[med-svn] [python-pbcore] branch upstream updated (a8e05e3 -> 56e8b41)

[Afif Elghraoui]

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

      from  a8e05e3   Imported Upstream version 1.2.4+dfsg
       new  56e8b41   Imported Upstream version 1.2.6+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                                    |    7 +
 LICENSES.txt => PKG-INFO                         |   12 +-
 LICENSES.txt => pbcore.egg-info/PKG-INFO         |   12 +-
 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 +
 requirements.txt => pbcore.egg-info/requires.txt |    3 +-
 pbcore.egg-info/top_level.txt                    |    1 +
 pbcore/__init__.py                               |    2 +-
 pbcore/chemistry/resources/mapping.xml           |   30 +
 pbcore/io/BasH5IO.py                             |    5 +-
 pbcore/io/align/BamAlignment.py                  |    4 +
 pbcore/io/align/BamIO.py                         |   12 +
 pbcore/io/align/CmpH5IO.py                       |    4 +
 pbcore/io/align/PacBioBamIndex.py                |    6 +-
 pbcore/io/align/_AlignmentMixin.py               |   13 +
 pbcore/io/dataset/DataSetIO.py                   |  189 +-
 pbcore/io/dataset/DataSetMembers.py              |   54 +-
 pbcore/io/dataset/DataSetReader.py               |   14 +-
 pbcore/io/dataset/DataSetValidator.py            |    2 +
 pbcore/io/dataset/DataSetWriter.py               |   85 +-
 pbcore/io/dataset/DataSetXsd.py                  |  501 +++---
 pbcore/io/dataset/EntryPoints.py                 |    3 +
 pbcore/io/dataset/__init__.py                    |   16 -
 pbcore/io/dataset/_pbbase.py                     | 2042 ++++++++++++----------
 pbcore/io/dataset/_pbds.py                       | 1898 +++++++++++---------
 pbcore/io/dataset/_pbmeta.py                     |  620 ++++---
 pbcore/io/dataset/_pbpn.py                       |  628 +++++--
 pbcore/io/dataset/_pbrk.py                       |  410 ++---
 pbcore/io/dataset/_pbsample.py                   |  132 +-
 pbcore/io/dataset/utils.py                       |    3 +
 setup.cfg                                        |    6 +
 tests/test_pbcore_io_AlnFileReaders.py           |    7 +
 tests/test_pbdataset.py                          |   62 +-
 tests/test_pbdataset_subtypes.py                 |   71 +-
 39 files changed, 4097 insertions(+), 2989 deletions(-)
 delete mode 100644 .circleci/installHDF5.sh
 delete mode 100644 .gitignore
 copy LICENSES.txt => PKG-INFO (90%)
 copy LICENSES.txt => pbcore.egg-info/PKG-INFO (90%)
 create mode 100644 pbcore.egg-info/SOURCES.txt
 create mode 100644 pbcore.egg-info/dependency_links.txt
 create mode 100644 pbcore.egg-info/entry_points.txt
 create mode 100644 pbcore.egg-info/not-zip-safe
 create mode 100644 pbcore.egg-info/pbr.json
 copy requirements.txt => pbcore.egg-info/requires.txt (86%)
 create mode 100644 pbcore.egg-info/top_level.txt

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