[med-svn] [python-pbcore] 03/08: Merge tag 'upstream/1.2.7+dfsg'

[Afif Elghraoui]

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afif-guest pushed a commit to branch master
in repository python-pbcore.

commit 79f6474a2d2315978bbbeefbe92766beec6e7627
Merge: 41d7f1c b924872
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Sun Dec 13 17:12:22 2015 -0800

    Merge tag 'upstream/1.2.7+dfsg'
    
    Upstream version 1.2.7+dfsg

 .circleci/installHDF5.sh                           |   14 +
 .gitignore                                         |   13 +
 CHANGELOG.org                                      |    8 +
 PKG-INFO                                           |   69 -
 circle.yml                                         |    1 +
 pbcore.egg-info/PKG-INFO                           |   69 -
 pbcore.egg-info/SOURCES.txt                        |  199 --
 pbcore.egg-info/dependency_links.txt               |    1 -
 pbcore.egg-info/entry_points.txt                   |    3 -
 pbcore.egg-info/not-zip-safe                       |    1 -
 pbcore.egg-info/pbr.json                           |    1 -
 pbcore.egg-info/requires.txt                       |    3 -
 pbcore.egg-info/top_level.txt                      |    1 -
 pbcore/__init__.py                                 |    2 +-
 pbcore/data/empty.ccs.bam                          |  Bin 507 -> 540 bytes
 ...52550000001823085912221377_s1_X0.scraps.bam.pbi |  Bin 0 -> 1574 bytes
 ...550000001823085912221377_s1_X0.subreads.bam.bai |  Bin 16 -> 0 bytes
 pbcore/io/BasH5IO.py                               |   10 -
 pbcore/io/FastaIO.py                               |   12 +-
 pbcore/io/align/BamAlignment.py                    |    2 +-
 pbcore/io/align/BamIO.py                           |   13 +-
 pbcore/io/align/CmpH5IO.py                         |    6 +-
 pbcore/io/align/PacBioBamIndex.py                  |    7 +-
 pbcore/io/dataset/DataSetIO.py                     |  294 +-
 pbcore/io/dataset/DataSetMembers.py                |   71 +-
 pbcore/io/dataset/DataSetXsd.py                    | 3772 ++++++++++++++------
 pbcore/io/dataset/EntryPoints.py                   |    3 +-
 pbcore/io/dataset/_pbbase.py                       | 1063 +++---
 pbcore/io/dataset/_pbds.py                         | 3639 -------------------
 pbcore/io/dataset/_pbmeta.py                       |  520 ++-
 pbcore/io/dataset/_pbpn.py                         |  939 -----
 pbcore/io/dataset/_pbrk.py                         |  234 +-
 pbcore/io/dataset/_pbsample.py                     |  130 +-
 pbcore/io/dataset/utils.py                         |   55 +-
 pbcore/io/opener.py                                |    3 +-
 requirements-dev.txt                               |    1 -
 requirements.txt                                   |    2 +-
 setup.cfg                                          |    6 -
 setup.py                                           |   27 +-
 tests/test_pbcore_io_BasH5Reader.py                |   20 +-
 tests/test_pbcore_io_GffIO.py                      |    7 +
 tests/test_pbdataset.py                            |  109 +-
 tests/test_pbdataset_subtypes.py                   |   21 +-
 43 files changed, 4145 insertions(+), 7206 deletions(-)

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