Merge pull request #1920 from gregcaporaso/190-release

fixing issues and updating version strings for 1.9.0

ChangeLog.md

@@ -1,5 +1,5 @@
-QIIME 1.9.0-rc2
-===============
+QIIME 1.9.0
+===========
 
 New scripts
 -----------
@@ -45,7 +45,7 @@ Features
 * ``cluster_jobs_fp`` in the QIIME config file now defaults to ``start_parallel_jobs.py``. ``seconds_to_sleep`` now defaults to 1.
 * Added ``--negate_sample_id_fp`` option to ``filter_samples_from_otu_table.py`` (see [#1117](https://github.com/biocore/qiime/issues/1117)).
 * Added ``--percent_variation_below_one`` flag to ``make_2d_plots.py`` for when the percent variation is actually below 1 and not a relative measure.
-* The default confidence threshold for the Naive Bayes taxonomy assigners (RDP Classifier and mothur) is now ``0.50``, as [recommended by the RDP Classifier developers](https://rdp.cme.msu.edu/classifier/class_help.jsp#conf) for partial sequences. 
+* The default confidence threshold for the Naive Bayes taxonomy assigners (RDP Classifier and mothur) is now ``0.50``, as [recommended by the RDP Classifier developers](https://rdp.cme.msu.edu/classifier/class_help.jsp#conf) for partial sequences.
 
 Usability enhancements
 ----------------------

doc/_templates/layout.html

@@ -24,11 +24,14 @@
 
     <h3><a href="{{ pathto('index') }}">Site index</a></h3>
     <ul><li><ul>
-    <li><a href="{{ pathto('index')}}">Home</a><br /></li>
+    <li><a href="http://www.qiime.org">Home</a><br /></li>
     <li><a href="{{ pathto('install/index')}}">Install</a><br /></li>
     <li><a href="{{ pathto('tutorials/index')}}">Tutorials</a><br /></li>
     <li><a href="{{ pathto('scripts/index')}}">Scripts</a><br /></li>
-    <li><a href="{{ pathto('documentation/index')}}">Documentation</a><br /></li>
+    <li><a href="http://help.qiime.org">Help</a><br /></li>
+    <li><a href="http://qiime.org/home_static/dataFiles.html">Resources</a><br /></li>
+    <li><a href="{{ pathto('documentation/index')}}">File Formats</a><br /></li>
+    <li><a href="http://workshops.qiime.org">Workshops</a><br /></li>
     <li><a href="http://qiime.wordpress.com">Blog</a><br /></li>
     <li><a href="{{ pathto('developer/index')}}">Developer</a><br /></li>
     </ul></li></ul>

doc/conf.py

@@ -46,9 +46,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.9.0-rc2'
+version = '1.9.0'
 # The full version, including alpha/beta/rc tags.
-release = '1.9.0-rc2'
+release = '1.9.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/documentation/index.rst

@@ -6,9 +6,9 @@
 
 .. index:: Documentation
 
-===================
-QIIME Documentation
-===================
+==================
+QIIME File Formats
+==================
 
 These pages document various aspects of QIIME, including scripts, file formats, and parameters files. If you're instead looking for tutorials to guide you through different types of analyses, you should refer to the `QIIME tutorials <../tutorials/index.html>`_.
 

doc/index.rst

@@ -1,77 +1,15 @@
-
-.. QIIME documentation master file, created by
-   sphinx-quickstart on Mon Jan 25 12:57:02 2010.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
 ###################################################
 QIIME: Quantitative Insights Into Microbial Ecology
 ###################################################
-QIIME (canonically pronounced 'Chime') is a pipeline for performing microbial community analysis that integrates many third party tools which have become standard in the field. QIIME can run on a laptop, a supercomputer, and systems in between such as multicore desktops.  Linux and Mac OS X are supported natively, and Windows, Linux, and Mac OS X are supported via the `QIIME virtual box <./install/virtual_box.html>`_.
-
-**The quickest way to start using QIIME is with the** `QIIME virtual box <./install/virtual_box.html>`_. To stay up-to-date on what's new with QIIME, you should subscribe to the `blog <http://qiime.wordpress.com>`_.
-
-Rather than reimplementing commonly used algorithms, QIIME wraps popular implementations of those algorithms. This allows us to make use of the many excellent tools available in this area, and allows faster integration of new tools. If you use tools that you think would be useful additions to QIIME, consider submitting a feature request by `creating a new issue on our GitHub issue tracker <https://github.com/biocore/qiime/issues>`_ and labelling it as an *enhancement*. You will need to create a free GitHub account in order to create an issue.
-
-A standard QIIME analysis begins with sequence data from one or more sequencing platforms, including Sanger, Roche/454, and Illumina GAIIx. QIIME can perform library de-multiplexing and quality filtering; denoising with AmpliconNoise or the QIIME Denoiser; OTU and representative set picking with uclust, cdhit, mothur, BLAST, or other tools; taxonomy assignment with uclust, BLAST, the RDP classifier, mothur, or rtax; sequence alignment with PyNAST, muscle, infernal, or other tools; phylogeny reconstruction with FastTree, raxml, clearcut, or other tools; alpha diversity and rarefaction, including visualization of results, using over 20 metrics including Phylogenetic Diversity, chao1, and observed species; beta diversity and rarefaction, including visualization of results, using over 25 metrics including weighted and unweighted UniFrac, Euclidean distance, and Bray-Curtis; summarization and visualization of taxonomic composition of samples using area, bar and pie charts along with distance histograms; and many other features. While QIIME is primarily used for analysis of amplicon data, many of the downstream analysis pipeline (such as alpha rarefaction and jackknifed beta diversity) can be performed on any type of `sample x observation tables if they are formatted correctly <./documentation/file_formats.html#otu-table-format>`_.
-
-QIIME includes parallelization capabilities for many of the computationally intensive steps. By default, these are configured to utilize a mutli-core environment, and are easily configured to run in a cluster environment. QIIME is built in Python using the open-source PyCogent_ toolkit. It makes extensive use of unit tests, and is highly modular to facilitate custom analyses.
-
-Blog and Mailing List
-=====================
-We recommend that all QIIME users keep an eye on the QIIME blog for important announcements. You can `subscribe to the RSS feed <http://qiime.wordpress.com/feed/>`_ or `sign up for e-mail notifications on the front page of the blog <http://qiime.wordpress.com>`_. This is a very low traffic list (typically around one message per month), and we will not share subscriber information with anyone.
-
-Downloading and installing QIIME
-================================
-
-There are several ways to get a working install of QIIME.
-
-The easiest is to use our virtual machines:
-
- * 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>`_.
-
- * Amazon EC2 image: A QIIME EC2 image can be loaded in the Amazon Web Services cloud. For details, `see EC2 documentation <./install/vm_ec2.html>`_.
-
-Alternatively, there are a few choices for automated installation of QIIME.
-
- * qiime-deploy: The `qiime-deploy <https://github.com/qiime/qiime-deploy>`_ tool can be used to easily install various versions of QIIME natively on Linux systems.
- * MacQIIME: `MacQIIME <http://www.wernerlab.org/software/macqiime>`_ includes a nearly-full installation of QIIME for Mac OS X users.
-
-If you are instead interested in a native install of QIIME, you can choose between the QIIME base install, which provides access to the most commonly used features of QIIME (with default parameters), or the QIIME full install. For both, you should begin with the `QIIME installation guide <./install/install.html>`_. For most users, the QIIME base install will be sufficient, at least when getting started.
-
-If installing QIIME natively, you'll need to choose between the release and development version of QIIME.
-
- * Stable Release: Currently the most stable version of QIIME is our |release| release, which you can `download here <https://pypi.python.org/pypi/qiime>`_. If you don't know whether you want to install the release or development version of QIIME, you most likely want the release version.
-
- * 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::
-
-	git clone git://github.com/biocore/qiime.git Qiime
-
-
-Learning QIIME
-==========================
-After installing QIIME, you should move on to the `QIIME Illumina Overview Tutorial <./tutorials/illumina_overview_tutorial.html>`_ to analyze an example data set. As you begin using QIIME on your own data, you'll want to refer to the `QIIME tutorials <./tutorials/index.html>`_  and the `QIIME documentation <./documentation/index.html>`_.
-
-Contact Us
-==========
-To get help with using QIIME, please visit http://help.qiime.org.
-
-Users can also submit bug reports and feature requests via our `GitHub issue tracker <https://github.com/biocore/qiime/issues>`_.
-
-QIIME Development
-=================
-
-QIIME is an open-source project, primarily developed in the `Knight Lab <http://www.knightlab.ucsd.edu>`_ at the University of Colorado at Boulder, the `Caporaso Lab <http://caporasolab.us>`_ at Northern Arizona University and the `Clemente Lab <http://clemente-lab.github.io>`_ at Icahn School of Medicine at Mount Sinai. If you are interested in getting involved, check out the `developer notes <./developer/index.html>`_.
-
-Citing QIIME
-============
-If you use QIIME for any published research, please include the following citation:
-
-	**QIIME allows analysis of high-throughput community sequencing data**
-
-	J Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D Bushman, Elizabeth K Costello, Noah Fierer, Antonio Gonzalez Pena, Julia K Goodrich, Jeffrey I Gordon, Gavin A Huttley, Scott T Kelley, Dan Knights, Jeremy E Koenig, Ruth E Ley, Catherine A Lozupone, Daniel McDonald, Brian D Muegge, Meg Pirrung, Jens Reeder, Joel R Sevinsky, Peter J Turnbaugh, William A Walters, Jeremy Widmann, Tanya Yatsunenko, Jesse Zaneveld and Rob Knight; Nature Methods, 2010; doi:10.1038/nmeth.f.303
 
+This is the main entry point into the QIIME documentation. If you're looking for information about QIIME, you should start on the `QIIME homepage <http://www.qiime.org>`_.
 
-You can find the `QIIME paper here <http://www.nature.com/nmeth/journal/v7/n5/full/nmeth.f.303.html>`_, and the data presented in this paper can be found `here <ftp://ftp.microbio.me/qiime/QIIME_NM_2010.tgz>`_.
+.. toctree::
+   :maxdepth: 1
+   :glob:
 
-.. _PyCogent: http://www.pycogent.org
+   install/index
+   tutorials/index
+   scripts/index
+   documentation/index
+   developer/index

doc/install/index.rst

@@ -8,6 +8,7 @@ Installing QIIME
    :maxdepth: 1
    :glob:
 
-   ./*
-
-
+   install
+   virtual_box
+   upgrade
+   qiime_config

doc/install/vm_ec2.rst

@@ -1,22 +1,3 @@
 .. _ec2:
 
-======================
-QIIME Amazon EC2 Image
-======================
-
-As a consequence of QIIME's *pipeline* architecture, **QIIME has a lot of dependencies and can (but doesn't have to) be very challenging to install**. The QIIME Amazon EC2 Image gets around the difficulty of installation by providing a functioning QIIME full install inside an Ubuntu Linux virtual machine that runs on the Amazon Cloud.
-
-Users will need their own Amazon Web Services (AWS) account to make use of the compute resources available in the Amazon Cloud. Those resources are typically rented by the hour. Note that those fees cover your use of Amazon's hardware. Use of QIIME itself, as always, is free.
-
-To get started working with the QIIME Amazon EC2 Image, see :ref:`working_with_ec2`.
-
-The Amazon Machine Identifiers (AMIs) for all QIIME releases are listed on the `QIIME Resources page <http://qiime.org/home_static/dataFiles.html>`_.
-
-As of this writing, `Amazon has an open call for proposals <http://aws.amazon.com/grants/>`_ for grants related to using AWS resources for research and education. 
-
-Acknowledgements
-================
-The QIIME Amazon EC2 Image was developed using an AWS in Education (for Researchers) grant of compute resource time.
-
-.. _AWS: http://aws.amazon.com/
-.. _AWS console: http://aws.amazon.com/console/
+This page has been replaced with the `QIIME AWS tutorial <../tutorials/working_with_aws.html>`_.

doc/scripts/index.rst

@@ -1,7 +1,7 @@
 .. _index:
 
 =============
-QIIME scripts
+QIIME Scripts
 =============
 
 All QIIME analyses are performed using python (``.py``) scripts. See `the QIIME install guide <../install/install.html>`_ if you need help getting the QIIME scripts installed.

doc/vb_files/Before_you_start/0.QIIME_version.txt

@@ -1,3 +1,3 @@
 QIIME virtual machine 1.8.0 for 64 bit machines
 
-Important: All the software to run QIIME is already installed in this virtual machine. The main software requierements are installed in /software/, to access this folder we have created a direct link to it in the Desktop. 
+Important: All the software to run QIIME is already installed in this virtual machine. The main software requirements are installed in /software/, to access this folder we have created a direct link to it in the Desktop. 

qiime/__init__.py

@@ -18,7 +18,7 @@
                "Daniel McDonald",
                "Catherine Lozupone"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc2"
+__version__ = "1.9.0"
 __maintainer__ = "Greg Caporaso"
 __email__ = "[email protected]"
 

qiime/add_alpha_to_mapping_file.py

@@ -6,7 +6,7 @@
 __copyright__ = "Copyright 2011, The QIIME project"
 __credits__ = ["Yoshiki Vazquez-Baeza", "Antonio Gonzalez-Pena"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc2"
+__version__ = "1.9.0"
 __maintainer__ = "Yoshiki Vazquez-Baeza"
 __email__ = "[email protected]"
 

qiime/add_qiime_labels.py

@@ -5,7 +5,7 @@
 __copyright__ = "Copyright 2011, The QIIME Project"
 __credits__ = ["William Walters", "Emily TerAvest"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc2"
+__version__ = "1.9.0"
 __maintainer__ = "William Walters"
 __email__ = "[email protected]"
 

qiime/adjust_seq_orientation.py

@@ -6,7 +6,7 @@
 __copyright__ = "Copyright 2011, The QIIME Project"
 __credits__ = ["Greg Caporaso", "Antonio Gonzalez Pena"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc2"
+__version__ = "1.9.0"
 __maintainer__ = "Greg Caporaso"
 __email__ = "[email protected]"
 

qiime/align_seqs.py

@@ -8,7 +8,7 @@
     "Jeremy Widmann",
     "Kyle Bittinger"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc2"
+__version__ = "1.9.0"
 __maintainer__ = "Greg Caporaso"
 __email__ = "[email protected]"
 

qiime/alpha_diversity.py

@@ -6,7 +6,7 @@
                "William Van Treuren", "Jose Antonio Navas Molina",
                "Jai Ram Rideout"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc2"
+__version__ = "1.9.0"
 __maintainer__ = "Justin Kuczynski"
 __email__ = "[email protected]"
 

qiime/assign_taxonomy.py

@@ -7,7 +7,7 @@
 __credits__ = ["Rob Knight", "Greg Caporaso", "Kyle Bittinger",
                "Antonio Gonzalez Pena", "David Soergel", "Jai Ram Rideout"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc2"
+__version__ = "1.9.0"
 __maintainer__ = "Greg Caporaso"
 __email__ = "[email protected]"
 

qiime/barcode.py

@@ -5,7 +5,7 @@
 __copyright__ = "Copyright 2011, The QIIME Project"
 __credits__ = ["Justin Kuczynski"]  # remember to add yourself
 __license__ = "GPL"
-__version__ = "1.9.0-rc2"
+__version__ = "1.9.0"
 __maintainer__ = "Justin Kuczynski"
 __email__ = "[email protected]"
 

qiime/beta_diversity.py

@@ -6,7 +6,7 @@
                "Jose Carlos Clemente Litran", "Jai Ram Rideout",
                "Jose Antonio Navas Molina"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc2"
+__version__ = "1.9.0"
 __maintainer__ = "Justin Kuczynski"
 __email__ = "[email protected]"
 

qiime/beta_metrics.py

@@ -4,7 +4,7 @@
 __copyright__ = "Copyright 2011, The QIIME Project"
 __credits__ = ["Rob Knight", "Justin Kuczynski"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc2"
+__version__ = "1.9.0"
 __maintainer__ = "Justin Kuczynski"
 __email__ = "[email protected]"
 

qiime/biplots.py

@@ -5,7 +5,7 @@
 __copyright__ = "Copyright 2011, The QIIME Project"
 __credits__ = ["Dan Knights", "Justin Kuczynski"]  # remember to add yourself
 __license__ = "GPL"
-__version__ = "1.9.0-rc2"
+__version__ = "1.9.0"
 __maintainer__ = "Dan Knights"
 __email__ = "[email protected]"
 

qiime/categorized_dist_scatterplot.py

@@ -6,7 +6,7 @@
 __copyright__ = "Copyright 2011, The QIIME Project"
 __credits__ = ["Justin Kuczynski"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc2"
+__version__ = "1.9.0"
 __maintainer__ = "Justin Kuczynski"
 __email__ = "[email protected]"
 

qiime/check_id_map.py

@@ -43,7 +43,7 @@
 __copyright__ = "Copyright 2011, The QIIME Project"
 __credits__ = ["Rob Knight", "William Walters"]  # remember to add yourself
 __license__ = "GPL"
-__version__ = "1.9.0-rc2"
+__version__ = "1.9.0"
 __maintainer__ = "William Walters"
 __email__ = "[email protected]"
 

qiime/clean_raxml_parsimony_tree.py

@@ -6,7 +6,7 @@
 __copyright__ = "Copyright 2011, The QIIME project"
 __credits__ = ["Jesse Stombaugh"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc2"
+__version__ = "1.9.0"
 __maintainer__ = "Jesse Stombaugh"
 __email__ = "[email protected]"
 

qiime/cluster_quality.py

@@ -4,7 +4,7 @@
 __copyright__ = "Copyright 2011, The QIIME Project"
 __credits__ = ["Justin Kuczynski"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc2"
+__version__ = "1.9.0"
 __maintainer__ = "Justin Kuczynski"
 __email__ = "[email protected]"
 """ computes cluster quality the default way, bet/within"""

qiime/collate_alpha.py

@@ -4,7 +4,7 @@
 __copyright__ = "Copyright 2011, The QIIME Project"
 __credits__ = ["Justin Kuczynski"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc2"
+__version__ = "1.9.0"
 __maintainer__ = "Justin Kuczynski"
 __email__ = "[email protected]"
 

qiime/colors.py

@@ -6,7 +6,7 @@
 # remember to add yourself
 __credits__ = ["Rob Knight", "Jesse Stombaugh", "Yoshiki Vazquez-Baeza"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc2"
+__version__ = "1.9.0"
 __maintainer__ = "Jesse Stombaugh"
 __email__ = "[email protected]"
 

qiime/compare_alpha_diversity.py

@@ -6,7 +6,7 @@
 __copyright__ = "Copyright 2011, The QIIME project"
 __credits__ = ["William Van Treuren", "Greg Caporaso", "Jai Ram Rideout"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc2"
+__version__ = "1.9.0"
 __maintainer__ = "William Van Treuren"
 __email__ = "[email protected]"
 

qiime/compare_categories.py

@@ -6,7 +6,7 @@
 __credits__ = ["Jai Ram Rideout", "Michael Dwan", "Logan Knecht",
                "Damien Coy", "Levi McCracken"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc2"
+__version__ = "1.9.0"
 __maintainer__ = "Jai Ram Rideout"
 __email__ = "[email protected]"
 

qiime/compare_distance_matrices.py

@@ -6,7 +6,7 @@
 __credits__ = ["Jai Ram Rideout", "Michael Dwan", "Logan Knecht",
                "Damien Coy", "Levi McCracken", "Greg Caporaso"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc2"
+__version__ = "1.9.0"
 __maintainer__ = "Jai Ram Rideout"
 __email__ = "[email protected]"
 

qiime/compare_taxa_summaries.py

@@ -5,7 +5,7 @@
 __copyright__ = "Copyright 2012, The QIIME project"
 __credits__ = ["Jai Ram Rideout", "Greg Caporaso"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc2"
+__version__ = "1.9.0"
 __maintainer__ = "Jai Ram Rideout"
 __email__ = "[email protected]"
 

qiime/compare_trajectories.py

@@ -5,7 +5,7 @@
 __credits__ = ["Jose Antonio Navas Molina", "Antonio Gonzalez Pena",
                "Yoshiki Vazquez Baeza"]
 __license__ = "GPL"
-__version__ = "1.9.0-rc2"
+__version__ = "1.9.0"
 __maintainer__ = "Jose Antonio Navas Molina"
 __email__ = "[email protected]"