Merge pull request #1816 from jairideout/190-rc1

QIIME 1.9.0 release candidate 1, redux

ChangeLog.md

@@ -1,5 +1,5 @@
-QIIME 1.8.0-dev (changes since 1.8.0 go here)
-=============================================
+QIIME 1.9.0-rc1
+===============
 * Added new ``observation_metadata_correlation.py`` script. This script allows the calculation of correlations between feature abundances and continuous-valued metadata. This script replaces the continuous-valued correlation functionality that was in ``otu_category_significance.py`` in QIIME 1.7.0 and earlier.
 * ``split_otu_table.py`` now allows multiple fields to be passed to split a biom table, and
 optionally a mapping file. Check out the new documentation for the naming conventions
@@ -101,6 +101,8 @@ optionally a mapping file. Check out the new documentation for the naming conven
 * Fixed bug that resulted in samples being mislabeled in ``make_otu_heatmap.py`` when one of the following options was passed: ``--category``, ``--map_fname``, ``--sample_tree``, or ``--suppress_column_clustering``. This is discussed in [#1790](https://github.com/biocore/qiime/issues/1790).
 * Added ``--negate_sample_id_fp`` option to ``filter_samples_from_otu_table.py`` (see [#1117](https://github.com/biocore/qiime/issues/1117)).
 * Added three new workflow scripts for facilitating initial QIIME processing of already-demultiplexed fastq files, as these are commonly being provided by sequencing centers. These are: ``multiple_split_libraries_fastq.py``, ``multiple_join_paired_ends.py``, and ``multiple_extract_barcodes.py``.
+* Added ``differential_abundance.py`` to supplement ``group_significance.py`` for to support metagenomeSeq's fitZIG algorithm and DESeq2's negative binomial algorithm.  Note that the input for this is a unnormalized, raw BIOM table.
+* Added ``normalize_table.py`` to support normalization algorithms in addition to rarefaction. Supported methods are metagenomeSeq's CSS and DESeq's variance stabilizing transformation.
 
 QIIME 1.8.0 (11 Dec 2013)
 =========================

doc/conf.py

@@ -46,9 +46,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.8.0-dev'
+version = '1.9.0-rc1'
 # The full version, including alpha/beta/rc tags.
-release = '1.8.0-dev'
+release = '1.9.0-rc1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

qiime/__init__.py

@@ -18,7 +18,7 @@
                "Daniel McDonald",
                "Catherine Lozupone"]
 __license__ = "GPL"
-__version__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __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__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __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__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __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__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __maintainer__ = "Greg Caporaso"
 __email__ = "[email protected]"
 

qiime/align_seqs.py

@@ -8,7 +8,7 @@
     "Jeremy Widmann",
     "Kyle Bittinger"]
 __license__ = "GPL"
-__version__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __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__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __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__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __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__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __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__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __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__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __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__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __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__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __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__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __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__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __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__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __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__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __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__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __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__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __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__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __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__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __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__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __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__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __maintainer__ = "Jose Antonio Navas Molina"
 __email__ = "[email protected]"
 

qiime/compute_taxonomy_ratios.py

@@ -11,7 +11,7 @@
 __copyright__ = "Copyright 2014, The QIIME project"
 __credits__ = ["Daniel McDonald"]
 __license__ = "GPL"
-__version__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __maintainer__ = "Daniel McDonald"
 __email__ = "[email protected]"
 

qiime/convert_fastaqual_fastq.py

@@ -4,7 +4,7 @@
 __copyright__ = "Copyright 2011, The QIIME project"
 __credits__ = ["Adam Robbins-Pianka, Abhisaar Yadav"]
 __license__ = "GPL"
-__version__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __maintainer__ = "Adam Robbins-Pianka"
 __email__ = "[email protected]"
 

qiime/core_microbiome.py

@@ -6,7 +6,7 @@
 __copyright__ = "Copyright 2011, The QIIME project"
 __credits__ = ["Greg Caporaso", "Jai Ram Rideout"]
 __license__ = "GPL"
-__version__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __maintainer__ = "Greg Caporaso"
 __email__ = "[email protected]"
 

qiime/demultiplex_fasta.py

@@ -13,7 +13,7 @@
     "Jens Reeder",
     "Emily TerAvest"]  # remember to add yourself
 __license__ = "GPL"
-__version__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __maintainer__ = "William Walters"
 __email__ = "[email protected]"
 

qiime/denoise_wrapper.py

@@ -7,7 +7,7 @@
 __copyright__ = "Copyright 2011, The QIIME Project"
 __credits__ = ["Jens Reeder", "Greg Caporaso"]
 __license__ = "GPL"
-__version__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __maintainer__ = "Justin Kuczynski"
 __email__ = "[email protected]"
 

qiime/denoiser/__init__.py

@@ -5,7 +5,7 @@
 # remember to add yourself if you make changes
 __credits__ = ["Jens Reeder", "Rob Knight"]
 __license__ = "GPL"
-__version__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __maintainer__ = "Jens Reeder"
 __email__ = "[email protected]"
 

qiime/denoiser/cluster_utils.py

@@ -7,7 +7,7 @@
 # remember to add yourself if you make changes
 __credits__ = ["Jens Reeder", "Rob Knight", "Nigel Cook", "Jai Ram Rideout"]
 __license__ = "GPL"
-__version__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __maintainer__ = "Jens Reeder"
 __email__ = "[email protected]"
 

qiime/denoiser/denoise_postprocess.py

@@ -5,7 +5,7 @@
 # remember to add yourself if you make changes
 __credits__ = ["Jens Reeder", "Rob Knight"]
 __license__ = "GPL"
-__version__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __maintainer__ = "Jens Reeder"
 __email__ = "[email protected]"
 

qiime/denoiser/denoise_worker.py

@@ -7,7 +7,7 @@
 # remember to add yourself if you make changes
 __credits__ = ["Jens Reeder", "Rob Knight", "Nigel Cook"]
 __license__ = "GPL"
-__version__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __maintainer__ = "Jens Reeder"
 __email__ = "[email protected]"
 

qiime/denoiser/flowgram_clustering.py

@@ -7,7 +7,7 @@
 # remember to add yourself if you make changes
 __credits__ = ["Jens Reeder", "Rob Knight", "Nigel Cook", "Jai Ram Rideout"]
 __license__ = "GPL"
-__version__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __maintainer__ = "Jens Reeder"
 __email__ = "[email protected]"
 

qiime/denoiser/flowgram_filter.py

@@ -7,7 +7,7 @@
 # remember to add yourself if you make changes
 __credits__ = ["Jens Reeder", "Rob Knight", "Yoshiki Vazquez Baeza"]
 __license__ = "GPL"
-__version__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __maintainer__ = "Jens Reeder"
 __email__ = "[email protected]"
 

qiime/denoiser/make_cluster_jobs.py

@@ -7,7 +7,7 @@
 # remember to add yourself if you make changes
 __credits__ = ["Jens Reeder", "Rob Knight", "Jai Ram Rideout"]
 __license__ = "GPL"
-__version__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __maintainer__ = "Jens Reeder"
 __email__ = "[email protected]"
 

qiime/denoiser/preprocess.py

@@ -7,7 +7,7 @@
 # remember to add yourself if you make changes
 __credits__ = ["Jens Reeder", "Rob Knight", "Jai Ram Rideout"]
 __license__ = "GPL"
-__version__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __maintainer__ = "Jens Reeder"
 __email__ = "[email protected]"
 

qiime/denoiser/utils.py

@@ -8,7 +8,7 @@
 # remember to add yourself if you make changes
 __credits__ = ["Jens Reeder", "Rob Knight", "Jai Ram Rideout"]
 __license__ = "GPL"
-__version__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __maintainer__ = "Jens Reeder"
 __email__ = "[email protected]"
 

qiime/detrend.py

@@ -4,7 +4,7 @@
 __copyright__ = "Copyright 2012, The QIIME Project"
 __credits__ = ["Dan Knights", "Adam Robbins-Pianka"]
 __license__ = "GPL"
-__version__ = "1.8.0-dev"
+__version__ = "1.9.0-rc1"
 __maintainer__ = "Dan Knights"
 __email__ = "[email protected]"