GitHub stats (generated with Matplotlib's github_stats.py) for 2012/12/18 - 2013/05/14 (tag: 1.6.0)
These lists are automatically generated, and may be incomplete or contain duplicates.
The following 21 authors contributed 988 commits.
- Adam Robbins-Pianka
- Antonio Gonzalez
- Catherine Lozupone
- Dan Knights
- Daniel McDonald
- Greg Caporaso
- Jai Ram Rideout
- Jose Carlos Clemente
- Jose Navas
- Justin Kuczynski
- Kyle Bittinger
- Luke Ursell
- Meg Pirrung
- Tony Walters
- William Van Treuren
- Yoshiki Vázquez Baeza
- johnjohnchase
- kpatnode
- paulomat
- zachcp
- zech
We closed a total of 487 issues, 159 pull requests and 328 regular issues; this is the full list:
Pull Requests (159):
- :ghpull:
962: updated for 1.7.0 - :ghpull:
961: added note on usearch61 - :ghpull:
960: updated automated script documentation - :ghpull:
943: Added usearch61 chimera checking (denovo and ref) to identify_chimeric_s... - :ghpull:
913: Fixing illumina quality chars to return only printable chars - :ghpull:
954: compare_alpha_diversity.py improvements - :ghpull:
952: Issue 808 - :ghpull:
955: Issue 112 - :ghpull:
953: updated to correctly handle zero otus in the core - :ghpull:
951: Issue 885 - :ghpull:
945: completed otu picking "tutorial" - :ghpull:
947: otu_cateogry_significance.py warnings now suppressed - :ghpull:
948: Fixed read-only permissions in tests. - :ghpull:
938: update qiime config parser to expand env variables - :ghpull:
939: Fix input_fps option type for count_seqs.py - :ghpull:
942: Remove deprecated options in split_otu_table.py - :ghpull:
940: Fixes issue 289 - :ghpull:
896: Update denoise_wrapper.py - :ghpull:
925: Update the blast_db option type across all QIIME scripts - :ghpull:
930: Retrieve qiime_scripts_dir on the fly - :ghpull:
917: Fixes Issue 779 - :ghpull:
936: Multiple corrections to the docs - :ghpull:
923: fixes #705 - :ghpull:
932: split_libraries.py disallows -s without -q. - :ghpull:
934: fixes issue #773 - :ghpull:
933: Inline comments in parameters files now ignored. - :ghpull:
935: Issue313 - :ghpull:
931: tutorial updates - :ghpull:
928: Pick otus desc usearchqf - :ghpull:
926: load_remote_mapping_file.py now handles headers with leading digits. - :ghpull:
922: summarize_taxa.py provides an informative error message on no obs metadata - :ghpull:
929: Reworded script text to (hopefully) be clearer. - :ghpull:
916: Modified pycogent_backports/usearch.py to correctly pass HALT_EXEC for u... - :ghpull:
924: Check id map columns - :ghpull:
921: Fixes issue #903 - :ghpull:
912: Adding new option 'blast_db' and fixing parallel_blast.py - :ghpull:
915: fixes #764 - :ghpull:
821: Fixing ci_type and metrics option type of... - :ghpull:
910: Alternative hypothesis is now explicitly stated. - :ghpull:
898: Remove std dev reporting for LOO error estimates in supervised learning, fixes issue #798 - :ghpull:
909: RExecutor tests now respect qiime temp dir. - :ghpull:
911: summarize_taxa.py now writes output tables in BIOM and TSV formats. - :ghpull:
906: compare_categories.py now respects QIIME temp dir. - :ghpull:
901: Added support for non-diagonal zeros in Moran's I. - :ghpull:
900: File handles are now properly closed. - :ghpull:
880: some edits on top of @johnchase's SourceTracker tutorial - :ghpull:
875: new: make_bipartite_network.py - :ghpull:
893: increased max acceptable p-value to reduce freq of stochastic test failures - :ghpull:
892: officially removed per_library_stats.py in favor of print_biom_table_summary.py - :ghpull:
882: Change -o option type for cluster_quality.py - :ghpull:
890: added function write small test data set files to output_dir - :ghpull:
840: Add descriptive error to add_alpha_to_mapping_file - :ghpull:
879: fixed failure on metadata category with spaces - :ghpull:
877: Doc edits - :ghpull:
873: Addd --output_fp option to relatedness.py - :ghpull:
872: Add option to save the output of fix_arb_fasta.py - :ghpull:
871: Add --output_fp to print_metadata_stats.py - :ghpull:
775: changed {} to None as default function parameters and more - :ghpull:
867: Add taxonomy as a valid string - :ghpull:
870: Modified qiime/pick_otus.py so reference based OTU picking (usearch 5.X ... - :ghpull:
869: addresses one of the stochastic failures noted in #864 - :ghpull:
848: addition of usearch 6.1 wrappers for otu picking and renaming of qiime otu picking workflows - :ghpull:
855: A few fixes to qiime_test_data stuff - :ghpull:
841: Adding plot_stderr_and_stddev in run_alpha_rarefaction - :ghpull:
846: Minor fixes to make_distance_comparison_plots.py - :ghpull:
842: Removed link to svn_documentation. - :ghpull:
815: Fixing option types and example definition - :ghpull:
820: Fixing --metrics option type for beta_diversity.py - :ghpull:
822: Fixing scaling_method and vectors_algorithm option types for ... - :ghpull:
823: Fixing metrics option type of parallel_alpha_diversity.py - :ghpull:
835: Fixing metrics option of parallel_beta_diversity.py - :ghpull:
836: Fixing chart_type option type for plot_taxa_summary - :ghpull:
837: Fixing methods option type for relatedness.py - :ghpull:
838: Fixing input_dir option type for process_qseq.py - :ghpull:
832: updated to address #831 - :ghpull:
814: Fixing option types for jackknifed_beta_diversity.py - :ghpull:
816: Fixing --sort_by option type of pick_rep_set.py - :ghpull:
818: Fixing --dir-prefix option type of split_libraries.py - :ghpull:
819: Fixing --truncate_option option type for truncate_reverse_primer.py - :ghpull:
828: Upped timeouts of some workflow tests. - :ghpull:
826: fixed supervised_learning.py script test failure - :ghpull:
824: merge qiime_test_data into qiime - :ghpull:
812: Fixes issue #811 - :ghpull:
734: New option type - 'multiple_choice' - :ghpull:
800: Fixing --tree_fp option type - :ghpull:
807: supervised_learning.py handles input directories - :ghpull:
795: Increased number of stochastic p-value trials. - :ghpull:
782: Otu category significance - :ghpull:
801: Fixing --metric option type of cluster_quality.py - :ghpull:
802: Fixing --coord_fnames and --background_color option types for ... - :ghpull:
803: Fixing --conversion_type option type for convert_fastaqual_fastq.py - :ghpull:
804: Fixing option types for demultiplex_fasta.py - :ghpull:
805: Fixing --map_fname option type in denoise_wrapper.py - :ghpull:
806: Fixing --output_fasta_fp option type for extract_seqs_by_sample_id.py - :ghpull:
797: New OTUs' metadata are now handled correctly. - :ghpull:
793: simsam.py now handles superset mapping file. - :ghpull:
792: addresses #789 - :ghpull:
786: Added -m/--mapping_fp option to simsam.py - :ghpull:
771: reverting #659 - this isn't actually working for me - :ghpull:
770: updated to use default depth for compare_alpha_diversity.py - :ghpull:
659: Update collate_alpha.py to avoid directories - :ghpull:
740: Added support for plotting empty distributions in box plots. - :ghpull:
767: fixes #766 - :ghpull:
763: added flags to suppress different analysis types - :ghpull:
761: Removed make_cluster_jobs.py test. - :ghpull:
733: Quick fixes - :ghpull:
753: Checking in tests fix for te 1.0 - :ghpull:
759: Solves issue #758 -- a truly monumental commit - :ghpull:
741: Fixes issue #711 - :ghpull:
736: Change read mode for parameter files -- issue 727 - :ghpull:
742: Fixed performance bug in make_otu_heatmap_html.py. - :ghpull:
730: partially addresses #688 - :ghpull:
721: Fixing the option types for ampliconnoise.py - :ghpull:
720: Ported mc_t_two_sample fix from PyCogent. - :ghpull:
715: Use 'choice' option type for --binning_method - :ghpull:
680: Fixes #672, explicitly checks type of opts.input_dir - :ghpull:
661: Convert fastaqual fastq - :ghpull:
714: major refactoring of workflow tests and organization of workflow code - :ghpull:
647: Modifying exclude_seqs_by_blast.py in order to store the output... - :ghpull:
704: Changed timeout from 120 to 240 seconds. - :ghpull:
696: Add note to the coding guidelines - :ghpull:
692: Fixing issue #685 - :ghpull:
687: a complete refactoring and renaming of core_qiime_analyses.py (now core_diversity_analyses.py) - :ghpull:
689: Resolves issue #686. - :ghpull:
683: Fix issue #677 - :ghpull:
681: Modified a single line in parse_classic_otu_table to allow it to correct... - :ghpull:
682: fixing issue #676. beta_diversity.py -r now only warns when run on samples with no data - :ghpull:
675: Fixed changes for TE 1.0 - :ghpull:
671: Modified pick_otus.py and usearch.py to allow modulation of reverse stra... - :ghpull:
667: getResults now uses the BIOM table API more effectively - :ghpull:
665: Extract adjacent distances from distance matrix - :ghpull:
651: Relatedness speedup - :ghpull:
664: updated links that were to svn version of documentation. - :ghpull:
654: update denoising_454 tutorial - :ghpull:
655: Updated to reference biom-format 1.1.2. - :ghpull:
577: Modified add_qiime_labels.py script to use a standard metadata mapping f... - :ghpull:
630: Further improvements to timeseries filtering. - :ghpull:
645: Update doc/scripts/beta_diversity_metrics.rst - :ghpull:
649: use BIOM Table API instead of per-element lookups - :ghpull:
627: Added support for variable-size distance classes in Mantel correlogram. - :ghpull:
609: Add is_valid_git_refname and is_valid_git_sha1 - :ghpull:
612: Modified the compare_alpha_diversity library, script, and tests to resol... - :ghpull:
606: Backported changes to rdp_classifier.py in PyCogent - :ghpull:
607: Fixing error with distance_matrix_from_mapping.py in Clout - :ghpull:
602: Adding functionality to calculate linear distance from Latitude/Longitude point - :ghpull:
596: Collated alpha map - :ghpull:
591: added sample_count_by_category - :ghpull:
589: 160dev update - updated all version information to 1.6.0-dev - :ghpull:
587: Updated version. - :ghpull:
586: Added .gitattributes. - :ghpull:
585: updated handling of nan to address test failure - :ghpull:
584: Updated version info for 1.6.0 release. - :ghpull:
581: updated version and status strings and references to the version... - :ghpull:
578: ChangeLog updated for QIIME 1.6.0 - :ghpull:
580: fix for issue #579 - :ghpull:
576: updated all script rst files for QIIME 1.6.0 - :ghpull:
575: Misc. fixes to compare_alpha_diversity.py. - :ghpull:
515: Compare alpha diversity.py - :ghpull:
573: Tutorial organization
Issues (328):
- :ghissue:
957: update/clean up change log - :ghissue:
962: updated for 1.7.0 - :ghissue:
959: update any necessary dependencies on install page - :ghissue:
958: generate script rst files - :ghissue:
961: added note on usearch61 - :ghissue:
960: updated automated script documentation - :ghissue:
629: '--barcode_qual_c' option from process_iseq.py breaks the XML file parser - :ghissue:
943: Added usearch61 chimera checking (denovo and ref) to identify_chimeric_s... - :ghissue:
913: Fixing illumina quality chars to return only printable chars - :ghissue:
954: compare_alpha_diversity.py improvements - :ghissue:
808: filtering document - :ghissue:
952: Issue 808 - :ghissue:
955: Issue 112 - :ghissue:
112: transform_coordinate_matrices.py - sample ID map option needs more extensive documentation - :ghissue:
944: Usearch61 chimera tutorial change1 - :ghissue:
600: map_reads_to_reference.py fails with uninformative error when not enough memory - :ghissue:
642: compute_core_microbiome.py fails in plotting step. - :ghissue:
953: updated to correctly handle zero otus in the core - :ghissue:
884: Compare alpha div improvement - :ghissue:
850: complete new otu_picking tutorial - :ghissue:
885: core_diversity_analysis.py qiime_test_data documentation error - :ghissue:
951: Issue 885 - :ghissue:
712: otu_category_significance.py prints warnings to stdout - :ghissue:
851: revise open reference otu picking workflow documentation - :ghissue:
945: completed otu picking "tutorial" - :ghissue:
946: Issue 885 - :ghissue:
947: otu_cateogry_significance.py warnings now suppressed - :ghissue:
703: test_convert_fastaqual_fastq.py permissions issue - :ghissue:
948: Fixed read-only permissions in tests. - :ghissue:
297: RDP assign_taxonomy wrapper skips seqs that are too short - :ghissue:
927: Ot ucat - :ghissue:
63: Tests for assign taxonomy produce awkward output if RDP classifier isn't present - :ghissue:
684: supervised_learning.py cannot handle all mapping files that check_id_map.py blesses - :ghissue:
673: pick_otus.py script documentation inconsistent for usearch/usearch_qf - :ghissue:
762: core_diversity_analyses fails on biom table without observation metadata - :ghissue:
639: Add note on setting cluster_jobs_fp to parallel documentation - :ghissue:
843: HALT_EXEC parameter to qiime.pick_otus.usearch_qf doesn't work - :ghissue:
908: documentation for open reference OTU picking needs to be updated - :ghissue:
406: pick_otus.py using uclust_ref misnames new cluster IDs - :ghissue:
313: replace /home/qiime with $HOME in install doc - :ghissue:
772: updates to illumina overview tutorial - :ghissue:
938: update qiime config parser to expand env variables - :ghissue:
632: Fix option types on qiime scripts for Galaxy integration - :ghissue:
939: Fix input_fps option type for count_seqs.py - :ghissue:
417: split_otu_table.py fail, option-c - :ghissue:
942: Remove deprecated options in split_otu_table.py - :ghissue:
937: qiime_config should support environment variables - :ghissue:
289: identify_chimeric_seqs.py path issue on some linux systems - :ghissue:
940: Fixes issue 289 - :ghissue:
773: Change -i to -m for the mapping file option in print_metadata_stats.py - :ghissue:
896: Update denoise_wrapper.py - :ghissue:
641: split_libraries allows for changes to sequences that denoiser can't follow - :ghissue:
925: Update the blast_db option type across all QIIME scripts - :ghissue:
881: all_tests.py output directory requirement and qiime_config requirement - :ghissue:
930: Retrieve qiime_scripts_dir on the fly - :ghissue:
700: pool_by_metadata.py - :ghissue:
779: filter_distance_matrix can give traceback - :ghissue:
917: Fixes Issue 779 - :ghissue:
724: Old link for ampliconnoise installation notes in print_qiime_config.py - :ghissue:
760: general documentation corrections - :ghissue:
707: misleading link in overview tutorial - :ghissue:
936: Multiple corrections to the docs - :ghissue:
705: jackknifed_beta_diveristy.py runs tree_compare.py on one too many trees - :ghissue:
923: fixes #705 - :ghissue:
876: split_libraries.py doesn't notify when passing min qual flag (-s) but no qual file - :ghissue:
932: split_libraries.py disallows -s without -q. - :ghissue:
934: fixes issue #773 - :ghissue:
738: qiime parameters doesn't accept comments after configuration line - :ghissue:
933: Inline comments in parameters files now ignored. - :ghissue:
935: Issue313 - :ghissue:
931: tutorial updates - :ghissue:
928: Pick otus desc usearchqf - :ghissue:
710: load_remote_mapping_file.py can't handle headers that start with numbers - :ghissue:
926: load_remote_mapping_file.py now handles headers with leading digits. - :ghissue:
219: summarize_taxa_through_plots.py - fails on OTU table containing samples with zero OTUs - :ghissue:
922: summarize_taxa.py provides an informative error message on no obs metadata - :ghissue:
929: Reworded script text to (hopefully) be clearer. - :ghissue:
907: Fix help text for filter_samples_from_otu_table.py - :ghissue:
916: Modified pycogent_backports/usearch.py to correctly pass HALT_EXEC for u... - :ghissue:
924: Check id map columns - :ghissue:
903: detrend.py fails when passing a PC file - :ghissue:
921: Fixes issue #903 - :ghissue:
10: choice option type with the append action should be used for passing metrics to scripts - :ghissue:
861: QIIME.org frontpage does not mention the qiime-deploy - :ghissue:
912: Adding new option 'blast_db' and fixing parallel_blast.py - :ghissue:
613: make_3d_plots.py with continuous coloring and scientific notation - :ghissue:
676: beta_diversity.py handles problematic samples different when running in one-versus-all v all-versus-all modes - :ghissue:
764: assign_taxonomy's -m flag doesn't mention tax2tree - :ghissue:
915: fixes #764 - :ghissue:
717: Outdated page needs to be removed from SVN documentation - :ghissue:
745: replace sphinx tutorials with IPython Notebook tutorials - :ghissue:
878: supervised_learning.py doesn't parse files correctly - :ghissue:
821: Fixing ci_type and metrics option type of... - :ghissue:
798: Std dev of error should be removed for LOO in supervised_learning.py - :ghissue:
839: pick_otus.py -m usearch_ref fails when -r is not an absolute path - :ghissue:
566: add_qiime_labels.py should be updated to use metadata mapping file - :ghissue:
891: Support for denoising, chimera checking etc. with core_qiime_analysis.py - :ghissue:
862: summarize_otu_by_cat.py - :ghissue:
904: detrend.py not working - :ghissue:
685: make_3d_plots.py produced an uninformative warning message "Warning: invalid value encountered in divide" - :ghissue:
657: one-tailed t-test output in make_distance_boxplots.py should contain additional description - :ghissue:
910: Alternative hypothesis is now explicitly stated. - :ghissue:
810: add check for SourceTracker to print_qiime_config.py - :ghissue:
898: Remove std dev reporting for LOO error estimates in supervised learning, fixes issue #798 - :ghissue:
909: RExecutor tests now respect qiime temp dir. - :ghissue:
163: taxonomy tables to biom format (confirm that these can go directly into VAMPS) - :ghissue:
911: summarize_taxa.py now writes output tables in BIOM and TSV formats. - :ghissue:
895: Add Emperor to Jenkins - :ghissue:
906: compare_categories.py now respects QIIME temp dir. - :ghissue:
901: Added support for non-diagonal zeros in Moran's I. - :ghissue:
899: simsam.py doesn't close file handles after writing - :ghissue:
900: File handles are now properly closed. - :ghissue:
880: some edits on top of @johnchase's SourceTracker tutorial - :ghissue:
787: test_downstream.py randomly fails - :ghissue:
875: new: make_bipartite_network.py - :ghissue:
893: increased max acceptable p-value to reduce freq of stochastic test failures - :ghissue:
592: port per_library_stats.py to biom-format - :ghissue:
892: officially removed per_library_stats.py in favor of print_biom_table_summary.py - :ghissue:
620: compare_alpha_diversity.py defaults to one-tailed t-test - :ghissue:
650: replace per_library_stats.py with biom version of this script - :ghissue:
789: define a simsam_range function - :ghissue:
868: usearch61_ref should create an empty failures file if there are no failures - :ghissue:
882: Change -o option type for cluster_quality.py - :ghissue:
890: added function write small test data set files to output_dir - :ghissue:
883: beta_diversity_through_plots.py not using mapping headers - :ghissue:
719: SourceTracker Turorial - :ghissue:
827: add_alpha_to_mapping_file.py gives uninformative error when --depth doesn't exist - :ghissue:
840: Add descriptive error to add_alpha_to_mapping_file - :ghissue:
864: stochastic failures from test_pick_open_reference_otus.py - :ghissue:
765: Summarize_taxonomy_through_plots fails with multiword metadata - :ghissue:
879: fixed failure on metadata category with spaces - :ghissue:
877: Doc edits - :ghissue:
873: Addd --output_fp option to relatedness.py - :ghissue:
872: Add option to save the output of fix_arb_fasta.py - :ghissue:
871: Add --output_fp to print_metadata_stats.py - :ghissue:
775: changed {} to None as default function parameters and more - :ghissue:
716: make_distance_boxplots.py should (optionally?) ignore empty distributions - :ghissue:
71: tests leaving processes behind - :ghissue:
863: make_distance_boxplot.py - :ghissue:
799: Jenkins randomly crashes - :ghissue:
866: parse_classic_otu_table will fail when header key is taxonomy - :ghissue:
867: Add taxonomy as a valid string - :ghissue:
870: Modified qiime/pick_otus.py so reference based OTU picking (usearch 5.X ... - :ghissue:
677: Biplots change the results based on how many OTUs you want to display - :ghissue:
869: addresses one of the stochastic failures noted in #864 - :ghissue:
732: parallel_map_reads_to_reference.py infinitely hangs if usearch isn't present - :ghissue:
785: subsampled open reference otu picking workflow should work with usearch - :ghissue:
833: pick_reference_otus_through_otu_table.py should work with usearch_ref - :ghissue:
708: proposed renaming of otu picking workflow scripts - :ghissue:
848: addition of usearch 6.1 wrappers for otu picking and renaming of qiime otu picking workflows - :ghissue:
610: Type of input_dir option in process_qseq.py is wrong - :ghissue:
853: run_script_usage_tests should order the scripts that it tests - :ghissue:
852: run_script_usage_tests still references qiime_test_data repository - :ghissue:
854: print_qiime_config.py shouldn't search for qiime_test_data_dir key - :ghissue:
855: A few fixes to qiime_test_data stuff - :ghissue:
811: qiime.split import error - :ghissue:
603: get_qiime_library_version bug with older git versions - :ghissue:
844: Added application controller framework for usearch6.1 (open and closed r... - :ghissue:
841: Adding plot_stderr_and_stddev in run_alpha_rarefaction - :ghissue:
846: Minor fixes to make_distance_comparison_plots.py - :ghissue:
831: update qiime.util to import option_parsing code from pycogent_backports - :ghissue:
830: Remove svn_documentation from QIIME website? - :ghissue:
842: Removed link to svn_documentation. - :ghissue:
815: Fixing option types and example definition - :ghissue:
820: Fixing --metrics option type for beta_diversity.py - :ghissue:
822: Fixing scaling_method and vectors_algorithm option types for ... - :ghissue:
823: Fixing metrics option type of parallel_alpha_diversity.py - :ghissue:
835: Fixing metrics option of parallel_beta_diversity.py - :ghissue:
836: Fixing chart_type option type for plot_taxa_summary - :ghissue:
837: Fixing methods option type for relatedness.py - :ghissue:
838: Fixing input_dir option type for process_qseq.py - :ghissue:
832: updated to address #831 - :ghissue:
814: Fixing option types for jackknifed_beta_diversity.py - :ghissue:
816: Fixing --sort_by option type of pick_rep_set.py - :ghissue:
818: Fixing --dir-prefix option type of split_libraries.py - :ghissue:
819: Fixing --truncate_option option type for truncate_reverse_primer.py - :ghissue:
828: Upped timeouts of some workflow tests. - :ghissue:
813: supervised_learning.py test failure - :ghissue:
826: fixed supervised_learning.py script test failure - :ghissue:
590: Merge qiime_test_data repo into QIIME - :ghissue:
824: merge qiime_test_data into qiime - :ghissue:
812: Fixes issue #811 - :ghissue:
734: New option type - 'multiple_choice' - :ghissue:
769: Allow minimum rather than exact version of R, see issue #624 - :ghissue:
800: Fixing --tree_fp option type - :ghissue:
809: QIIME blog contains incorrect link to latest greengenes release - :ghissue:
791: History expansion in sample_ids_from_metadata_description - :ghissue:
807: supervised_learning.py handles input directories - :ghissue:
788: filter_fasta.py doesn't describe what --valid_states is - :ghissue:
794: test_compare_taxa_summaries.py randomly fails - :ghissue:
795: Increased number of stochastic p-value trials. - :ghissue:
782: Otu category significance - :ghissue:
801: Fixing --metric option type of cluster_quality.py - :ghissue:
802: Fixing --coord_fnames and --background_color option types for ... - :ghissue:
803: Fixing --conversion_type option type for convert_fastaqual_fastq.py - :ghissue:
804: Fixing option types for demultiplex_fasta.py - :ghissue:
805: Fixing --map_fname option type in denoise_wrapper.py - :ghissue:
806: Fixing --output_fasta_fp option type for extract_seqs_by_sample_id.py - :ghissue:
797: New OTUs' metadata are now handled correctly. - :ghissue:
796: simsam.py handles missing metadata incorrectly - :ghissue:
793: simsam.py now handles superset mapping file. - :ghissue:
792: addresses #789 - :ghissue:
784: Output new mapping file from simsam.py - :ghissue:
786: Added -m/--mapping_fp option to simsam.py - :ghissue:
780: Remove nightly Clout run - :ghissue:
778: Be more efficient with QIIME builds - :ghissue:
755: Hook Jenkins up to GitHub - :ghissue:
757: Migrate Jenkins to caporaso-lab production server - :ghissue:
771: reverting #659 - this isn't actually working for me - :ghissue:
711: compare_alpha_diversities.py should have a default depth - :ghissue:
770: updated to use default depth for compare_alpha_diversity.py - :ghissue:
746: set up nightly testing with jenkins - :ghissue:
659: Update collate_alpha.py to avoid directories - :ghissue:
740: Added support for plotting empty distributions in box plots. - :ghissue:
713: TopiaryExplorer-related failure in test_format.py - :ghissue:
766: define get_adjacent_coordinates function (similar to qiime.group.get_adjacent_distances) - :ghissue:
767: fixes #766 - :ghissue:
754: Coverage - :ghissue:
763: added flags to suppress different analysis types - :ghissue:
761: Removed make_cluster_jobs.py test. - :ghissue:
622: transform_coordinate_matrices.py leaves file behind in current directory - :ghissue:
611: Two option types from plot_semivariogram.py are wrong - :ghissue:
758: Error in Illumina processing tutorial - :ghissue:
733: Quick fixes - :ghissue:
753: Checking in tests fix for te 1.0 - :ghissue:
759: Solves issue #758 -- a truly monumental commit - :ghissue:
601: add ability to toggle between different taxa summary plots to support comparison - :ghissue:
741: Fixes issue #711 - :ghissue:
727: Parameters file are not parsed with U - :ghissue:
736: Change read mode for parameter files -- issue 727 - :ghissue:
731: make_otu_heatmap_html.py slow on large tables - :ghissue:
742: Fixed performance bug in make_otu_heatmap_html.py. - :ghissue:
730: partially addresses #688 - :ghissue:
269: Allow suppress row/column clustering in make_otu_heatmap.py - :ghissue:
83: incorporate bi-plots into core_qiime_analyses.py - :ghissue:
721: Fixing the option types for ampliconnoise.py - :ghissue:
720: Ported mc_t_two_sample fix from PyCogent. - :ghissue:
634: Store the output ofexclude_seqs_by_blast.pyin a directory - :ghissue:
660: convert_fastaqual_fastq.py is very slow, needs attention - :ghissue:
477: refactor core_qiime_analyses.py to perform only downstream processing - :ghissue:
715: Use 'choice' option type for --binning_method - :ghissue:
698: split workflow.py into qiime/workflow/util.py and other sub-modules - :ghissue:
699: replace workflow test data with the new small test set defined in #582 - :ghissue:
672: process_sff.py - fails when using -f without -o - :ghissue:
680: Fixes #672, explicitly checks type of opts.input_dir - :ghissue:
661: Convert fastaqual fastq - :ghissue:
714: major refactoring of workflow tests and organization of workflow code - :ghissue:
647: Modifying exclude_seqs_by_blast.py in order to store the output... - :ghissue:
702: assign_taxonomy.py -m mothur raises a KeyError - :ghissue:
704: Changed timeout from 120 to 240 seconds. - :ghissue:
582: compile very small test data set for use in slow unit tests - :ghissue:
696: Add note to the coding guidelines - :ghissue:
695: per_library_stats.py raises an exception - :ghissue:
692: Fixing issue #685 - :ghissue:
687: a complete refactoring and renaming of core_qiime_analyses.py (now core_diversity_analyses.py) - :ghissue:
689: Resolves issue #686. - :ghissue:
683: Fix issue #677 - :ghissue:
678: bug in parse_otu_table - :ghissue:
681: Modified a single line in parse_classic_otu_table to allow it to correct... - :ghissue:
682: fixing issue #676. beta_diversity.py -r now only warns when run on samples with no data - :ghissue:
652: Updates for TE 1.0 - :ghissue:
675: Fixed changes for TE 1.0 - :ghissue:
670: Add option to disable reverse strand matching for pick_otus.py -m usearch - :ghissue:
671: Modified pick_otus.py and usearch.py to allow modulation of reverse stra... - :ghissue:
666: alpha_rarefaction could improve on the use of the BIOM Table API - :ghissue:
667: getResults now uses the BIOM table API more effectively - :ghissue:
665: Extract adjacent distances from distance matrix - :ghissue:
651: Relatedness speedup - :ghissue:
663: workshop tutorial template FileLinks points to the wrong location - :ghissue:
664: updated links that were to svn version of documentation. - :ghissue:
654: update denoising_454 tutorial - :ghissue:
662: Multi-threading Not Working in jackknifed_beta_diversity.py - :ghissue:
467: compare_alpha_diversity.py degrees of freedom bug/multiple corrections bug - :ghissue:
656: Update doc/tutorials/denoising_454_data.rst - :ghissue:
655: Updated to reference biom-format 1.1.2. - :ghissue:
577: Modified add_qiime_labels.py script to use a standard metadata mapping f... - :ghissue:
653: request to create parallel version of mothur OTU picking - :ghissue:
638: should per_library_stats.py be renamed print_biom_stats.py and ported to biom-format? - :ghissue:
453: function to be used for exploring time series relevant subsampling - :ghissue:
630: Further improvements to timeseries filtering. - :ghissue:
616: Add a parallel_denoiser script - :ghissue:
645: Update doc/scripts/beta_diversity_metrics.rst - :ghissue:
646: filter_samples_from_otu_table.py documentation is incorrect - :ghissue:
648: otu_category_significance.py is not using BIOM methods well - :ghissue:
649: use BIOM Table API instead of per-element lookups - :ghissue:
618: beta_diversity_through_plots.py should throw output directory exists message over stderr - :ghissue:
621: in filter_samples_from_otu_table.py consider default -n from 0 to 1 - :ghissue:
617: Small Changes to Parallel Documentation - :ghissue:
627: Added support for variable-size distance classes in Mantel correlogram. - :ghissue:
636: retain_unassigned_reads acts differently in demultiplex_fasta.py vs. split_libraries.py - :ghissue:
635: Replace spaces with underscores in BIOM_TABLE_TYPE options in convert_biom.py - :ghissue:
625: Add option to summarize_taxa.py to output .biom files - :ghissue:
609: Add is_valid_git_refname and is_valid_git_sha1 - :ghissue:
612: Modified the compare_alpha_diversity library, script, and tests to resol... - :ghissue:
626: Add new option file "multiple_choice" - :ghissue:
606: Backported changes to rdp_classifier.py in PyCogent - :ghissue:
614: Outdated page on QIIME website - :ghissue:
615: denoise_wrapper.py errors when there are multiple input files - :ghissue:
607: Fixing error with distance_matrix_from_mapping.py in Clout - :ghissue:
602: Adding functionality to calculate linear distance from Latitude/Longitude point - :ghissue:
220: Script convert_fastaqual_fastaq argument CONVERSION_TYPE fastq_to_fastaqual - :ghissue:
598: Paths in app deploy script - :ghissue:
555: align_seqs.py error on compy - :ghissue:
596: Collated alpha map - :ghissue:
538: remove qiime.format.get_ipynb_output_formatter ... - :ghissue:
456: Parameter to turn off alignment/tree building in OTU picking etc workflows? - :ghissue:
593: make_otu_table.py crashes on OTU maps with long lines - :ghissue:
591: added sample_count_by_category - :ghissue:
589: 160dev update - updated all version information to 1.6.0-dev - :ghissue:
587: Updated version. - :ghissue:
583: compare_alpha_diversities test failure - :ghissue:
586: Added .gitattributes. - :ghissue:
585: updated handling of nan to address test failure - :ghissue:
584: Updated version info for 1.6.0 release. - :ghissue:
581: updated version and status strings and references to the version... - :ghissue:
571: test documentation for w3c compliance and broken links - :ghissue:
574: update ChangeLog - :ghissue:
578: ChangeLog updated for QIIME 1.6.0 - :ghissue:
570: build new script rst files - :ghissue:
579: compare_alpha_diversity.py fails if there is nan in the array of alpha diversities - :ghissue:
580: fix for issue #579 - :ghissue:
576: updated all script rst files for QIIME 1.6.0 - :ghissue:
575: Misc. fixes to compare_alpha_diversity.py. - :ghissue:
498: compare_alpha_diversity.py script errors if mapping file not perfect match to IDs in collated_alpha file - :ghissue:
103: implement gini index for alpha diversity - :ghissue:
255: Good's coverage estimate - :ghissue:
515: Compare alpha diversity.py - :ghissue:
573: Tutorial organization