[med-svn] [python-pbcore] branch master updated (620c3bb -> b642087)

[Afif Elghraoui]

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

      from  620c3bb   releasing package python-pbcore version 1.2.10+dfsg-1
       new  114e570   Imported Upstream version 1.2.11+dfsg
       new  c63a73c   Merge tag 'upstream/1.2.11+dfsg'
       new  88ce0b1   Update patches
       new  b642087   releasing package python-pbcore version 1.2.11+dfsg-1

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Summary of changes:
 .circleci/installHDF5.sh                           |    2 +-
 CHANGELOG.org                                      |    5 +
 Makefile                                           |    5 +
 debian/changelog                                   |    7 +
 debian/patches/ignore-pyxb.patch                   |    7 +
 pbcore/__init__.py                                 |    2 +-
 pbcore/chemistry/resources/mapping.xml             |   60 +-
 pbcore/data/__init__.py                            |    3 +
 pbcore/data/empty.aligned_subreads.bam             |  Bin 0 -> 728 bytes
 ...gned.bam.pbi => empty.aligned_subreads.bam.pbi} |  Bin
 pbcore/io/GffIO.py                                 |   70 +-
 pbcore/io/align/BamIO.py                           |   26 +-
 pbcore/io/align/CmpH5IO.py                         |    6 +-
 pbcore/io/align/PacBioBamIndex.py                  |   10 +-
 pbcore/io/dataset/DataSetErrors.py                 |   34 +
 pbcore/io/dataset/DataSetIO.py                     |  339 +++---
 pbcore/io/dataset/DataSetMembers.py                |  850 +++++++++------
 .../Process.py => io/dataset/DataSetMetaTypes.py}  |   86 +-
 pbcore/io/dataset/DataSetReader.py                 |   46 +-
 pbcore/{sequence.py => io/dataset/DataSetUtils.py} |   72 +-
 pbcore/io/dataset/DataSetValidator.py              |   41 +-
 pbcore/io/dataset/DataSetWriter.py                 |   43 +-
 pbcore/io/dataset/__init__.py                      |   35 +
 pbcore/io/dataset/utils.py                         |  172 ++-
 requirements-dev.txt                               |    2 +-
 tests/test_pbcore_io_AlnFileReaders.py             |   12 +-
 tests/test_pbcore_io_GffIO.py                      |   11 +
 tests/test_pbdataset.py                            | 1090 ++++----------------
 tests/test_pbdataset_filters.py                    |  373 +++++++
 tests/test_pbdataset_metadata.py                   |  114 ++
 tests/test_pbdataset_split.py                      |  506 +++++++++
 tests/test_pbdataset_subtypes.py                   |  205 ++--
 tests/test_pbdataset_utils.py                      |  183 ++++
 tests/utils.py                                     |   40 +
 34 files changed, 2812 insertions(+), 1645 deletions(-)
 create mode 100644 pbcore/data/empty.aligned_subreads.bam
 copy pbcore/data/{datasets/empty_lambda.aligned.bam.pbi => empty.aligned_subreads.bam.pbi} (100%)
 copy pbcore/{util/Process.py => io/dataset/DataSetMetaTypes.py} (50%)
 copy pbcore/{sequence.py => io/dataset/DataSetUtils.py} (53%)
 create mode 100644 tests/test_pbdataset_filters.py
 create mode 100644 tests/test_pbdataset_metadata.py
 create mode 100644 tests/test_pbdataset_split.py
 create mode 100644 tests/test_pbdataset_utils.py
 create mode 100644 tests/utils.py

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