Merge pull request #210 from jchodera/master

Add testing for py35
choderalab · Feb 12, 2016 · a60ca61 · a60ca61
2 parents 9c4acd6 + 5876dac
commit a60ca61
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Showing 8 changed files with 117 additions and 41 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -1,26 +1,41 @@
 language: c
-
-branches:
-  only:
-    - master
+sudo: false
+addons:
+  apt:
+    sources:
+    - ubuntu-toolchain-r-test
+    packages:
+      - g++
+      - gfortran
+      - valgrind
+      - csh
+      - g++-multilib
+      - gcc-multilib
 
 install:
-  - source devtools/ci/install.sh
+  - source devtools/travis-ci/install.sh
   - export PYTHONUNBUFFERED=true
+  - export CC=gcc
+  - export CXX=g++
 
 script:
-  # this builds the binary, unpacks it, and runs the tests
+  - conda config --add channels ${ORGNAME}
   - conda build devtools/conda-recipe
-
+  - source activate _test
+  - conda install --yes --quiet pip nose nose-timer
+  - cd devtools && nosetests $PACKAGENAME --nocapture --verbosity=2 --with-doctest --with-timer && cd ..
 env:
   matrix:
-    - CONDA_PY=2.7
-    - CONDA_PY=3.3
-    - CONDA_PY=3.4    
+    - python=2.7  CONDA_PY=27
+    - python=3.4  CONDA_PY=34
+    - python=3.5  CONDA_PY=35
 
   global:
+    - ORGNAME="omnia"
+    - PACKAGENAME="pymbar"
     # encrypted BINSTAR_TOKEN for push of dev package to binstar
     - secure: "lu3EsyPF+woAABbZyctdFUPfTkAUOyC7k7LsDmWBMrV6ctpvYkomDFS65NAElXDOnmPzxMpn4+f0V2+tNqD4sM/9erDfM2MkJH+tRznNkAAZFoxbxeZCmzV4zSzNvAKlopasHSXt2mbhzbDnhrIToAssQZMHp13pNlBMEq86hKc="
 
 after_success:
-  - source devtools/ci/after_sucess.sh
+  - echo "after_success"
+  - ./devtools/travis-ci/after_success.sh
diff --git a/devtools/ci/after_sucess.sh b/devtools/ci/after_sucess.sh
diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml
@@ -11,7 +11,7 @@ requirements:
     - numpy
     - scipy
     - setuptools
-    - numexpr   
+    - numexpr
     - six
   run:
     - python
@@ -24,7 +24,7 @@ test:
   requires:
     - nose
     - setuptools
-    - statsmodels    
+    - statsmodels
   imports:
     - pymbar
   commands:

diff --git a/devtools/travis-ci/after_success.sh b/devtools/travis-ci/after_success.sh
@@ -0,0 +1,36 @@
+#!/bin/bash
+# Must be invoked with $PACKAGENAME
+
+echo $TRAVIS_PULL_REQUEST $TRAVIS_BRANCH
+PUSH_DOCS_TO_S3=false
+
+if [ "$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
+
+
+# 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
+
+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 install --yes `conda build devtools/conda-recipe --output`
+    pip install numpydoc s3cmd msmb_theme
+    conda install --yes `cat docs/requirements.txt | xargs`
+
+    conda list -e
+
+    (cd docs && make html && cd -)
+    ls -lt docs/_build
+    pwd
+    python devtools/ci/push-docs-to-s3.py
+fi
diff --git a/devtools/travis-ci/index.html b/devtools/travis-ci/index.html
@@ -0,0 +1 @@
+<html><head><meta http-equiv="refresh" content="0;URL='/latest'"/></head></html>
diff --git a/devtools/ci/install.sh → devtools/travis-ci/install.sh b/devtools/ci/install.sh → devtools/travis-ci/install.sh
@@ -1,17 +1,20 @@
+#!/bin/bash
+pushd .
+
+# Install Miniconda
+cd $HOME
 MINICONDA=Miniconda-latest-Linux-x86_64.sh
 MINICONDA_MD5=$(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"
+bash $MINICONDA -b -p miniconda
 
-sudo ln -s /usr/bin/g++ /usr/bin/g++44
+# Configure miniconda
 export PATH=$HOME/miniconda/bin:$PATH
+conda install --yes conda-build jinja2 anaconda-client pip
+conda config --add channels omnia
 
-conda update --yes conda
-conda config --add channels http://conda.binstar.org/omnia
-conda install --yes conda-build
-
+popd
diff --git a/devtools/travis-ci/push-docs-to-s3.py b/devtools/travis-ci/push-docs-to-s3.py
@@ -0,0 +1,39 @@
+import os
+import pip
+import tempfile
+import subprocess
+import pymbar.version
+
+
+BUCKET_NAME = 'pymbar.org'
+if not pymbar.version.release:
+    PREFIX = 'latest'
+else:
+    PREFIX = pymbar.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')
+# The secret key is available as a secure environment variable
+# on travis-ci to push the build documentation to Amazon S3.
+with tempfile.NamedTemporaryFile('w') as f:
+    f.write('''[default]
+access_key = {AWS_ACCESS_KEY_ID}
+secret_key = {AWS_SECRET_ACCESS_KEY}
+'''.format(**os.environ))
+    f.flush()
+
+    template = ('s3cmd --guess-mime-type --config {config} '
+                'sync docs/_build/ s3://{bucket}/{prefix}/')
+    cmd = template.format(
+            config=f.name,
+            bucket=BUCKET_NAME,
+            prefix=PREFIX)
+    return_val = subprocess.call(cmd.split())
+
+    # Sync index file.
+    template = ('s3cmd --guess-mime-type --config {config} '
+                'sync devtools/ci/index.html s3://{bucket}/')
+    cmd = template.format(
+            config=f.name,
+            bucket=BUCKET_NAME)
+    return_val = subprocess.call(cmd.split())
diff --git a/setup.cfg b/setup.cfg
@@ -1,3 +1,6 @@
 [nosetests]
 verbosity=2
 with-doctest=1
+
+[metadata]
+description-file = README.md