Merge pull request #1135 from ElDeveloper/alpha-0.1-release

MAINT: Updates for 0.1 alpha release

Author: antgonza

CHANGELOG.md

@@ -0,0 +1,6 @@
+# Qiita changelog
+
+Version 0.1.0 (2015-04-29)
+--------------------------
+
+Initial alpha release.

INSTALL.md

@@ -9,7 +9,15 @@ Install the non-python dependencies
 * [PostgreSQL](http://www.postgresql.org/download/) (we have tested most extensively with 9.3)
 * [redis-server](http://redis.io) (we have tested most extensively with 2.8.17)
 
-Install both of these packages according to the instructions on their websites. You'll then need to ensure that the postgres binaries (for example, ``psql``) are in your executable search path (``$PATH`` environment variable).
+Install both of these packages according to the instructions on their websites.
+You'll then need to ensure that the postgres binaries (for example, ``psql``)
+are in your executable search path (``$PATH`` environment variable). For
+example if you are using Postgres.app on OS X, you can do this by addint
+the following line to your `.bash_profile`:
+
+```bash
+export PATH=$PATH:/Applications/Postgres.app/Contents/Versions/9.3/bin/
+```
 
 Install Qiita and its python dependencies
 -----------------------------------------
@@ -29,7 +37,7 @@ After these commands are executed, you will need to:
 
   ```bash
   cd
-  curl -O https://raw.githubusercontent.com/biocore/qiita/master/qiita_core/support_files/config_test.txt > config_test.txt
+  curl -O https://raw.githubusercontent.com/biocore/qiita/master/qiita_core/support_files/config_test.txt
   ```
 
 2. Set your `QIITA_CONFIG_FP` environment variable to point to that file:
@@ -46,10 +54,15 @@ After these commands are executed, you will need to:
   qiita_env make --no-load-ontologies
   ```
 
-4. Finally you can start the server:
+4. Start the redis server:
+  ```bash
+  redis-server
+  ```
+
+5. Finally you can start the server:
 
   ```bash
-  qiita_env start_cluster demo test reserved && sleep 30
+  qiita_env start_cluster qiita_general && sleep 30
   qiita webserver start
   ```
 

MANIFEST.in

@@ -1,4 +1,4 @@
-include README.md
+include README.rst
 include INSTALL.md
 include LICENSE
 

README.md

@@ -0,0 +1,18 @@
+Qiita
+=====
+
+|Build Status| |Coverage Status| |Gitter|
+
+Qiita (canonically pronounced *cheetah*) is an analysis environment for microbiome (and other "comparative -omics") datasets. You can find the public Qiita server at `http://qiita.microbio.me <http://qiita.microbio.me>`__.
+
+Qiita is currently in alpha status. We are very open to community contributions and feedback. If you're interested in contributing to Qiita, see `CONTRIBUTING.md <https://github.com/biocore/qiita/blob/master/CONTRIBUTING.md>`__. If you'd like to report bugs or request features, you can do that in the `Qiita issue tracker <https://github.com/biocore/qiita/issues>`__.
+
+To install and configure your own Qiita server, see `INSTALL.md <https://github.com/biocore/qiita/blob/master/INSTALL.md>`__.
+
+
+.. |Build Status| image:: https://travis-ci.org/biocore/qiita.png?branch=master
+   :target: https://travis-ci.org/biocore/qiita
+.. |Coverage Status| image:: https://coveralls.io/repos/biocore/qiita/badge.png?branch=master
+   :target: https://coveralls.io/r/biocore/qiita
+.. |Gitter| image:: https://badges.gitter.im/Join%20Chat.svg
+   :target: https://gitter.im/biocore/qiita?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge

README.rst

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "0.0.1-dev"
+__version__ = "0.1.0"

qiita_core/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "0.0.1-dev"
+__version__ = "0.1.0"

qiita_db/__init__.py

@@ -94,7 +94,7 @@ def _add_ontology_data(conn):
               "To download the file again, delete the existing file first."
               % fp)
     else:
-        url = 'ftp://thebeast.colorado.edu/pub/qiita/qiita_ontoandvocab.sql.gz'
+        url = 'ftp://ftp.microbio.me/pub/qiita/qiita_ontoandvocab.sql.gz'
         try:
             urlretrieve(url, fp)
         except:
@@ -121,13 +121,13 @@ def _download_reference_files(conn):
         mkdir(reference_base_dir)
 
     files = {'tree': (get_reference_fp('gg_13_8-97_otus.tree'),
-                      'ftp://thebeast.colorado.edu/greengenes_release/'
+                      'ftp://ftp.microbio.me/greengenes_release/'
                       'gg_13_8_otus/trees/97_otus.tree'),
              'taxonomy': (get_reference_fp('gg_13_8-97_otu_taxonomy.txt'),
-                          'ftp://thebeast.colorado.edu/greengenes_release/'
+                          'ftp://ftp.microbio.me/greengenes_release/'
                           'gg_13_8_otus/taxonomy/97_otu_taxonomy.txt'),
              'sequence': (get_reference_fp('gg_13_8-97_otus.fasta'),
-                          'ftp://thebeast.colorado.edu/greengenes_release/'
+                          'ftp://ftp.microbio.me/greengenes_release/'
                           'gg_13_8_otus/rep_set/97_otus.fasta')}
 
     for file_type, (local_fp, url) in viewitems(files):
@@ -231,6 +231,11 @@ def make_environment(load_ontologies, download_reference, add_demo_user):
             ('[email protected]', 4,
              '$2a$12$gnUi8Qg.0tvW243v889BhOBhWLIHyIJjjgaG6dxuRJkUM8nXG9Efe',
              'Demo', 'Qitta Dev', '1345 Colorado Avenue', '303-492-1984')""")
+        conn.execute("""
+            INSERT INTO qiita.analysis (email, name, description, dflt,
+                                        analysis_status_id)
+            VALUES
+            ('[email protected]', '[email protected]', 'dflt', 't', 1)""")
 
         print('Demo user successfully created')
 

qiita_db/environment_manager.py

@@ -11,7 +11,6 @@
 from .util import load_template_to_dataframe
 from .constants import TARGET_GENE_DATA_TYPES
 
-__version__ = "0.0.1-dev"
 
 __all__ = ['SampleTemplate', 'PrepTemplate', 'load_template_to_dataframe',
            'TARGET_GENE_DATA_TYPES']

qiita_db/metadata_template/__init__.py

@@ -13,4 +13,4 @@
     'IE': 10
 }
 
-__version__ = "0.0.1-dev"
+__version__ = "0.1.0"

qiita_pet/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "0.0.1-dev"
+__version__ = "0.1.0"

qiita_ware/__init__.py

@@ -10,11 +10,11 @@
 from setuptools import setup
 from glob import glob
 
-__version__ = "0.0.1-dev"
+__version__ = "0.1.0"
 
 
 classes = """
-    Development Status :: 2 - Pre-Alpha
+    Development Status :: 3 - Alpha
     License :: OSI Approved :: BSD License
     Topic :: Scientific/Engineering :: Bio-Informatics
     Topic :: Software Development :: Libraries :: Application Frameworks
@@ -26,7 +26,8 @@
     Operating System :: MacOS :: MacOS X
 """
 
-long_description = """Qiita: Spot Patterns"""
+with open('README.rst') as f:
+    long_description = f.read()
 
 classifiers = [s.strip() for s in classes.split('\n') if s]
 
@@ -43,7 +44,9 @@
                 'qiita_db',
                 'qiita_db/metadata_template/',
                 'qiita_pet',
+                'qiita_pet/uimodules',
                 'qiita_pet/handlers',
+                'qiita_pet/handlers/study_handlers',
                 'qiita_ware'
                 ],
       package_data={'qiita_core': ['support_files/config_test.txt'],