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updated __version__ and __status__ strings and references to the vers…

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commit f30d6398be6c09418cdcb149e68556187bc4560d 1 parent b706c51
@gregcaporaso gregcaporaso authored
Showing with 599 additions and 599 deletions.
  1. +1 −1  README
  2. +2 −2 doc/conf.py
  3. +1 −1  doc/index.rst
  4. +3 −3 doc/install/install.rst
  5. +1 −1  doc/install/upgrade.rst
  6. +1 −1  doc/install/virtual_box.rst
  7. +2 −2 qiime/__init__.py
  8. +2 −2 qiime/add_alpha_to_mapping_file.py
  9. +2 −2 qiime/add_qiime_labels.py
  10. +2 −2 qiime/adjust_seq_orientation.py
  11. +2 −2 qiime/align_seqs.py
  12. +2 −2 qiime/alpha_diversity.py
  13. +2 −2 qiime/assign_taxonomy.py
  14. +2 −2 qiime/barcode.py
  15. +2 −2 qiime/beta_diversity.py
  16. +2 −2 qiime/beta_metrics.py
  17. +2 −2 qiime/biplots.py
  18. +2 −2 qiime/categorized_dist_scatterplot.py
  19. +2 −2 qiime/check_id_map.py
  20. +2 −2 qiime/clean_raxml_parsimony_tree.py
  21. +2 −2 qiime/cluster_quality.py
  22. +2 −2 qiime/collate_alpha.py
  23. +2 −2 qiime/colors.py
  24. +2 −2 qiime/compare_alpha_diversity.py
  25. +2 −2 qiime/compare_categories.py
  26. +2 −2 qiime/compare_distance_matrices.py
  27. +2 −2 qiime/compare_taxa_summaries.py
  28. +2 −2 qiime/convert_fastaqual_fastq.py
  29. +2 −2 qiime/core_microbiome.py
  30. +2 −2 qiime/demultiplex_fasta.py
  31. +2 −2 qiime/denoise_wrapper.py
  32. +2 −2 qiime/denoiser/__init__.py
  33. +2 −2 qiime/denoiser/cluster_utils.py
  34. +2 −2 qiime/denoiser/denoise_postprocess.py
  35. +2 −2 qiime/denoiser/denoise_worker.py
  36. +2 −2 qiime/denoiser/flowgram_clustering.py
  37. +2 −2 qiime/denoiser/flowgram_filter.py
  38. +2 −2 qiime/denoiser/make_cluster_jobs.py
  39. +2 −2 qiime/denoiser/preprocess.py
  40. +2 −2 qiime/denoiser/utils.py
  41. +2 −2 qiime/detrend.py
  42. +2 −2 qiime/distance_matrix_from_mapping.py
  43. +2 −2 qiime/exclude_seqs_by_blast.py
  44. +2 −2 qiime/filter.py
  45. +2 −2 qiime/filter_alignment.py
  46. +2 −2 qiime/filter_otus_by_sample.py
  47. +2 −2 qiime/format.py
  48. +2 −2 qiime/golay.py
  49. +2 −2 qiime/group.py
  50. +2 −2 qiime/hamming.py
  51. +2 −2 qiime/hierarchical_cluster.py
  52. +2 −2 qiime/identify_chimeric_seqs.py
  53. +2 −2 qiime/insert_seqs_into_tree.py
  54. +2 −2 qiime/longitudinal_otu_category_significance.py
  55. +2 −2 qiime/make_2d_plots.py
  56. +2 −2 qiime/make_3d_plots.py
  57. +2 −2 qiime/make_bootstrapped_tree.py
  58. +2 −2 qiime/make_distance_boxplots.py
  59. +2 −2 qiime/make_distance_histograms.py
  60. +2 −2 qiime/make_fastq.py
  61. +2 −2 qiime/make_library_id_lists.py
  62. +2 −2 qiime/make_otu_heatmap.py
  63. +2 −2 qiime/make_otu_heatmap_html.py
  64. +2 −2 qiime/make_otu_network.py
  65. +2 −2 qiime/make_otu_table.py
  66. +2 −2 qiime/make_per_library_sff.py
  67. +2 −2 qiime/make_phylogeny.py
  68. +2 −2 qiime/make_rarefaction_plots.py
  69. +2 −2 qiime/map_reads_to_reference.py
  70. +2 −2 qiime/merge_mapping_files.py
  71. +2 −2 qiime/nmds.py
  72. +2 −2 qiime/otu_category_significance.py
  73. +2 −2 qiime/parallel/__init__.py
  74. +2 −2 qiime/parallel/align_seqs.py
  75. +2 −2 qiime/parallel/alpha_diversity.py
  76. +2 −2 qiime/parallel/assign_taxonomy.py
  77. +2 −2 qiime/parallel/beta_diversity.py
  78. +2 −2 qiime/parallel/blast.py
  79. +2 −2 qiime/parallel/identify_chimeric_seqs.py
  80. +2 −2 qiime/parallel/map_reads_to_reference.py
  81. +2 −2 qiime/parallel/multiple_rarefactions.py
  82. +2 −2 qiime/parallel/pick_otus.py
  83. +2 −2 qiime/parallel/poller.py
  84. +2 −2 qiime/parallel/util.py
  85. +2 −2 qiime/parse.py
  86. +2 −2 qiime/pick_otus.py
  87. +2 −2 qiime/pick_rep_set.py
  88. +2 −2 qiime/pick_subsampled_reference_otus_through_otu_table.py
  89. +2 −2 qiime/plot_rank_abundance_graph.py
  90. +2 −2 qiime/plot_semivariogram.py
  91. +2 −2 qiime/plot_taxa_summary.py
  92. +2 −2 qiime/principal_coordinates.py
  93. +2 −2 qiime/process_sff.py
  94. +2 −2 qiime/pycogent_backports/__init__.py
  95. +2 −2 qiime/pycogent_backports/tax2tree.py
  96. +2 −2 qiime/quality.py
  97. +2 −2 qiime/quality_scores_plot.py
  98. +2 −2 qiime/rarefaction.py
  99. +2 −2 qiime/relatedness_library.py
  100. +2 −2 qiime/remote.py
  101. +2 −2 qiime/shared_phylotypes.py
  102. +2 −2 qiime/simsam.py
  103. +2 −2 qiime/sort.py
  104. +2 −2 qiime/split.py
  105. +2 −2 qiime/split_libraries.py
  106. +2 −2 qiime/split_libraries_fastq.py
  107. +2 −2 qiime/stats.py
  108. +2 −2 qiime/submit_to_mgrast.py
  109. +2 −2 qiime/summarize_taxa.py
  110. +2 −2 qiime/supervised_learning.py
  111. +2 −2 qiime/support_files/R/util.r
  112. +2 −2 qiime/support_files/js/otu_count_display.js
  113. +2 −2 qiime/support_files/qiime_config_n3phele
  114. +2 −2 qiime/support_files/test_js/test_otu_count_display.html
  115. +2 −2 qiime/test.py
  116. +2 −2 qiime/transform_coordinate_matrices.py
  117. +2 −2 qiime/tree_compare.py
  118. +2 −2 qiime/trim_sff_primers.py
  119. +2 −2 qiime/truncate_fasta_qual_files.py
  120. +2 −2 qiime/truncate_reverse_primer.py
  121. +2 −2 qiime/util.py
  122. +2 −2 qiime/validate_demultiplexed_fasta.py
  123. +2 −2 qiime/workflow.py
  124. +2 −2 scripts/add_alpha_to_mapping_file.py
  125. +2 −2 scripts/add_qiime_labels.py
  126. +2 −2 scripts/add_taxa.py
  127. +2 −2 scripts/adjust_seq_orientation.py
  128. +2 −2 scripts/align_seqs.py
  129. +2 −2 scripts/alpha_diversity.py
  130. +2 −2 scripts/alpha_rarefaction.py
  131. +2 −2 scripts/ampliconnoise.py
  132. +2 −2 scripts/assign_taxonomy.py
  133. +2 −2 scripts/beta_diversity.py
  134. +2 −2 scripts/beta_diversity_through_plots.py
  135. +2 −2 scripts/beta_significance.py
  136. +2 −2 scripts/blast_wrapper.py
  137. +2 −2 scripts/categorized_dist_scatterplot.py
  138. +2 −2 scripts/check_id_map.py
  139. +2 −2 scripts/clean_raxml_parsimony_tree.py
  140. +2 −2 scripts/cluster_quality.py
  141. +2 −2 scripts/collate_alpha.py
  142. +2 −2 scripts/compare_3d_plots.py
  143. +2 −2 scripts/compare_alpha_diversity.py
  144. +2 −2 scripts/compare_categories.py
  145. +2 −2 scripts/compare_distance_matrices.py
  146. +2 −2 scripts/compare_taxa_summaries.py
  147. +2 −2 scripts/compute_core_microbiome.py
  148. +2 −2 scripts/conditional_uncovered_probability.py
  149. +2 −2 scripts/consensus_tree.py
  150. +2 −2 scripts/convert_fastaqual_fastq.py
  151. +2 −2 scripts/convert_otu_table_to_unifrac_sample_mapping.py
  152. +2 −2 scripts/convert_unifrac_sample_mapping_to_otu_table.py
  153. +2 −2 scripts/core_qiime_analyses.py
  154. +2 −2 scripts/count_seqs.py
  155. +2 −2 scripts/demultiplex_fasta.py
  156. +2 −2 scripts/denoise_wrapper.py
  157. +2 −2 scripts/denoiser.py
  158. +2 −2 scripts/denoiser_preprocess.py
  159. +2 −2 scripts/denoiser_worker.py
  160. +2 −2 scripts/detrend.py
  161. +2 −2 scripts/dissimilarity_mtx_stats.py
  162. +2 −2 scripts/distance_matrix_from_mapping.py
  163. +2 −2 scripts/exclude_seqs_by_blast.py
  164. +2 −2 scripts/extract_seqs_by_sample_id.py
  165. +2 −2 scripts/filter_alignment.py
  166. +2 −2 scripts/filter_distance_matrix.py
  167. +2 −2 scripts/filter_fasta.py
  168. +2 −2 scripts/filter_otus_by_sample.py
  169. +2 −2 scripts/filter_otus_from_otu_table.py
  170. +2 −2 scripts/filter_samples_from_otu_table.py
  171. +2 −2 scripts/filter_taxa_from_otu_table.py
  172. +2 −2 scripts/filter_tree.py
  173. +2 −2 scripts/fix_arb_fasta.py
  174. +2 −2 scripts/identify_chimeric_seqs.py
  175. +2 −2 scripts/identify_missing_files.py
  176. +2 −2 scripts/inflate_denoiser_output.py
  177. +2 −2 scripts/insert_seqs_into_tree.py
  178. +2 −2 scripts/jackknifed_beta_diversity.py
  179. +2 −2 scripts/load_remote_mapping_file.py
  180. +2 −2 scripts/make_2d_plots.py
  181. +2 −2 scripts/make_3d_plots.py
  182. +2 −2 scripts/make_bootstrapped_tree.py
  183. +2 −2 scripts/make_distance_boxplots.py
  184. +2 −2 scripts/make_distance_comparison_plots.py
  185. +2 −2 scripts/make_distance_histograms.py
  186. +2 −2 scripts/make_fastq.py
  187. +2 −2 scripts/make_library_id_lists.py
  188. +2 −2 scripts/make_otu_heatmap.py
  189. +2 −2 scripts/make_otu_heatmap_html.py
  190. +2 −2 scripts/make_otu_network.py
  191. +2 −2 scripts/make_otu_table.py
  192. +2 −2 scripts/make_per_library_sff.py
  193. +2 −2 scripts/make_phylogeny.py
  194. +2 −2 scripts/make_prefs_file.py
  195. +4 −4 scripts/make_qiime_py_file.py
  196. +2 −2 scripts/make_qiime_rst_file.py
  197. +2 −2 scripts/make_rarefaction_plots.py
  198. +2 −2 scripts/make_tep.py
  199. +2 −2 scripts/map_reads_to_reference.py
  200. +2 −2 scripts/merge_mapping_files.py
  201. +2 −2 scripts/merge_otu_maps.py
  202. +2 −2 scripts/merge_otu_tables.py
  203. +2 −2 scripts/multiple_rarefactions.py
  204. +2 −2 scripts/multiple_rarefactions_even_depth.py
  205. +2 −2 scripts/neighbor_joining.py
  206. +2 −2 scripts/nmds.py
  207. +2 −2 scripts/otu_category_significance.py
  208. +2 −2 scripts/parallel_align_seqs_pynast.py
  209. +2 −2 scripts/parallel_alpha_diversity.py
  210. +2 −2 scripts/parallel_assign_taxonomy_blast.py
  211. +2 −2 scripts/parallel_assign_taxonomy_rdp.py
  212. +2 −2 scripts/parallel_beta_diversity.py
  213. +2 −2 scripts/parallel_blast.py
  214. +2 −2 scripts/parallel_identify_chimeric_seqs.py
  215. +2 −2 scripts/parallel_map_reads_to_reference.py
  216. +2 −2 scripts/parallel_multiple_rarefactions.py
  217. +2 −2 scripts/parallel_pick_otus_blast.py
  218. +2 −2 scripts/parallel_pick_otus_trie.py
  219. +2 −2 scripts/parallel_pick_otus_uclust_ref.py
  220. +2 −2 scripts/per_library_stats.py
  221. +2 −2 scripts/pick_otus.py
  222. +2 −2 scripts/pick_otus_through_otu_table.py
  223. +2 −2 scripts/pick_reference_otus_through_otu_table.py
  224. +2 −2 scripts/pick_rep_set.py
  225. +2 −2 scripts/pick_subsampled_reference_otus_through_otu_table.py
  226. +2 −2 scripts/plot_rank_abundance_graph.py
  227. +2 −2 scripts/plot_semivariogram.py
  228. +2 −2 scripts/plot_taxa_summary.py
  229. +2 −2 scripts/poller.py
  230. +2 −2 scripts/poller_example.py
  231. +2 −2 scripts/principal_coordinates.py
  232. +2 −2 scripts/print_qiime_config.py
  233. +2 −2 scripts/process_iseq.py
  234. +2 −2 scripts/process_qseq.py
  235. +2 −2 scripts/process_sff.py
  236. +2 −2 scripts/quality_scores_plot.py
  237. +2 −2 scripts/relatedness.py
  238. +2 −2 scripts/shared_phylotypes.py
  239. +2 −2 scripts/simsam.py
  240. +2 −2 scripts/single_rarefaction.py
  241. +2 −2 scripts/sort_otu_table.py
  242. +2 −2 scripts/split_fasta_on_sample_ids.py
  243. +2 −2 scripts/split_libraries.py
  244. +2 −2 scripts/split_libraries_fastq.py
  245. +2 −2 scripts/split_otu_table.py
  246. +2 −2 scripts/split_otu_table_by_taxonomy.py
  247. +2 −2 scripts/start_parallel_jobs.py
  248. +2 −2 scripts/start_parallel_jobs_sc.py
  249. +2 −2 scripts/start_parallel_jobs_torque.py
  250. +2 −2 scripts/submit_to_mgrast.py
  251. +2 −2 scripts/subsample_fasta.py
  252. +2 −2 scripts/summarize_otu_by_cat.py
  253. +2 −2 scripts/summarize_taxa.py
  254. +2 −2 scripts/summarize_taxa_through_plots.py
  255. +2 −2 scripts/supervised_learning.py
  256. +2 −2 scripts/transform_coordinate_matrices.py
  257. +2 −2 scripts/tree_compare.py
  258. +2 −2 scripts/trflp_file_to_otu_table.py
  259. +2 −2 scripts/trim_sff_primers.py
  260. +2 −2 scripts/truncate_fasta_qual_files.py
  261. +2 −2 scripts/truncate_reverse_primer.py
  262. +2 −2 scripts/unweight_fasta.py
  263. +2 −2 scripts/upgma_cluster.py
  264. +2 −2 scripts/validate_demultiplexed_fasta.py
  265. +2 −2 setup.py
  266. +2 −2 tests/__init__.py
  267. +2 −2 tests/all_tests.py
  268. +2 −2 tests/test_add_alpha_to_mapping_file.py
  269. +2 −2 tests/test_add_qiime_labels.py
  270. +2 −2 tests/test_adjust_seq_orientation.py
  271. +2 −2 tests/test_align_seqs.py
  272. +2 −2 tests/test_alpha_diversity.py
  273. +2 −2 tests/test_assign_taxonomy.py
  274. +2 −2 tests/test_barcode.py
  275. +2 −2 tests/test_beta_diversity.py
  276. +2 −2 tests/test_beta_metrics.py
  277. +2 −2 tests/test_biplots.py
  278. +2 −2 tests/test_categorized_dist_scatterplot.py
  279. +2 −2 tests/test_check_id_map.py
  280. +2 −2 tests/test_clean_raxml_parsimony_tree.py
  281. +2 −2 tests/test_cluster_quality.py
  282. +2 −2 tests/test_collate_alpha.py
  283. +2 −2 tests/test_colors.py
  284. +2 −2 tests/test_compare_alpha_diversity.py
  285. +2 −2 tests/test_compare_categories.py
  286. +2 −2 tests/test_compare_distance_matrices.py
  287. +2 −2 tests/test_compare_taxa_summaries.py
  288. +2 −2 tests/test_convert_fastaqual_fastq.py
  289. +2 −2 tests/test_core_microbiome.py
  290. +2 −2 tests/test_demultiplex_fasta.py
  291. +2 −2 tests/test_denoise_wrapper.py
  292. +2 −2 tests/test_denoiser/test_cluster_util.py
  293. +2 −2 tests/test_denoiser/test_denoise_postprocess.py
  294. +2 −2 tests/test_denoiser/test_denoiser.py
  295. +2 −2 tests/test_denoiser/test_flowgram_clustering.py
  296. +2 −2 tests/test_denoiser/test_flowgram_filter.py
  297. +2 −2 tests/test_denoiser/test_make_cluster_jobs.py
  298. +2 −2 tests/test_denoiser/test_preprocess.py
  299. +2 −2 tests/test_denoiser/test_settings.py
  300. +2 −2 tests/test_denoiser/test_utils.py
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2  README
@@ -10,7 +10,7 @@ The definitive source for information on QIIME is the QIIME website at `http://w
Dependencies
------------
-QIIME requires Python_ 2.7, Numpy_ 1.5.1, and PyCogent_ 1.5.1.
+QIIME requires Python_ 2.7.3, Numpy_ 1.5.1, and PyCogent_ 1.5.3.
Required
^^^^^^^^
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4 doc/conf.py
@@ -45,9 +45,9 @@
# built documents.
#
# The short X.Y version.
-version = '1.5.0-dev'
+version = '1.6.0'
# The full version, including alpha/beta/rc tags.
-release = '1.5.0-dev'
+release = '1.6.0'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
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2  doc/index.rst
@@ -26,7 +26,7 @@ Download QIIME
* Virtual Box: The QIIME Virtual Box is an Ubuntu Linux virtual machine, pre-loaded with QIIME and its dependencies. This is the quickest way to start using QIIME. To get the Virtual Box, please `see Virtual Box documentation <./install/virtual_box.html>`_.
- * Stable Release: Currently the most stable version of QIIME is our |release| release, which you can `download here <https://github.com/downloads/qiime/qiime/Qiime-1.5.0.tar.gz>`_.
+ * Stable Release: Currently the most stable version of QIIME is our |release| release, which you can `download here <https://github.com/downloads/qiime/qiime/Qiime-1.6.0.tar.gz>`_.
* Development Version: QIIME is under very active development. To get the latest development version of QIIME, you access our git repository, which is hosted on GitHub. While this code is subject to minor changes in interface, it will provide access to the latest and greatest features. The official web documentation is likely to be out-of-date with respect to the development software. You should instead refer to the documentation in Qiime/doc. Check out the latest version of QIIME using git with the command::
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6 doc/install/install.rst
@@ -110,7 +110,7 @@ First, change to the directory where you would like to download QIIME::
Stable Release
^^^^^^^^^^^^^^
-Currently the most stable version of QIIME is our |release| release, which you can download from `here <https://github.com/downloads/qiime/qiime/Qiime-1.5.0.tar.gz>`_.
+Currently the most stable version of QIIME is our |release| release, which you can download from `here <https://github.com/downloads/qiime/qiime/Qiime-1.6.0.tar.gz>`_.
Latest Development Version
^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -129,8 +129,8 @@ After downloading the QIIME release tar file you'll need to unpack the code. For
Unpack the release Qiime tar file with the commands::
cd /home/qiime_user
- tar -xvzf Qiime-1.5.0.tar.gz
- ln -s /home/qiime/Qiime-1.5.0 /home/qiime/Qiime
+ tar -xvzf Qiime-1.6.0.tar.gz
+ ln -s /home/qiime/Qiime-1.6.0 /home/qiime/Qiime
If you have downloaded the development version from GitHub, QIIME is already unpacked.
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2  doc/install/upgrade.rst
@@ -4,7 +4,7 @@ Upgrading to the latest version of QIIME
========================================
This page documents how to install a new version of QIIME from an installation of the previous version. It should also be possible to follow the steps to upgrade from older versions to the most recent version, but it's best to review all steps in that case to ensure that you won't be performing unnecessary steps.
-For a detailed history of the most notable changes between versions see the `QIIME ChangeLog <https://github.com/qiime/qiime/blob/master/ChangeLog>`_. This points to the most recent version, so will usually also give a preview of the changes that are coming in the next version of QIIME.
+For a detailed history of the most notable changes between versions see the `QIIME ChangeLog <https://github.com/qiime/qiime/blob/master/ChangeLog.md>`_. This points to the most recent version, so will usually also give a preview of the changes that are coming in the next version of QIIME.
1.5.0 to 1.5.0-dev (Linux)
--------------------------
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2  doc/install/virtual_box.rst
@@ -90,5 +90,5 @@ If this doesn't work, you might need to instead hit F9 to enter the BIOS. See th
Briefly, on booting the system, hit F9. Enter Advanced Options -> Processor Options -> Intel(R) Virtualization Technology and then hit Enable.
.. _CloVR: http://clovr.org
-.. _64-bit QIIME Virtual Box: ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/QIIME-1.5.0-amd64.vdi.gz
+.. _64-bit QIIME Virtual Box: ftp://thebeast.colorado.edu/pub/QIIME-v1.6.0-dependencies/QIIME-1.6.0-amd64.vdi.gz
.. _VirtualBox: http://www.virtualbox.org/wiki/Downloads
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4 qiime/__init__.py
@@ -4,10 +4,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Rob Knight", "Greg Caporaso", "Jeremy Widmann", "Kyle Bittinger", "Justin Kuczynski", "William Walters", "Jesse Zaneveld", "Dan Knights", "Jesse Stombaugh", "Micah Hamady", "Julia Goodrich", "Meg Pirrung", "Jens Reeder", "Daniel McDonald", "Catherine Lozupone"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
__all__ = ['align_seqs',
'alpha_diversity',
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4 qiime/add_alpha_to_mapping_file.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Yoshiki Vazquez-Baeza", "Antonio Gonzalez-Pena"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Yoshiki Vazquez-Baeza"
__email__ = "yoshiki89@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from copy import deepcopy
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4 qiime/add_qiime_labels.py
@@ -5,10 +5,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
from os.path import join, basename
from glob import glob
View
4 qiime/adjust_seq_orientation.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso", "Antonio Gonzalez Pena"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from os.path import split, splitext
from cogent.parse.fasta import MinimalFastaParser
View
4 qiime/align_seqs.py
@@ -4,10 +4,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Rob Knight", "Greg Caporaso", "Jeremy Widmann", "Kyle Bittinger"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""Contains code for aligning sequences, using several techniques.
View
4 qiime/alpha_diversity.py
@@ -5,10 +5,10 @@
__credits__ = ["Justin Kuczynski", "Rob Knight", "Greg Caporaso",
"William Van Treuren"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""Contains code for performing alpha diversity analyses within each sample.
View
4 qiime/assign_taxonomy.py
@@ -5,10 +5,10 @@
__credits__ = ["Rob Knight", "Greg Caporaso", "Kyle Bittinger",
"Antonio Gonzalez Pena", "David Soergel", "Jai Ram Rideout"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
import logging
View
4 qiime/barcode.py
@@ -5,10 +5,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Justin Kuczynski"] #remember to add yourself
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""
provides functions, used to assign a possibly error-fraught DNA
View
4 qiime/beta_diversity.py
@@ -5,10 +5,10 @@
__credits__ = ["Justin Kuczynski", "Rob Knight", "Greg Caporaso",
"Jose Carlos Clemente Litran", "Jai Ram Rideout"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""Contains code for performing beta diversity analyses of different samples.
View
4 qiime/beta_metrics.py
@@ -4,10 +4,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Rob Knight", "Justin Kuczynski"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""contains metrics for use with beta_diversity.py
View
4 qiime/biplots.py
@@ -5,10 +5,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Dan Knights", "Justin Kuczynski"] #remember to add yourself
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Dan Knights"
__email__ = "daniel.knights@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
from qiime.parse import parse_otu_table
from numpy import array,apply_along_axis,dot,delete,argsort
View
4 qiime/categorized_dist_scatterplot.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Justin Kuczynski"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from qiime.parse import parse_metadata_state_descriptions
View
4 qiime/check_id_map.py
@@ -43,10 +43,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Rob Knight","William Walters"] #remember to add yourself
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "William Walters"
__email__ = "william.a.walters@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
from collections import defaultdict
from string import letters, digits, upper
View
4 qiime/clean_raxml_parsimony_tree.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Jesse Stombaugh"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jesse Stombaugh"
__email__ = "jesse.stombaugh@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
from random import choice
View
4 qiime/cluster_quality.py
@@ -4,10 +4,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Justin Kuczynski"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
""" computes cluster quality the default way, bet/within"""
def clust_qual_ratio(dists, map_data, category):
View
4 qiime/collate_alpha.py
@@ -4,10 +4,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Justin Kuczynski"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""takes as input alpha diveristy files, format:
file: one rarefaction depth/iteration
View
4 qiime/colors.py
@@ -5,10 +5,10 @@
__copyright__ = "Copyright 2011, The QIIME Project" #consider project name
__credits__ = ["Rob Knight","Jesse Stombaugh"] #remember to add yourself
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jesse Stombaugh"
__email__ = "jesse.stombaugh@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
"""Code for coloring series based on prefs file.
"""
View
4 qiime/compare_alpha_diversity.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["William Van Treuren", "Greg Caporaso", "Jai Ram Rideout"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "William Van Treuren"
__email__ = "vantreur@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
from numpy import array, isnan, min as np_min
from qiime.format import format_p_value_for_num_iters
View
4 qiime/compare_categories.py
@@ -6,10 +6,10 @@
__credits__ = ["Jai Ram Rideout", "Michael Dwan", "Logan Knecht",
"Damien Coy", "Levi McCracken"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jai Ram Rideout"
__email__ = "jai.rideout@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""Contains functions used in the compare_categories.py script."""
View
4 qiime/compare_distance_matrices.py
@@ -6,10 +6,10 @@
__credits__ = ["Jai Ram Rideout", "Michael Dwan", "Logan Knecht",
"Damien Coy", "Levi McCracken", "Greg Caporaso"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jai Ram Rideout"
__email__ = "jai.rideout@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""Contains functions used in the compare_distance_matrices.py script."""
View
4 qiime/compare_taxa_summaries.py
@@ -5,10 +5,10 @@
__copyright__ = "Copyright 2012, The QIIME project"
__credits__ = ["Jai Ram Rideout", "Greg Caporaso"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jai Ram Rideout"
__email__ = "jai.rideout@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""Contains functions used in the compare_taxa_summaries.py script."""
View
4 qiime/convert_fastaqual_fastq.py
@@ -4,10 +4,10 @@
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Adam Robbins-Pianka, Abhisaar Yadav"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Adam Robbins-Pianka"
__email__ = "adam.robbinspianka@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
# Reviewed by William Walters
View
4 qiime/core_microbiome.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso", "Jai Ram Rideout"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from numpy import array
from biom.exception import TableException
View
4 qiime/demultiplex_fasta.py
@@ -5,10 +5,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters", "Rob Knight", "Micah Hamady", "Greg Caporaso", "Kyle Bittinger","Jesse Stombaugh","Jens Reeder"] #remember to add yourself
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "William Walters"
__email__ = "william.a.walters@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
from string import upper
from itertools import izip
View
4 qiime/denoise_wrapper.py
@@ -7,10 +7,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jens Reeder", "Greg Caporaso"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from os import system, listdir, remove, rmdir
from os.path import exists, split
View
4 qiime/denoiser/__init__.py
@@ -4,10 +4,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jens Reeder", "Rob Knight"]#remember to add yourself if you make changes
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jens Reeder"
__email__ = "jens.reeder@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
__all__ = [\
'cluster_utils.py',
View
4 qiime/denoiser/cluster_utils.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jens Reeder", "Rob Knight", "Nigel Cook"]#remember to add yourself if you make changes
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jens Reeder"
__email__ = "jens.reeder@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from os import remove, system
from string import join, lowercase
View
4 qiime/denoiser/denoise_postprocess.py
@@ -4,10 +4,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jens Reeder", "Rob Knight"]#remember to add yourself if you make changes
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jens Reeder"
__email__ = "jens.reeder@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from optparse import OptionParser
from itertools import imap
View
4 qiime/denoiser/denoise_worker.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jens Reeder", "Rob Knight", "Nigel Cook"]#remember to add yourself if you make changes
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jens Reeder"
__email__ = "jens.reeder@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from os import remove, makedirs
from os.path import exists, split, dirname
View
4 qiime/denoiser/flowgram_clustering.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jens Reeder", "Rob Knight", "Nigel Cook"]#remember to add yourself if you make changes
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jens Reeder"
__email__ = "jens.reeder@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from os import remove, popen, makedirs, rename
from os.path import exists
View
4 qiime/denoiser/flowgram_filter.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jens Reeder", "Rob Knight", "Yoshiki Vazquez Baeza"]#remember to add yourself if you make changes
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jens Reeder"
__email__ = "jens.reeder@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from re import compile, search
from itertools import imap
View
4 qiime/denoiser/make_cluster_jobs.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jens Reeder", "Rob Knight"]#remember to add yourself if you make changes
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jens Reeder"
__email__ = "jens.reeder@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from os.path import exists
from os import remove, rename, rmdir, makedirs
View
4 qiime/denoiser/preprocess.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jens Reeder", "Rob Knight"]#remember to add yourself if you make changes
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jens Reeder"
__email__ = "jens.reeder@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from itertools import imap
from os import remove
View
4 qiime/denoiser/utils.py
@@ -7,10 +7,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jens Reeder", "Rob Knight", "Jai Ram Rideout"]#remember to add yourself if you make changes
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jens Reeder"
__email__ = "jens.reeder@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
import sys
from os import remove, makedirs, access, X_OK, R_OK
View
4 qiime/detrend.py
@@ -4,10 +4,10 @@
__copyright__ = "Copyright 2012, The QIIME Project"
__credits__ = ["Dan Knights"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Dan Knights"
__email__ = "danknights@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from os.path import split, splitext, join, exists
from os import remove
View
4 qiime/distance_matrix_from_mapping.py
@@ -7,10 +7,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Antonio Gonzalez Pena"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Antonio Gonzalez Pena"
__email__ = "antgonza@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""Contains code for performing distance matrix analyses of a column from a mapping file.
View
4 qiime/exclude_seqs_by_blast.py
@@ -15,10 +15,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jesse Zaneveld","Rob Knight"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jesse Zaneveld"
__email__ = "zaneveld@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
View
4 qiime/filter.py
@@ -7,10 +7,10 @@
__credits__ = ["Greg Caporaso", "Will Van Treuren", "Daniel McDonald",
"Jai Ram Rideout"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from collections import defaultdict
from random import shuffle, sample
View
4 qiime/filter_alignment.py
@@ -24,10 +24,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso", "Justin Kuczynski", "Dan Knights"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Dan Knights"
__email__ = "danknights@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""Contains code for filtering alignments before building trees from them
"""
View
4 qiime/filter_otus_by_sample.py
@@ -5,10 +5,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jesse Stombaugh"] #remember to add yourself
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jesse Stombaugh"
__email__ = "jesse.stombaugh@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
from string import strip
View
4 qiime/format.py
@@ -6,10 +6,10 @@
"Antonio Gonzalez Pena", "Daniel McDonald", "Jai Ram Rideout"]
#remember to add yourself if you make changes
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
import numpy
from numpy import isnan, log10, median
View
4 qiime/golay.py
@@ -5,10 +5,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Justin Kuczynski"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""
module provides golay encoding/decoding of DNA barcodes.
View
4 qiime/group.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Jai Ram Rideout", "Jeremy Widmann"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jai Ram Rideout"
__email__ = "jai.rideout@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from numpy import array
from cogent.maths.stats.test import is_symmetric_and_hollow
View
4 qiime/hamming.py
@@ -13,10 +13,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Micah Hamady", "Rob Knight"]#remember to add yourself if you make changes
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
# current encoding scheme
View
4 qiime/hierarchical_cluster.py
@@ -4,10 +4,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Justin Kuczynski"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""runs upgma or nj on a distance matrix file, writes the resulting tree
with distances to specified output file
View
4 qiime/identify_chimeric_seqs.py
@@ -23,10 +23,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso","Jens Reeder"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
#NOTE: The next ChimeraSlayer release will have an option to increase the number of
# iterations performed. Currently the hard coded default is 100, which leads to
View
4 qiime/insert_seqs_into_tree.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Jesse Stombaugh"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jesse Stombaugh"
__email__ = "jesse.stombaugh@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
from cogent.core.tree import PhyloNode
from cogent.parse.tree import DndParser
View
4 qiime/longitudinal_otu_category_significance.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Catherine Lozupone", "Jai Ram Rideout"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Catherine Lozupone"
__email__ = "lozupone@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
from collections import defaultdict
from numpy import zeros
View
4 qiime/make_2d_plots.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jesse Stombaugh", "Jose Antonio Navas Molina"] #remember to add yourself
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jesse Stombaugh"
__email__ = "jesse.stombaugh@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
import re
from matplotlib import use
View
4 qiime/make_3d_plots.py
@@ -6,10 +6,10 @@
__credits__ = ["Jesse Stombaugh", "Rob Knight", "Micah Hamady", "Dan Knights",\
"Antonio Gonzalez Pena", "Yoshiki Vazquez Baeza"] #remember to add yourself
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jesse Stombaugh"
__email__ = "jesse.stombaugh@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
import os
import re
View
4 qiime/make_bootstrapped_tree.py
@@ -4,10 +4,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Justin Kuczynski"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""takes a tree and bootstrap support file and writes a pdf, colored by
bootstrap support
View
4 qiime/make_distance_boxplots.py
@@ -5,10 +5,10 @@
__copyright__ = "Copyright 2012, The QIIME project"
__credits__ = ["Jai Ram Rideout"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jai Ram Rideout"
__email__ = "jai.rideout@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""Contains functions used in the make_distance_boxplots.py script."""
View
4 qiime/make_distance_histograms.py
@@ -6,10 +6,10 @@
__credits__ = ["Jeremy Widmann","Rob Knight","Jesse Stombaugh",
"Jai Ram Rideout"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jeremy Widmann"
__email__ = "jeremy.widmann@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
from matplotlib import use
use('Agg',warn=False)
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4 qiime/make_fastq.py
@@ -4,10 +4,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Rob Knight"] #remember to add yourself if you make changes
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Kyle Bittinger"
__email__ = "kylebittinger@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""Generates fastq file for ERA submission from paired fasta and qual files.
View
4 qiime/make_library_id_lists.py
@@ -10,10 +10,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Rob Knight"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Kyle Bittinger"
__email__ = "kylebittinger@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
def get_ids(lines, field, bad_ids=None, debug=False):
"""Make dict of lib:ids"""
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4 qiime/make_otu_heatmap.py
@@ -7,10 +7,10 @@
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Dan Knights"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Dan Knights"
__email__ = "daniel.knights@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
from numpy import array,concatenate,asarray,transpose,log,invert,asarray,\
View
4 qiime/make_otu_heatmap_html.py
@@ -7,10 +7,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jesse Stombaugh", "Jose Carlos Clemente Litran"] #remember to add yourself
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jesse Stombaugh"
__email__ = "jesse.stombaugh@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
from numpy import array,concatenate,asarray,transpose,log,invert,asarray,\
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4 qiime/make_otu_network.py
@@ -5,10 +5,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Julia Goodrich"] #remember to add yourself
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jose Clemente"
__email__ = "jose.clemente@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""
View
4 qiime/make_otu_table.py
@@ -4,10 +4,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Rob Knight", "Justin Kuczynski"] #remember to add yourself
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""Makes sample x OTU table from OTU map and taxonomy.
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4 qiime/make_per_library_sff.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Kyle Bittinger"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Kyle Bittinger"
__email__ = "kylebittinger@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
import itertools
import os
View
4 qiime/make_phylogeny.py
@@ -5,10 +5,10 @@
__credits__ = ["Rob Knight", "Justin Kuczynski", "Daniel McDonald",
"Jai Ram Rideout"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""Contains code for making a phylogeny from aligned sequences, using several techniques.
View
4 qiime/make_rarefaction_plots.py
@@ -5,10 +5,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Meg Pirrung", "Jesse Stombaugh", "Antonio Gonzalez Pena", "Will Van Treuren"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jesse Stombaugh"
__email__ = "jesse.stombaugh@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
from matplotlib import use
use('Agg',warn=False)
View
4 qiime/map_reads_to_reference.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from os.path import join, splitext, exists
from cogent.parse.blast import MinimalBlatParser9
View
4 qiime/merge_mapping_files.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from qiime.parse import parse_mapping_file
View
4 qiime/nmds.py
@@ -10,10 +10,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Justin Kuczynski"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
def nmds(file,dimensions=2):
View
4 qiime/otu_category_significance.py
@@ -7,10 +7,10 @@
__credits__ = ["Catherine Lozupone", "Jesse Stombaugh", "Dan Knights",
"Jai Ram Rideout"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Catherine Lozupone"
__email__ = "lozupone@colorado.edu"
-__status__ = "Development"
+__status__ = "Release"
from optparse import OptionParser
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4 qiime/parallel/__init__.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Rob Knight", "Greg Caporaso", "Jeremy Widmann", "Kyle Bittinger", "Justin Kuczynski", "William Walters", "Jesse Zaneveld", "Dan Knights", "Jesse Stombaugh", "Micah Hamady", "Julia Goodrich", "Meg Pirrung", "Jens Reeder", "Daniel McDonald", "Catherine Lozupone"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
__all__ = ['parallel_rdp',\
'util']
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4 qiime/parallel/align_seqs.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from cogent.app.formatdb import build_blast_db_from_fasta_path
from qiime.align_seqs import compute_min_alignment_length
View
4 qiime/parallel/alpha_diversity.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from os.path import join, split
from qiime.parallel.util import ParallelWrapper
View
4 qiime/parallel/assign_taxonomy.py
@@ -5,10 +5,10 @@
__copyright__ = "Copyright 2012, The QIIME project"
__credits__ = ["Jai Ram Rideout"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jai Ram Rideout"
__email__ = "jai.rideout@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from cogent.app.formatdb import build_blast_db_from_fasta_path
from qiime.parallel.util import ParallelWrapper
View
4 qiime/parallel/beta_diversity.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from os.path import join, split, splitext
from cogent.util.misc import create_dir
View
4 qiime/parallel/blast.py
@@ -5,10 +5,10 @@
__copyright__ = "Copyright 2012, The QIIME project"
__credits__ = ["Jai Ram Rideout"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jai Ram Rideout"
__email__ = "jai.rideout@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from os.path import split, splitext
from cogent.app.formatdb import build_blast_db_from_fasta_path
View
4 qiime/parallel/identify_chimeric_seqs.py
@@ -5,10 +5,10 @@
__copyright__ = "Copyright 2012, The QIIME project"
__credits__ = ["Jai Ram Rideout"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Jai Ram Rideout"
__email__ = "jai.rideout@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from os.path import split
from shutil import copy
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4 qiime/parallel/map_reads_to_reference.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from os.path import join
from qiime.make_otu_table import make_otu_table
View
4 qiime/parallel/multiple_rarefactions.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from qiime.parallel.util import ParallelWrapper
View
4 qiime/parallel/pick_otus.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso", "Jens Reeder"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from cogent.app.formatdb import build_blast_db_from_fasta_path
from qiime.parallel.util import ParallelWrapper, BufferedWriter
View
4 qiime/parallel/poller.py
@@ -13,10 +13,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
def get_function_handle(s):
last_dot = s.rindex('.')
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4 qiime/parallel/util.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso", "Jens Reeder", "Jai Ram Rideout"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from math import ceil
from os.path import split, splitext, join
View
4 qiime/parse.py
@@ -7,10 +7,10 @@
"Justin Kuczynski", "Cathy Lozupone", "Jens Reeder",
"Antonio Gonzalez Pena", "Jai Ram Rideout"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from string import strip
from collections import defaultdict
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4 qiime/pick_otus.py
@@ -3,10 +3,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Rob Knight","Greg Caporaso", "Kyle Bittinger","Jens Reeder", "William Walters", "Jose Carlos Clemente Litran", "Adam Robbins-Pianka"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""Contains code for OTU picking, using several techniques.
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4 qiime/pick_rep_set.py
@@ -4,10 +4,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Rob Knight","Greg Caporaso", "Kyle Bittinger"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Daniel McDonald"
__email__ = "wasade@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
"""Contains code for picking representative set of seqs, several techniques.
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4 qiime/pick_subsampled_reference_otus_through_otu_table.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from os import makedirs
from os.path import split, splitext, getsize, exists
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4 qiime/plot_rank_abundance_graph.py
@@ -6,10 +6,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jens Reeder"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
from matplotlib import use
use('Agg',warn=False)
View
4 qiime/plot_semivariogram.py
@@ -10,10 +10,10 @@
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Antonio Gonzalez Pena"]
__license__ = "GPL"
-__version__ = "1.5.0-dev"
+__version__ = "1.6.0"
__maintainer__ = "Antonio Gonzalez Pena"
__email__ = "antgonza@gmail.com"
-__status__ = "Development"
+__status__ = "Release"
class FitModel(object):
"""This class defines the available models and their functions for a
View
4 qiime/plot_taxa_summary.py