Merge branch 'master' of https://github.com/biocore/qiita into cart

Author: squirrelo

.travis.yml

@@ -14,15 +14,13 @@ before_install:
   # Update conda itself
   - conda update --yes conda
 install:
-  - conda create --yes -n env_name python=$PYTHON_VERSION pip nose openpyxl=1.8.2 pandas>=0.15 pyzmq flake8
-  - conda install --yes -n env_name python=$PYTHON_VERSION h5py>=2.3.1
+  # install a few of the dependencies that pip would otherwise try to install
+  # when intalling scikit-bio
+  - conda create --yes -n env_name python=$PYTHON_VERSION pip nose flake8 pyzmq networkx pyparsing natsort mock 'pandas>=0.15' 'matplotlib>=1.1.0' 'scipy>0.13.0' 'numpy>= 1.7' 'h5py>=2.3.1' 'future==0.13.0'
   - source activate env_name
-  - pip install coveralls cogent burrito qcli burrito-fillings ipython[all]==2.4.1
+  - pip install coveralls ipython[all]==2.4.1
   - pip install https://github.com/biocore/mustached-octo-ironman/archive/master.zip
-  - pip install https://github.com/biocore/qiime/archive/master.zip --no-deps
   - pip install .
-  # upgrade click, older versions of click do not have __version__
-  - pip install -U click
 script:
   - export MOI_CONFIG_FP=`pwd`/qiita_core/support_files/config_test.txt
   - ipython profile create qiita_general --parallel
@@ -32,9 +30,6 @@ script:
   - if [ ${TEST_ADD_STUDIES} == "False" ]; then qiita_test_install ; fi
   - if [ ${TEST_ADD_STUDIES} == "False" ]; then nosetests --with-doctest --with-coverage ; fi
   - if [ ${TEST_ADD_STUDIES} == "False" ]; then flake8 qiita_* setup.py scripts/qiita scripts/qiita_env scripts/qiita_test_install ; fi
-  # we need to run the test suite from setup.py for coveralls to grab the info
-  # - coverage run setup.py test
-  # - coverage report -m
 services:
   - redis-server
 after_success:

qiita_pet/handlers/stats.py

@@ -59,7 +59,7 @@ def get(self):
 
         # Pull a random public study from the database
         public_studies = Study.get_by_status('public')
-        study = Study(choice(public_studies)) if public_studies else None
+        study = Study(choice(list(public_studies))) if public_studies else None
         if study is None:
             random_study_info = None
             random_study_title = None

setup.py

@@ -75,7 +75,7 @@
       scripts=glob('scripts/*'),
       extras_require={'test': ["nose >= 0.10.1", "pep8", 'mock'],
                       'doc': ["Sphinx >= 1.2.2", "sphinx-bootstrap-theme"]},
-      install_requires=['psycopg2', 'click == 1.0', 'future==0.13.0',
+      install_requires=['psycopg2', 'click >= 3.3', 'future==0.13.0',
                         'bcrypt', 'pandas >= 0.15', 'numpy >= 1.7',
                         'tornado==3.1.1', 'toredis', 'redis',
                         'ipython[all] >= 2.4.1, < 2.5', 'pyparsing',