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updated __version__ and __status__ strings and references to the vers…

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1 parent b706c51 commit f30d6398be6c09418cdcb149e68556187bc4560d @gregcaporaso gregcaporaso committed Dec 18, 2012
Showing 374 changed files with 747 additions and 747 deletions.
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2 README
@@ -10,7 +10,7 @@ The definitive source for information on QIIME is the QIIME website at `http://w
Dependencies
------------
-QIIME requires Python_ 2.7, Numpy_ 1.5.1, and PyCogent_ 1.5.1.
+QIIME requires Python_ 2.7.3, Numpy_ 1.5.1, and PyCogent_ 1.5.3.
Required
^^^^^^^^
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@@ -45,9 +45,9 @@
# built documents.
#
# The short X.Y version.
-version = '1.5.0-dev'
+version = '1.6.0'
# The full version, including alpha/beta/rc tags.
-release = '1.5.0-dev'
+release = '1.6.0'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
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@@ -26,7 +26,7 @@ Download QIIME
* Virtual Box: The QIIME Virtual Box is an Ubuntu Linux virtual machine, pre-loaded with QIIME and its dependencies. This is the quickest way to start using QIIME. To get the Virtual Box, please `see Virtual Box documentation <./install/virtual_box.html>`_.
- * Stable Release: Currently the most stable version of QIIME is our |release| release, which you can `download here <https://github.com/downloads/qiime/qiime/Qiime-1.5.0.tar.gz>`_.
+ * Stable Release: Currently the most stable version of QIIME is our |release| release, which you can `download here <https://github.com/downloads/qiime/qiime/Qiime-1.6.0.tar.gz>`_.
* Development Version: QIIME is under very active development. To get the latest development version of QIIME, you access our git repository, which is hosted on GitHub. While this code is subject to minor changes in interface, it will provide access to the latest and greatest features. The official web documentation is likely to be out-of-date with respect to the development software. You should instead refer to the documentation in Qiime/doc. Check out the latest version of QIIME using git with the command::
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@@ -110,7 +110,7 @@ First, change to the directory where you would like to download QIIME::
Stable Release
^^^^^^^^^^^^^^
-Currently the most stable version of QIIME is our |release| release, which you can download from `here <https://github.com/downloads/qiime/qiime/Qiime-1.5.0.tar.gz>`_.
+Currently the most stable version of QIIME is our |release| release, which you can download from `here <https://github.com/downloads/qiime/qiime/Qiime-1.6.0.tar.gz>`_.
Latest Development Version
^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -129,8 +129,8 @@ After downloading the QIIME release tar file you'll need to unpack the code. For
Unpack the release Qiime tar file with the commands::
cd /home/qiime_user
- tar -xvzf Qiime-1.5.0.tar.gz
- ln -s /home/qiime/Qiime-1.5.0 /home/qiime/Qiime
+ tar -xvzf Qiime-1.6.0.tar.gz
+ ln -s /home/qiime/Qiime-1.6.0 /home/qiime/Qiime
If you have downloaded the development version from GitHub, QIIME is already unpacked.
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@@ -4,7 +4,7 @@ Upgrading to the latest version of QIIME
========================================
This page documents how to install a new version of QIIME from an installation of the previous version. It should also be possible to follow the steps to upgrade from older versions to the most recent version, but it's best to review all steps in that case to ensure that you won't be performing unnecessary steps.
-For a detailed history of the most notable changes between versions see the `QIIME ChangeLog <https://github.com/qiime/qiime/blob/master/ChangeLog>`_. This points to the most recent version, so will usually also give a preview of the changes that are coming in the next version of QIIME.
+For a detailed history of the most notable changes between versions see the `QIIME ChangeLog <https://github.com/qiime/qiime/blob/master/ChangeLog.md>`_. This points to the most recent version, so will usually also give a preview of the changes that are coming in the next version of QIIME.
1.5.0 to 1.5.0-dev (Linux)
--------------------------
@@ -90,5 +90,5 @@ If this doesn't work, you might need to instead hit F9 to enter the BIOS. See th
Briefly, on booting the system, hit F9. Enter Advanced Options -> Processor Options -> Intel(R) Virtualization Technology and then hit Enable.
.. _CloVR: http://clovr.org
-.. _64-bit QIIME Virtual Box: ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/QIIME-1.5.0-amd64.vdi.gz
+.. _64-bit QIIME Virtual Box: ftp://thebeast.colorado.edu/pub/QIIME-v1.6.0-dependencies/QIIME-1.6.0-amd64.vdi.gz
.. _VirtualBox: http://www.virtualbox.org/wiki/Downloads
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@@ -4,10 +4,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Rob Knight", "Greg Caporaso", "Jeremy Widmann", "Kyle Bittinger", "Justin Kuczynski", "William Walters", "Jesse Zaneveld", "Dan Knights", "Jesse Stombaugh", "Micah Hamady", "Julia Goodrich", "Meg Pirrung", "Jens Reeder", "Daniel McDonald", "Catherine Lozupone"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
__all__ = ['align_seqs',
'alpha_diversity',
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Yoshiki Vazquez-Baeza", "Antonio Gonzalez-Pena"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Yoshiki Vazquez-Baeza"
__email__ = "yoshiki89@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from copy import deepcopy
@@ -5,10 +5,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
from os.path import join, basename
from glob import glob
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso", "Antonio Gonzalez Pena"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from os.path import split, splitext
from cogent.parse.fasta import MinimalFastaParser
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@@ -4,10 +4,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Rob Knight", "Greg Caporaso", "Jeremy Widmann", "Kyle Bittinger"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""Contains code for aligning sequences, using several techniques.
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@@ -5,10 +5,10 @@
__credits__ = ["Justin Kuczynski", "Rob Knight", "Greg Caporaso",
"William Van Treuren"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""Contains code for performing alpha diversity analyses within each sample.
View
@@ -5,10 +5,10 @@
__credits__ = ["Rob Knight", "Greg Caporaso", "Kyle Bittinger",
"Antonio Gonzalez Pena", "David Soergel", "Jai Ram Rideout"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
import logging
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@@ -5,10 +5,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Justin Kuczynski"] #remember to add yourself
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""
provides functions, used to assign a possibly error-fraught DNA
View
@@ -5,10 +5,10 @@
__credits__ = ["Justin Kuczynski", "Rob Knight", "Greg Caporaso",
"Jose Carlos Clemente Litran", "Jai Ram Rideout"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""Contains code for performing beta diversity analyses of different samples.
View
@@ -4,10 +4,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Rob Knight", "Justin Kuczynski"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""contains metrics for use with beta_diversity.py
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@@ -5,10 +5,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Dan Knights", "Justin Kuczynski"] #remember to add yourself
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Dan Knights"
__email__ = "daniel.knights@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
from qiime.parse import parse_otu_table
from numpy import array,apply_along_axis,dot,delete,argsort
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Justin Kuczynski"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from qiime.parse import parse_metadata_state_descriptions
View
@@ -43,10 +43,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Rob Knight","William Walters"] #remember to add yourself
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "William Walters"
__email__ = "william.a.walters@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
from collections import defaultdict
from string import letters, digits, upper
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Jesse Stombaugh"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jesse Stombaugh"
__email__ = "jesse.stombaugh@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
from random import choice
View
@@ -4,10 +4,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Justin Kuczynski"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
""" computes cluster quality the default way, bet/within"""
def clust_qual_ratio(dists, map_data, category):
View
@@ -4,10 +4,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Justin Kuczynski"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""takes as input alpha diveristy files, format:
file: one rarefaction depth/iteration
View
@@ -5,10 +5,10 @@
__copyright__ = "Copyright 2011, The QIIME Project" #consider project name
__credits__ = ["Rob Knight","Jesse Stombaugh"] #remember to add yourself
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jesse Stombaugh"
__email__ = "jesse.stombaugh@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
"""Code for coloring series based on prefs file.
"""
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["William Van Treuren", "Greg Caporaso", "Jai Ram Rideout"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "William Van Treuren"
__email__ = "vantreur@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
from numpy import array, isnan, min as np_min
from qiime.format import format_p_value_for_num_iters
@@ -6,10 +6,10 @@
__credits__ = ["Jai Ram Rideout", "Michael Dwan", "Logan Knecht",
"Damien Coy", "Levi McCracken"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jai Ram Rideout"
__email__ = "jai.rideout@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""Contains functions used in the compare_categories.py script."""
@@ -6,10 +6,10 @@
__credits__ = ["Jai Ram Rideout", "Michael Dwan", "Logan Knecht",
"Damien Coy", "Levi McCracken", "Greg Caporaso"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jai Ram Rideout"
__email__ = "jai.rideout@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""Contains functions used in the compare_distance_matrices.py script."""
@@ -5,10 +5,10 @@
__copyright__ = "Copyright 2012, The QIIME project"
__credits__ = ["Jai Ram Rideout", "Greg Caporaso"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jai Ram Rideout"
__email__ = "jai.rideout@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""Contains functions used in the compare_taxa_summaries.py script."""
@@ -4,10 +4,10 @@
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Adam Robbins-Pianka, Abhisaar Yadav"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Adam Robbins-Pianka"
__email__ = "adam.robbinspianka@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
# Reviewed by William Walters
View
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso", "Jai Ram Rideout"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from numpy import array
from biom.exception import TableException
@@ -5,10 +5,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters", "Rob Knight", "Micah Hamady", "Greg Caporaso", "Kyle Bittinger","Jesse Stombaugh","Jens Reeder"] #remember to add yourself
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "William Walters"
__email__ = "william.a.walters@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
from string import upper
from itertools import izip
View
@@ -7,10 +7,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jens Reeder", "Greg Caporaso"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from os import system, listdir, remove, rmdir
from os.path import exists, split
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