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afif pushed a commit to branch master
in repository emperor.

commit e5755c43a54b023052cb313eb357e4d84c3f9c0a
Merge: ed7d170 da2580e
Author: Afif Elghraoui <a...@ghraoui.name>
Date:   Wed Oct 12 23:13:13 2016 -0700

    Merge tag 'upstream/0.9.3+dfsg'
    
    Upstream version 0.9.3+dfsg

 .gitignore                                         |    42 +
 .travis.yml                                        |     7 +
 ChangeLog.md                                       |    90 +
 INSTALL.md                                         |    28 +
 LICENSE.md                                         |   223 +
 MANIFEST.in                                        |    15 +
 README.md                                          |    34 +
 doc/description_index.html                         |   209 +
 doc/img/axes_menu.png                              |   Bin 0 -> 16003 bytes
 doc/img/colors_menu.png                            |   Bin 0 -> 16257 bytes
 doc/img/description_1.png                          |   Bin 0 -> 66096 bytes
 doc/img/emperor_heading.png                        |   Bin 0 -> 12582 bytes
 doc/img/favicon.ico                                |   Bin 0 -> 5558 bytes
 doc/img/key_menu.png                               |   Bin 0 -> 17838 bytes
 doc/img/labels_menu.png                            |   Bin 0 -> 19279 bytes
 doc/img/options_menu.png                           |   Bin 0 -> 15108 bytes
 doc/img/parallel_plots.png                         |   Bin 0 -> 208007 bytes
 doc/img/sample_1.png                               |   Bin 0 -> 78421 bytes
 doc/img/scaling_menu.png                           |   Bin 0 -> 21444 bytes
 doc/img/tutorial/1.png                             |   Bin 0 -> 134941 bytes
 doc/img/tutorial/10.png                            |   Bin 0 -> 137743 bytes
 doc/img/tutorial/11.png                            |   Bin 0 -> 125936 bytes
 doc/img/tutorial/2.png                             |   Bin 0 -> 104168 bytes
 doc/img/tutorial/6.png                             |   Bin 0 -> 108753 bytes
 doc/img/tutorial/capture_2.png                     |   Bin 0 -> 100097 bytes
 doc/img/tutorial/exes.png                          |   Bin 0 -> 102868 bytes
 doc/img/tutorial/rotating_1.png                    |   Bin 0 -> 148230 bytes
 doc/img/tutorial/rotating_2.png                    |   Bin 0 -> 156729 bytes
 doc/img/tutorial/treta.png                         |   Bin 0 -> 191814 bytes
 doc/img/view_menu.png                              |   Bin 0 -> 20196 bytes
 doc/img/visibility_menu.png                        |   Bin 0 -> 27290 bytes
 doc/index.html                                     |   178 +
 doc/installation_index.html                        |   202 +
 doc/tutorial_index.html                            |   245 +
 emperor/__init__.py                                |    13 +
 emperor/biplots.py                                 |   110 +
 emperor/filter.py                                  |    72 +
 emperor/format.py                                  |   723 +
 emperor/pycogent_backports/__init__.py             |    12 +
 emperor/pycogent_backports/procrustes.py           |   157 +
 emperor/qiime_backports/__init__.py                |    13 +
 emperor/qiime_backports/biplots.py                 |    55 +
 emperor/qiime_backports/filter.py                  |   120 +
 emperor/qiime_backports/format.py                  |    40 +
 emperor/qiime_backports/make_3d_plots.py           |    67 +
 emperor/qiime_backports/parse.py                   |   270 +
 emperor/qiime_backports/util.py                    |   423 +
 emperor/sort.py                                    |    87 +
 emperor/support_files/css/colorPicker.css          |    31 +
 emperor/support_files/css/d3.parcoords.css         |    40 +
 .../css/images/ui-bg_flat_0_aaaaaa_40x100.png      |   Bin 0 -> 180 bytes
 .../css/images/ui-bg_flat_75_ffffff_40x100.png     |   Bin 0 -> 178 bytes
 .../css/images/ui-bg_glass_55_fbf9ee_1x400.png     |   Bin 0 -> 120 bytes
 .../css/images/ui-bg_glass_65_ffffff_1x400.png     |   Bin 0 -> 105 bytes
 .../css/images/ui-bg_glass_75_dadada_1x400.png     |   Bin 0 -> 111 bytes
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 .../css/images/ui-bg_glass_95_fef1ec_1x400.png     |   Bin 0 -> 119 bytes
 .../ui-bg_highlight-soft_75_cccccc_1x100.png       |   Bin 0 -> 101 bytes
 .../css/images/ui-icons_222222_256x240.png         |   Bin 0 -> 4369 bytes
 .../css/images/ui-icons_2e83ff_256x240.png         |   Bin 0 -> 4369 bytes
 .../css/images/ui-icons_454545_256x240.png         |   Bin 0 -> 4369 bytes
 .../css/images/ui-icons_888888_256x240.png         |   Bin 0 -> 4369 bytes
 .../css/images/ui-icons_cd0a0a_256x240.png         |   Bin 0 -> 4369 bytes
 .../support_files/css/jquery-ui-1.8.16.custom.css  |   568 +
 emperor/support_files/css/jquery-ui2.css           |   567 +
 emperor/support_files/css/spectrum.css             |   408 +
 emperor/support_files/emperor/css/emperor.css      |   284 +
 emperor/support_files/emperor/js/emperor.js        |  2430 ++
 emperor/support_files/img/emperor.png              |   Bin 0 -> 8747 bytes
 emperor/support_files/img/favicon.ico              |   Bin 0 -> 5558 bytes
 emperor/support_files/img/pause.png                |   Bin 0 -> 2919 bytes
 emperor/support_files/img/play.png                 |   Bin 0 -> 2946 bytes
 emperor/support_files/img/reset.png                |   Bin 0 -> 2965 bytes
 emperor/support_files/js/FileSaver.min.js          |     2 +
 emperor/support_files/js/THREEx.screenshot.js      |   130 +
 emperor/support_files/js/Three.js                  | 37637 +++++++++++++++++++
 emperor/support_files/js/d3.parcoords.js           |   568 +
 emperor/support_files/js/d3.v3.min.js              |     5 +
 emperor/support_files/js/jquery-1.7.1.min.js       |     4 +
 .../js/jquery-ui-1.8.17.custom.min.js              |   356 +
 emperor/support_files/js/jquery.colorPicker.js     |   328 +
 emperor/support_files/js/js/AudioObject.js         |   172 +
 emperor/support_files/js/js/Car.js                 |   364 +
 emperor/support_files/js/js/DAT.GUI.min.js         |    53 +
 emperor/support_files/js/js/Detector.js            |    58 +
 emperor/support_files/js/js/ImprovedNoise.js       |    71 +
 emperor/support_files/js/js/PRNG.js                |    11 +
 .../support_files/js/js/RequestAnimationFrame.js   |    22 +
 emperor/support_files/js/js/ShaderExtras.js        |  1779 +
 emperor/support_files/js/js/ShaderSkin.js          |   752 +
 emperor/support_files/js/js/ShaderTerrain.js       |   306 +
 emperor/support_files/js/js/SimplexNoise.js        |   316 +
 emperor/support_files/js/js/Sparks.js              |   832 +
 emperor/support_files/js/js/Stats.js               |     8 +
 emperor/support_files/js/js/Tween.js               |    13 +
 emperor/support_files/js/js/ctm/CTMLoader.js       |   821 +
 emperor/support_files/js/js/ctm/CTMWorker.js       |    19 +
 emperor/support_files/js/js/ctm/ctm.js             |   626 +
 .../support_files/js/js/ctm/license/OpenCTM.txt    |    20 +
 .../support_files/js/js/ctm/license/js-lzma.txt    |    19 +
 .../support_files/js/js/ctm/license/js-openctm.txt |    19 +
 emperor/support_files/js/js/ctm/lzma.js            |   510 +
 .../js/js/postprocessing/BloomPass.js              |   100 +
 .../js/js/postprocessing/DotScreenPass.js          |    52 +
 .../js/js/postprocessing/EffectComposer.js         |   136 +
 .../support_files/js/js/postprocessing/FilmPass.js |    51 +
 .../support_files/js/js/postprocessing/MaskPass.js |    86 +
 .../js/js/postprocessing/RenderPass.js             |    51 +
 .../support_files/js/js/postprocessing/SavePass.js |    52 +
 .../js/js/postprocessing/ShaderPass.js             |    51 +
 .../js/js/postprocessing/TexturePass.js            |    37 +
 emperor/support_files/js/specifications.txt        |     1 +
 emperor/support_files/js/spectrum.js               |  1566 +
 emperor/util.py                                    |   488 +
 images/emperor-logos.ai                            |  1197 +
 scripts/make_emperor.py                            |   627 +
 setup.py                                           |    61 +
 tests/all_tests.py                                 |   183 +
 .../scripts_test_data/make_emperor/Fasting_Map.txt |    11 +
 .../make_emperor/Fasting_Map_modified.txt          |    11 +
 tests/scripts_test_data/make_emperor/biplot.txt    |     4 +
 .../pcoa_unweighted_unifrac_rarefaction_110_0.txt  |    14 +
 .../pcoa_unweighted_unifrac_rarefaction_110_1.txt  |    14 +
 .../scripts_test_data/make_emperor/makefolders.sh  |    10 +
 .../make_emperor/otu_table_L3.txt                  |     9 +
 .../make_emperor/unweighted_unifrac_pc.txt         |    14 +
 .../pcoa_unweighted_unifrac_rarefaction_110_0.txt  |    14 +
 .../pcoa_unweighted_unifrac_rarefaction_110_1.txt  |    14 +
 .../pcoa_unweighted_unifrac_rarefaction_110_2.txt  |    14 +
 .../pcoa_unweighted_unifrac_rarefaction_110_3.txt  |    14 +
 .../pcoa_unweighted_unifrac_rarefaction_110_4.txt  |    14 +
 .../pcoa_unweighted_unifrac_rarefaction_110_5.txt  |    14 +
 .../pcoa_unweighted_unifrac_rarefaction_110_6.txt  |    14 +
 .../pcoa_unweighted_unifrac_rarefaction_110_7.txt  |    14 +
 .../pcoa_unweighted_unifrac_rarefaction_110_8.txt  |    14 +
 .../pcoa_unweighted_unifrac_rarefaction_110_9.txt  |    14 +
 tests/test_biplots.py                              |   243 +
 tests/test_filter.py                               |    91 +
 tests/test_format.py                               |  1516 +
 tests/test_pycogent_backports/test_procrustes.py   |   139 +
 tests/test_qiime_backports/test_biplots.py         |   108 +
 tests/test_qiime_backports/test_filter.py          |   130 +
 tests/test_qiime_backports/test_format.py          |    44 +
 tests/test_qiime_backports/test_make_3d_plots.py   |   104 +
 tests/test_qiime_backports/test_parse.py           |   390 +
 tests/test_qiime_backports/test_util.py            |   543 +
 tests/test_sort.py                                 |   235 +
 tests/test_util.py                                 |   501 +
 148 files changed, 62594 insertions(+)

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