[med-svn] [python-pbcore] branch upstream updated (56e8b41 -> b924872)

[Afif Elghraoui]

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afif-guest pushed a change to branch upstream
in repository python-pbcore.

      from  56e8b41   Imported Upstream version 1.2.6+dfsg
       new  b924872   Imported Upstream version 1.2.7+dfsg

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 .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(-)
 create mode 100644 .circleci/installHDF5.sh
 create mode 100644 .gitignore
 delete mode 100644 PKG-INFO
 delete mode 100644 pbcore.egg-info/PKG-INFO
 delete mode 100644 pbcore.egg-info/SOURCES.txt
 delete mode 100644 pbcore.egg-info/dependency_links.txt
 delete mode 100644 pbcore.egg-info/entry_points.txt
 delete mode 100644 pbcore.egg-info/not-zip-safe
 delete mode 100644 pbcore.egg-info/pbr.json
 delete mode 100644 pbcore.egg-info/requires.txt
 delete mode 100644 pbcore.egg-info/top_level.txt
 create mode 100644 pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.scraps.bam.pbi
 delete mode 100644 pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam.bai
 mode change 100755 => 100644 pbcore/io/dataset/DataSetXsd.py
 mode change 100755 => 100644 pbcore/io/dataset/_pbbase.py
 delete mode 100755 pbcore/io/dataset/_pbds.py
 mode change 100755 => 100644 pbcore/io/dataset/_pbmeta.py
 delete mode 100755 pbcore/io/dataset/_pbpn.py
 mode change 100755 => 100644 pbcore/io/dataset/_pbrk.py
 mode change 100755 => 100644 pbcore/io/dataset/_pbsample.py

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