Sync with master

CHANGELOG.md

@@ -1,8 +1,10 @@
 # Qiita changelog
 
+Version 0.2.0-dev (Changes since version 0.2.0 go here)
+-------------------------------------------------------
 
-Qiita 0.1.0-dev (changes since Qiita 0.1.0 go here)
----------------------------------------------------
+Version 0.2.0 (2015-08-25)
+--------------------------
 
 * Creating an empty RawData is no longer needed in order to add a PrepTemplate.
 Now, the PrepTemplate is required in order to add a RawData to a study. This is

qiita_core/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "0.1.0-dev"
+__version__ = "0.2.0-dev"

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_core/support_files/config_test.cfg

@@ -63,7 +63,7 @@ USER =
 PASSWORD =
 
 # The email to have messages sent from
-EMAIL = donotreply@qiita.colorado.edu
+EMAIL = example@domain.com
 
 # ----------------------------- Redis settings --------------------------------
 [redis]
@@ -126,7 +126,7 @@ EBI_CENTER_NAME = CCME-COLORADO
 
 # This string (with an underscore) will be prefixed to your EBI submission and
 # study aliases
-EBI_ORGANIZATION_PREFIX = qiime
+EBI_ORGANIZATION_PREFIX = example_organization
 
 
 # ----------------------------- IPython settings -----------------------------

qiita_db/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "0.1.0-dev"
+__version__ = "0.2.0-dev"

qiita_db/environment_manager.py

@@ -120,7 +120,7 @@ def _insert_processed_params(ref):
         TRN.execute()
 
 
-def _download_reference_files(conn):
+def _download_reference_files():
     print('Downloading reference files')
     if not exists(reference_base_dir):
         mkdir(reference_base_dir)
@@ -242,7 +242,8 @@ def make_environment(load_ontologies, download_reference, add_demo_user):
             sql = """INSERT INTO qiita.analysis (email, name, description,
                                                  dflt, analysis_status_id)
                      VALUES ('demo@microbio.me', 'demo@microbio.me-dflt',
-                             'dflt', 't', 1)"""
+                             'dflt', 't', 1)
+                     RETURNING analysis_id"""
             TRN.add(sql)
             analysis_id = TRN.execute_fetchlast()
 

qiita_db/metadata_template/test/__init__.py

@@ -5,5 +5,3 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
-
-__version__ = "0.0.1-dev"

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()

qiita_db/test/__init__.py

@@ -5,5 +5,3 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
-
-__version__ = "0.0.1-dev"

qiita_pet/__init__.py

@@ -13,4 +13,4 @@
     'IE': 10
 }
 
-__version__ = "0.1.0-dev"
+__version__ = "0.2.0-dev"

qiita_pet/handlers/__init__.py

@@ -8,5 +8,3 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
-
-__version__ = "0.0.1-dev"

qiita_ware/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "0.1.0-dev"
+__version__ = "0.2.0-dev"

setup.py

@@ -10,7 +10,7 @@
 from setuptools import setup
 from glob import glob
 
-__version__ = "0.1.0-dev"
+__version__ = "0.2.0-dev"
 
 
 classes = """
@@ -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
       )