From ac2e825e6561705effedbfb1a7cda0f94844efaa Mon Sep 17 00:00:00 2001 From: Greg Caporaso Date: Fri, 9 Jan 2015 14:55:28 -0700 Subject: [PATCH 1/8] REL: updated version strings for 1.9.0-rc2 --- ChangeLog.md | 2 +- doc/conf.py | 4 ++-- qiime/__init__.py | 2 +- qiime/add_alpha_to_mapping_file.py | 2 +- qiime/add_qiime_labels.py | 2 +- qiime/adjust_seq_orientation.py | 2 +- qiime/align_seqs.py | 2 +- qiime/alpha_diversity.py | 2 +- qiime/assign_taxonomy.py | 2 +- qiime/barcode.py | 2 +- qiime/beta_diversity.py | 2 +- qiime/beta_metrics.py | 2 +- qiime/biplots.py | 2 +- qiime/categorized_dist_scatterplot.py | 2 +- qiime/check_id_map.py | 2 +- qiime/clean_raxml_parsimony_tree.py | 2 +- qiime/cluster_quality.py | 2 +- qiime/collate_alpha.py | 2 +- qiime/colors.py | 2 +- qiime/compare_alpha_diversity.py | 2 +- qiime/compare_categories.py | 2 +- qiime/compare_distance_matrices.py | 2 +- qiime/compare_taxa_summaries.py | 2 +- qiime/compare_trajectories.py | 2 +- qiime/compute_taxonomy_ratios.py | 2 +- qiime/convert_fastaqual_fastq.py | 2 +- qiime/core_microbiome.py | 2 +- qiime/demultiplex_fasta.py | 2 +- qiime/denoise_wrapper.py | 2 +- qiime/denoiser/__init__.py | 2 +- qiime/denoiser/cluster_utils.py | 2 +- qiime/denoiser/denoise_postprocess.py | 2 +- qiime/denoiser/denoise_worker.py | 2 +- qiime/denoiser/flowgram_clustering.py | 2 +- qiime/denoiser/flowgram_filter.py | 2 +- qiime/denoiser/make_cluster_jobs.py | 2 +- qiime/denoiser/preprocess.py | 2 +- qiime/denoiser/utils.py | 2 +- qiime/detrend.py | 2 +- qiime/differential_abundance.py | 2 +- qiime/distance_matrix_from_mapping.py | 2 +- qiime/estimate_observation_richness.py | 2 +- qiime/exclude_seqs_by_blast.py | 2 +- qiime/extract_barcodes.py | 2 +- qiime/filter.py | 2 +- qiime/filter_alignment.py | 2 +- qiime/filter_otus_by_sample.py | 2 +- qiime/format.py | 2 +- qiime/golay.py | 2 +- qiime/group.py | 2 +- qiime/hamming.py | 2 +- qiime/hierarchical_cluster.py | 2 +- qiime/identify_chimeric_seqs.py | 2 +- qiime/join_paired_ends.py | 2 +- qiime/make_2d_plots.py | 2 +- qiime/make_bipartite_network.py | 2 +- qiime/make_bootstrapped_tree.py | 2 +- qiime/make_distance_boxplots.py | 2 +- qiime/make_fastq.py | 2 +- qiime/make_library_id_lists.py | 2 +- qiime/make_otu_heatmap.py | 2 +- qiime/make_otu_network.py | 2 +- qiime/make_otu_table.py | 2 +- qiime/make_per_library_sff.py | 2 +- qiime/make_phylogeny.py | 2 +- qiime/make_rarefaction_plots.py | 2 +- qiime/map_reads_to_reference.py | 2 +- qiime/nmds.py | 2 +- qiime/normalize_table.py | 2 +- qiime/otu_significance.py | 2 +- qiime/parallel/__init__.py | 2 +- qiime/parallel/align_seqs.py | 2 +- qiime/parallel/alpha_diversity.py | 2 +- qiime/parallel/assign_taxonomy.py | 2 +- qiime/parallel/beta_diversity.py | 2 +- qiime/parallel/blast.py | 2 +- qiime/parallel/identify_chimeric_seqs.py | 2 +- qiime/parallel/map_reads_to_reference.py | 2 +- qiime/parallel/merge_otus.py | 2 +- qiime/parallel/multiple_rarefactions.py | 2 +- qiime/parallel/pick_otus.py | 2 +- qiime/parallel/poller.py | 2 +- qiime/parallel/util.py | 2 +- qiime/parse.py | 2 +- qiime/pick_otus.py | 2 +- qiime/pick_rep_set.py | 2 +- qiime/plot_rank_abundance_graph.py | 2 +- qiime/plot_semivariogram.py | 2 +- qiime/plot_taxa_summary.py | 2 +- qiime/principal_coordinates.py | 2 +- qiime/process_sff.py | 2 +- qiime/pycogent_backports/__init__.py | 2 +- qiime/quality_scores_plot.py | 2 +- qiime/rarefaction.py | 2 +- qiime/relatedness_library.py | 2 +- qiime/remote.py | 2 +- qiime/shared_phylotypes.py | 2 +- qiime/simsam.py | 2 +- qiime/sort.py | 2 +- qiime/split.py | 2 +- qiime/split_libraries.py | 2 +- qiime/split_libraries_fastq.py | 2 +- qiime/split_libraries_lea_seq.py | 2 +- qiime/stats.py | 2 +- qiime/summarize_taxa.py | 2 +- qiime/supervised_learning.py | 2 +- qiime/support_files/R/util.r | 2 +- qiime/support_files/js/otu_count_display.js | 2 +- qiime/support_files/test_js/test_otu_count_display.html | 2 +- qiime/test.py | 2 +- qiime/transform_coordinate_matrices.py | 2 +- qiime/tree_compare.py | 2 +- qiime/trim_sff_primers.py | 2 +- qiime/truncate_fasta_qual_files.py | 2 +- qiime/truncate_reverse_primer.py | 2 +- qiime/util.py | 2 +- qiime/validate_demultiplexed_fasta.py | 2 +- qiime/workflow/__init__.py | 2 +- qiime/workflow/ampliconnoise.py | 2 +- qiime/workflow/core_diversity_analyses.py | 2 +- qiime/workflow/downstream.py | 2 +- qiime/workflow/pick_open_reference_otus.py | 2 +- qiime/workflow/preprocess.py | 2 +- qiime/workflow/upstream.py | 2 +- qiime/workflow/util.py | 2 +- scripts/add_alpha_to_mapping_file.py | 2 +- scripts/add_qiime_labels.py | 2 +- scripts/adjust_seq_orientation.py | 2 +- scripts/align_seqs.py | 2 +- scripts/alpha_diversity.py | 2 +- scripts/alpha_rarefaction.py | 2 +- scripts/ampliconnoise.py | 2 +- scripts/assign_taxonomy.py | 2 +- scripts/beta_diversity.py | 2 +- scripts/beta_diversity_through_plots.py | 2 +- scripts/beta_significance.py | 2 +- scripts/blast_wrapper.py | 2 +- scripts/categorized_dist_scatterplot.py | 2 +- scripts/check_id_map.py | 2 +- scripts/clean_raxml_parsimony_tree.py | 2 +- scripts/cluster_quality.py | 2 +- scripts/collapse_samples.py | 2 +- scripts/collate_alpha.py | 2 +- scripts/compare_alpha_diversity.py | 2 +- scripts/compare_categories.py | 2 +- scripts/compare_distance_matrices.py | 2 +- scripts/compare_taxa_summaries.py | 2 +- scripts/compare_trajectories.py | 2 +- scripts/compute_core_microbiome.py | 2 +- scripts/compute_taxonomy_ratios.py | 2 +- scripts/conditional_uncovered_probability.py | 2 +- scripts/consensus_tree.py | 2 +- scripts/convert_fastaqual_fastq.py | 2 +- scripts/convert_unifrac_sample_mapping_to_otu_table.py | 2 +- scripts/core_diversity_analyses.py | 2 +- scripts/count_seqs.py | 2 +- scripts/demultiplex_fasta.py | 2 +- scripts/denoise_wrapper.py | 2 +- scripts/denoiser.py | 2 +- scripts/denoiser_preprocess.py | 2 +- scripts/denoiser_worker.py | 2 +- scripts/detrend.py | 2 +- scripts/differential_abundance.py | 2 +- scripts/dissimilarity_mtx_stats.py | 2 +- scripts/distance_matrix_from_mapping.py | 2 +- scripts/estimate_observation_richness.py | 2 +- scripts/exclude_seqs_by_blast.py | 2 +- scripts/extract_barcodes.py | 2 +- scripts/extract_reads_from_interleaved_file.py | 2 +- scripts/extract_seqs_by_sample_id.py | 2 +- scripts/filter_alignment.py | 2 +- scripts/filter_distance_matrix.py | 2 +- scripts/filter_fasta.py | 2 +- scripts/filter_otus_by_sample.py | 2 +- scripts/filter_otus_from_otu_table.py | 2 +- scripts/filter_samples_from_otu_table.py | 2 +- scripts/filter_taxa_from_otu_table.py | 2 +- scripts/filter_tree.py | 2 +- scripts/fix_arb_fasta.py | 2 +- scripts/group_significance.py | 2 +- scripts/identify_chimeric_seqs.py | 2 +- scripts/identify_missing_files.py | 2 +- scripts/identify_paired_differences.py | 2 +- scripts/inflate_denoiser_output.py | 2 +- scripts/jackknifed_beta_diversity.py | 2 +- scripts/join_paired_ends.py | 2 +- scripts/load_remote_mapping_file.py | 2 +- scripts/make_2d_plots.py | 2 +- scripts/make_bipartite_network.py | 2 +- scripts/make_bootstrapped_tree.py | 2 +- scripts/make_distance_boxplots.py | 2 +- scripts/make_distance_comparison_plots.py | 2 +- scripts/make_fastq.py | 2 +- scripts/make_library_id_lists.py | 2 +- scripts/make_otu_heatmap.py | 2 +- scripts/make_otu_network.py | 2 +- scripts/make_otu_table.py | 2 +- scripts/make_per_library_sff.py | 2 +- scripts/make_phylogeny.py | 2 +- scripts/make_prefs_file.py | 2 +- scripts/make_qiime_py_file.py | 4 ++-- scripts/make_rarefaction_plots.py | 2 +- scripts/make_tep.py | 2 +- scripts/map_reads_to_reference.py | 2 +- scripts/merge_mapping_files.py | 2 +- scripts/merge_otu_maps.py | 2 +- scripts/merge_otu_tables.py | 2 +- scripts/multiple_extract_barcodes.py | 2 +- scripts/multiple_join_paired_ends.py | 2 +- scripts/multiple_rarefactions.py | 2 +- scripts/multiple_rarefactions_even_depth.py | 2 +- scripts/multiple_split_libraries_fastq.py | 2 +- scripts/neighbor_joining.py | 2 +- scripts/nmds.py | 2 +- scripts/normalize_table.py | 2 +- scripts/observation_metadata_correlation.py | 2 +- scripts/otu_category_significance.py | 2 +- scripts/parallel_align_seqs_pynast.py | 2 +- scripts/parallel_alpha_diversity.py | 2 +- scripts/parallel_assign_taxonomy_blast.py | 2 +- scripts/parallel_assign_taxonomy_rdp.py | 2 +- scripts/parallel_assign_taxonomy_uclust.py | 2 +- scripts/parallel_beta_diversity.py | 2 +- scripts/parallel_blast.py | 2 +- scripts/parallel_identify_chimeric_seqs.py | 2 +- scripts/parallel_map_reads_to_reference.py | 2 +- scripts/parallel_merge_otu_tables.py | 2 +- scripts/parallel_multiple_rarefactions.py | 2 +- scripts/parallel_pick_otus_blast.py | 2 +- scripts/parallel_pick_otus_sortmerna.py | 2 +- scripts/parallel_pick_otus_trie.py | 2 +- scripts/parallel_pick_otus_uclust_ref.py | 2 +- scripts/parallel_pick_otus_usearch61_ref.py | 2 +- scripts/pick_closed_reference_otus.py | 2 +- scripts/pick_de_novo_otus.py | 2 +- scripts/pick_open_reference_otus.py | 2 +- scripts/pick_otus.py | 2 +- scripts/pick_rep_set.py | 2 +- scripts/plot_rank_abundance_graph.py | 2 +- scripts/plot_semivariogram.py | 2 +- scripts/plot_taxa_summary.py | 2 +- scripts/poller.py | 2 +- scripts/principal_coordinates.py | 2 +- scripts/print_metadata_stats.py | 2 +- scripts/print_qiime_config.py | 2 +- scripts/process_iseq.py | 2 +- scripts/process_qseq.py | 2 +- scripts/process_sff.py | 2 +- scripts/quality_scores_plot.py | 2 +- scripts/relatedness.py | 2 +- scripts/shared_phylotypes.py | 2 +- scripts/simsam.py | 2 +- scripts/single_rarefaction.py | 2 +- scripts/sort_otu_table.py | 2 +- scripts/split_libraries.py | 2 +- scripts/split_libraries_fastq.py | 2 +- scripts/split_libraries_lea_seq.py | 2 +- scripts/split_otu_table.py | 2 +- scripts/split_otu_table_by_taxonomy.py | 2 +- scripts/split_sequence_file_on_sample_ids.py | 2 +- scripts/start_parallel_jobs.py | 2 +- scripts/start_parallel_jobs_sc.py | 2 +- scripts/start_parallel_jobs_torque.py | 2 +- scripts/subsample_fasta.py | 2 +- scripts/summarize_taxa.py | 2 +- scripts/summarize_taxa_through_plots.py | 2 +- scripts/supervised_learning.py | 2 +- scripts/transform_coordinate_matrices.py | 2 +- scripts/tree_compare.py | 2 +- scripts/trflp_file_to_otu_table.py | 2 +- scripts/trim_sff_primers.py | 2 +- scripts/truncate_fasta_qual_files.py | 2 +- scripts/truncate_reverse_primer.py | 2 +- scripts/unweight_fasta.py | 2 +- scripts/upgma_cluster.py | 2 +- scripts/validate_demultiplexed_fasta.py | 2 +- scripts/validate_mapping_file.py | 2 +- setup.py | 2 +- tests/__init__.py | 2 +- tests/all_tests.py | 2 +- tests/test_add_alpha_to_mapping_file.py | 2 +- tests/test_add_qiime_labels.py | 2 +- tests/test_adjust_seq_orientation.py | 2 +- tests/test_align_seqs.py | 2 +- tests/test_alpha_diversity.py | 2 +- tests/test_assign_taxonomy.py | 2 +- tests/test_barcode.py | 2 +- tests/test_beta_diversity.py | 2 +- tests/test_beta_metrics.py | 2 +- tests/test_biplots.py | 2 +- tests/test_categorized_dist_scatterplot.py | 2 +- tests/test_clean_raxml_parsimony_tree.py | 2 +- tests/test_cluster_quality.py | 2 +- tests/test_collate_alpha.py | 2 +- tests/test_colors.py | 2 +- tests/test_compare_alpha_diversity.py | 2 +- tests/test_compare_categories.py | 2 +- tests/test_compare_distance_matrices.py | 2 +- tests/test_compare_taxa_summaries.py | 2 +- tests/test_compare_trajectories.py | 2 +- tests/test_compute_taxonomy_ratios.py | 2 +- tests/test_convert_fastaqual_fastq.py | 2 +- tests/test_core_microbiome.py | 2 +- tests/test_demultiplex_fasta.py | 2 +- tests/test_denoise_wrapper.py | 2 +- tests/test_denoiser/test_cluster_util.py | 2 +- tests/test_denoiser/test_denoise_postprocess.py | 2 +- tests/test_denoiser/test_denoiser.py | 2 +- tests/test_denoiser/test_flowgram_clustering.py | 2 +- tests/test_denoiser/test_flowgram_filter.py | 2 +- tests/test_denoiser/test_make_cluster_jobs.py | 2 +- tests/test_denoiser/test_preprocess.py | 2 +- tests/test_denoiser/test_settings.py | 2 +- tests/test_denoiser/test_utils.py | 2 +- tests/test_detrend.py | 2 +- tests/test_differential_abundance.py | 2 +- tests/test_distance_matrix_from_mapping.py | 2 +- tests/test_estimate_observation_richness.py | 2 +- tests/test_exclude_seqs_by_blast.py | 2 +- tests/test_extract_barcodes.py | 2 +- tests/test_filter.py | 2 +- tests/test_filter_alignment.py | 2 +- tests/test_filter_otus_by_sample.py | 2 +- tests/test_format.py | 2 +- tests/test_golay.py | 2 +- tests/test_group.py | 2 +- tests/test_hamming.py | 2 +- tests/test_hierarchical_cluster.py | 2 +- tests/test_identify_chimeric_seqs.py | 2 +- tests/test_join_paired_ends.py | 2 +- tests/test_make_2d_plots.py | 2 +- tests/test_make_bipartite_network.py | 2 +- tests/test_make_bootstrapped_tree.py | 2 +- tests/test_make_distance_boxplots.py | 2 +- tests/test_make_fastq.py | 2 +- tests/test_make_library_id_lists.py | 2 +- tests/test_make_otu_heatmap.py | 2 +- tests/test_make_otu_network.py | 2 +- tests/test_make_otu_table.py | 2 +- tests/test_make_per_library_sff.py | 2 +- tests/test_make_phylogeny.py | 2 +- tests/test_make_rarefaction_plots.py | 2 +- tests/test_map_reads_to_reference.py | 2 +- tests/test_normalize_table.py | 2 +- tests/test_otu_significance.py | 2 +- tests/test_parallel/test_align_seqs.py | 2 +- tests/test_parallel/test_alpha_diversity.py | 2 +- tests/test_parallel/test_assign_taxonomy.py | 2 +- tests/test_parallel/test_beta_diversity.py | 2 +- tests/test_parallel/test_blast.py | 2 +- tests/test_parallel/test_identify_chimeric_seqs.py | 2 +- tests/test_parallel/test_map_reads_to_reference.py | 2 +- tests/test_parallel/test_merge_otus.py | 2 +- tests/test_parallel/test_multiple_rarefactions.py | 2 +- tests/test_parallel/test_pick_otus.py | 2 +- tests/test_parallel/test_util.py | 2 +- tests/test_parse.py | 2 +- tests/test_pick_otus.py | 2 +- tests/test_pick_rep_set.py | 2 +- tests/test_plot_rank_abundance_graph.py | 2 +- tests/test_plot_semivariogram.py | 2 +- tests/test_plot_taxa_summary.py | 2 +- tests/test_principal_coordinates.py | 2 +- tests/test_process_sff.py | 2 +- tests/test_quality_scores_plot.py | 2 +- tests/test_rarefaction.py | 2 +- tests/test_relatedness.py | 2 +- tests/test_remote.py | 2 +- tests/test_shared_phylotypes.py | 2 +- tests/test_simsam.py | 2 +- tests/test_sort.py | 2 +- tests/test_split.py | 2 +- tests/test_split_libraries.py | 2 +- tests/test_split_libraries_fastq.py | 2 +- tests/test_split_libraries_lea_seq.py | 2 +- tests/test_stats.py | 2 +- tests/test_summarize_taxa.py | 2 +- tests/test_supervised_learning.py | 2 +- tests/test_transform_coordinate_matrices.py | 2 +- tests/test_tree_compare.py | 2 +- tests/test_trim_sff_primers.py | 2 +- tests/test_truncate_fasta_qual_files.py | 2 +- tests/test_truncate_reverse_primer.py | 2 +- tests/test_util.py | 2 +- tests/test_validate_demultiplexed_fasta.py | 2 +- tests/test_validate_mapping_file.py | 2 +- tests/test_workflow/test_ampliconnoise.py | 2 +- tests/test_workflow/test_core_diversity_analyses.py | 2 +- tests/test_workflow/test_downstream.py | 2 +- tests/test_workflow/test_pick_open_reference_otus.py | 2 +- tests/test_workflow/test_preprocess.py | 2 +- tests/test_workflow/test_upstream.py | 2 +- tests/test_workflow/test_util.py | 2 +- 393 files changed, 395 insertions(+), 395 deletions(-) diff --git a/ChangeLog.md b/ChangeLog.md index efe91e9d23..c70c72b8bb 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -1,4 +1,4 @@ -QIIME 1.9.0-rc1 +QIIME 1.9.0-rc2 =============== * 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 diff --git a/doc/conf.py b/doc/conf.py index cf6c8fabd4..77ad16b724 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -46,9 +46,9 @@ # built documents. # # The short X.Y version. -version = '1.9.0-rc1' +version = '1.9.0-rc2' # The full version, including alpha/beta/rc tags. -release = '1.9.0-rc1' +release = '1.9.0-rc2' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/qiime/__init__.py b/qiime/__init__.py index 024f6a4846..17b693f0ef 100644 --- a/qiime/__init__.py +++ b/qiime/__init__.py @@ -18,7 +18,7 @@ "Daniel McDonald", "Catherine Lozupone"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/add_alpha_to_mapping_file.py b/qiime/add_alpha_to_mapping_file.py index e98c69d420..d6701daf15 100755 --- a/qiime/add_alpha_to_mapping_file.py +++ b/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-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Yoshiki Vazquez-Baeza" __email__ = "yoshiki89@gmail.com" diff --git a/qiime/add_qiime_labels.py b/qiime/add_qiime_labels.py index 0bf7f91d13..56ac3c9eb3 100755 --- a/qiime/add_qiime_labels.py +++ b/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-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/qiime/adjust_seq_orientation.py b/qiime/adjust_seq_orientation.py index b3dd351be4..7261c6dbd3 100755 --- a/qiime/adjust_seq_orientation.py +++ b/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-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/align_seqs.py b/qiime/align_seqs.py index 3b03fe15ed..8243b0b3bf 100644 --- a/qiime/align_seqs.py +++ b/qiime/align_seqs.py @@ -8,7 +8,7 @@ "Jeremy Widmann", "Kyle Bittinger"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/alpha_diversity.py b/qiime/alpha_diversity.py index d800654151..c10ae14ae7 100644 --- a/qiime/alpha_diversity.py +++ b/qiime/alpha_diversity.py @@ -6,7 +6,7 @@ "William Van Treuren", "Jose Antonio Navas Molina", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/assign_taxonomy.py b/qiime/assign_taxonomy.py index f99a8d5910..74739f27d7 100644 --- a/qiime/assign_taxonomy.py +++ b/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-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/barcode.py b/qiime/barcode.py index 7567838512..dbd9048599 100644 --- a/qiime/barcode.py +++ b/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-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/beta_diversity.py b/qiime/beta_diversity.py index d874ced1b6..10fa9b929d 100644 --- a/qiime/beta_diversity.py +++ b/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-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/beta_metrics.py b/qiime/beta_metrics.py index ca0309de5e..5c0bd49ce6 100644 --- a/qiime/beta_metrics.py +++ b/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-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/biplots.py b/qiime/biplots.py index 7b39b2cd55..4f9d9e16f1 100644 --- a/qiime/biplots.py +++ b/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-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Dan Knights" __email__ = "daniel.knights@colorado.edu" diff --git a/qiime/categorized_dist_scatterplot.py b/qiime/categorized_dist_scatterplot.py index 9224063879..9ce415b491 100755 --- a/qiime/categorized_dist_scatterplot.py +++ b/qiime/categorized_dist_scatterplot.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/check_id_map.py b/qiime/check_id_map.py index 1d4070a494..b6e54550e7 100644 --- a/qiime/check_id_map.py +++ b/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-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/qiime/clean_raxml_parsimony_tree.py b/qiime/clean_raxml_parsimony_tree.py index cd97705c3d..821bda64c8 100644 --- a/qiime/clean_raxml_parsimony_tree.py +++ b/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-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/cluster_quality.py b/qiime/cluster_quality.py index e1f4377e72..cab32b29bb 100644 --- a/qiime/cluster_quality.py +++ b/qiime/cluster_quality.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" """ computes cluster quality the default way, bet/within""" diff --git a/qiime/collate_alpha.py b/qiime/collate_alpha.py index 7d2adc4607..33aabc0983 100644 --- a/qiime/collate_alpha.py +++ b/qiime/collate_alpha.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/colors.py b/qiime/colors.py index e078127e30..2bb827ce45 100644 --- a/qiime/colors.py +++ b/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-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/compare_alpha_diversity.py b/qiime/compare_alpha_diversity.py index 2f50185d91..aad231dac4 100644 --- a/qiime/compare_alpha_diversity.py +++ b/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-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Van Treuren" __email__ = "vantreur@colorado.edu" diff --git a/qiime/compare_categories.py b/qiime/compare_categories.py index b89872e8c3..e82429f849 100755 --- a/qiime/compare_categories.py +++ b/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-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/compare_distance_matrices.py b/qiime/compare_distance_matrices.py index ebf073b23f..f5a2140014 100755 --- a/qiime/compare_distance_matrices.py +++ b/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-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/compare_taxa_summaries.py b/qiime/compare_taxa_summaries.py index 08fc788e7e..8a38e26792 100755 --- a/qiime/compare_taxa_summaries.py +++ b/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-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/compare_trajectories.py b/qiime/compare_trajectories.py index a466893d10..90848e0e98 100644 --- a/qiime/compare_trajectories.py +++ b/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-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jose Antonio Navas Molina" __email__ = "josenavasmolina@gmail.com" diff --git a/qiime/compute_taxonomy_ratios.py b/qiime/compute_taxonomy_ratios.py index 94eff52960..38d1cf639f 100644 --- a/qiime/compute_taxonomy_ratios.py +++ b/qiime/compute_taxonomy_ratios.py @@ -11,7 +11,7 @@ __copyright__ = "Copyright 2014, The QIIME project" __credits__ = ["Daniel McDonald"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Daniel McDonald" __email__ = "mcdonadt@colorado.edu" diff --git a/qiime/convert_fastaqual_fastq.py b/qiime/convert_fastaqual_fastq.py index 69ddeff7e9..f102ecd2a0 100644 --- a/qiime/convert_fastaqual_fastq.py +++ b/qiime/convert_fastaqual_fastq.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Adam Robbins-Pianka, Abhisaar Yadav"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Adam Robbins-Pianka" __email__ = "adam.robbinspianka@colorado.edu" diff --git a/qiime/core_microbiome.py b/qiime/core_microbiome.py index af568d7ddc..846f8a91c1 100644 --- a/qiime/core_microbiome.py +++ b/qiime/core_microbiome.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/demultiplex_fasta.py b/qiime/demultiplex_fasta.py index 4cf7921265..3a1cfc925c 100755 --- a/qiime/demultiplex_fasta.py +++ b/qiime/demultiplex_fasta.py @@ -13,7 +13,7 @@ "Jens Reeder", "Emily TerAvest"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/qiime/denoise_wrapper.py b/qiime/denoise_wrapper.py index 0a4059faf9..2d3c604643 100644 --- a/qiime/denoise_wrapper.py +++ b/qiime/denoise_wrapper.py @@ -7,7 +7,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/denoiser/__init__.py b/qiime/denoiser/__init__.py index 2b6adf3ef4..c9e9db7b1e 100644 --- a/qiime/denoiser/__init__.py +++ b/qiime/denoiser/__init__.py @@ -5,7 +5,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/cluster_utils.py b/qiime/denoiser/cluster_utils.py index b2a706bd58..2cd011ede7 100644 --- a/qiime/denoiser/cluster_utils.py +++ b/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__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/denoise_postprocess.py b/qiime/denoiser/denoise_postprocess.py index d3e9fd5174..9768ebc183 100644 --- a/qiime/denoiser/denoise_postprocess.py +++ b/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__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/denoise_worker.py b/qiime/denoiser/denoise_worker.py index a74f4430dd..634d85fb5e 100644 --- a/qiime/denoiser/denoise_worker.py +++ b/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__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/flowgram_clustering.py b/qiime/denoiser/flowgram_clustering.py index c6711957e1..56461e6616 100644 --- a/qiime/denoiser/flowgram_clustering.py +++ b/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__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/flowgram_filter.py b/qiime/denoiser/flowgram_filter.py index 9d1411a969..a666c2bd7f 100644 --- a/qiime/denoiser/flowgram_filter.py +++ b/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__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/make_cluster_jobs.py b/qiime/denoiser/make_cluster_jobs.py index 359fb5a4c4..b2a0569780 100755 --- a/qiime/denoiser/make_cluster_jobs.py +++ b/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__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/preprocess.py b/qiime/denoiser/preprocess.py index 26119b281e..7eec12c510 100644 --- a/qiime/denoiser/preprocess.py +++ b/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__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/denoiser/utils.py b/qiime/denoiser/utils.py index efb45b472c..313e2ae8f5 100644 --- a/qiime/denoiser/utils.py +++ b/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__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/qiime/detrend.py b/qiime/detrend.py index 485016151b..5fc07442f7 100644 --- a/qiime/detrend.py +++ b/qiime/detrend.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2012, The QIIME Project" __credits__ = ["Dan Knights", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Dan Knights" __email__ = "danknights@gmail.com" diff --git a/qiime/differential_abundance.py b/qiime/differential_abundance.py index 5be4ea10cf..df433006c9 100755 --- a/qiime/differential_abundance.py +++ b/qiime/differential_abundance.py @@ -17,7 +17,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Sophie Weiss", "Joseph Paulson"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Sophie Weiss" __email__ = "sophie.sjw@gmail.com" diff --git a/qiime/distance_matrix_from_mapping.py b/qiime/distance_matrix_from_mapping.py index 3951047268..a778840189 100644 --- a/qiime/distance_matrix_from_mapping.py +++ b/qiime/distance_matrix_from_mapping.py @@ -7,7 +7,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Antonio Gonzalez Pena", "Andrew J. King"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/qiime/estimate_observation_richness.py b/qiime/estimate_observation_richness.py index 64d7cd27d8..3eba581d0e 100755 --- a/qiime/estimate_observation_richness.py +++ b/qiime/estimate_observation_richness.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/exclude_seqs_by_blast.py b/qiime/exclude_seqs_by_blast.py index 2d754ba84c..04d407e1b1 100644 --- a/qiime/exclude_seqs_by_blast.py +++ b/qiime/exclude_seqs_by_blast.py @@ -17,7 +17,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jesse Zaneveld", "Rob Knight", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jesse Zaneveld" __email__ = "zaneveld@gmail.com" diff --git a/qiime/extract_barcodes.py b/qiime/extract_barcodes.py index 3beec47a73..31d6953953 100644 --- a/qiime/extract_barcodes.py +++ b/qiime/extract_barcodes.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "william.a.walters@gmail.com" diff --git a/qiime/filter.py b/qiime/filter.py index ace45d3e9a..356b5d35bd 100644 --- a/qiime/filter.py +++ b/qiime/filter.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Will Van Treuren", "Daniel McDonald", "Jai Ram Rideout", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/filter_alignment.py b/qiime/filter_alignment.py index 6a4bcb2a26..523c6ba5df 100755 --- a/qiime/filter_alignment.py +++ b/qiime/filter_alignment.py @@ -21,7 +21,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Justin Kuczynski", "Dan Knights"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/filter_otus_by_sample.py b/qiime/filter_otus_by_sample.py index a2a9a0bb97..199d56fff8 100644 --- a/qiime/filter_otus_by_sample.py +++ b/qiime/filter_otus_by_sample.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jesse Stombaugh"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/format.py b/qiime/format.py index 21456af3e2..2e5a7fb00b 100755 --- a/qiime/format.py +++ b/qiime/format.py @@ -6,7 +6,7 @@ "Antonio Gonzalez Pena", "Daniel McDonald", "Jai Ram Rideout"] # remember to add yourself if you make changes __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/golay.py b/qiime/golay.py index e975475aa7..b725b45675 100644 --- a/qiime/golay.py +++ b/qiime/golay.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/group.py b/qiime/group.py index 17d27789be..7a280f80d9 100755 --- a/qiime/group.py +++ b/qiime/group.py @@ -8,7 +8,7 @@ "Greg Caporaso", "Jeremy Widmann"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/hamming.py b/qiime/hamming.py index d9fa3e01f9..0c56d7d0d8 100644 --- a/qiime/hamming.py +++ b/qiime/hamming.py @@ -15,7 +15,7 @@ # remember to add yourself if you make changes __credits__ = ["Micah Hamady", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/hierarchical_cluster.py b/qiime/hierarchical_cluster.py index 962e896387..f2c26d9273 100644 --- a/qiime/hierarchical_cluster.py +++ b/qiime/hierarchical_cluster.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/identify_chimeric_seqs.py b/qiime/identify_chimeric_seqs.py index a3dc93d53a..8104bfca7f 100755 --- a/qiime/identify_chimeric_seqs.py +++ b/qiime/identify_chimeric_seqs.py @@ -28,7 +28,7 @@ __credits__ = ["Greg Caporaso", "Jens Reeder", "William Walters", "Jai Ram Rideout", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/join_paired_ends.py b/qiime/join_paired_ends.py index f981a4f826..258c5ab7d4 100644 --- a/qiime/join_paired_ends.py +++ b/qiime/join_paired_ends.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Mike Robeson"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Mike Robeson" __email__ = "robesonms@ornl.gov" diff --git a/qiime/make_2d_plots.py b/qiime/make_2d_plots.py index 80b2bc2b60..6f8ae7c497 100644 --- a/qiime/make_2d_plots.py +++ b/qiime/make_2d_plots.py @@ -7,7 +7,7 @@ # remember to add yourself __credits__ = ["Jesse Stombaugh", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/make_bipartite_network.py b/qiime/make_bipartite_network.py index ff3d34d032..d2264ae3c2 100644 --- a/qiime/make_bipartite_network.py +++ b/qiime/make_bipartite_network.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Will Van Treuren, Julia Goodrich"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Will Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/qiime/make_bootstrapped_tree.py b/qiime/make_bootstrapped_tree.py index 30015e1f89..f86aaaef0d 100644 --- a/qiime/make_bootstrapped_tree.py +++ b/qiime/make_bootstrapped_tree.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/make_distance_boxplots.py b/qiime/make_distance_boxplots.py index 4ccd6f09a8..ac654e5fd0 100755 --- a/qiime/make_distance_boxplots.py +++ b/qiime/make_distance_boxplots.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/make_fastq.py b/qiime/make_fastq.py index ee22269e2e..b8b73ed216 100644 --- a/qiime/make_fastq.py +++ b/qiime/make_fastq.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight"] # remember to add yourself if you make changes __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/qiime/make_library_id_lists.py b/qiime/make_library_id_lists.py index ff11d3269a..2c1aa65e8a 100644 --- a/qiime/make_library_id_lists.py +++ b/qiime/make_library_id_lists.py @@ -10,7 +10,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/qiime/make_otu_heatmap.py b/qiime/make_otu_heatmap.py index b94a7f5500..b3234d0908 100644 --- a/qiime/make_otu_heatmap.py +++ b/qiime/make_otu_heatmap.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Dan Knights", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Dan Knights" __email__ = "daniel.knights@colorado.edu" diff --git a/qiime/make_otu_network.py b/qiime/make_otu_network.py index fe49ed1fa5..5e639a3bff 100644 --- a/qiime/make_otu_network.py +++ b/qiime/make_otu_network.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Julia Goodrich"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jose Clemente" __email__ = "jose.clemente@gmail.com" diff --git a/qiime/make_otu_table.py b/qiime/make_otu_table.py index 0f70d0f518..612c81d955 100644 --- a/qiime/make_otu_table.py +++ b/qiime/make_otu_table.py @@ -5,7 +5,7 @@ __credits__ = ["Rob Knight", "Justin Kuczynski", "Adam Robbins-Pianka", "Sami Pietila"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/make_per_library_sff.py b/qiime/make_per_library_sff.py index b4c10d478f..69f28740ed 100644 --- a/qiime/make_per_library_sff.py +++ b/qiime/make_per_library_sff.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Kyle Bittinger"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/qiime/make_phylogeny.py b/qiime/make_phylogeny.py index dfae6cade5..bb334f3e8b 100644 --- a/qiime/make_phylogeny.py +++ b/qiime/make_phylogeny.py @@ -5,7 +5,7 @@ __credits__ = ["Rob Knight", "Justin Kuczynski", "Daniel McDonald", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/make_rarefaction_plots.py b/qiime/make_rarefaction_plots.py index 6b69a63209..9c7b1abf95 100644 --- a/qiime/make_rarefaction_plots.py +++ b/qiime/make_rarefaction_plots.py @@ -7,7 +7,7 @@ "Will Van Treuren", "Yoshiki Vazquez Baeza", "Jai Ram Rideout", "Evan Bolyen"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/map_reads_to_reference.py b/qiime/map_reads_to_reference.py index 63d49d8e76..edc8b37a53 100644 --- a/qiime/map_reads_to_reference.py +++ b/qiime/map_reads_to_reference.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/nmds.py b/qiime/nmds.py index 1b2b31c4ea..d6306a3761 100644 --- a/qiime/nmds.py +++ b/qiime/nmds.py @@ -10,7 +10,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/normalize_table.py b/qiime/normalize_table.py index b92bb9de3e..892db3609a 100755 --- a/qiime/normalize_table.py +++ b/qiime/normalize_table.py @@ -15,7 +15,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Sophie Weiss", "Joseph Paulson"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Sophie Weiss" __email__ = "sophie.sjw@gmail.com" diff --git a/qiime/otu_significance.py b/qiime/otu_significance.py index 71143a2aea..b4abb9f3c7 100644 --- a/qiime/otu_significance.py +++ b/qiime/otu_significance.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2013, The QIIME project" __credits__ = ["Will Van Treuren", "Luke Ursell", "Catherine Lozupone"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Luke Ursell" __email__ = "lkursell@gmail.com" diff --git a/qiime/parallel/__init__.py b/qiime/parallel/__init__.py index e955bf5970..dbafb65971 100644 --- a/qiime/parallel/__init__.py +++ b/qiime/parallel/__init__.py @@ -20,7 +20,7 @@ "Daniel McDonald", "Catherine Lozupone"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/align_seqs.py b/qiime/parallel/align_seqs.py index 69fcf119a3..3e302f912a 100644 --- a/qiime/parallel/align_seqs.py +++ b/qiime/parallel/align_seqs.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/alpha_diversity.py b/qiime/parallel/alpha_diversity.py index 0841fc8555..688260474a 100644 --- a/qiime/parallel/alpha_diversity.py +++ b/qiime/parallel/alpha_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/assign_taxonomy.py b/qiime/parallel/assign_taxonomy.py index e7ba01ff95..6d8e056f8a 100644 --- a/qiime/parallel/assign_taxonomy.py +++ b/qiime/parallel/assign_taxonomy.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/parallel/beta_diversity.py b/qiime/parallel/beta_diversity.py index ade9d03b83..287ac387ee 100644 --- a/qiime/parallel/beta_diversity.py +++ b/qiime/parallel/beta_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/blast.py b/qiime/parallel/blast.py index 4efa4b0f83..d03f901cab 100755 --- a/qiime/parallel/blast.py +++ b/qiime/parallel/blast.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/parallel/identify_chimeric_seqs.py b/qiime/parallel/identify_chimeric_seqs.py index 5b58698f5f..7444ef0781 100755 --- a/qiime/parallel/identify_chimeric_seqs.py +++ b/qiime/parallel/identify_chimeric_seqs.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/parallel/map_reads_to_reference.py b/qiime/parallel/map_reads_to_reference.py index 199c1ff833..8914acbb7b 100644 --- a/qiime/parallel/map_reads_to_reference.py +++ b/qiime/parallel/map_reads_to_reference.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/merge_otus.py b/qiime/parallel/merge_otus.py index 16bec04b63..946bd9b0e2 100644 --- a/qiime/parallel/merge_otus.py +++ b/qiime/parallel/merge_otus.py @@ -10,7 +10,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Daniel McDonald", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Daniel McDonald" __email__ = "mcdonadt@colorado.edu" diff --git a/qiime/parallel/multiple_rarefactions.py b/qiime/parallel/multiple_rarefactions.py index c875363cb9..8769f7ca2a 100644 --- a/qiime/parallel/multiple_rarefactions.py +++ b/qiime/parallel/multiple_rarefactions.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/pick_otus.py b/qiime/parallel/pick_otus.py index 03ccabe892..eeec05daab 100644 --- a/qiime/parallel/pick_otus.py +++ b/qiime/parallel/pick_otus.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jens Reeder", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/poller.py b/qiime/parallel/poller.py index 5ad807eb3a..f0d76a317f 100755 --- a/qiime/parallel/poller.py +++ b/qiime/parallel/poller.py @@ -13,7 +13,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parallel/util.py b/qiime/parallel/util.py index 3ea88ab39d..3f0a0e9287 100644 --- a/qiime/parallel/util.py +++ b/qiime/parallel/util.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Jens Reeder", "Jai Ram Rideout", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/parse.py b/qiime/parse.py index be3a9027b9..179d839f60 100644 --- a/qiime/parse.py +++ b/qiime/parse.py @@ -8,7 +8,7 @@ "Antonio Gonzalez Pena", "Jai Ram Rideout", "Will Van Treuren", "Yoshiki Vazquez-Baeza", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/pick_otus.py b/qiime/pick_otus.py index 31165f2430..bed884b758 100644 --- a/qiime/pick_otus.py +++ b/qiime/pick_otus.py @@ -5,7 +5,7 @@ "William Walters", "Jose Carlos Clemente Litran", "Adam Robbins-Pianka", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/pick_rep_set.py b/qiime/pick_rep_set.py index 303959ef30..9afa990607 100644 --- a/qiime/pick_rep_set.py +++ b/qiime/pick_rep_set.py @@ -5,7 +5,7 @@ __credits__ = ["Rob Knight", "Greg Caporaso", "Kyle Bittinger", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Daniel McDonald" __email__ = "wasade@gmail.com" diff --git a/qiime/plot_rank_abundance_graph.py b/qiime/plot_rank_abundance_graph.py index 814c1660f6..694d21cd7a 100644 --- a/qiime/plot_rank_abundance_graph.py +++ b/qiime/plot_rank_abundance_graph.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Emily TerAvest"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/plot_semivariogram.py b/qiime/plot_semivariogram.py index 960c6ed5de..7aaacb30a2 100644 --- a/qiime/plot_semivariogram.py +++ b/qiime/plot_semivariogram.py @@ -13,7 +13,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Antonio Gonzalez Pena"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/qiime/plot_taxa_summary.py b/qiime/plot_taxa_summary.py index eb918faeea..26fb0c230c 100644 --- a/qiime/plot_taxa_summary.py +++ b/qiime/plot_taxa_summary.py @@ -7,7 +7,7 @@ __credits__ = ["Jesse Stobmaugh", "Julia Goodrich", "Micah Hamady"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/principal_coordinates.py b/qiime/principal_coordinates.py index 43cbab0554..989f9929c7 100644 --- a/qiime/principal_coordinates.py +++ b/qiime/principal_coordinates.py @@ -8,7 +8,7 @@ "Catherine Lozupone", "Emily TerAvest", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/process_sff.py b/qiime/process_sff.py index 53cc8fbddf..95081abc88 100644 --- a/qiime/process_sff.py +++ b/qiime/process_sff.py @@ -29,7 +29,7 @@ "Adam Robbins-Pianka", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/qiime/pycogent_backports/__init__.py b/qiime/pycogent_backports/__init__.py index bc5d2790ec..5ebe02024f 100644 --- a/qiime/pycogent_backports/__init__.py +++ b/qiime/pycogent_backports/__init__.py @@ -18,6 +18,6 @@ "Daniel McDonald", "Catherine Lozupone"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/quality_scores_plot.py b/qiime/quality_scores_plot.py index 872e1c28bd..0770168ad9 100755 --- a/qiime/quality_scores_plot.py +++ b/qiime/quality_scores_plot.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/qiime/rarefaction.py b/qiime/rarefaction.py index fc929bc3a7..4e7d54c88c 100644 --- a/qiime/rarefaction.py +++ b/qiime/rarefaction.py @@ -6,7 +6,7 @@ __credits__ = ["Justin Kuczynski", "Jose Carlos Clemente Litran", "Rob Knight", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/relatedness_library.py b/qiime/relatedness_library.py index bbf611ad95..27e65e0dd4 100644 --- a/qiime/relatedness_library.py +++ b/qiime/relatedness_library.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["William Van Treuren"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/qiime/remote.py b/qiime/remote.py index c560317f28..5147b163a6 100755 --- a/qiime/remote.py +++ b/qiime/remote.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/shared_phylotypes.py b/qiime/shared_phylotypes.py index d24af7271d..23bbb3792c 100644 --- a/qiime/shared_phylotypes.py +++ b/qiime/shared_phylotypes.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder, Justin Kuczynski", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jose Clemente" __email__ = "jose.clemente@gmail.com" diff --git a/qiime/simsam.py b/qiime/simsam.py index bc7b8e3892..1396af8573 100755 --- a/qiime/simsam.py +++ b/qiime/simsam.py @@ -7,7 +7,7 @@ __credits__ = ["Justin Kuczynski", "Rob Knight", "Jai Ram Rideout", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/sort.py b/qiime/sort.py index 4911a0abdb..95a5ae74cb 100644 --- a/qiime/sort.py +++ b/qiime/sort.py @@ -13,7 +13,7 @@ __credits__ = ["Greg Caporaso", "Rob Knight", "Daniel McDonald", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/split.py b/qiime/split.py index de8d1f66a5..47f99a9125 100644 --- a/qiime/split.py +++ b/qiime/split.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Daniel McDonald", "Will Van Treuren"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/split_libraries.py b/qiime/split_libraries.py index f0e8496aad..99ef9a0dae 100644 --- a/qiime/split_libraries.py +++ b/qiime/split_libraries.py @@ -30,7 +30,7 @@ "Jesse Stombaugh", "William Walters", "Jens Reeder", "Emily TerAvest", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "rob@spot.colorado.edu, william.a.walters@colorado.edu" diff --git a/qiime/split_libraries_fastq.py b/qiime/split_libraries_fastq.py index 5985e10bfa..3ceb870032 100644 --- a/qiime/split_libraries_fastq.py +++ b/qiime/split_libraries_fastq.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/split_libraries_lea_seq.py b/qiime/split_libraries_lea_seq.py index a001d967e3..b8650f7ac6 100644 --- a/qiime/split_libraries_lea_seq.py +++ b/qiime/split_libraries_lea_seq.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Charudatta Navare", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Charudatta Navare" __email__ = "charudatta.navare@gmail.com" diff --git a/qiime/stats.py b/qiime/stats.py index ea96f62a2c..014a4eb47e 100644 --- a/qiime/stats.py +++ b/qiime/stats.py @@ -8,7 +8,7 @@ "Jose Carlos Clemente Litran", "Greg Caporaso", "Will Van Treuren"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/qiime/summarize_taxa.py b/qiime/summarize_taxa.py index 73a6d2e319..03bfdad0b9 100644 --- a/qiime/summarize_taxa.py +++ b/qiime/summarize_taxa.py @@ -6,7 +6,7 @@ "Rob Knight", "Catherine Lozupone", "Justin Kuczynski", "Julia Goodrich", "Antonio Gonzalez Pena", "Jose Carlos Clemente Litran"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Daniel McDonald" __email__ = "wasade@gmail.com" diff --git a/qiime/supervised_learning.py b/qiime/supervised_learning.py index cd585a36e4..5904fe1ce0 100644 --- a/qiime/supervised_learning.py +++ b/qiime/supervised_learning.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Dan Knights", "Luke Ursell", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Dan Knights" __email__ = "danknights@gmail.com" diff --git a/qiime/support_files/R/util.r b/qiime/support_files/R/util.r index 7acb152583..84bab74142 100644 --- a/qiime/support_files/R/util.r +++ b/qiime/support_files/R/util.r @@ -4,7 +4,7 @@ # __copyright__ = "Copyright 2011, The QIIME Project" # __credits__ = ["Dan Knights"] # __license__ = "GPL" -# __version__ = "1.9.0-rc1" +# __version__ = "1.9.0-rc2" # __maintainer__ = "Dan Knights" # __email__ = "daniel.knights@colorado.edu" # diff --git a/qiime/support_files/js/otu_count_display.js b/qiime/support_files/js/otu_count_display.js index 91f80f982e..31f3aab08d 100644 --- a/qiime/support_files/js/otu_count_display.js +++ b/qiime/support_files/js/otu_count_display.js @@ -6,7 +6,7 @@ __author__ = "Jesse Stombaugh" __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jesse Stombaugh"] #remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Rob Knight" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/support_files/test_js/test_otu_count_display.html b/qiime/support_files/test_js/test_otu_count_display.html index 469ce6c71c..53fa391938 100644 --- a/qiime/support_files/test_js/test_otu_count_display.html +++ b/qiime/support_files/test_js/test_otu_count_display.html @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" #consider project name __credits__ = ["Jesse Stombaugh"] #remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/qiime/test.py b/qiime/test.py index e436b48029..163c7af5ba 100644 --- a/qiime/test.py +++ b/qiime/test.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/transform_coordinate_matrices.py b/qiime/transform_coordinate_matrices.py index 7e11d58fb7..0e67e06337 100644 --- a/qiime/transform_coordinate_matrices.py +++ b/qiime/transform_coordinate_matrices.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Justin Kuczynski", "Kyle Patnode", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/tree_compare.py b/qiime/tree_compare.py index 7dbf3974fc..eb41c03db1 100644 --- a/qiime/tree_compare.py +++ b/qiime/tree_compare.py @@ -13,7 +13,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/qiime/trim_sff_primers.py b/qiime/trim_sff_primers.py index 3c8abfa92c..3f74eca38e 100644 --- a/qiime/trim_sff_primers.py +++ b/qiime/trim_sff_primers.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", 'Kyle Bittinger', "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/qiime/truncate_fasta_qual_files.py b/qiime/truncate_fasta_qual_files.py index 6e503c6a18..96fac3fc3a 100755 --- a/qiime/truncate_fasta_qual_files.py +++ b/qiime/truncate_fasta_qual_files.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/qiime/truncate_reverse_primer.py b/qiime/truncate_reverse_primer.py index 0440f470e9..11429bb069 100755 --- a/qiime/truncate_reverse_primer.py +++ b/qiime/truncate_reverse_primer.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Emily TerAvest"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/qiime/util.py b/qiime/util.py index e682000cfe..f6f5d219dc 100644 --- a/qiime/util.py +++ b/qiime/util.py @@ -8,7 +8,7 @@ "Levi McCracken", "Damien Coy", "Yoshiki Vazquez Baeza", "Will Van Treuren", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/validate_demultiplexed_fasta.py b/qiime/validate_demultiplexed_fasta.py index 52946f2ed2..059b956a15 100755 --- a/qiime/validate_demultiplexed_fasta.py +++ b/qiime/validate_demultiplexed_fasta.py @@ -7,7 +7,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Anton Walters", "Emily TerAvest"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Anton Walters" __email__ = "william.a.walters@gmail.com" diff --git a/qiime/workflow/__init__.py b/qiime/workflow/__init__.py index 2a272bb3d7..8de00a076b 100644 --- a/qiime/workflow/__init__.py +++ b/qiime/workflow/__init__.py @@ -21,6 +21,6 @@ "Daniel McDonald", "Catherine Lozupone"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/workflow/ampliconnoise.py b/qiime/workflow/ampliconnoise.py index 80014a7a2b..bf3c026a63 100755 --- a/qiime/workflow/ampliconnoise.py +++ b/qiime/workflow/ampliconnoise.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Kyle Bittinger", "Justin Kuczynski", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/workflow/core_diversity_analyses.py b/qiime/workflow/core_diversity_analyses.py index edd8c0322c..cd0ddf78b3 100644 --- a/qiime/workflow/core_diversity_analyses.py +++ b/qiime/workflow/core_diversity_analyses.py @@ -23,7 +23,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/workflow/downstream.py b/qiime/workflow/downstream.py index 023d7a7d08..d516862d69 100644 --- a/qiime/workflow/downstream.py +++ b/qiime/workflow/downstream.py @@ -8,7 +8,7 @@ "Jesse Stombaugh", "Yoshiki Vazquez Baeza", "Jai Ram Rideout", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/workflow/pick_open_reference_otus.py b/qiime/workflow/pick_open_reference_otus.py index ac7df1e50a..d119081a1c 100644 --- a/qiime/workflow/pick_open_reference_otus.py +++ b/qiime/workflow/pick_open_reference_otus.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/workflow/preprocess.py b/qiime/workflow/preprocess.py index 05d09915e4..66c130a39d 100644 --- a/qiime/workflow/preprocess.py +++ b/qiime/workflow/preprocess.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/qiime/workflow/upstream.py b/qiime/workflow/upstream.py index d6e8c746e7..b48df52a17 100644 --- a/qiime/workflow/upstream.py +++ b/qiime/workflow/upstream.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Kyle Bittinger", "Justin Kuczynski", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/qiime/workflow/util.py b/qiime/workflow/util.py index 6034835040..b395995833 100755 --- a/qiime/workflow/util.py +++ b/qiime/workflow/util.py @@ -8,7 +8,7 @@ "Kyle Bittinger", "Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/add_alpha_to_mapping_file.py b/scripts/add_alpha_to_mapping_file.py index 98fe051256..22c1586998 100755 --- a/scripts/add_alpha_to_mapping_file.py +++ b/scripts/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-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Yoshiki Vazquez-Baeza" __email__ = "yoshiki89@gmail.com" diff --git a/scripts/add_qiime_labels.py b/scripts/add_qiime_labels.py index 82838b24fb..a106e533bf 100755 --- a/scripts/add_qiime_labels.py +++ b/scripts/add_qiime_labels.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/adjust_seq_orientation.py b/scripts/adjust_seq_orientation.py index 8f53912b49..2405212ecb 100755 --- a/scripts/adjust_seq_orientation.py +++ b/scripts/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-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/scripts/align_seqs.py b/scripts/align_seqs.py index 4b9c8b2c22..fd09b7f277 100755 --- a/scripts/align_seqs.py +++ b/scripts/align_seqs.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/alpha_diversity.py b/scripts/alpha_diversity.py index 4a4fb43df8..74d11ee448 100755 --- a/scripts/alpha_diversity.py +++ b/scripts/alpha_diversity.py @@ -7,7 +7,7 @@ __credits__ = ["Justin Kuczynski", "Rob Knight", "Jose Antonio Navas Molina", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/alpha_rarefaction.py b/scripts/alpha_rarefaction.py index 4f50001b8e..0dfd635981 100755 --- a/scripts/alpha_rarefaction.py +++ b/scripts/alpha_rarefaction.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/ampliconnoise.py b/scripts/ampliconnoise.py index 705e9f159a..16bdd65762 100755 --- a/scripts/ampliconnoise.py +++ b/scripts/ampliconnoise.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Jose A. Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/assign_taxonomy.py b/scripts/assign_taxonomy.py index ec1751ef9b..3ac6f50c02 100755 --- a/scripts/assign_taxonomy.py +++ b/scripts/assign_taxonomy.py @@ -7,7 +7,7 @@ __credits__ = ["Rob Knight", "Greg Caporaso", "Kyle Bittinger", "Antonio Gonzalez Pena", "David Soergel", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/scripts/beta_diversity.py b/scripts/beta_diversity.py index 5fcb6b2a9c..3e02dadf9b 100755 --- a/scripts/beta_diversity.py +++ b/scripts/beta_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Rob Knight", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/beta_diversity_through_plots.py b/scripts/beta_diversity_through_plots.py index 3bb0e2306e..90aaad3ec1 100755 --- a/scripts/beta_diversity_through_plots.py +++ b/scripts/beta_diversity_through_plots.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Kestrel Gorlick"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/beta_significance.py b/scripts/beta_significance.py index df41d58250..fc2fbb30a1 100755 --- a/scripts/beta_significance.py +++ b/scripts/beta_significance.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Jose Antonio Navas", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/blast_wrapper.py b/scripts/blast_wrapper.py index f631128565..1b367e256d 100755 --- a/scripts/blast_wrapper.py +++ b/scripts/blast_wrapper.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jesse Stombaugh"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/categorized_dist_scatterplot.py b/scripts/categorized_dist_scatterplot.py index 9ef0838362..c2b5556d11 100755 --- a/scripts/categorized_dist_scatterplot.py +++ b/scripts/categorized_dist_scatterplot.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/check_id_map.py b/scripts/check_id_map.py index 885b49533c..d78671753a 100755 --- a/scripts/check_id_map.py +++ b/scripts/check_id_map.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Luke Ursell"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/clean_raxml_parsimony_tree.py b/scripts/clean_raxml_parsimony_tree.py index 49486e177e..c5c7cb5c9b 100755 --- a/scripts/clean_raxml_parsimony_tree.py +++ b/scripts/clean_raxml_parsimony_tree.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Jesse Stombaugh"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/scripts/cluster_quality.py b/scripts/cluster_quality.py index d7ca38cf63..52e2995da8 100755 --- a/scripts/cluster_quality.py +++ b/scripts/cluster_quality.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/collapse_samples.py b/scripts/collapse_samples.py index dfdaffddc8..e15d4aacef 100755 --- a/scripts/collapse_samples.py +++ b/scripts/collapse_samples.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/collate_alpha.py b/scripts/collate_alpha.py index 572b47a646..664a3d13a5 100755 --- a/scripts/collate_alpha.py +++ b/scripts/collate_alpha.py @@ -15,7 +15,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/compare_alpha_diversity.py b/scripts/compare_alpha_diversity.py index 54c2dd007e..add18361fa 100755 --- a/scripts/compare_alpha_diversity.py +++ b/scripts/compare_alpha_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["William Van Treuren", "Greg Caparaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Van Treuren" __email__ = "vantreur@colorado.edu" diff --git a/scripts/compare_categories.py b/scripts/compare_categories.py index 1d21198ccc..8bd6a76337 100755 --- a/scripts/compare_categories.py +++ b/scripts/compare_categories.py @@ -6,7 +6,7 @@ __credits__ = ["Logan Knecht", "Michael Dwan", "Damien Coy", "Jai Ram Rideout", "Levi McCracken"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/scripts/compare_distance_matrices.py b/scripts/compare_distance_matrices.py index 38e7b9a32a..11f43be4e6 100755 --- a/scripts/compare_distance_matrices.py +++ b/scripts/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-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/scripts/compare_taxa_summaries.py b/scripts/compare_taxa_summaries.py index 739335ad57..0f4b35de59 100755 --- a/scripts/compare_taxa_summaries.py +++ b/scripts/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-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/scripts/compare_trajectories.py b/scripts/compare_trajectories.py index b08ceddd40..3b25fcd001 100755 --- a/scripts/compare_trajectories.py +++ b/scripts/compare_trajectories.py @@ -6,7 +6,7 @@ __credits__ = ["Jose Antonio Navas Molina", "Antonio Gonzalez Pena", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jose Antonio Navas Molina" __email__ = "josenavasmolina@gmail.com" diff --git a/scripts/compute_core_microbiome.py b/scripts/compute_core_microbiome.py index fbec42b0b0..36c16630b0 100755 --- a/scripts/compute_core_microbiome.py +++ b/scripts/compute_core_microbiome.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/compute_taxonomy_ratios.py b/scripts/compute_taxonomy_ratios.py index 16fb454369..cba1034d38 100755 --- a/scripts/compute_taxonomy_ratios.py +++ b/scripts/compute_taxonomy_ratios.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2014, The QIIME project" __credits__ = ["Daniel McDonald", "Greg Caporaso", "Jai Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Daniel McDonald" __email__ = "mcdonadt@colorado.edu" diff --git a/scripts/conditional_uncovered_probability.py b/scripts/conditional_uncovered_probability.py index 7f459572da..0b4776bcd6 100755 --- a/scripts/conditional_uncovered_probability.py +++ b/scripts/conditional_uncovered_probability.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Jose Antonio Navas Molina", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" __status__ = "Development" diff --git a/scripts/consensus_tree.py b/scripts/consensus_tree.py index 2c2525e263..2cfa6f3de3 100755 --- a/scripts/consensus_tree.py +++ b/scripts/consensus_tree.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "justinak@gmail.com" diff --git a/scripts/convert_fastaqual_fastq.py b/scripts/convert_fastaqual_fastq.py index 5bcfe01772..913da0cbfd 100755 --- a/scripts/convert_fastaqual_fastq.py +++ b/scripts/convert_fastaqual_fastq.py @@ -5,7 +5,7 @@ __credits__ = ["Adam Robbins-Pianka, Abhisaar Yadav", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Adam Robbins-Pianka" __email__ = "adam.robbinspianka@colorado.edu" diff --git a/scripts/convert_unifrac_sample_mapping_to_otu_table.py b/scripts/convert_unifrac_sample_mapping_to_otu_table.py index fc9b58770b..ba23b2b7b4 100755 --- a/scripts/convert_unifrac_sample_mapping_to_otu_table.py +++ b/scripts/convert_unifrac_sample_mapping_to_otu_table.py @@ -5,7 +5,7 @@ __credits__ = ["Catherine Lozupone", "Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Cathy Lozupone" __email__ = "lozupone@colorado.edu" diff --git a/scripts/core_diversity_analyses.py b/scripts/core_diversity_analyses.py index bc4fabd39d..3925d6f72b 100755 --- a/scripts/core_diversity_analyses.py +++ b/scripts/core_diversity_analyses.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/count_seqs.py b/scripts/count_seqs.py index f54cac6144..7728300722 100755 --- a/scripts/count_seqs.py +++ b/scripts/count_seqs.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/demultiplex_fasta.py b/scripts/demultiplex_fasta.py index 05f59fc9e9..75a1802fee 100755 --- a/scripts/demultiplex_fasta.py +++ b/scripts/demultiplex_fasta.py @@ -13,7 +13,7 @@ "Jens Reeder", "Jose Antonio Navas Molina"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/scripts/denoise_wrapper.py b/scripts/denoise_wrapper.py index 0da4550be1..1bd245ac7f 100755 --- a/scripts/denoise_wrapper.py +++ b/scripts/denoise_wrapper.py @@ -8,7 +8,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/scripts/denoiser.py b/scripts/denoiser.py index 88f4380c76..ee53b7b753 100755 --- a/scripts/denoiser.py +++ b/scripts/denoiser.py @@ -8,7 +8,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/scripts/denoiser_preprocess.py b/scripts/denoiser_preprocess.py index a3ba2c38a8..36b47b40f8 100755 --- a/scripts/denoiser_preprocess.py +++ b/scripts/denoiser_preprocess.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/scripts/denoiser_worker.py b/scripts/denoiser_worker.py index 5e7ed953e5..c39cd24884 100755 --- a/scripts/denoiser_worker.py +++ b/scripts/denoiser_worker.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/scripts/detrend.py b/scripts/detrend.py index ef00e4f1f7..dfba04d504 100755 --- a/scripts/detrend.py +++ b/scripts/detrend.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME Project" __credits__ = ["Dan Knights"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Dan Knights" __email__ = "danknights@gmail.com" diff --git a/scripts/differential_abundance.py b/scripts/differential_abundance.py index 0e6ec78f10..b6baed8ebb 100755 --- a/scripts/differential_abundance.py +++ b/scripts/differential_abundance.py @@ -12,7 +12,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Sophie Weiss"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Sophie Weiss" __email__ = "sophie.sjw@gmail.com" diff --git a/scripts/dissimilarity_mtx_stats.py b/scripts/dissimilarity_mtx_stats.py index c8ac0934b3..c31c66e237 100755 --- a/scripts/dissimilarity_mtx_stats.py +++ b/scripts/dissimilarity_mtx_stats.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/distance_matrix_from_mapping.py b/scripts/distance_matrix_from_mapping.py index 0531909b5c..47a6497b9e 100755 --- a/scripts/distance_matrix_from_mapping.py +++ b/scripts/distance_matrix_from_mapping.py @@ -7,7 +7,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Antonio Gonzalez Pena", "Andrew J. King"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/scripts/estimate_observation_richness.py b/scripts/estimate_observation_richness.py index 08418e8e61..a353e7c7fc 100755 --- a/scripts/estimate_observation_richness.py +++ b/scripts/estimate_observation_richness.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/scripts/exclude_seqs_by_blast.py b/scripts/exclude_seqs_by_blast.py index aea654f94a..5452544524 100755 --- a/scripts/exclude_seqs_by_blast.py +++ b/scripts/exclude_seqs_by_blast.py @@ -26,7 +26,7 @@ "Jose Antonio Navas Molina", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jesse Zaneveld" __email__ = "zaneveld@gmail.com" diff --git a/scripts/extract_barcodes.py b/scripts/extract_barcodes.py index 2c20de7786..499d710191 100755 --- a/scripts/extract_barcodes.py +++ b/scripts/extract_barcodes.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "william.a.walters@gmail.com" diff --git a/scripts/extract_reads_from_interleaved_file.py b/scripts/extract_reads_from_interleaved_file.py index 5f3ef0d3fb..376b7410f8 100755 --- a/scripts/extract_reads_from_interleaved_file.py +++ b/scripts/extract_reads_from_interleaved_file.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Antonio Gonzalez Pena"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/scripts/extract_seqs_by_sample_id.py b/scripts/extract_seqs_by_sample_id.py index 85f3a93359..180fe8da7d 100755 --- a/scripts/extract_seqs_by_sample_id.py +++ b/scripts/extract_seqs_by_sample_id.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/filter_alignment.py b/scripts/filter_alignment.py index f390dcc373..4a8dabb79b 100755 --- a/scripts/filter_alignment.py +++ b/scripts/filter_alignment.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Justin Kuczynski", "Dan Knights", "Doug Wendel", "William Walters", "John Chase"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/filter_distance_matrix.py b/scripts/filter_distance_matrix.py index 4bc0a47e8c..89e2ebb929 100755 --- a/scripts/filter_distance_matrix.py +++ b/scripts/filter_distance_matrix.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2010, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/filter_fasta.py b/scripts/filter_fasta.py index c68e2dd698..1a95866cb1 100755 --- a/scripts/filter_fasta.py +++ b/scripts/filter_fasta.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jens Reeder", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/filter_otus_by_sample.py b/scripts/filter_otus_by_sample.py index dfb266ce26..8696235c91 100755 --- a/scripts/filter_otus_by_sample.py +++ b/scripts/filter_otus_by_sample.py @@ -8,7 +8,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jesse Stombaugh"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/scripts/filter_otus_from_otu_table.py b/scripts/filter_otus_from_otu_table.py index c729ecbd97..919f64ad9d 100755 --- a/scripts/filter_otus_from_otu_table.py +++ b/scripts/filter_otus_from_otu_table.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/filter_samples_from_otu_table.py b/scripts/filter_samples_from_otu_table.py index cc0f1829c1..d5eeadae0a 100755 --- a/scripts/filter_samples_from_otu_table.py +++ b/scripts/filter_samples_from_otu_table.py @@ -11,7 +11,7 @@ "Daniel McDonald", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/filter_taxa_from_otu_table.py b/scripts/filter_taxa_from_otu_table.py index 9a5535a4e1..fa7b0e9131 100755 --- a/scripts/filter_taxa_from_otu_table.py +++ b/scripts/filter_taxa_from_otu_table.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/filter_tree.py b/scripts/filter_tree.py index a27e174fbf..4023c47dd0 100755 --- a/scripts/filter_tree.py +++ b/scripts/filter_tree.py @@ -10,7 +10,7 @@ "Daniel McDonald", "Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Van Treuren" __email__ = "vantreur@colorado.edu" diff --git a/scripts/fix_arb_fasta.py b/scripts/fix_arb_fasta.py index 99f012cfc0..e1e1032fdd 100755 --- a/scripts/fix_arb_fasta.py +++ b/scripts/fix_arb_fasta.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "Daniel McDonald", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/group_significance.py b/scripts/group_significance.py index b70104287c..a65add847b 100755 --- a/scripts/group_significance.py +++ b/scripts/group_significance.py @@ -9,7 +9,7 @@ "Jesse Stombaugh", "Doug Wendel", "Dan Knights", "Greg Caporaso", "Jai Ram Rideout", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Will Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/scripts/identify_chimeric_seqs.py b/scripts/identify_chimeric_seqs.py index 14335e956b..762bb231e5 100755 --- a/scripts/identify_chimeric_seqs.py +++ b/scripts/identify_chimeric_seqs.py @@ -12,7 +12,7 @@ "Jens Reeder", "William Walters"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/identify_missing_files.py b/scripts/identify_missing_files.py index a784966b10..f79b6d9373 100755 --- a/scripts/identify_missing_files.py +++ b/scripts/identify_missing_files.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/identify_paired_differences.py b/scripts/identify_paired_differences.py index 8b3e83b269..b18d29e821 100755 --- a/scripts/identify_paired_differences.py +++ b/scripts/identify_paired_differences.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2013, The QIIME project" __credits__ = ["Greg Caporaso", "Jose Carlos Clemente Litran"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/inflate_denoiser_output.py b/scripts/inflate_denoiser_output.py index ab25d4b4e1..6b4f34f419 100755 --- a/scripts/inflate_denoiser_output.py +++ b/scripts/inflate_denoiser_output.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/jackknifed_beta_diversity.py b/scripts/jackknifed_beta_diversity.py index 1db6e94623..f829856b6f 100755 --- a/scripts/jackknifed_beta_diversity.py +++ b/scripts/jackknifed_beta_diversity.py @@ -9,7 +9,7 @@ "Justin Kuczynski", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/join_paired_ends.py b/scripts/join_paired_ends.py index 62dd303683..8c28262b17 100755 --- a/scripts/join_paired_ends.py +++ b/scripts/join_paired_ends.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Mike Robeson"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Mike Robeson" __email__ = "robesonms@ornl.gov" diff --git a/scripts/load_remote_mapping_file.py b/scripts/load_remote_mapping_file.py index 229f3b8469..24ca18024f 100755 --- a/scripts/load_remote_mapping_file.py +++ b/scripts/load_remote_mapping_file.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/scripts/make_2d_plots.py b/scripts/make_2d_plots.py index ee3ae9f900..8491f1e43d 100755 --- a/scripts/make_2d_plots.py +++ b/scripts/make_2d_plots.py @@ -8,7 +8,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jesse Stombaugh", "Jose Antonio Navas Molina", "John Chase"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/scripts/make_bipartite_network.py b/scripts/make_bipartite_network.py index 2368cfdbae..b1db6f92ca 100755 --- a/scripts/make_bipartite_network.py +++ b/scripts/make_bipartite_network.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2013, The QIIME project" __credits__ = ["Will Van Treuren, Julia Goodrich, Luke Ursell"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Will Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/scripts/make_bootstrapped_tree.py b/scripts/make_bootstrapped_tree.py index 4027143b67..e79ed07b9b 100755 --- a/scripts/make_bootstrapped_tree.py +++ b/scripts/make_bootstrapped_tree.py @@ -9,7 +9,7 @@ "Jesse Stombaugh", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/make_distance_boxplots.py b/scripts/make_distance_boxplots.py index 3f7f055a32..bf625eee90 100755 --- a/scripts/make_distance_boxplots.py +++ b/scripts/make_distance_boxplots.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/scripts/make_distance_comparison_plots.py b/scripts/make_distance_comparison_plots.py index 20b54587ea..803b14a33d 100755 --- a/scripts/make_distance_comparison_plots.py +++ b/scripts/make_distance_comparison_plots.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/scripts/make_fastq.py b/scripts/make_fastq.py index ae49309899..f464d54407 100755 --- a/scripts/make_fastq.py +++ b/scripts/make_fastq.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "Jens Reeder"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/scripts/make_library_id_lists.py b/scripts/make_library_id_lists.py index 7d4fb2034c..5b4df1340e 100755 --- a/scripts/make_library_id_lists.py +++ b/scripts/make_library_id_lists.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "Doug Wendel"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/scripts/make_otu_heatmap.py b/scripts/make_otu_heatmap.py index 52a451ccef..3c016e48c4 100755 --- a/scripts/make_otu_heatmap.py +++ b/scripts/make_otu_heatmap.py @@ -10,7 +10,7 @@ "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Dan Knights" __email__ = "daniel.knights@colorado.edu" diff --git a/scripts/make_otu_network.py b/scripts/make_otu_network.py index 137eca37f0..7464f66047 100755 --- a/scripts/make_otu_network.py +++ b/scripts/make_otu_network.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Julia Goodrich", "Jose Carlos Clemente Litran"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jose Clemente" __email__ = "jose.clemente@gmail.com" diff --git a/scripts/make_otu_table.py b/scripts/make_otu_table.py index 68121f9872..e6b1c42759 100755 --- a/scripts/make_otu_table.py +++ b/scripts/make_otu_table.py @@ -12,7 +12,7 @@ "Adam Robbins-Pianka", "Sami Pietila"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/make_per_library_sff.py b/scripts/make_per_library_sff.py index 4257a1dddf..af0e95b7fc 100755 --- a/scripts/make_per_library_sff.py +++ b/scripts/make_per_library_sff.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "Daniel McDonald", "Kyle Bittinger"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/scripts/make_phylogeny.py b/scripts/make_phylogeny.py index 28c438b4f9..4a71bd62d9 100755 --- a/scripts/make_phylogeny.py +++ b/scripts/make_phylogeny.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/make_prefs_file.py b/scripts/make_prefs_file.py index b3137ff002..83faee2538 100755 --- a/scripts/make_prefs_file.py +++ b/scripts/make_prefs_file.py @@ -9,7 +9,7 @@ "Jeremy Widmann", "Antonio Gonzalez Pena"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/scripts/make_qiime_py_file.py b/scripts/make_qiime_py_file.py index a5c2193298..7309c88016 100755 --- a/scripts/make_qiime_py_file.py +++ b/scripts/make_qiime_py_file.py @@ -10,7 +10,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" @@ -88,7 +88,7 @@ def main(): __copyright__ = "COPYRIGHT" __credits__ = ["AUTHOR_NAME"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "AUTHOR_NAME" __email__ = "AUTHOR_EMAIL" """ % strftime('%d %b %Y') diff --git a/scripts/make_rarefaction_plots.py b/scripts/make_rarefaction_plots.py index ce2d01c41c..5aac4c477a 100755 --- a/scripts/make_rarefaction_plots.py +++ b/scripts/make_rarefaction_plots.py @@ -7,7 +7,7 @@ __credits__ = ["Meg Pirrung", "Jesse Stombaugh", "John Chase", "Jai Ram Rideout", "Evan Bolyen"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/scripts/make_tep.py b/scripts/make_tep.py index f94a916d49..61b431c8a2 100755 --- a/scripts/make_tep.py +++ b/scripts/make_tep.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Meg Pirrung", "Jesse Stombaugh", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Meg Pirrung" __email__ = "meganap@gmail.com" diff --git a/scripts/map_reads_to_reference.py b/scripts/map_reads_to_reference.py index 6a93e0708d..1dd8182758 100755 --- a/scripts/map_reads_to_reference.py +++ b/scripts/map_reads_to_reference.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/merge_mapping_files.py b/scripts/merge_mapping_files.py index 2832527151..6e667702cd 100755 --- a/scripts/merge_mapping_files.py +++ b/scripts/merge_mapping_files.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/merge_otu_maps.py b/scripts/merge_otu_maps.py index c9148f69c8..99654c171e 100755 --- a/scripts/merge_otu_maps.py +++ b/scripts/merge_otu_maps.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Dan Knights"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/merge_otu_tables.py b/scripts/merge_otu_tables.py index 8cfbe085dd..e691d494da 100755 --- a/scripts/merge_otu_tables.py +++ b/scripts/merge_otu_tables.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/multiple_extract_barcodes.py b/scripts/multiple_extract_barcodes.py index d4d62c3155..e01b38fc35 100755 --- a/scripts/multiple_extract_barcodes.py +++ b/scripts/multiple_extract_barcodes.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/multiple_join_paired_ends.py b/scripts/multiple_join_paired_ends.py index 36ad09b5de..0bcbe86c6e 100755 --- a/scripts/multiple_join_paired_ends.py +++ b/scripts/multiple_join_paired_ends.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/multiple_rarefactions.py b/scripts/multiple_rarefactions.py index 6e2d88cbc5..b44a543a2e 100755 --- a/scripts/multiple_rarefactions.py +++ b/scripts/multiple_rarefactions.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/multiple_rarefactions_even_depth.py b/scripts/multiple_rarefactions_even_depth.py index bc95166fe2..2a095e63b8 100755 --- a/scripts/multiple_rarefactions_even_depth.py +++ b/scripts/multiple_rarefactions_even_depth.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/multiple_split_libraries_fastq.py b/scripts/multiple_split_libraries_fastq.py index 0aa9d6613f..2aff431894 100755 --- a/scripts/multiple_split_libraries_fastq.py +++ b/scripts/multiple_split_libraries_fastq.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/neighbor_joining.py b/scripts/neighbor_joining.py index a5458d00f6..007ab6dcc0 100755 --- a/scripts/neighbor_joining.py +++ b/scripts/neighbor_joining.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/nmds.py b/scripts/nmds.py index 5624e4cc5c..d103c90689 100755 --- a/scripts/nmds.py +++ b/scripts/nmds.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/normalize_table.py b/scripts/normalize_table.py index caee7b4b93..6a3be97a0b 100755 --- a/scripts/normalize_table.py +++ b/scripts/normalize_table.py @@ -11,7 +11,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Sophie Weiss"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Sophie Weiss" __email__ = "sophie.sjw@gmail.com" diff --git a/scripts/observation_metadata_correlation.py b/scripts/observation_metadata_correlation.py index 96b8fb771f..a28f9616e9 100755 --- a/scripts/observation_metadata_correlation.py +++ b/scripts/observation_metadata_correlation.py @@ -6,7 +6,7 @@ "Jesse Stombaugh", "Doug Wendel", "Dan Knights", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Will Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/scripts/otu_category_significance.py b/scripts/otu_category_significance.py index 7e5fb1d03f..1d02fc754c 100755 --- a/scripts/otu_category_significance.py +++ b/scripts/otu_category_significance.py @@ -7,7 +7,7 @@ __credits__ = ["Catherine Lozupone", "Jesse Stombaugh", "Doug Wendel", "Dan Knights", "Greg Caporaso", "Luke Ursell"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Doug Wendel" __email__ = "wendel@colorado.edu" diff --git a/scripts/parallel_align_seqs_pynast.py b/scripts/parallel_align_seqs_pynast.py index 9ba8c0d8cf..d44c402085 100755 --- a/scripts/parallel_align_seqs_pynast.py +++ b/scripts/parallel_align_seqs_pynast.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_alpha_diversity.py b/scripts/parallel_alpha_diversity.py index d324975658..1fd510b7f3 100755 --- a/scripts/parallel_alpha_diversity.py +++ b/scripts/parallel_alpha_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_assign_taxonomy_blast.py b/scripts/parallel_assign_taxonomy_blast.py index ca483447b5..017f647214 100755 --- a/scripts/parallel_assign_taxonomy_blast.py +++ b/scripts/parallel_assign_taxonomy_blast.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_assign_taxonomy_rdp.py b/scripts/parallel_assign_taxonomy_rdp.py index 1647e2ce2a..7b1601cb0d 100755 --- a/scripts/parallel_assign_taxonomy_rdp.py +++ b/scripts/parallel_assign_taxonomy_rdp.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Antonio Gonzalez Pena", "William Walters", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_assign_taxonomy_uclust.py b/scripts/parallel_assign_taxonomy_uclust.py index 2af94f852c..76b013f845 100755 --- a/scripts/parallel_assign_taxonomy_uclust.py +++ b/scripts/parallel_assign_taxonomy_uclust.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_beta_diversity.py b/scripts/parallel_beta_diversity.py index 3ff1e118bd..bbe5425cb7 100755 --- a/scripts/parallel_beta_diversity.py +++ b/scripts/parallel_beta_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina", "Emily TerAvest"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_blast.py b/scripts/parallel_blast.py index 3e9eaeba9b..aa5c10a0e4 100755 --- a/scripts/parallel_blast.py +++ b/scripts/parallel_blast.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_identify_chimeric_seqs.py b/scripts/parallel_identify_chimeric_seqs.py index c5c3eb22a5..397e1c3782 100755 --- a/scripts/parallel_identify_chimeric_seqs.py +++ b/scripts/parallel_identify_chimeric_seqs.py @@ -6,7 +6,7 @@ __credits__ = ["Greg Caporaso", "Jens Reeder", "Jai Ram Rideout", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_map_reads_to_reference.py b/scripts/parallel_map_reads_to_reference.py index ee5e24207e..4d0193178e 100755 --- a/scripts/parallel_map_reads_to_reference.py +++ b/scripts/parallel_map_reads_to_reference.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_merge_otu_tables.py b/scripts/parallel_merge_otu_tables.py index f6772552b2..513e51f382 100755 --- a/scripts/parallel_merge_otu_tables.py +++ b/scripts/parallel_merge_otu_tables.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Daniel McDonald", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Daniel McDonald" __email__ = "mcdonadt@colorado.edu" diff --git a/scripts/parallel_multiple_rarefactions.py b/scripts/parallel_multiple_rarefactions.py index d2f59b7f8b..e6d9266339 100755 --- a/scripts/parallel_multiple_rarefactions.py +++ b/scripts/parallel_multiple_rarefactions.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_pick_otus_blast.py b/scripts/parallel_pick_otus_blast.py index 92361d1002..61748ead6e 100755 --- a/scripts/parallel_pick_otus_blast.py +++ b/scripts/parallel_pick_otus_blast.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Dan Knights", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_pick_otus_sortmerna.py b/scripts/parallel_pick_otus_sortmerna.py index 3f646a262b..8a97ef88f7 100755 --- a/scripts/parallel_pick_otus_sortmerna.py +++ b/scripts/parallel_pick_otus_sortmerna.py @@ -7,7 +7,7 @@ from __future__ import division __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jenya Kopylov" __email__ = "jenya.kopylov@gmail.com" diff --git a/scripts/parallel_pick_otus_trie.py b/scripts/parallel_pick_otus_trie.py index 710c8608d5..74434897c6 100755 --- a/scripts/parallel_pick_otus_trie.py +++ b/scripts/parallel_pick_otus_trie.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/scripts/parallel_pick_otus_uclust_ref.py b/scripts/parallel_pick_otus_uclust_ref.py index 66a493c93e..fe6d329bed 100755 --- a/scripts/parallel_pick_otus_uclust_ref.py +++ b/scripts/parallel_pick_otus_uclust_ref.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/parallel_pick_otus_usearch61_ref.py b/scripts/parallel_pick_otus_usearch61_ref.py index 48148e8ca0..fd6e8c94c7 100755 --- a/scripts/parallel_pick_otus_usearch61_ref.py +++ b/scripts/parallel_pick_otus_usearch61_ref.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/pick_closed_reference_otus.py b/scripts/pick_closed_reference_otus.py index 4541221866..d8f2c38b60 100755 --- a/scripts/pick_closed_reference_otus.py +++ b/scripts/pick_closed_reference_otus.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/pick_de_novo_otus.py b/scripts/pick_de_novo_otus.py index b8b912582e..b2a19854e7 100755 --- a/scripts/pick_de_novo_otus.py +++ b/scripts/pick_de_novo_otus.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Kyle Bittinger"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/pick_open_reference_otus.py b/scripts/pick_open_reference_otus.py index 6e546dd643..dc6fd2e03f 100755 --- a/scripts/pick_open_reference_otus.py +++ b/scripts/pick_open_reference_otus.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/pick_otus.py b/scripts/pick_otus.py index 5ca0fbaffd..29a464e426 100755 --- a/scripts/pick_otus.py +++ b/scripts/pick_otus.py @@ -8,7 +8,7 @@ "Jens Reeder", "William Walters", "Jose Carlos Clemente Litran", "Jai Ram Rideout", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/pick_rep_set.py b/scripts/pick_rep_set.py index 2048f4bd00..c57b1a12f3 100755 --- a/scripts/pick_rep_set.py +++ b/scripts/pick_rep_set.py @@ -7,7 +7,7 @@ __credits__ = ["Rob Knight", "Greg Caporaso", "Kyle Bittinger", "Jai Ram Rideout", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Daniel McDonald" __email__ = "wasade@gmail.com" diff --git a/scripts/plot_rank_abundance_graph.py b/scripts/plot_rank_abundance_graph.py index bf9ae70b47..5f92eff6e2 100755 --- a/scripts/plot_rank_abundance_graph.py +++ b/scripts/plot_rank_abundance_graph.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/plot_semivariogram.py b/scripts/plot_semivariogram.py index 02b2e94102..2493281124 100755 --- a/scripts/plot_semivariogram.py +++ b/scripts/plot_semivariogram.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Antonio Gonzalez Pena, Kyle Patnode", "Yoshiki Vazquez-Baeza"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/scripts/plot_taxa_summary.py b/scripts/plot_taxa_summary.py index a733a493bb..205a1c3329 100755 --- a/scripts/plot_taxa_summary.py +++ b/scripts/plot_taxa_summary.py @@ -7,7 +7,7 @@ __credits__ = ["Jesse Stombaugh", "Julia Goodrich", "Justin Kuczynski", "John Chase", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" """ diff --git a/scripts/poller.py b/scripts/poller.py index 96eae3ada0..72ff248cea 100755 --- a/scripts/poller.py +++ b/scripts/poller.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/principal_coordinates.py b/scripts/principal_coordinates.py index a6e6797c70..0fd2d56673 100755 --- a/scripts/principal_coordinates.py +++ b/scripts/principal_coordinates.py @@ -7,7 +7,7 @@ __credits__ = ["Justin Kuczynski", "Rob Knight", "Antonio Gonzalez Pena", "Catherine Lozupone", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/scripts/print_metadata_stats.py b/scripts/print_metadata_stats.py index 46f14b4f71..ebd2f680d8 100755 --- a/scripts/print_metadata_stats.py +++ b/scripts/print_metadata_stats.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Daniel McDonald", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Daniel McDonald" __email__ = "mcdonadt@colorado.edu" diff --git a/scripts/print_qiime_config.py b/scripts/print_qiime_config.py index cca451a2dd..3e57729842 100755 --- a/scripts/print_qiime_config.py +++ b/scripts/print_qiime_config.py @@ -7,7 +7,7 @@ "Justin Kuczynski", "Jai Ram Rideout", "Greg Caporaso", "Emily TerAvest"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/process_iseq.py b/scripts/process_iseq.py index 67d7bc881a..86224bf301 100755 --- a/scripts/process_iseq.py +++ b/scripts/process_iseq.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/process_qseq.py b/scripts/process_qseq.py index f70881d676..1031f9eab6 100755 --- a/scripts/process_qseq.py +++ b/scripts/process_qseq.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/process_sff.py b/scripts/process_sff.py index 18f7576157..aaf7fa2575 100755 --- a/scripts/process_sff.py +++ b/scripts/process_sff.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "Kyle Bittinger", "Jesse Stombaugh"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/scripts/quality_scores_plot.py b/scripts/quality_scores_plot.py index b9e8b6afc8..50d0db4ff8 100755 --- a/scripts/quality_scores_plot.py +++ b/scripts/quality_scores_plot.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/relatedness.py b/scripts/relatedness.py index c18eea72b6..67b67bf54d 100755 --- a/scripts/relatedness.py +++ b/scripts/relatedness.py @@ -8,7 +8,7 @@ "Jose Antonio Navas Molina", "Yoshiki Vazquez Baeza", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/scripts/shared_phylotypes.py b/scripts/shared_phylotypes.py index d056ac8e52..e7d3b5c8c8 100755 --- a/scripts/shared_phylotypes.py +++ b/scripts/shared_phylotypes.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jose Clemente" __email__ = "jose.clemente@gmail.com" diff --git a/scripts/simsam.py b/scripts/simsam.py index 2d7ea375c2..0976cdc44c 100755 --- a/scripts/simsam.py +++ b/scripts/simsam.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Jai Ram Rideout", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/single_rarefaction.py b/scripts/single_rarefaction.py index 76b681eaf7..bfbc48da75 100755 --- a/scripts/single_rarefaction.py +++ b/scripts/single_rarefaction.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/sort_otu_table.py b/scripts/sort_otu_table.py index b53ee307f8..8b1bd2f4dd 100755 --- a/scripts/sort_otu_table.py +++ b/scripts/sort_otu_table.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Daniel McDonald", "Emily TerAvest", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/split_libraries.py b/scripts/split_libraries.py index 2381929b69..8826a86434 100755 --- a/scripts/split_libraries.py +++ b/scripts/split_libraries.py @@ -9,7 +9,7 @@ "Jens Reeder", "Jose Antonio Navas Molina", "Jai Ram Rideout"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/scripts/split_libraries_fastq.py b/scripts/split_libraries_fastq.py index f59a6dc9bf..3bdc84ef32 100755 --- a/scripts/split_libraries_fastq.py +++ b/scripts/split_libraries_fastq.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Emily TerAvest"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/split_libraries_lea_seq.py b/scripts/split_libraries_lea_seq.py index d410e61334..a19b616507 100755 --- a/scripts/split_libraries_lea_seq.py +++ b/scripts/split_libraries_lea_seq.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Charudatta Navare", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Charudatta Navare" __email__ = "charudatta.navare@gmail.com" diff --git a/scripts/split_otu_table.py b/scripts/split_otu_table.py index d7d2df2c46..f775b655d4 100755 --- a/scripts/split_otu_table.py +++ b/scripts/split_otu_table.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Antonio Gonzalez Pena", "Yoshiki Vazquez Baeza", "Will Van Treuren"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/split_otu_table_by_taxonomy.py b/scripts/split_otu_table_by_taxonomy.py index 320b4db3a8..41088dcb8d 100755 --- a/scripts/split_otu_table_by_taxonomy.py +++ b/scripts/split_otu_table_by_taxonomy.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2010, The QIIME project" __credits__ = ["Greg Caporaso", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/split_sequence_file_on_sample_ids.py b/scripts/split_sequence_file_on_sample_ids.py index e93cff15a9..8509c1bc3a 100755 --- a/scripts/split_sequence_file_on_sample_ids.py +++ b/scripts/split_sequence_file_on_sample_ids.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/start_parallel_jobs.py b/scripts/start_parallel_jobs.py index 883c01fc75..5518a5ec6b 100755 --- a/scripts/start_parallel_jobs.py +++ b/scripts/start_parallel_jobs.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/start_parallel_jobs_sc.py b/scripts/start_parallel_jobs_sc.py index 595cee47d4..f6bce67182 100755 --- a/scripts/start_parallel_jobs_sc.py +++ b/scripts/start_parallel_jobs_sc.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/start_parallel_jobs_torque.py b/scripts/start_parallel_jobs_torque.py index 4711d20a37..170fb57d3b 100755 --- a/scripts/start_parallel_jobs_torque.py +++ b/scripts/start_parallel_jobs_torque.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Rob Knight", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/subsample_fasta.py b/scripts/subsample_fasta.py index b7dac14c31..8f6e2d2dce 100755 --- a/scripts/subsample_fasta.py +++ b/scripts/subsample_fasta.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "william.a.walters@gmail.com" diff --git a/scripts/summarize_taxa.py b/scripts/summarize_taxa.py index c00645db0f..5b48d108ee 100755 --- a/scripts/summarize_taxa.py +++ b/scripts/summarize_taxa.py @@ -9,7 +9,7 @@ "Jesse Stombaugh", "Jose Carlos Clemente Litran", "Greg Caporaso", "Jai Ram Rideout", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Daniel McDonald" __email__ = "wasade@gmail.com" diff --git a/scripts/summarize_taxa_through_plots.py b/scripts/summarize_taxa_through_plots.py index bea9c8aa32..3da39e5c7f 100755 --- a/scripts/summarize_taxa_through_plots.py +++ b/scripts/summarize_taxa_through_plots.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Jesse Stombaugh"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/scripts/supervised_learning.py b/scripts/supervised_learning.py index c95e1f16b8..5f22e48743 100755 --- a/scripts/supervised_learning.py +++ b/scripts/supervised_learning.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Dan Knights", "Luke Ursell"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Dan Knights" __email__ = "daniel.knights@colorado.edu" diff --git a/scripts/transform_coordinate_matrices.py b/scripts/transform_coordinate_matrices.py index 8c26adc572..5469d4ecaf 100755 --- a/scripts/transform_coordinate_matrices.py +++ b/scripts/transform_coordinate_matrices.py @@ -7,7 +7,7 @@ __credits__ = ["Greg Caporaso", "Justin Kuczynski", "Jose Carlos Clemente Litran", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/scripts/tree_compare.py b/scripts/tree_compare.py index 2ff0d856ba..5d9d03b4f3 100755 --- a/scripts/tree_compare.py +++ b/scripts/tree_compare.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/trflp_file_to_otu_table.py b/scripts/trflp_file_to_otu_table.py index 757f23012a..100059f2b9 100755 --- a/scripts/trflp_file_to_otu_table.py +++ b/scripts/trflp_file_to_otu_table.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Antonio Gonzalez Pena", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/scripts/trim_sff_primers.py b/scripts/trim_sff_primers.py index 6834a226a1..9b3252ceb4 100755 --- a/scripts/trim_sff_primers.py +++ b/scripts/trim_sff_primers.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "Kyle Bittinger"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/scripts/truncate_fasta_qual_files.py b/scripts/truncate_fasta_qual_files.py index 4366fcbbbb..19d85c5b36 100755 --- a/scripts/truncate_fasta_qual_files.py +++ b/scripts/truncate_fasta_qual_files.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/truncate_reverse_primer.py b/scripts/truncate_reverse_primer.py index b24c2dc064..a701f843d2 100755 --- a/scripts/truncate_reverse_primer.py +++ b/scripts/truncate_reverse_primer.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/scripts/unweight_fasta.py b/scripts/unweight_fasta.py index 583afc21fd..2acad6a3ad 100755 --- a/scripts/unweight_fasta.py +++ b/scripts/unweight_fasta.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/upgma_cluster.py b/scripts/upgma_cluster.py index 33b126c007..136cc8ebb8 100755 --- a/scripts/upgma_cluster.py +++ b/scripts/upgma_cluster.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/scripts/validate_demultiplexed_fasta.py b/scripts/validate_demultiplexed_fasta.py index 950d762831..a0e57f877c 100755 --- a/scripts/validate_demultiplexed_fasta.py +++ b/scripts/validate_demultiplexed_fasta.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Anton Walters"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Anton Walters" __email__ = "william.a.walters@gmail.com" diff --git a/scripts/validate_mapping_file.py b/scripts/validate_mapping_file.py index 5511d49fb8..5e4b91261a 100755 --- a/scripts/validate_mapping_file.py +++ b/scripts/validate_mapping_file.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/setup.py b/setup.py index 31a242decf..5a3513d74e 100644 --- a/setup.py +++ b/setup.py @@ -17,7 +17,7 @@ __credits__ = ["Greg Caporaso", "Kyle Bittinger", "Jai Ram Rideout", "Yoshiki Vazquez Baeza", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "qiime.help@gmail.com" diff --git a/tests/__init__.py b/tests/__init__.py index b9584fc8c4..cf82c7ae41 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -16,7 +16,7 @@ "Daniel McDonald", "Catherine Lozupone"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" __status__ = "Development" diff --git a/tests/all_tests.py b/tests/all_tests.py index efafa1045e..d55ecf1c34 100755 --- a/tests/all_tests.py +++ b/tests/all_tests.py @@ -17,7 +17,7 @@ __credits__ = ["Rob Knight", "Greg Caporaso", "Jai Ram Rideout", "Yoshiki Vazquez Baeza"] # remember to add yourself if you make changes __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_add_alpha_to_mapping_file.py b/tests/test_add_alpha_to_mapping_file.py index ab3bd4cff0..39a367409d 100755 --- a/tests/test_add_alpha_to_mapping_file.py +++ b/tests/test_add_alpha_to_mapping_file.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Yoshiki Vazquez-Baeza"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Yoshiki Vazquez-Baeza" __email__ = "yoshiki89@gmail.com" diff --git a/tests/test_add_qiime_labels.py b/tests/test_add_qiime_labels.py index c44edf3fa5..a1e7ecf7a0 100755 --- a/tests/test_add_qiime_labels.py +++ b/tests/test_add_qiime_labels.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/tests/test_adjust_seq_orientation.py b/tests/test_adjust_seq_orientation.py index 3b60cc1293..08b4859323 100755 --- a/tests/test_adjust_seq_orientation.py +++ b/tests/test_adjust_seq_orientation.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_align_seqs.py b/tests/test_align_seqs.py index 435d7ae01e..efea352e04 100644 --- a/tests/test_align_seqs.py +++ b/tests/test_align_seqs.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jeremy Widmann"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_alpha_diversity.py b/tests/test_alpha_diversity.py index 77b65bb3e9..49cdb181d4 100644 --- a/tests/test_alpha_diversity.py +++ b/tests/test_alpha_diversity.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Rob Knight", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_assign_taxonomy.py b/tests/test_assign_taxonomy.py index d947a5098a..ebc5a16a93 100644 --- a/tests/test_assign_taxonomy.py +++ b/tests/test_assign_taxonomy.py @@ -8,7 +8,7 @@ __credits__ = ["Greg Caporaso", "Kyle Bittinger", "David Soergel", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_barcode.py b/tests/test_barcode.py index 43c010ec22..06eea95b56 100644 --- a/tests/test_barcode.py +++ b/tests/test_barcode.py @@ -5,7 +5,7 @@ # remember to add yourself if you make changes __credits__ = ["Justin Kuczynski", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_beta_diversity.py b/tests/test_beta_diversity.py index b9e6240835..f5e2bbf69e 100644 --- a/tests/test_beta_diversity.py +++ b/tests/test_beta_diversity.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Rob Knight", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_beta_metrics.py b/tests/test_beta_metrics.py index e7b3222ede..d4f2680255 100644 --- a/tests/test_beta_metrics.py +++ b/tests/test_beta_metrics.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "justin kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_biplots.py b/tests/test_biplots.py index 5d97409e60..f0e5a80479 100755 --- a/tests/test_biplots.py +++ b/tests/test_biplots.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_categorized_dist_scatterplot.py b/tests/test_categorized_dist_scatterplot.py index 5e063d75ac..e88d8a0616 100755 --- a/tests/test_categorized_dist_scatterplot.py +++ b/tests/test_categorized_dist_scatterplot.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_clean_raxml_parsimony_tree.py b/tests/test_clean_raxml_parsimony_tree.py index bc9500e89c..fdc912f974 100755 --- a/tests/test_clean_raxml_parsimony_tree.py +++ b/tests/test_clean_raxml_parsimony_tree.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Jesse Stombaugh"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/tests/test_cluster_quality.py b/tests/test_cluster_quality.py index 78b10c6894..21e5bb5c5b 100644 --- a/tests/test_cluster_quality.py +++ b/tests/test_cluster_quality.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_collate_alpha.py b/tests/test_collate_alpha.py index 039b1b6d59..a7c8bb84bb 100644 --- a/tests/test_collate_alpha.py +++ b/tests/test_collate_alpha.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["justin kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_colors.py b/tests/test_colors.py index 9f6b125f34..ea54740ea7 100644 --- a/tests/test_colors.py +++ b/tests/test_colors.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["Jesse Stombaugh"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/tests/test_compare_alpha_diversity.py b/tests/test_compare_alpha_diversity.py index 920bf6021e..1a461704b5 100755 --- a/tests/test_compare_alpha_diversity.py +++ b/tests/test_compare_alpha_diversity.py @@ -7,7 +7,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["William Van Treuren", "Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Van Treuren" __email__ = "vantreur@colorado.edu" diff --git a/tests/test_compare_categories.py b/tests/test_compare_categories.py index d3833433cb..8b19a7a9a4 100644 --- a/tests/test_compare_categories.py +++ b/tests/test_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-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_compare_distance_matrices.py b/tests/test_compare_distance_matrices.py index 62dded402f..7c97343160 100644 --- a/tests/test_compare_distance_matrices.py +++ b/tests/test_compare_distance_matrices.py @@ -6,7 +6,7 @@ __credits__ = ["Jai Ram Rideout", "Michael Dwan", "Logan Knecht", "Damien Coy", "Levi McCracken"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_compare_taxa_summaries.py b/tests/test_compare_taxa_summaries.py index 498a0cf3e0..421b42d046 100644 --- a/tests/test_compare_taxa_summaries.py +++ b/tests/test_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-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_compare_trajectories.py b/tests/test_compare_trajectories.py index ec2a6ab85f..691aaf59e2 100644 --- a/tests/test_compare_trajectories.py +++ b/tests/test_compare_trajectories.py @@ -6,7 +6,7 @@ __credits__ = ["Jose Antonio Navas Molina", "Antonio Gonzalez Pena", "Yoshiki Vazquez Baeza", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jose Antonio Navas Molina" __email__ = "josenavasmolina@gmail.com" diff --git a/tests/test_compute_taxonomy_ratios.py b/tests/test_compute_taxonomy_ratios.py index 6d37daf0fb..015347e0e9 100644 --- a/tests/test_compute_taxonomy_ratios.py +++ b/tests/test_compute_taxonomy_ratios.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Daniel McDonald"] __license__ = "BSD" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Daniel McDonald" __email__ = "mcdonadt@colorado.edu" diff --git a/tests/test_convert_fastaqual_fastq.py b/tests/test_convert_fastaqual_fastq.py index 6023d3189f..dcf569321f 100755 --- a/tests/test_convert_fastaqual_fastq.py +++ b/tests/test_convert_fastaqual_fastq.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Adam Robbins-Pianka", "Abhisaar Yadav", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Adam Robbins-Pianka" __email__ = "adam.robbinspianka@colorado.edu" diff --git a/tests/test_core_microbiome.py b/tests/test_core_microbiome.py index b733ca09a8..e7686c0d3b 100755 --- a/tests/test_core_microbiome.py +++ b/tests/test_core_microbiome.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_demultiplex_fasta.py b/tests/test_demultiplex_fasta.py index 83e93121cc..d6de8209e5 100755 --- a/tests/test_demultiplex_fasta.py +++ b/tests/test_demultiplex_fasta.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "William Walters"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/tests/test_denoise_wrapper.py b/tests/test_denoise_wrapper.py index e996263d69..ed5ea73ebc 100644 --- a/tests/test_denoise_wrapper.py +++ b/tests/test_denoise_wrapper.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_denoiser/test_cluster_util.py b/tests/test_denoiser/test_cluster_util.py index ba4680aa5a..88f809c640 100644 --- a/tests/test_denoiser/test_cluster_util.py +++ b/tests/test_denoiser/test_cluster_util.py @@ -6,7 +6,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_denoise_postprocess.py b/tests/test_denoiser/test_denoise_postprocess.py index 7677163466..adeb603c76 100644 --- a/tests/test_denoiser/test_denoise_postprocess.py +++ b/tests/test_denoiser/test_denoise_postprocess.py @@ -8,7 +8,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_denoiser.py b/tests/test_denoiser/test_denoiser.py index 1ee6c73bd7..3d6c9be4bf 100644 --- a/tests/test_denoiser/test_denoiser.py +++ b/tests/test_denoiser/test_denoiser.py @@ -8,7 +8,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_flowgram_clustering.py b/tests/test_denoiser/test_flowgram_clustering.py index 87250c350b..f39e3d9e90 100644 --- a/tests/test_denoiser/test_flowgram_clustering.py +++ b/tests/test_denoiser/test_flowgram_clustering.py @@ -6,7 +6,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Nigel Cook"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_flowgram_filter.py b/tests/test_denoiser/test_flowgram_filter.py index f711896c9c..94f5c375ae 100644 --- a/tests/test_denoiser/test_flowgram_filter.py +++ b/tests/test_denoiser/test_flowgram_filter.py @@ -6,7 +6,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_make_cluster_jobs.py b/tests/test_denoiser/test_make_cluster_jobs.py index bf0871991c..fb1827ed0b 100644 --- a/tests/test_denoiser/test_make_cluster_jobs.py +++ b/tests/test_denoiser/test_make_cluster_jobs.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_preprocess.py b/tests/test_denoiser/test_preprocess.py index 4e79a34244..0e6bcb41c3 100644 --- a/tests/test_denoiser/test_preprocess.py +++ b/tests/test_denoiser/test_preprocess.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_settings.py b/tests/test_denoiser/test_settings.py index 6fbf482985..3ee3dd9de5 100644 --- a/tests/test_denoiser/test_settings.py +++ b/tests/test_denoiser/test_settings.py @@ -8,7 +8,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_denoiser/test_utils.py b/tests/test_denoiser/test_utils.py index 3eb9b841e4..124799d4fb 100644 --- a/tests/test_denoiser/test_utils.py +++ b/tests/test_denoiser/test_utils.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Jens Reeder", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jens Reeder" __email__ = "jens.reeder@gmail.com" diff --git a/tests/test_detrend.py b/tests/test_detrend.py index dcd9c05714..40da5c95a7 100644 --- a/tests/test_detrend.py +++ b/tests/test_detrend.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Dan Knights"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Dan Knights" __email__ = "daniel.knights@colorado.edu" diff --git a/tests/test_differential_abundance.py b/tests/test_differential_abundance.py index bf17d14daf..c2526545c4 100644 --- a/tests/test_differential_abundance.py +++ b/tests/test_differential_abundance.py @@ -15,7 +15,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Sophie Weiss"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Sophie Weiss" __email__ = "sophie.sjw@gmail.com" diff --git a/tests/test_distance_matrix_from_mapping.py b/tests/test_distance_matrix_from_mapping.py index 7cd7af4325..5f62ae64ec 100644 --- a/tests/test_distance_matrix_from_mapping.py +++ b/tests/test_distance_matrix_from_mapping.py @@ -10,7 +10,7 @@ "Michael S. Robeson", ] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/tests/test_estimate_observation_richness.py b/tests/test_estimate_observation_richness.py index 4ebc592b2c..411323713c 100644 --- a/tests/test_estimate_observation_richness.py +++ b/tests/test_estimate_observation_richness.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_exclude_seqs_by_blast.py b/tests/test_exclude_seqs_by_blast.py index ccdabb4bb7..ef595a1249 100644 --- a/tests/test_exclude_seqs_by_blast.py +++ b/tests/test_exclude_seqs_by_blast.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jesse Zaneveld", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jesse Zaneveld" __email__ = "zaneveld@gmail.com" diff --git a/tests/test_extract_barcodes.py b/tests/test_extract_barcodes.py index 111696eabf..a311dd00f7 100644 --- a/tests/test_extract_barcodes.py +++ b/tests/test_extract_barcodes.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["William Walters", "Daniel McDonald"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/tests/test_filter.py b/tests/test_filter.py index 3792ad4ec5..45a256d548 100755 --- a/tests/test_filter.py +++ b/tests/test_filter.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_filter_alignment.py b/tests/test_filter_alignment.py index 1bfc630b86..bc0e376086 100755 --- a/tests/test_filter_alignment.py +++ b/tests/test_filter_alignment.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Dan Knights"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_filter_otus_by_sample.py b/tests/test_filter_otus_by_sample.py index 67d160ae3d..7450678cbf 100644 --- a/tests/test_filter_otus_by_sample.py +++ b/tests/test_filter_otus_by_sample.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["Jesse Stombaugh"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/tests/test_format.py b/tests/test_format.py index 8f1f95971f..35de7a5a18 100755 --- a/tests/test_format.py +++ b/tests/test_format.py @@ -9,7 +9,7 @@ "Jai Ram Rideout", "Jose Antonio Navas Molina"] # remember to add yourself if you make changes __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_golay.py b/tests/test_golay.py index a61bdc4c3e..1fca3d4fc7 100644 --- a/tests/test_golay.py +++ b/tests/test_golay.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_group.py b/tests/test_group.py index c7f3400446..00df45bc14 100755 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -8,7 +8,7 @@ "Greg Caporaso", "Jeremy Widmann"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_hamming.py b/tests/test_hamming.py index bb97bb4b26..12f86e6248 100755 --- a/tests/test_hamming.py +++ b/tests/test_hamming.py @@ -10,7 +10,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["Micah Hamady", "Rob Knight"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_hierarchical_cluster.py b/tests/test_hierarchical_cluster.py index da8b19a7b8..233efaa0b4 100644 --- a/tests/test_hierarchical_cluster.py +++ b/tests/test_hierarchical_cluster.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["justin kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_identify_chimeric_seqs.py b/tests/test_identify_chimeric_seqs.py index 5c35e2b26d..3a19661c4d 100755 --- a/tests/test_identify_chimeric_seqs.py +++ b/tests/test_identify_chimeric_seqs.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jens Reeder", "William Walters"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_join_paired_ends.py b/tests/test_join_paired_ends.py index f77d3f02c1..e923c697f2 100644 --- a/tests/test_join_paired_ends.py +++ b/tests/test_join_paired_ends.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Mike Robeson"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Mike Robeson" __email__ = "robesonms@ornl.gov" diff --git a/tests/test_make_2d_plots.py b/tests/test_make_2d_plots.py index c104dddcc6..0ab5352d64 100644 --- a/tests/test_make_2d_plots.py +++ b/tests/test_make_2d_plots.py @@ -6,7 +6,7 @@ # remember to add yourself __credits__ = ["Jesse Stombaugh", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/tests/test_make_bipartite_network.py b/tests/test_make_bipartite_network.py index 8dc48376f5..d5b71a39d7 100755 --- a/tests/test_make_bipartite_network.py +++ b/tests/test_make_bipartite_network.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2013, The QIIME project" __credits__ = ["Will Van Treuren"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Will Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/tests/test_make_bootstrapped_tree.py b/tests/test_make_bootstrapped_tree.py index 013d1571cb..c19f504c05 100644 --- a/tests/test_make_bootstrapped_tree.py +++ b/tests/test_make_bootstrapped_tree.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["justin kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_make_distance_boxplots.py b/tests/test_make_distance_boxplots.py index c0bd5aeb2d..216d357328 100644 --- a/tests/test_make_distance_boxplots.py +++ b/tests/test_make_distance_boxplots.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_make_fastq.py b/tests/test_make_fastq.py index 83fdd9c796..85b53e02a3 100644 --- a/tests/test_make_fastq.py +++ b/tests/test_make_fastq.py @@ -9,7 +9,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["Rob Knight"] # remember to add yourself if you make changes __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/tests/test_make_library_id_lists.py b/tests/test_make_library_id_lists.py index efd8231fee..55eeae5c09 100644 --- a/tests/test_make_library_id_lists.py +++ b/tests/test_make_library_id_lists.py @@ -8,7 +8,7 @@ # remember to add yourself if you make changes __credits__ = ["Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/tests/test_make_otu_heatmap.py b/tests/test_make_otu_heatmap.py index 5d1a425665..5060c89b94 100644 --- a/tests/test_make_otu_heatmap.py +++ b/tests/test_make_otu_heatmap.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Dan Knights"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Dan Knights" __email__ = "daniel.knights@colorado.edu" diff --git a/tests/test_make_otu_network.py b/tests/test_make_otu_network.py index 8b836009c1..4351f9b2cd 100644 --- a/tests/test_make_otu_network.py +++ b/tests/test_make_otu_network.py @@ -6,7 +6,7 @@ # remember to add yourself __credits__ = ["Julia Goodrich", "Jose Carlos Clemente Litran"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jose Clemente" __email__ = "jose.clemente@gmail.com" diff --git a/tests/test_make_otu_table.py b/tests/test_make_otu_table.py index 4445628ceb..cd0e8b02d3 100644 --- a/tests/test_make_otu_table.py +++ b/tests/test_make_otu_table.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["Rob Knight", "Justin Kuczynski", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_make_per_library_sff.py b/tests/test_make_per_library_sff.py index 5229134b63..cf2231bfd9 100644 --- a/tests/test_make_per_library_sff.py +++ b/tests/test_make_per_library_sff.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Kyle Bittinger"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/tests/test_make_phylogeny.py b/tests/test_make_phylogeny.py index fdb5d03e6f..d5ec31273e 100644 --- a/tests/test_make_phylogeny.py +++ b/tests/test_make_phylogeny.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Rob Knight"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_make_rarefaction_plots.py b/tests/test_make_rarefaction_plots.py index aa16e6da1e..6db9bf114a 100755 --- a/tests/test_make_rarefaction_plots.py +++ b/tests/test_make_rarefaction_plots.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jesse Stombaugh", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/tests/test_map_reads_to_reference.py b/tests/test_map_reads_to_reference.py index a951d5bf48..5065268f0a 100755 --- a/tests/test_map_reads_to_reference.py +++ b/tests/test_map_reads_to_reference.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_normalize_table.py b/tests/test_normalize_table.py index ca26e375aa..c303f987fa 100644 --- a/tests/test_normalize_table.py +++ b/tests/test_normalize_table.py @@ -16,7 +16,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Sophie Weiss"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Sophie Weiss" __email__ = "sophie.sjw@gmail.com" diff --git a/tests/test_otu_significance.py b/tests/test_otu_significance.py index 3662dd06f8..7350cbfaf9 100755 --- a/tests/test_otu_significance.py +++ b/tests/test_otu_significance.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2013, The QIIME project" __credits__ = ["Luke Ursell", "Will Van Treuren", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Luke Ursell" __email__ = "lkursell@gmail.com" diff --git a/tests/test_parallel/test_align_seqs.py b/tests/test_parallel/test_align_seqs.py index 3b73c35a7f..a9ac541e65 100755 --- a/tests/test_parallel/test_align_seqs.py +++ b/tests/test_parallel/test_align_seqs.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_parallel/test_alpha_diversity.py b/tests/test_parallel/test_alpha_diversity.py index aeac617166..3909ec0c6d 100755 --- a/tests/test_parallel/test_alpha_diversity.py +++ b/tests/test_parallel/test_alpha_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_parallel/test_assign_taxonomy.py b/tests/test_parallel/test_assign_taxonomy.py index cdb0dcfcf7..6fee2cc399 100755 --- a/tests/test_parallel/test_assign_taxonomy.py +++ b/tests/test_parallel/test_assign_taxonomy.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_parallel/test_beta_diversity.py b/tests/test_parallel/test_beta_diversity.py index 9985221494..aaf7530f95 100755 --- a/tests/test_parallel/test_beta_diversity.py +++ b/tests/test_parallel/test_beta_diversity.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_parallel/test_blast.py b/tests/test_parallel/test_blast.py index 33efc305d2..d98603503e 100755 --- a/tests/test_parallel/test_blast.py +++ b/tests/test_parallel/test_blast.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_parallel/test_identify_chimeric_seqs.py b/tests/test_parallel/test_identify_chimeric_seqs.py index 2af19c14a4..9927b3cae0 100755 --- a/tests/test_parallel/test_identify_chimeric_seqs.py +++ b/tests/test_parallel/test_identify_chimeric_seqs.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_parallel/test_map_reads_to_reference.py b/tests/test_parallel/test_map_reads_to_reference.py index c50e3eb412..355520c3c9 100755 --- a/tests/test_parallel/test_map_reads_to_reference.py +++ b/tests/test_parallel/test_map_reads_to_reference.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_parallel/test_merge_otus.py b/tests/test_parallel/test_merge_otus.py index 904252ba85..78d833a86f 100644 --- a/tests/test_parallel/test_merge_otus.py +++ b/tests/test_parallel/test_merge_otus.py @@ -10,7 +10,7 @@ __copyright__ = "Copyright 2013, The QIIME Project" __credits__ = ["Daniel McDonald", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Daniel McDonald" __email__ = "mcdonadt@colorado.edu" diff --git a/tests/test_parallel/test_multiple_rarefactions.py b/tests/test_parallel/test_multiple_rarefactions.py index 50eb6c8c49..b2caf229b4 100755 --- a/tests/test_parallel/test_multiple_rarefactions.py +++ b/tests/test_parallel/test_multiple_rarefactions.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_parallel/test_pick_otus.py b/tests/test_parallel/test_pick_otus.py index 3adbbfb335..bef77636a6 100755 --- a/tests/test_parallel/test_pick_otus.py +++ b/tests/test_parallel/test_pick_otus.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jens Reeder"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_parallel/test_util.py b/tests/test_parallel/test_util.py index 492b02b703..ac32ca7b65 100755 --- a/tests/test_parallel/test_util.py +++ b/tests/test_parallel/test_util.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_parse.py b/tests/test_parse.py index 4da35b2189..fe020445b6 100644 --- a/tests/test_parse.py +++ b/tests/test_parse.py @@ -8,7 +8,7 @@ "Jai Ram Rideout", "Will Van Treuren", "Yoshiki Vazquez-Baeza", "Jose Antonio Navas Molina"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_pick_otus.py b/tests/test_pick_otus.py index bbddc8bb3d..c613263531 100755 --- a/tests/test_pick_otus.py +++ b/tests/test_pick_otus.py @@ -13,7 +13,7 @@ "William Walters", "Jose Carlos Clemente Litran"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_pick_rep_set.py b/tests/test_pick_rep_set.py index 4a3e1486fb..54f52829ee 100644 --- a/tests/test_pick_rep_set.py +++ b/tests/test_pick_rep_set.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Rob Knight", "Kyle Bittinger", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Daniel McDonald" __email__ = "wasade@gmail.com" diff --git a/tests/test_plot_rank_abundance_graph.py b/tests/test_plot_rank_abundance_graph.py index 20ab3dd120..50683ac456 100755 --- a/tests/test_plot_rank_abundance_graph.py +++ b/tests/test_plot_rank_abundance_graph.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_plot_semivariogram.py b/tests/test_plot_semivariogram.py index e3878a06dd..8570587ff9 100644 --- a/tests/test_plot_semivariogram.py +++ b/tests/test_plot_semivariogram.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Antonio Gonzalez Pena"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Antonio Gonzalez Pena" __email__ = "antgonza@gmail.com" diff --git a/tests/test_plot_taxa_summary.py b/tests/test_plot_taxa_summary.py index 5bcd5496f1..aba192f8c2 100644 --- a/tests/test_plot_taxa_summary.py +++ b/tests/test_plot_taxa_summary.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["Jesse Stombaugh", "Julia Goodrich"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jesse Stombaugh" __email__ = "jesse.stombaugh@colorado.edu" diff --git a/tests/test_principal_coordinates.py b/tests/test_principal_coordinates.py index 7739e60143..6ad73b8a6d 100644 --- a/tests/test_principal_coordinates.py +++ b/tests/test_principal_coordinates.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_process_sff.py b/tests/test_process_sff.py index 4b2c529cd9..ff67437479 100644 --- a/tests/test_process_sff.py +++ b/tests/test_process_sff.py @@ -25,7 +25,7 @@ "Jesse Stombaugh", "Adam Robbins-Pianka"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/tests/test_quality_scores_plot.py b/tests/test_quality_scores_plot.py index 407ee385d0..e4952a0ff4 100755 --- a/tests/test_quality_scores_plot.py +++ b/tests/test_quality_scores_plot.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/tests/test_rarefaction.py b/tests/test_rarefaction.py index eb60d9c43d..3f55f50d7f 100644 --- a/tests/test_rarefaction.py +++ b/tests/test_rarefaction.py @@ -5,7 +5,7 @@ __credits__ = ["justin kuczynski", "Rob Knight", "Jose Carlos Clemente Litran", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_relatedness.py b/tests/test_relatedness.py index 03100f5e22..ae6f6fb5ec 100644 --- a/tests/test_relatedness.py +++ b/tests/test_relatedness.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["William Van Treuren"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Van Treuren" __email__ = "wdwvt1@gmail.com" diff --git a/tests/test_remote.py b/tests/test_remote.py index e1550fdfd9..271a48793a 100644 --- a/tests/test_remote.py +++ b/tests/test_remote.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2012, The QIIME project" __credits__ = ["Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_shared_phylotypes.py b/tests/test_shared_phylotypes.py index 9fdcc06ac6..33397b9820 100644 --- a/tests/test_shared_phylotypes.py +++ b/tests/test_shared_phylotypes.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Jens Reeder", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jose Clemente" __email__ = "jose.clemente@gmail.com" diff --git a/tests/test_simsam.py b/tests/test_simsam.py index 73e6793038..79b83d89be 100755 --- a/tests/test_simsam.py +++ b/tests/test_simsam.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kucyznski", "Jai Ram Rideout", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kucyznski" __email__ = "justinak@gmail.com" diff --git a/tests/test_sort.py b/tests/test_sort.py index 7d9737ff48..8760680d92 100755 --- a/tests/test_sort.py +++ b/tests/test_sort.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Daniel McDonald", "Yoshiki Vazquez Baeza"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_split.py b/tests/test_split.py index 9c02a17bb8..7021d0108f 100755 --- a/tests/test_split.py +++ b/tests/test_split.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Will Van Treuren"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_split_libraries.py b/tests/test_split_libraries.py index e250f832e8..aceb286e18 100644 --- a/tests/test_split_libraries.py +++ b/tests/test_split_libraries.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Rob Knight", "William Walters", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/tests/test_split_libraries_fastq.py b/tests/test_split_libraries_fastq.py index 6c70aef52a..f8aa9c05a2 100755 --- a/tests/test_split_libraries_fastq.py +++ b/tests/test_split_libraries_fastq.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_split_libraries_lea_seq.py b/tests/test_split_libraries_lea_seq.py index 8b45b590c2..e4ffbae680 100644 --- a/tests/test_split_libraries_lea_seq.py +++ b/tests/test_split_libraries_lea_seq.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2014, The QIIME Project" __credits__ = ["Charudatta Navare"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Charudatta Navare" __email__ = "charudatta.navare@gmail.com" diff --git a/tests/test_stats.py b/tests/test_stats.py index 159b3cb9ee..f7ad491598 100644 --- a/tests/test_stats.py +++ b/tests/test_stats.py @@ -7,7 +7,7 @@ "Damien Coy", "Levi McCracken", "Andrew Cochran", "Will Van Treuren"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Jai Ram Rideout" __email__ = "jai.rideout@gmail.com" diff --git a/tests/test_summarize_taxa.py b/tests/test_summarize_taxa.py index d8619fbde5..e4bb82790c 100644 --- a/tests/test_summarize_taxa.py +++ b/tests/test_summarize_taxa.py @@ -11,7 +11,7 @@ "Antonio Gonzalez Pena", "Jose Carlos Clemente Litran"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Daniel McDonald" __email__ = "wasade@gmail.com" diff --git a/tests/test_supervised_learning.py b/tests/test_supervised_learning.py index b04e08bb7a..9fd8b685c2 100644 --- a/tests/test_supervised_learning.py +++ b/tests/test_supervised_learning.py @@ -7,7 +7,7 @@ # remember to add yourself if you make changes __credits__ = ["Dan Knights", "Luke Ursell"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Dan Knights" __email__ = "daniel.knights@colorado.edu" diff --git a/tests/test_transform_coordinate_matrices.py b/tests/test_transform_coordinate_matrices.py index aebceda5ee..3b62b18009 100755 --- a/tests/test_transform_coordinate_matrices.py +++ b/tests/test_transform_coordinate_matrices.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_tree_compare.py b/tests/test_tree_compare.py index cd2d728c0a..6027822717 100644 --- a/tests/test_tree_compare.py +++ b/tests/test_tree_compare.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Justin Kuczynski", "Daniel McDonald"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Justin Kuczynski" __email__ = "justinak@gmail.com" diff --git a/tests/test_trim_sff_primers.py b/tests/test_trim_sff_primers.py index f91bd7bb40..67c0530491 100644 --- a/tests/test_trim_sff_primers.py +++ b/tests/test_trim_sff_primers.py @@ -10,7 +10,7 @@ # remember to add yourself if you make changes __credits__ = ["Rob Knight", 'Kyle Bittinger'] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Kyle Bittinger" __email__ = "kylebittinger@gmail.com" diff --git a/tests/test_truncate_fasta_qual_files.py b/tests/test_truncate_fasta_qual_files.py index b016140a8f..74238bb524 100755 --- a/tests/test_truncate_fasta_qual_files.py +++ b/tests/test_truncate_fasta_qual_files.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters", "Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/tests/test_truncate_reverse_primer.py b/tests/test_truncate_reverse_primer.py index 1a93a6e10b..af2f84f701 100755 --- a/tests/test_truncate_reverse_primer.py +++ b/tests/test_truncate_reverse_primer.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/tests/test_util.py b/tests/test_util.py index 437104627c..8f509541db 100755 --- a/tests/test_util.py +++ b/tests/test_util.py @@ -69,7 +69,7 @@ "Levi McCracken", "Damien Coy", "Yoshiki Vazquez Baeza", "Will Van Treuren", "Luke Ursell"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_validate_demultiplexed_fasta.py b/tests/test_validate_demultiplexed_fasta.py index 5eba04e882..5d2bddb527 100755 --- a/tests/test_validate_demultiplexed_fasta.py +++ b/tests/test_validate_demultiplexed_fasta.py @@ -7,7 +7,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Anton Walters"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Anton Walters" __email__ = "william.a.walters@gmail.com" diff --git a/tests/test_validate_mapping_file.py b/tests/test_validate_mapping_file.py index 72c44f124b..b005caa74d 100755 --- a/tests/test_validate_mapping_file.py +++ b/tests/test_validate_mapping_file.py @@ -4,7 +4,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" # consider project name __credits__ = ["Rob Knight", "William Walters"] # remember to add yourself __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "william.a.walters@colorado.edu" diff --git a/tests/test_workflow/test_ampliconnoise.py b/tests/test_workflow/test_ampliconnoise.py index 838bd3d679..441fd356f6 100755 --- a/tests/test_workflow/test_ampliconnoise.py +++ b/tests/test_workflow/test_ampliconnoise.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Kyle Bittinger", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_workflow/test_core_diversity_analyses.py b/tests/test_workflow/test_core_diversity_analyses.py index 357ef2b97d..508704300b 100755 --- a/tests/test_workflow/test_core_diversity_analyses.py +++ b/tests/test_workflow/test_core_diversity_analyses.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_workflow/test_downstream.py b/tests/test_workflow/test_downstream.py index e8b77d4547..c0fc2003b9 100755 --- a/tests/test_workflow/test_downstream.py +++ b/tests/test_workflow/test_downstream.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Kyle Bittinger", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_workflow/test_pick_open_reference_otus.py b/tests/test_workflow/test_pick_open_reference_otus.py index feff9d9724..51e0daf8ce 100755 --- a/tests/test_workflow/test_pick_open_reference_otus.py +++ b/tests/test_workflow/test_pick_open_reference_otus.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_workflow/test_preprocess.py b/tests/test_workflow/test_preprocess.py index 8225133219..8333aa5f89 100755 --- a/tests/test_workflow/test_preprocess.py +++ b/tests/test_workflow/test_preprocess.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["William Walters"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "William Walters" __email__ = "William.A.Walters@colorado.edu" diff --git a/tests/test_workflow/test_upstream.py b/tests/test_workflow/test_upstream.py index a881c247fc..c61193d685 100755 --- a/tests/test_workflow/test_upstream.py +++ b/tests/test_workflow/test_upstream.py @@ -5,7 +5,7 @@ __copyright__ = "Copyright 2011, The QIIME project" __credits__ = ["Greg Caporaso", "Kyle Bittinger", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" diff --git a/tests/test_workflow/test_util.py b/tests/test_workflow/test_util.py index 8c61092ae9..b9d1375abf 100755 --- a/tests/test_workflow/test_util.py +++ b/tests/test_workflow/test_util.py @@ -6,7 +6,7 @@ __copyright__ = "Copyright 2011, The QIIME Project" __credits__ = ["Greg Caporaso", "Kyle Bittinger", "Jai Ram Rideout"] __license__ = "GPL" -__version__ = "1.9.0-rc1" +__version__ = "1.9.0-rc2" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" From 0a6709da6cf7efad479dacb200eb5145212402a8 Mon Sep 17 00:00:00 2001 From: Greg Caporaso Date: Fri, 9 Jan 2015 15:04:21 -0700 Subject: [PATCH 2/8] REL: partially addresses #1818 --- ChangeLog.md | 1 + 1 file changed, 1 insertion(+) diff --git a/ChangeLog.md b/ChangeLog.md index c70c72b8bb..8f1d896e46 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -103,6 +103,7 @@ optionally a mapping file. Check out the new documentation for the naming conven * 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. +* Added ``start_parallel_jobs_slurm.py``, which allows for parallel job submission using [slurm](https://computing.llnl.gov/linux/slurm/). QIIME 1.8.0 (11 Dec 2013) ========================= From 7563e5bc02a8977fc8c505c39d384ee1dd743918 Mon Sep 17 00:00:00 2001 From: Greg Caporaso Date: Fri, 9 Jan 2015 15:58:35 -0700 Subject: [PATCH 3/8] DOC: improved doc, fixes #1841 --- scripts/pick_open_reference_otus.py | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/scripts/pick_open_reference_otus.py b/scripts/pick_open_reference_otus.py index dc6fd2e03f..6c45f04713 100755 --- a/scripts/pick_open_reference_otus.py +++ b/scripts/pick_open_reference_otus.py @@ -296,11 +296,14 @@ 'reference and any reads which fail to hit are discarded (a quality ' 'filter); pass 0.0 to disable [default:%default]'), make_option('--step1_otu_map_fp', type='existing_filepath', - help='reference OTU picking OTU map (to avoid rebuilding if one has ' - 'already been built)'), + help='reference OTU picking OTU map, to avoid rebuilding if one has ' + 'already been built. This must be an OTU map generated by this ' + 'workflow, not (for example) pick_closed_reference_otus.py.'), make_option('--step1_failures_fasta_fp', type='existing_filepath', - help='reference OTU picking failures fasta filepath (to avoid ' - 'rebuilding if one has already been built)'), + help='reference OTU picking failures fasta filepath, to avoid ' + 'rebuilding if one has already been built. This must be a ' + 'failures file generated by this workflow, not (for example) ' + 'pick_closed_reference_otus.py.'), make_option('--minimum_failure_threshold', type='int', default='100000', help='The minimum number of sequences that must fail to hit the ' 'reference for subsampling to be performed. If fewer than this ' From 50f2479d4384023fde5a81783234dca9e65e67be Mon Sep 17 00:00:00 2001 From: Greg Caporaso Date: Fri, 9 Jan 2015 16:00:16 -0700 Subject: [PATCH 4/8] DOC: improved clarity of help text, fixes #1840 --- scripts/collapse_samples.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/collapse_samples.py b/scripts/collapse_samples.py index e15d4aacef..cc8dd859cb 100755 --- a/scripts/collapse_samples.py +++ b/scripts/collapse_samples.py @@ -56,7 +56,7 @@ script_info['optional_options'] = [ make_option('--collapse_mode', type='choice', choices=collapse_modes, help="the mechanism for collapsing counts within groups; " - "valid options are: %s" % ' '.join(collapse_modes), default='sum'), + "valid options are: %s" % ', '.join(collapse_modes), default='sum'), make_option('--normalize', help='Normalize observation counts to relative abundances, so the ' 'counts within each sample sum to 1.0. [default: %default]', From af18451c6917cf6a27756394c023b6538f298c73 Mon Sep 17 00:00:00 2001 From: Greg Caporaso Date: Fri, 9 Jan 2015 16:05:23 -0700 Subject: [PATCH 5/8] DOC: updated dependency list, fixes #1827 --- doc/install/install.rst | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/doc/install/install.rst b/doc/install/install.rst index 7e1b2ae64d..1f028ea02d 100644 --- a/doc/install/install.rst +++ b/doc/install/install.rst @@ -149,6 +149,11 @@ If you plan to use SourceTracker with QIIME: * SourceTracker 0.9.5 (`src `_) (license: GPL) +For joining paired end reads, with ``join_paired_ends.py`` and ``multiple_join_paired_ends.py``: + +* ea-utils 1.1.2-537 (`web `_) (license: MIT) +* SeqPrep v1.1 (`src `_) (license: MIT) + For improved performance with large BIOM files, or if you're working with BIOM format 2.x files: * HDF5 (`web_hdf5 `_) From 9c5ebf8ce9e4105a5213572f0975de3754a14032 Mon Sep 17 00:00:00 2001 From: Greg Caporaso Date: Fri, 9 Jan 2015 16:08:29 -0700 Subject: [PATCH 6/8] MAINT: updated URLs, fixes #1823 --- doc/tutorials/category_comparison.rst | 2 +- doc/tutorials/creating_distance_comparison_plots.rst | 2 +- doc/tutorials/distance_matrix_comparison.rst | 2 +- doc/tutorials/filtering_contamination_otus.rst | 2 +- doc/tutorials/procrustes_analysis.rst | 2 +- doc/tutorials/shotgun_analysis.rst | 2 +- doc/tutorials/source_tracking.rst | 2 +- doc/tutorials/taxa_summary_comparison.rst | 2 +- examples/ipynb/Fungal-ITS-analysis.ipynb | 2 +- examples/ipynb/illumina_overview_tutorial.ipynb | 2 +- .../ipynb/illumina_overview_tutorial_workshop_template.ipynb | 2 +- 11 files changed, 11 insertions(+), 11 deletions(-) diff --git a/doc/tutorials/category_comparison.rst b/doc/tutorials/category_comparison.rst index 7bb03babfd..8f3dd4832b 100644 --- a/doc/tutorials/category_comparison.rst +++ b/doc/tutorials/category_comparison.rst @@ -12,7 +12,7 @@ This tutorial explains the use of several different mapping file category compar Input Files ----------- -You can obtain the files used in this tutorial `here `_. The files are taken from a study (Fierer et al., 2010) where samples were collected from the fingertips of three individuals and the keys of their keyboards. Researchers found that an individual's fingertip samples clustered very closely with his or her corresponding keyboard samples. These results have potential application in the field of forensic science. Throughout this tutorial, we will explore various ways of determining whether the clustering of fingertip and keyboard samples is statistically significant by analyzing the groups of samples. +You can obtain the files used in this tutorial `here `_. The files are taken from a study (Fierer et al., 2010) where samples were collected from the fingertips of three individuals and the keys of their keyboards. Researchers found that an individual's fingertip samples clustered very closely with his or her corresponding keyboard samples. These results have potential application in the field of forensic science. Throughout this tutorial, we will explore various ways of determining whether the clustering of fingertip and keyboard samples is statistically significant by analyzing the groups of samples. Output Files ------------ diff --git a/doc/tutorials/creating_distance_comparison_plots.rst b/doc/tutorials/creating_distance_comparison_plots.rst index ea352cabf5..d0bc363a53 100644 --- a/doc/tutorials/creating_distance_comparison_plots.rst +++ b/doc/tutorials/creating_distance_comparison_plots.rst @@ -18,7 +18,7 @@ Input Files ----------- The first part of this tutorial that details how to use `make_distance_boxplots.py <../scripts/make_distance_boxplots.html>`_ uses the dataset found in the `QIIME tutorial <./tutorial.html>`_. It assumes that you have already performed the beta diversity step to generate a distance matrix which will be used as input to these scripts. You can use any of the distance matrices that are generated by this step as input to these scripts. You will also use the mapping file for this dataset as input to the scripts. All commands assume you are within the top-level directory of the QIIME tutorial's data directory. -The second part of this tutorial that details how to use `make_distance_comparison_plots.py <../scripts/make_distance_comparison_plots.html>`_ uses the dataset from a study that transplanted samples from one part of the body to another (Costello et al., 2009). The metadata mapping file can be found here: `download mapping file `_ and the unweighted UniFrac distance matrix can be found here: `download distance matrix `_. +The second part of this tutorial that details how to use `make_distance_comparison_plots.py <../scripts/make_distance_comparison_plots.html>`_ uses the dataset from a study that transplanted samples from one part of the body to another (Costello et al., 2009). The metadata mapping file can be found here: `download mapping file `_ and the unweighted UniFrac distance matrix can be found here: `download distance matrix `_. Plotting Within and Between Distances ------------------------------------- diff --git a/doc/tutorials/distance_matrix_comparison.rst b/doc/tutorials/distance_matrix_comparison.rst index 53ccf87f1a..66ce984d80 100644 --- a/doc/tutorials/distance_matrix_comparison.rst +++ b/doc/tutorials/distance_matrix_comparison.rst @@ -14,7 +14,7 @@ Please note that this tutorial does not attempt to cover every possible option t Input Files ----------- -You can obtain the files used in this tutorial `here `_. The files are taken from a study (Lauber et al., 2009) where 88 soil samples were collected at various regions around the world. pH was recorded for each of the soil samples. Using `distance_matrix_from_mapping.py <../scripts/distance_matrix_from_mapping.html>`_, we created a distance matrix containing differences in pH between each pair of samples. Throughout this tutorial, we will explore various ways of comparing these matrices for correlation. +You can obtain the files used in this tutorial `here `_. The files are taken from a study (Lauber et al., 2009) where 88 soil samples were collected at various regions around the world. pH was recorded for each of the soil samples. Using `distance_matrix_from_mapping.py <../scripts/distance_matrix_from_mapping.html>`_, we created a distance matrix containing differences in pH between each pair of samples. Throughout this tutorial, we will explore various ways of comparing these matrices for correlation. Output Files ------------ diff --git a/doc/tutorials/filtering_contamination_otus.rst b/doc/tutorials/filtering_contamination_otus.rst index 4b255888bf..b9ea93bb06 100755 --- a/doc/tutorials/filtering_contamination_otus.rst +++ b/doc/tutorials/filtering_contamination_otus.rst @@ -8,7 +8,7 @@ This tutorial explains how to use several QIIME scripts to filter all OTUs that To accomplish this task several scripts are used to first generate an OTU table of target OTUs to remove, then filter those OTUs from the original OTU table, and finally to perform a clean-up step to remove the control samples that would now have zero sequences associated with them. -The OTU table and mapping file (generated from the QIIME tutorial data set) are available `here `_. +The OTU table and mapping file (generated from the QIIME tutorial data set) are available `here `_. Once these files are downloaded and extracted, open a terminal and change to the directory of the extracted files to begin processing. diff --git a/doc/tutorials/procrustes_analysis.rst b/doc/tutorials/procrustes_analysis.rst index fc10235f4b..bce59d0a79 100644 --- a/doc/tutorials/procrustes_analysis.rst +++ b/doc/tutorials/procrustes_analysis.rst @@ -26,7 +26,7 @@ Do some initial set up for the tutorial. This version of the tutorial is based o :: cd - wget https://s3.amazonaws.com/s3-qiime_tutorial_files/moving_pictures_procrustes_demo.tgz + wget ftp://ftp.microbio.me/qiime/tutorial_files/moving_pictures_procrustes_demo.tgz tar -xzf moving_pictures_procrustes_demo.tgz screen cd moving_pictures_procrustes_demo diff --git a/doc/tutorials/shotgun_analysis.rst b/doc/tutorials/shotgun_analysis.rst index c0a64dd3a4..7c137863fd 100644 --- a/doc/tutorials/shotgun_analysis.rst +++ b/doc/tutorials/shotgun_analysis.rst @@ -12,7 +12,7 @@ QIIME can perform translated search to assign nucleic acid sequence reads to a r This tutorial is based on Guerrero Negro microbial mat metagenome data. This data was generated on Sanger, and contains approximately 120k sequences. You should begin by obtaining that data with the following command:: - curl -O https://s3.amazonaws.com/s3-qiime_tutorial_files/shotgun_analysis_gn.tgz + curl -O ftp://ftp.microbio.me/qiime/tutorial_files/shotgun_analysis_gn.tgz See below for the relevant references for this data set. diff --git a/doc/tutorials/source_tracking.rst b/doc/tutorials/source_tracking.rst index cfc92135d1..63c7da3a4b 100644 --- a/doc/tutorials/source_tracking.rst +++ b/doc/tutorials/source_tracking.rst @@ -12,7 +12,7 @@ This tutorial does not attempt to cover every possible usage of SourceTracker. I Tutorial data ------------- -You can obtain the files used in this tutorial `here `_. These are derived from `Hewitt et al., 2013 `_, where samples were collected from various surfaces in two different Neonatal Intensive Care Units (NICUs). The 16S rRNA was sequenced from these samples, and compared against pre-existing data sets using SourceTracker in order to predict the likely origin of the microbial contaminants on each NICU surface. +You can obtain the files used in this tutorial `here `_. These are derived from `Hewitt et al., 2013 `_, where samples were collected from various surfaces in two different Neonatal Intensive Care Units (NICUs). The 16S rRNA was sequenced from these samples, and compared against pre-existing data sets using SourceTracker in order to predict the likely origin of the microbial contaminants on each NICU surface. This tutorial begins with an OTU table. For information on various ways to generate OTU tables with QIIME, see :ref:`otu_picking`. diff --git a/doc/tutorials/taxa_summary_comparison.rst b/doc/tutorials/taxa_summary_comparison.rst index e4a2eb0ffd..ecce42741c 100644 --- a/doc/tutorials/taxa_summary_comparison.rst +++ b/doc/tutorials/taxa_summary_comparison.rst @@ -18,7 +18,7 @@ Please note that this tutorial does not attempt to cover every possible option t Input Files ----------- -You can obtain the files used in this tutorial `here `_. The files are derived from the `overview tutorial <./tutorial.html>`_. The unzipped directory will contain two taxa summary files named :file:`ts_rdp_0.60.txt` and :file:`ts_rdp_0.80.txt`. These taxa summaries were constructed from the overview tutorial representative sequence set by assigning taxonomy to it using the RDP classifier with two different confidence levels (0.60 and 0.80). The gg_otus_4feb2011 97% representative set was used as training input to the RDP classifier. +You can obtain the files used in this tutorial `here `_. The files are derived from the `overview tutorial <./tutorial.html>`_. The unzipped directory will contain two taxa summary files named :file:`ts_rdp_0.60.txt` and :file:`ts_rdp_0.80.txt`. These taxa summaries were constructed from the overview tutorial representative sequence set by assigning taxonomy to it using the RDP classifier with two different confidence levels (0.60 and 0.80). The gg_otus_4feb2011 97% representative set was used as training input to the RDP classifier. Output Files ------------ diff --git a/examples/ipynb/Fungal-ITS-analysis.ipynb b/examples/ipynb/Fungal-ITS-analysis.ipynb index 98abd93a05..9cecf9f09c 100644 --- a/examples/ipynb/Fungal-ITS-analysis.ipynb +++ b/examples/ipynb/Fungal-ITS-analysis.ipynb @@ -23,7 +23,7 @@ "cell_type": "code", "collapsed": true, "input": [ - "tutorial_url = \"https://s3.amazonaws.com/s3-qiime_tutorial_files/its-soils-tutorial.tgz\"\n", + "tutorial_url = \"ftp://ftp.microbio.me/qiime/tutorial_files/its-soils-tutorial.tgz\"\n", "reference_url = \"https://github.com/downloads/qiime/its-reference-otus/its_12_11_otus.tar.gz\"\n", "!wget $tutorial_url\n", "!wget $reference_url" diff --git a/examples/ipynb/illumina_overview_tutorial.ipynb b/examples/ipynb/illumina_overview_tutorial.ipynb index 05ef118d8c..7ac2d6bcf1 100644 --- a/examples/ipynb/illumina_overview_tutorial.ipynb +++ b/examples/ipynb/illumina_overview_tutorial.ipynb @@ -46,7 +46,7 @@ "cell_type": "code", "collapsed": false, "input": [ - "!(wget https://s3.amazonaws.com/s3-qiime_tutorial_files/moving_pictures_tutorial-1.9.0.tgz || curl -O https://s3.amazonaws.com/s3-qiime_tutorial_files/moving_pictures_tutorial-1.9.0.tgz)\n", + "!(wget ftp://ftp.microbio.me/qiime/tutorial_files/moving_pictures_tutorial-1.9.0.tgz || curl -O ftp://ftp.microbio.me/qiime/tutorial_files/moving_pictures_tutorial-1.9.0.tgz)\n", "!tar -xzf moving_pictures_tutorial-1.9.0.tgz" ], "language": "python", diff --git a/examples/ipynb/illumina_overview_tutorial_workshop_template.ipynb b/examples/ipynb/illumina_overview_tutorial_workshop_template.ipynb index 35f0e5f6b2..0e95ac25b6 100644 --- a/examples/ipynb/illumina_overview_tutorial_workshop_template.ipynb +++ b/examples/ipynb/illumina_overview_tutorial_workshop_template.ipynb @@ -50,7 +50,7 @@ "makedirs(working_dir)\n", "chdir(working_dir)\n", "\n", - "!wget https://s3.amazonaws.com/s3-qiime_tutorial_files/moving_pictures_tutorial-1.8.0.tgz\n", + "!wget ftp://ftp.microbio.me/qiime/tutorial_files/moving_pictures_tutorial-1.8.0.tgz\n", "!tar -xzf moving_pictures_tutorial-1.8.0.tgz\n", "\n", "# To use FileLink(s), but link to files in the user's working directory\n", From 9578aa7b9b1af8e9ecceaed95225167cb4193b24 Mon Sep 17 00:00:00 2001 From: Greg Caporaso Date: Fri, 9 Jan 2015 16:48:36 -0700 Subject: [PATCH 7/8] REL: starting cleaning up change log, partially addresses #1812 --- ChangeLog.md | 193 ++++++++++++++++++++++++++++----------------------- 1 file changed, 107 insertions(+), 86 deletions(-) diff --git a/ChangeLog.md b/ChangeLog.md index 8f1d896e46..b63c5f5ed5 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -1,109 +1,130 @@ QIIME 1.9.0-rc2 =============== -* 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 -(which have changed slightly) and an example. -* QIIME is now even easier to install! Removed ``qiime_scripts_dir``, ``python_exe_fp``, ``working_dir``, ``cloud_environment``, and ``template_alignment_lanemask_fp`` from the QIIME config file. If these values are present in your QIIME config file, they will be flagged as unrecognized by ``print_qiime_config.py -t`` and will be ignored by QIIME. QIIME will now use the ``python`` executable and QIIME scripts that are found in your ``PATH`` environment variable, and ``temp_dir`` will be used in place of ``working_dir`` (this value was used by some parts of parallel QIIME previously). ``filter_alignment.py`` will now use the 16S alignment Lane mask (Lane, D.J. 1991) by default if one is not provided via ``--lane_mask_fp``. -* Removed ``-Y``/``--python_exe_fp`` and ``-N`` options from ``parallel_merge_otu_tables.py`` script as these are not available in any of the other parallel QIIME scripts and we do not have good reason to support them (see QIIME 1.6.0 release notes below for more details). -* SciPy >= 0.13.0, pyqi 0.3.1, scikit-bio >= 0.2.2, < 0.3.0, and qiime-default-reference >= 0.1.1, < 0.2.0 are now required dependencies for a QIIME base install. -* Added new options to ``make_otu_heatmap.py``: ``--color_scheme``, which allows users to choose from different color schemes [here](http://matplotlib.org/examples/color/colormaps_reference.html); ``--observation_metadata_category``, which allows users to select a column other than taxonomy to use when labeling the rows; and ``--observation_metadata_level``, which allows the user to specify which level in the hierarchical metadata category to use in creating the row labels. -* ``-m/--mapping_fps`` is no longer required for split_libraries_fastq.py. The mapping file is not required when running with ``--barcode_type 'not-barcoded'``,but the mapping file would fail to validate when passing multiple sequence files and sample ids but a mapping file without barcodes (see #1400). + +New scripts +----------- + +* ``observation_metadata_correlation.py``: 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. +* ``compare_trajectories.py``: Allows analysis of volatility using different algorithms. +* ``compute_taxonomy_ratios.py``: Implements the microbial dysbiosis index (MD-index) from [Gevers et al 2014](http://www.ncbi.nlm.nih.gov/pubmed/24629344). +* ``collpase_samples.py``: Allows collapsing groups of samples in BIOM tables and mapping files based on their metadata (see [#1678](https://github.com/biocore/qiime/issues/1678)). This can be used, for example, to collapse samples belonging to a replicate group. This also has replaced ``summarize_otu_by_cat.py`` (see discussion on [#1798](https://github.com/biocore/qiime/issues/1798)). +* ``multiple_split_libraries_fastq.py``, ``multiple_join_paired_ends.py``, and ``multiple_extract_barcodes.py``: Facilitate initial QIIME processing of already-demultiplexed fastq files, as these are commonly being provided by sequencing centers. +* ``differential_abundance.py``: Supplements ``group_significance.py`` to support metagenomeSeq's fitZIG algorithm and DESeq2's negative binomial algorithm. The input for this is an unnormalized, raw BIOM table. +* ``normalize_table.py``: Adds support for BIOM table normalization algorithms in addition to rarefaction. Supported methods are metagenomeSeq's CSS and DESeq's variance stabilizing transformation. +* ``start_parallel_jobs_slurm.py``: Allows for parallel job submission using [slurm](https://computing.llnl.gov/linux/slurm/). +* ``split_libraries_lea_seq.py``: Allows for demultiplexing of sequences using the LEA-Seq protocol, described in [Faith et al. (2013)](http://www.sciencemag.org/content/341/6141/1237439). + +Features +-------- + +* ``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 (which have changed slightly) and an example. +* Added new options to ``make_otu_heatmap.py``: + * ``--color_scheme``, which allows users to choose from different color schemes [here](http://matplotlib.org/examples/color/colormaps_reference.html) + * ``--observation_metadata_category``, which allows users to select a column other than taxonomy to use when labeling the rows + * ``--observation_metadata_level``, which allows the user to specify which level in the hierarchical metadata category to use in creating the row labels. + * ``-g``/``--imagetype``, ``--dpi``, ``--width``, and ``--height``, which offer more control over the generation of heatmap figures. +* ``-m/--mapping_fps`` is no longer required for split_libraries_fastq.py. The mapping file is not required when running with ``--barcode_type 'not-barcoded'``,but the mapping file would fail to validate when passing multiple sequence files and sample ids but a mapping file without barcodes (see [#1400](https://github.com/biocore/qiime/issues/1400)). * Added alphabetical sorting option (based on boxplot labels) to ``make_distance_boxplots.py``. Sorting by boxplot median can now be performed by passing ``--sort median`` (this was previously invoked by passing ``--sort``). Sorting alphabetically can be performed by passing ``--sort alphabetical``. -* Removed ``insert_seqs_into_tree.py``. This code needs additional testing and documentation, and was not widely used. We plan to add this support back in the future, and progress on that can be followed on [#1499](https://github.com/biocore/qiime/issues/1499). -* The alpha diversity measures available in QIIME (e.g., ``alpha_diversity.py``) are now powered by [scikit-bio](http://scikit-bio.org/)! Click [here](http://scikit-bio.org/docs/latest/generated/skbio.diversity.alpha.html) to view the documentation for these measures. Several changes were made to ``alpha_diversity.py``: - - ``ACE`` is now ``ace`` - - ``chao1_confidence`` is now ``chao1_ci`` - - Added ``observed_otus``, which is equivalent to ``observed_species`` but is - generally a more accurate name. ``observed_species`` is retained for - backwards-compatibility. -* Removed options ``-c``/``--ci_type``, ``-a``/``--alpha``, and ``-f``/``--f_ratio`` from ``conditional_uncovered_probability.py`` as these weren't being used by the script (i.e., supplying different values didn't change the computed CIs because the default were always used). -* Removed ``tax2tree`` as a method in ``assign_taxonomy.py``. -* ANOSIM and PERMANOVA (available in ``compare_categories.py``) are considerably faster than previous implementations and provide more useful information in the output file. -* Added script ``compare_trajectories.py``, which provides access to analysis of volatility using different algorithms. -* Renamed ``compare_categories.py``'s BEST method to BIO-ENV to match the name used in R's vegan package (``vegan::bioenv``) and the name of the program in the original paper. Use ``compare_categories.py --method bioenv`` instead of ``compare_categories.py --method best``. The underlying implementation has also been rewritten and is considerably faster than before, and the output more closely matches the vegan package, as environmental variables are now scaled before computing Euclidean distances. -* Scripts that write an OTU table, will write BIOM files in HDF5 format. -* Changed default parameters for uclust-based OTU picking: ``max_accepts`` is now 1 (was 8), ``max_rejects`` is now 8 (was 500), ``stepwords`` is now 8 (was 20), and ``word_length`` is now 8 (was 12). These changes greatly reduce runtime, with minimal effect on the results. See Rideout et al., 2014 ([PeerJ pre-print](https://peerj.com/preprints/411/)) for more details. -* Disabled the prefilter by default in ``pick_open_reference_otus.py``. This change greatly reduces runtime, with minimal effect on the results. See Rideout et al., 2014 ([PeerJ pre-print](https://peerj.com/preprints/411/)) for more details. +* Scripts that write an OTU table will now write BIOM files in HDF5 format if HDF5 is installed. This improves performance for very large OTU tables. * ``merge_mapping_files.py`` can now take an argument to convert the header names to upper case, so it will merge for example a category named `treatment` and another one named `TREATMENT` from two different mapping files. * The script ``make_distance_histograms.py`` has been removed. This functionality should be accessed through ``make_distance_boxplots.py``. * Beta support has been added for performing subsampled open reference OTU picking using SortMeRNA ([Bioinformatics](http://www.ncbi.nlm.nih.gov/pubmed/23071270)(for the closed-reference steps) and SumaClust ([In Preparation](http://metabarcoding.org/sumatra)) (for the open reference steps). This can be accessed with ``pick_open_reference_otus.py -m sortmerna_sumaclust``. * Beta support has been added for performing closed-reference OTU picking using SortMeRNA ([Bioinformatics](http://www.ncbi.nlm.nih.gov/pubmed/23071270). This can be accessed with ``pick_closed_reference_otus.py -p params.txt`` where params.txt includes the line ``pick_otus:otu_picking_method sortmerna``. * Beta support has been added for performing de novo OTU picking using SumaClust ([In Preparation](http://metabarcoding.org/sumatra)). This can be accessed with ``pick_de_novo_otus.py -p params.txt`` where params.txt includes the line ``pick_otus:otu_picking_method sumaclust``. -* numpy version requirement has been updated to 1.7.1 or later. -* Updated to use [burrito](https://github.com/biocore/burrito) instead of scikit-bio for imports from the application controller framework, as the former is replacing the latter. -* QIIME now depends on [biom-format](https://github.com/biocore/biom-format) >= 2.1.2, < 2.2.0. -* the parameters ``--uclust_min_consensus_fraction`` and ``--uclust_similarity`` in assign taxonomy scripts have been changed to ``--min_consensus_fraction`` and ``--similarity`` since both of these parameters apply to the SortMeRNA taxon assigner as well. -* Renamed ``split_fasta_on_sample_ids_to_files.py`` to ``split_sequence_file_on_sample_ids_to_files.py``, which now supports splitting FASTQ files, as well. Added a parameter, ``file_type``, which is used to specify the type of the input file. -* Added --assign_taxonomy option to pick_closed_reference_otus.py to allow taxonomy assignment using a classifier, rather than the default of using the taxonomic assignment of the cluster centroid. +* Renamed ``split_fasta_on_sample_ids_to_files.py`` to ``split_sequence_file_on_sample_ids.py``, which now supports splitting FASTQ files, as well. Added a parameter, ``--file_type``, which is used to specify the type of the input file. +* Added ``--assign_taxonomy`` option to ``pick_closed_reference_otus.py`` to allow taxonomy assignment using a classifier, rather than the default of using the taxonomic assignment of the cluster centroid. +* Added ``--suppress_taxonomy_assignment`` option to ``pick_closed_reference_otus.py``. * Updated output of ``identify_paired_differences.py`` to include more information in the pseudo-mapping file that it generates. This includes the "pre" and "post" values for all of the analysis categories on a per-subject basis. This is useful for plotting with other tools, or for generating legends for the plots that are currently generated by the script (see [issue #1707](https://github.com/biocore/qiime/issues/1707)). -* Fasttree v1.x is no longer supported by ``make_phylogeny.py`` (see [issue #1516](https://github.com/biocore/qiime/issues/1516)). +* Added ``pick_otus_reference_seqs_fp`` to the QIIME config file. This is a filepath to reference sequences to use with QIIME's OTU picking scripts/workflows. See the [QIIME config docs](http://qiime.org/install/qiime_config.html) and [#1696](https://github.com/biocore/qiime/issues/1696) for more details. +* The QIIME config settings ``assign_taxonomy_id_to_taxonomy_fp``, ``assign_taxonomy_reference_seqs_fp``, ``pick_otus_reference_seqs_fp``, and ``pynast_template_alignment_fp`` now default to reference data files in the [qiime-default-reference project](http://github.com/biocore/qiime-default-reference). +* Installing QIIME via ``pip install qiime`` now works out-of-the-box by providing a functioning QIIME minimal (base) install (see [#1696](https://github.com/biocore/qiime/issues/1696)). +* ``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)). + +Bug fixes +--------- + * Relaxed sanity tests for ``compare_categories.py --method adonis`` so that unique values are only checked for categories that are non-numeric (see [issue #1316](https://github.com/biocore/qiime/issues/1360)). * ``core_diversity_analyses.py`` now requires ``--tree_fp`` unless ``--nonphylogenetic_diversity`` is passed (see [#1671](https://github.com/biocore/qiime/issues/1671)). * Fixed bug in ``assign_taxonomy.py -m blast`` and ``parallel_assign_taxonomy_blast.py`` that prevented multiple instances of either to run at the same time (see [#1768](https://github.com/biocore/qiime/issues/1768)). -* parallel_pick_otus_sortmerna.py added, and pick_closed_reference_otus.py and pick_open_reference_otus.py updated to use this functionality. -* Added new ``compute_taxonomy_ratios.py`` script, which implements the microbial dysbiosis index (MD-index) from [Gevers et al 2014](http://www.ncbi.nlm.nih.gov/pubmed/24629344). * Fixed bug where ``--phred_offset`` in ``split_libraries_fastq.py`` was ignored (see [#1656](https://github.com/biocore/qiime/issues/1656)). -* ``--tail_type`` option in ``compare_distance_matrices.py`` now accepts "two-sided" instead of "two sided" for specifying a two-sided alternative hypothesis. The new name is easier to specify via the command-line (quotes aren't needed because it is a single word). -* The Mantel test (``--method mantel``) and Mantel correlogram (``--method mantel_corr)`` in ``compare_distance_matrices.py`` are considerably faster than previous implementations. * Spaces in taxa will not cause an error when using ``--assignment_method=mothur`` in ``assign_taxonomy.py``. * Fixed bug where long axis labels were cut off in heatmaps generated by ``make_otu_heatmap.py`` (see [#1571](https://github.com/biocore/qiime/issues/1571)). -* Added new options ``-g``/``--imagetype``, ``--dpi``, ``--width``, and ``--height`` to ``make_otu_heatmap.py``, which offer more control over the generation of heatmap figures. -* Removed ``--output_dir`` optional option from ``make_otu_heatmap.py`` and replaced it with the required option ``--output_fp``. * Fixed bug where ``-S``/``--suppress_submit_jobs`` was being ignored by several of the parallel scripts (e.g. ``parallel_pick_otus_uclust_ref.py``) (see [#1665](https://github.com/biocore/qiime/issues/1665)). -* Simplified and improved QIIME documentation. -* ``print_qiime_config.py -t`` now tests a QIIME minimal (base) install instead of a QIIME full install. ``print_qiime_config.py -tf`` tests a QIIME full install. -* Added ``pick_otus_reference_seqs_fp`` to the QIIME config file. This is a filepath to reference sequences to use with QIIME's OTU picking scripts/workflows. See the [QIIME config docs](http://qiime.org/install/qiime_config.html) and [#1696](https://github.com/biocore/qiime/issues/1696) for more details. -* The QIIME config settings ``assign_taxonomy_id_to_taxonomy_fp``, ``assign_taxonomy_reference_seqs_fp``, ``pick_otus_reference_seqs_fp``, and ``pynast_template_alignment_fp`` now default to reference data files in the [qiime-default-reference project](http://github.com/biocore/qiime-default-reference). -* Installing QIIME via ``pip install qiime`` now works out-of-the-box by providing a functioning QIIME minimal (base) install (see [#1696](https://github.com/biocore/qiime/issues/1696)). -* ``cluster_jobs_fp`` in the QIIME config file now defaults to ``start_parallel_jobs.py``. ``seconds_to_sleep`` now defaults to 1. * Fixed bug where ``make_distance_comparison_plots.py`` would create empty groups (see [#1627](https://github.com/biocore/qiime/issues/1627)). -* Added ``--suppress_taxonomy_assignment`` option to ``pick_closed_reference_otus.py``. -* sumaclust v1.0.00, swarm 1.2.19, and sortmerna 2.0 are now optional dependencies (see the [QIIME install docs](http://qiime.org/install/install.html) for details). -* Errors raised by scripts are easier to read and include a supplementary message on how to get help (see [#1794](https://github.com/biocore/qiime/issues/1794)). -* Removed ``submit_to_mgrast.py`` script (see [#1780](https://github.com/biocore/qiime/issues/1780)). -* Added ``collpase_samples.py``, which can be used for collapsing groups of samples in BIOM tables and mapping files based on their metadata (see [#1678](https://github.com/biocore/qiime/issues/1678)). This can be used, for example, to collapse samples belonging to a replicate group. This also has replaced ``summarize_otu_by_cat.py`` (see discussion on [#1798](https://github.com/biocore/qiime/issues/1798)). * ``qiime/workflow/pick_open_reference_otus.py`` no longer copies the permission bits of the reference file which caused a file permission failure in some cases. -* Standardized use of underscores in option longnames. Affected scripts and options: - * ``scripts/compute_index.py`` - * `show-indices` is now `show_indices` - * ``scripts/demultiplex_fasta.py`` - * `start-numbering-at` is now `start_numbering_at` - * ``scripts/denoiser.py`` - * `low_cut-off` is now `low_cut_off` - * `high_cut-off` is now `high_cut_off` - * ``scripts/multiple_rarefactions.py`` - * `num-reps` is now `num_reps` - * ``scripts/multiple_rarefactions_even_depth.py`` - * `num-reps` is now `num_reps` - * ``scripts/parallel_multiple_rarefactions.py`` - * `num-reps` is now `num_reps` - * ``scripts/plot_rank_abundance_graph.py`` - * `no-legend` is now `no_legend` - * ``scripts/start_parallel_jobs_slurm.py`` - * `mem-per-cpu` is now `mem_per_cpu` - * ``scripts/split_libraries.py`` - * `min-seq-length` is now `min_seq_length` - * `max-seq-length` is now `max_seq_length` - * `trim-seq-length` is now `trim_seq_length` - * `min-qual-score` is now `min_qual_score` - * `keep-primer` is now `keep_primer` - * `keep-barcode` is now `keep_barcode` - * `max-ambig` is now `max_ambig` - * `max-homopolymer` is now `max_homopolymer` - * `max-primer-mismatch` is now `max_primer_mismatch` - * `barcode-type` is now `barcode_type` - * `dir-prefix` is now `dir_prefix` - * `max-barcode-errors` is now `max_barcode_errors` - * `start-numbering-at` is now `start_numbering_at` * Fixed bug in ``make_rarefaction_plots.py`` where ``--generate_per_sample_plots`` wasn't working (see [#1475](https://github.com/biocore/qiime/issues/1475)). -* Removed ``make_otu_heatmap_html.py`` in favor of ``make_otu_heatmap.py`` (see discussion on [#1724](https://github.com/biocore/qiime/issues/1724)). * 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. -* Added ``start_parallel_jobs_slurm.py``, which allows for parallel job submission using [slurm](https://computing.llnl.gov/linux/slurm/). + +Usability enhancements +---------------------- + +* Simplified and improved QIIME install documentation. +* Errors raised by scripts are easier to read and include a supplementary message on how to get help (see [#1794](https://github.com/biocore/qiime/issues/1794)). +* QIIME is now even easier to install! Removed ``qiime_scripts_dir``, ``python_exe_fp``, ``working_dir``, ``cloud_environment``, and ``template_alignment_lanemask_fp`` from the QIIME config file. If these values are present in your QIIME config file, they will be flagged as unrecognized by ``print_qiime_config.py -t`` and will be ignored by QIIME. QIIME will now use the ``python`` executable and QIIME scripts that are found in your ``PATH`` environment variable, and ``temp_dir`` will be used in place of ``working_dir`` (this value was used by some parts of parallel QIIME previously). ``filter_alignment.py`` will now use the 16S alignment Lane mask (Lane, D.J. 1991) by default if one is not provided via ``--lane_mask_fp``. +* ``--tail_type`` option in ``compare_distance_matrices.py`` now accepts "two-sided" instead of "two sided" for specifying a two-sided alternative hypothesis. The new name is easier to specify via the command-line (quotes aren't needed because it is a single word). +* ``print_qiime_config.py -t`` now tests a QIIME minimal (base) install instead of a QIIME full install. ``print_qiime_config.py -tf`` tests a QIIME full install. +* Standardized use of underscores in option longnames. Affected scripts and options: + * ``scripts/demultiplex_fasta.py`` + * `start-numbering-at` is now `start_numbering_at` + * ``scripts/denoiser.py`` + * `low_cut-off` is now `low_cut_off` + * `high_cut-off` is now `high_cut_off` + * ``scripts/multiple_rarefactions.py`` + * `num-reps` is now `num_reps` + * ``scripts/multiple_rarefactions_even_depth.py`` + * `num-reps` is now `num_reps` + * ``scripts/parallel_multiple_rarefactions.py`` + * `num-reps` is now `num_reps` + * ``scripts/plot_rank_abundance_graph.py`` + * `no-legend` is now `no_legend` + * ``scripts/split_libraries.py`` + * `min-seq-length` is now `min_seq_length` + * `max-seq-length` is now `max_seq_length` + * `trim-seq-length` is now `trim_seq_length` + * `min-qual-score` is now `min_qual_score` + * `keep-primer` is now `keep_primer` + * `keep-barcode` is now `keep_barcode` + * `max-ambig` is now `max_ambig` + * `max-homopolymer` is now `max_homopolymer` + * `max-primer-mismatch` is now `max_primer_mismatch` + * `barcode-type` is now `barcode_type` + * `dir-prefix` is now `dir_prefix` + * `max-barcode-errors` is now `max_barcode_errors` + * `start-numbering-at` is now `start_numbering_at` +* Removed ``--output_dir`` optional option from ``make_otu_heatmap.py`` and replaced it with the required option ``--output_fp``. + +Removal of outdated and unsupported functionality +------------------------------------------------- + +* Removed ``-Y``/``--python_exe_fp`` and ``-N`` options from ``parallel_merge_otu_tables.py`` script as these are not available in any of the other parallel QIIME scripts and we do not have good reason to support them (see QIIME 1.6.0 release notes below for more details). +* Removed ``insert_seqs_into_tree.py``. This code needs additional testing and documentation, and was not widely used. We plan to add this support back in the future, and progress on that can be followed on [#1499](https://github.com/biocore/qiime/issues/1499). +* ``summarize_otu_by_cat.py`` has been replaced with ``collapse_samples.py``. +* Removed options ``-c``/``--ci_type``, ``-a``/``--alpha``, and ``-f``/``--f_ratio`` from ``conditional_uncovered_probability.py`` as these weren't being used by the script (i.e., supplying different values didn't change the computed CIs because the default were always used). +* Removed ``tax2tree`` as a method in ``assign_taxonomy.py``. +* Fasttree v1.x is no longer supported by ``make_phylogeny.py`` (see [issue #1516](https://github.com/biocore/qiime/issues/1516)). +* Removed ``submit_to_mgrast.py`` script (see [#1780](https://github.com/biocore/qiime/issues/1780)). +* Removed ``make_otu_heatmap_html.py`` in favor of ``make_otu_heatmap.py`` (see discussion on [#1724](https://github.com/biocore/qiime/issues/1724)). + +Dependency changes +------------------ +* sumaclust v1.0.00, swarm 1.2.19, and sortmerna 2.0 are now optional dependencies (see the [QIIME install docs](http://qiime.org/install/install.html) for details). + +Miscellaneous +------------- + +* The alpha diversity measures available in QIIME (e.g., ``alpha_diversity.py``) are now powered by [scikit-bio](http://scikit-bio.org/)! Click [here](http://scikit-bio.org/docs/latest/generated/skbio.diversity.alpha.html) to view the documentation for these measures. Several changes were made to ``alpha_diversity.py``: + * ``ACE`` is now ``ace`` + * ``chao1_confidence`` is now ``chao1_ci`` + * Added ``observed_otus``, which is equivalent to ``observed_species`` but is generally a more accurate name. ``observed_species`` is retained for backward-compatibility. +* ANOSIM and PERMANOVA (available in ``compare_categories.py``) are now powered by [scikit-bio](http://scikit-bio.org/) and are approximately 1000 times faster than previous implementations. These additionally now provide more useful information in the output file. +* Renamed ``compare_categories.py``'s BEST method to BIO-ENV to match the name used in R's vegan package (``vegan::bioenv``) and the name of the program in the original paper. Use ``compare_categories.py --method bioenv`` instead of ``compare_categories.py --method best``. The underlying implementation has also been rewritten and is considerably faster than before, and the output more closely matches the vegan package, as environmental variables are now scaled before computing Euclidean distances. +* Changed default parameters for uclust-based OTU picking: ``max_accepts`` is now 1 (was 8), ``max_rejects`` is now 8 (was 500), ``stepwords`` is now 8 (was 20), and ``word_length`` is now 8 (was 12). These changes greatly reduce runtime, with minimal effect on the results. See Rideout et al., 2014 ([PeerJ pre-print](https://peerj.com/preprints/411/)) for more details. +* Disabled the prefilter by default in ``pick_open_reference_otus.py``. This change greatly reduces runtime, with minimal effect on the results. See Rideout et al., 2014 ([PeerJ pre-print](https://peerj.com/preprints/411/)) for more details. +* The parameters ``--uclust_min_consensus_fraction`` and ``--uclust_similarity`` in ``*_assign_taxonomy_*`` scripts have been changed to ``--min_consensus_fraction`` and ``--similarity`` since both of these parameters apply to the SortMeRNA taxon assigner as well. +* The Mantel test (``--method mantel``) and Mantel correlogram (``--method mantel_corr)`` in ``compare_distance_matrices.py`` are considerably faster than previous implementations. + + QIIME 1.8.0 (11 Dec 2013) ========================= From 897c37dc48a4611a1cb772a83dc3a69bb519f839 Mon Sep 17 00:00:00 2001 From: Greg Caporaso Date: Fri, 9 Jan 2015 16:56:06 -0700 Subject: [PATCH 8/8] REL: more updates to the changelog, still needs proof-reading and a final pass --- ChangeLog.md | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/ChangeLog.md b/ChangeLog.md index b63c5f5ed5..3cccf586df 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -93,6 +93,11 @@ Usability enhancements * `max-barcode-errors` is now `max_barcode_errors` * `start-numbering-at` is now `start_numbering_at` * Removed ``--output_dir`` optional option from ``make_otu_heatmap.py`` and replaced it with the required option ``--output_fp``. +* The parameters ``--uclust_min_consensus_fraction`` and ``--uclust_similarity`` in ``*_assign_taxonomy_*`` scripts have been changed to ``--min_consensus_fraction`` and ``--similarity`` since both of these parameters apply to the SortMeRNA taxon assigner as well. +* Several changes were made to ``alpha_diversity.py`` metric names: + * ``ACE`` is now ``ace`` + * ``chao1_confidence`` is now ``chao1_ci`` + * Added ``observed_otus``, which is equivalent to ``observed_species`` but is generally a more accurate name. ``observed_species`` is retained for backward-compatibility. Removal of outdated and unsupported functionality ------------------------------------------------- @@ -110,20 +115,15 @@ Dependency changes ------------------ * sumaclust v1.0.00, swarm 1.2.19, and sortmerna 2.0 are now optional dependencies (see the [QIIME install docs](http://qiime.org/install/install.html) for details). -Miscellaneous -------------- +Performance enhancements +------------------------ -* The alpha diversity measures available in QIIME (e.g., ``alpha_diversity.py``) are now powered by [scikit-bio](http://scikit-bio.org/)! Click [here](http://scikit-bio.org/docs/latest/generated/skbio.diversity.alpha.html) to view the documentation for these measures. Several changes were made to ``alpha_diversity.py``: - * ``ACE`` is now ``ace`` - * ``chao1_confidence`` is now ``chao1_ci`` - * Added ``observed_otus``, which is equivalent to ``observed_species`` but is generally a more accurate name. ``observed_species`` is retained for backward-compatibility. -* ANOSIM and PERMANOVA (available in ``compare_categories.py``) are now powered by [scikit-bio](http://scikit-bio.org/) and are approximately 1000 times faster than previous implementations. These additionally now provide more useful information in the output file. -* Renamed ``compare_categories.py``'s BEST method to BIO-ENV to match the name used in R's vegan package (``vegan::bioenv``) and the name of the program in the original paper. Use ``compare_categories.py --method bioenv`` instead of ``compare_categories.py --method best``. The underlying implementation has also been rewritten and is considerably faster than before, and the output more closely matches the vegan package, as environmental variables are now scaled before computing Euclidean distances. * Changed default parameters for uclust-based OTU picking: ``max_accepts`` is now 1 (was 8), ``max_rejects`` is now 8 (was 500), ``stepwords`` is now 8 (was 20), and ``word_length`` is now 8 (was 12). These changes greatly reduce runtime, with minimal effect on the results. See Rideout et al., 2014 ([PeerJ pre-print](https://peerj.com/preprints/411/)) for more details. * Disabled the prefilter by default in ``pick_open_reference_otus.py``. This change greatly reduces runtime, with minimal effect on the results. See Rideout et al., 2014 ([PeerJ pre-print](https://peerj.com/preprints/411/)) for more details. -* The parameters ``--uclust_min_consensus_fraction`` and ``--uclust_similarity`` in ``*_assign_taxonomy_*`` scripts have been changed to ``--min_consensus_fraction`` and ``--similarity`` since both of these parameters apply to the SortMeRNA taxon assigner as well. -* The Mantel test (``--method mantel``) and Mantel correlogram (``--method mantel_corr)`` in ``compare_distance_matrices.py`` are considerably faster than previous implementations. - +* The alpha diversity measures available in QIIME (e.g., ``alpha_diversity.py``) are now powered by [scikit-bio](http://scikit-bio.org/), and several of these methods are now considerably faster! See the scikit-bio docs on [alpha diversity](http://scikit-bio.org/docs/latest/generated/skbio.diversity.alpha.html) for more details on the methods. +* ANOSIM and PERMANOVA (available in ``compare_categories.py``) are now powered by [scikit-bio](http://scikit-bio.org/) and are approximately 1000 times faster than previous implementations. These additionally now provide more useful information in the output file. See the scikit-bio docs for [ANOSIM](http://scikit-bio.org/docs/latest/generated/generated/skbio.stats.distance.anosim.html) and [PERMANOVA](http://scikit-bio.org/docs/latest/generated/generated/skbio.stats.distance.permanova.html) for more detail. +* Renamed ``compare_categories.py``'s BEST method to BIO-ENV to match the name used in R's vegan package (``vegan::bioenv``) and the name of the program in the original paper. Use ``compare_categories.py --method bioenv`` instead of ``compare_categories.py --method best``. The underlying implementation has also been rewritten and is considerably faster than before, and the output more closely matches the vegan package, as environmental variables are now scaled before computing Euclidean distances. See the scikit-bio docs for [BIO-ENV](http://scikit-bio.org/docs/latest/generated/generated/skbio.stats.distance.bioenv.html) for more detail. +* The Mantel test (``--method mantel``) and Mantel correlogram (``--method mantel_corr)`` in ``compare_distance_matrices.py`` are considerably faster than previous implementations. See the scikit-bio docs for [Mantel](http://scikit-bio.org/docs/latest/generated/generated/skbio.stats.distance.mantel.html) for more detail. QIIME 1.8.0 (11 Dec 2013)