REL: Pre-Alpha release 0.0.1

INSTALL.md

@@ -1,13 +1,13 @@
 Dependencies
 ------------
 
-Qiita is a python package, with support for python 2.7 and 3.2, that depends on the following python libraries (all of them can be installed using pip):
+Qiita is a python package, with support for python 2.7, that depends on the following python libraries (all of them can be installed using pip):
 
 <!--
 * [pgbouncer](http://pgfoundry.org/projects/pgbouncer)
-* [IPython](https://github.com/ipython/ipython)
 -->
 
+* [IPython](https://github.com/ipython/ipython)
 * [tornado 3.1.1](http://www.tornadoweb.org/en/stable/)
 * [toredis](https://pypi.python.org/pypi/toredis)
 * [Psycopg2](http://initd.org/psycopg/download/)
@@ -26,24 +26,45 @@ Qiita is a python package, with support for python 2.7 and 3.2, that depends on
 And on the following packages:
 
 * [PostgresSQL 9.3](http://www.postgresql.org/download/)
-* [redis 2.8.0](https://pypi.python.org/pypi/redis/)
-
-<!--
 * [redis-server](http://redis.io)
--->
 
 Install
 -------
 
 Once you have [PostgresSQL](http://www.postgresql.org/download/) and [redis](https://pypi.python.org/pypi/redis/) installed (follow the instruction on their web site), simply run these commands to install qiita and configure the demo environment, replacing $QIITA_DIR for the path where qiita is installed
-(note that if you are not using Ubuntu you might need to follow the instructions in the next section):
+(note that if you are not using Ubuntu you might need to follow the instructions in the next section).
+
+```bash
+pip install numpy
+pip install cogent burrito qcli emperor pyzmq
+pip install https://github.com/biocore/qiime/archive/master.zip --no-deps
+pip install qiita-spots
+```
+
+After these commands are executed, you will need (1) download a [sample Qiita configuration file](https://raw.githubusercontent.com/biocore/qiita/a0628e54aef85b1a064d40d57ca981aaf082a120/qiita_core/support_files/config_test.txt), (2) set the `QIITA_CONFIG_FP` environment variable and (3) proceed to initialize your environment:
 
 ```bash
-echo "export QIITA_CONFIG_FP=$QIITA_DIR/qiita_core/support_files/config_demo.txt" >> ~/.bashrc
+# (1) use curl -O if using OS X
+wget https://github.com/biocore/qiita/blob/a0628e54aef85b1a064d40d57ca981aaf082a120/qiita_core/support_files/config_test.txt
+# (2) set the enviroment variable in your .bashrc
+echo "export QIITA_CONFIG_FP=config_test.txt" >> ~/.bashrc
 source ~/.bashrc
-pip install https://github.com/biocore/qiita/archive/master.zip
-qiita_env make_env --env demo
+# (3) start a test environment
+qiita_env make --no-load-ontologies
 ```
+
+Finally you need to start the server:
+
+```bash
+# IPython takes a while to get initialized so wait 30 seconds
+qiita_env start_cluster demo test reserved && sleep 30
+qiita webserver start
+
+```
+
+If all the above commands executed correctly, you should be able to go to http://localhost:8888 in your browser, to login use `demo@microbio.me` and `password` as the credentials.
+
+
 ## If using other operating systems that are not Ubuntu
 
 You will need to add the postgres user to the database. In order to do this, run:

qiita_pet/webserver.py

@@ -1,12 +1,8 @@
 # login code modified from https://gist.github.com/guillaumevincent/4771570
 import tornado.auth
 import tornado.escape
-import tornado.httpserver
-import tornado.ioloop
-import tornado.options
 import tornado.web
 import tornado.websocket
-from tornado.options import define, options
 from os.path import dirname, join
 from base64 import b64encode
 from uuid import uuid4
@@ -35,7 +31,6 @@
 from qiita_pet.handlers.download import DownloadHandler
 from qiita_db.util import get_mountpoint
 
-define("port", default=8888, help="run on the given port", type=int)
 
 DIRNAME = dirname(__file__)
 STATIC_PATH = join(DIRNAME, "static")
@@ -96,14 +91,3 @@ def __init__(self):
             "login_url": "/auth/login/"
         }
         tornado.web.Application.__init__(self, handlers, **settings)
-
-
-def main():
-    tornado.options.parse_command_line()
-    http_server = tornado.httpserver.HTTPServer(Application())
-    http_server.listen(options.port)
-    print("Tornado started on port", options.port)
-    tornado.ioloop.IOLoop.instance().start()
-
-if __name__ == "__main__":
-    main()

scripts/qiita

@@ -9,6 +9,8 @@
 # -----------------------------------------------------------------------------
 
 import click
+import tornado.httpserver
+import tornado.ioloop
 from psycopg2 import OperationalError
 
 from qiita_db.util import (get_filepath_types, get_filetypes,
@@ -58,6 +60,11 @@ def maintenance():
     pass
 
 
+@qiita.group()
+def webserver():
+    pass
+
+
 # #############################################################################
 # DB COMMANDS
 # #############################################################################
@@ -244,5 +251,24 @@ def status():
         print r_server.ttl('maintenance'), "seconds remaining"
 
 
+# #############################################################################
+# WEBSERVER COMMANDS
+# #############################################################################
+
+@webserver.command()
+@click.option('--port', required=False, type=int, help='Port where the '
+              'webserver will start', default=8888)
+def start(port):
+    # in order to use this command you need to have an IPython cluster running,
+    # for now this makes it so that you can use other sub-commands without
+    # having to do that. The solution will (perhaps) be to move this subcommand
+    # into an entirely different script.
+    from qiita_pet.webserver import Application
+
+    http_server = tornado.httpserver.HTTPServer(Application())
+    http_server.listen(port)
+    print("Qiita started on port", port)
+    tornado.ioloop.IOLoop.instance().start()
+
 if __name__ == '__main__':
     qiita()

setup.py

@@ -8,43 +8,43 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "0.1.0-dev"
+__version__ = "0.0.1"
 
 from setuptools import setup
 from glob import glob
 
 
 classes = """
-    Development Status :: 4 - Beta
+    Development Status :: 2 - Pre-Alpha
     License :: OSI Approved :: BSD License
     Topic :: Scientific/Engineering :: Bio-Informatics
     Topic :: Software Development :: Libraries :: Application Frameworks
     Topic :: Software Development :: Libraries :: Python Modules
     Programming Language :: Python
     Programming Language :: Python :: 2.7
     Programming Language :: Python :: Implementation :: CPython
-    Operating System :: OS Independent
     Operating System :: POSIX :: Linux
     Operating System :: MacOS :: MacOS X
 """
 
-long_description = """Qiita is a databasing and UI effort for QIIME"""
+long_description = """Qiita: Spot Patterns"""
 
 classifiers = [s.strip() for s in classes.split('\n') if s]
 
-setup(name='qiita',
+setup(name='qiita-spots',
       version=__version__,
       long_description=long_description,
       license="BSD",
-      description='Qiita',
+      description='Qiita: Spot Patterns',
       author="Qiita development team",
       author_email="mcdonadt@colorado.edu",
-      url='http://biocore.github.io/qiita',
+      url='https://github.com/biocore/qiita',
       test_suite='nose.collector',
       packages=['qiita_core',
                 'qiita_db',
                 'qiita_pet',
-                'qiita_ware',
+                'qiita_pet/handlers',
+                'qiita_ware'
                 ],
       package_data={'qiita_core': ['support_files/config_test.txt'],
                     'qiita_db': ['support_files/*.sql',
@@ -59,7 +59,16 @@
                                  'support_files/test_data/job/2_test_folder/*',
                                  'support_files/test_data/uploads/1/*',
                                  'support_files/test_data/templates/*',
-                                 'support_files/work_data/*']},
+                                 'support_files/work_data/*'],
+                    'qiita_pet': ['static/css/*.css', 'static/img/*.png',
+                                  'static/img/*.gif', 'static/img/*.ico',
+                                  'static/js/*.js', 'static/vendor/css/*.css',
+                                  'static/vendor/css/images/*.png',
+                                  'static/vendor/fonts/glyphicons*.*',
+                                  'static/vendor/images/*.png',
+                                  'static/vendor/js/*.js',
+                                  'results/admin/jobname/*.html',
+                                  'templates/*.html']},
       scripts=glob('scripts/*'),
       extras_require={'test': ["nose >= 0.10.1", "pep8", 'mock'],
                       'doc': ["Sphinx >= 1.2.2", "sphinx-bootstrap-theme"]},