Merge branch 'master' of https://github.com/biocore/qiita into version_0.2.0

Author: josenavas

qiita_core/configuration_manager.py

@@ -144,8 +144,8 @@ def __init__(self):
     def _get_main(self, config):
         """Get the configuration of the main section"""
         self.test_environment = config.getboolean('main', 'TEST_ENVIRONMENT')
-        default_base_data_dir = join(dirname(abspath(__file__)),
-                                     '..', 'qiita_db', 'support_files',
+        install_dir = dirname(dirname(abspath(__file__)))
+        default_base_data_dir = join(install_dir, 'qiita_db', 'support_files',
                                      'test_data')
         self.base_data_dir = config.get('main', 'BASE_DATA_DIR') or \
             default_base_data_dir

qiita_db/support_files/patches/31.sql

@@ -0,0 +1,3 @@
+-- August 24, 2015
+-- Delete all occurrences of '..' in the base_data_dir entry
+SELECT 42;

qiita_db/support_files/patches/python_patches/31.py

@@ -0,0 +1,11 @@
+from os.path import realpath
+from qiita_db.sql_connection import TRN
+
+with TRN:
+    TRN.add('SELECT base_data_dir FROM settings')
+    path = TRN.execute_fetchlast()
+
+    # if the path is non-canonical (it contains .. or other redundant symbols)
+    # this will update it, else it will leave as is
+    TRN.add("UPDATE settings SET base_data_dir = %s", (realpath(path),))
+    TRN.execute()

setup.py

@@ -90,14 +90,14 @@
                         'support_files/doc/source/_static/*.png'
                         ]},
       scripts=glob('scripts/*'),
-      extras_require={'test': ["nose >= 0.10.1", "pep8", 'mock'],
-                      'doc': ["Sphinx >= 1.2.2", "sphinx-bootstrap-theme"]},
+      extras_require={'test': ["nose >= 0.10.1", "pep8", 'mock']},
       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',
                         'h5py >= 2.3.1', 'biom-format', 'natsort', 'networkx',
                         'scikit-bio >= 0.2.3, < 0.3.0', 'wtforms == 2.0.1',
-                        'qiime >= 1.9.0, < 1.10.0', 'moi >= 0.2.0, < 0.3.0'],
+                        'qiime >= 1.9.0, < 1.10.0', 'moi >= 0.2.0, < 0.3.0',
+                        'sphinx-bootstrap-theme', 'Sphinx >= 1.2.2'],
       classifiers=classifiers
       )