[med-svn] [emperor] branch master updated (0dabb78 -> c80c5f5)

[Kerim Ölçer]

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kerimlcr-guest pushed a change to branch master
in repository emperor.

      from  0dabb78   Update VCS URLs
       new  c80c5f5   modified for new version

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Summary of changes:
 ChangeLog.md                                       |  105 +-
 INSTALL.md                                         |   56 +-
 LICENSE.md                                         |  312 +++--
 README.md                                          |   16 +-
 debian/changelog                                   |   16 +-
 debian/compat                                      |    2 +-
 debian/control                                     |   44 +-
 debian/patches/series                              |    2 +-
 debian/rules                                       |   52 +-
 debian/watch                                       |    2 +-
 doc/description_index.html                         |  112 +-
 doc/index.html                                     |  134 +-
 doc/tutorial_index.html                            |  107 +-
 emperor/__init__.py                                |   54 +-
 emperor/biplots.py                                 |  147 +-
 emperor/filter.py                                  |   84 +-
 emperor/format.py                                  |  717 +---------
 emperor/qiime_backports/__init__.py                |    4 +-
 emperor/qiime_backports/biplots.py                 |    6 +-
 emperor/qiime_backports/filter.py                  |   10 +-
 emperor/qiime_backports/make_3d_plots.py           |   10 +-
 emperor/qiime_backports/parse.py                   |   46 +-
 emperor/qiime_backports/util.py                    |    9 +-
 emperor/sort.py                                    |   84 +-
 emperor/util.py                                    |  648 ++++++---
 scripts/make_emperor.py                            |  633 +--------
 setup.py                                           |   86 +-
 tests/all_tests.py                                 |  220 ++-
 .../make_emperor/Fasting_Map_modified.txt          |   22 +-
 tests/scripts_test_data/make_emperor/biplot.txt    |    2 +-
 .../pcoa_unweighted_unifrac_rarefaction_110_0.txt  |   14 +-
 .../pcoa_unweighted_unifrac_rarefaction_110_1.txt  |   14 +-
 .../make_emperor/otu_table_L3.txt                  |    2 +-
 .../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                              |  490 ++++---
 tests/test_filter.py                               |  114 +-
 tests/test_format.py                               | 1467 +-------------------
 tests/test_qiime_backports/test_biplots.py         |   33 +-
 tests/test_qiime_backports/test_filter.py          |    5 +-
 tests/test_qiime_backports/test_make_3d_plots.py   |   20 +-
 tests/test_qiime_backports/test_parse.py           |    5 +-
 tests/test_qiime_backports/test_util.py            |   12 +-
 tests/test_sort.py                                 |  178 ++-
 tests/test_util.py                                 |  877 ++++++++----
 54 files changed, 2672 insertions(+), 4455 deletions(-)
 mode change 100755 => 100644 emperor/format.py
 mode change 100755 => 100644 tests/test_biplots.py
 mode change 100755 => 100644 tests/test_filter.py
 mode change 100755 => 100644 tests/test_format.py
 mode change 100755 => 100644 tests/test_sort.py
 mode change 100755 => 100644 tests/test_util.py

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