[med-svn] [python-pbcore] branch master updated (b642087 -> a60fd5b)

[Afif Elghraoui]

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

      from  b642087   releasing package python-pbcore version 1.2.11+dfsg-1
       new  4a2399d   New upstream version 1.4.2+dfsg
       new  f80c7e4   Merge tag 'upstream/1.4.2+dfsg'
       new  6d80e0f   Update patches
       new  0182f6e   d/control: use build profile declarations
       new  986f3a8   Add new tests dependency
       new  a60fd5b   Update changelog

The 6 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
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Summary of changes:
 .pylintrc                                          |   15 +
 CHANGELOG.org                                      |    8 +
 Makefile                                           |    6 +-
 README.md                                          |   12 +
 bamboo_build.sh                                    |   23 +
 bin/dataset.py                                     |   13 -
 bin/updateXSDs.py                                  |   18 +-
 debian/changelog                                   |    9 +
 debian/control                                     |    8 +-
 debian/patches/deprecate-dataset.patch             |   14 -
 debian/patches/enable-build-time-testing.patch     |    4 +-
 debian/patches/ignore-pyxb.patch                   |   40 +-
 debian/patches/remove-unnecessary-cython-dep.patch |    3 +-
 debian/patches/series                              |    1 -
 debian/tests/control                               |    1 +
 pbcore/__init__.py                                 |    2 +-
 pbcore/chemistry/chemistry.py                      |    9 +-
 pbcore/chemistry/resources/mapping.xml             |  170 +-
 pbcore/data/__init__.py                            |    3 +
 pbcore/data/chemistry.xml                          |    9 +
 pbcore/data/datasets/hdfsubread_dataset.xml        |    9 +-
 pbcore/data/datasets/subread.dataset.xml           |   25 +-
 .../datasets/transformed_rs_subread.dataset.xml    |   16 +-
 pbcore/io/BarcodeH5Reader.py                       |   22 +-
 pbcore/io/BasH5IO.py                               |   16 +-
 pbcore/io/VcfIO.py                                 |  179 ++
 pbcore/io/__init__.py                              |    1 +
 pbcore/io/_utils.py                                |   12 +-
 pbcore/io/align/BamIO.py                           |    7 +-
 pbcore/io/align/CmpH5IO.py                         |   10 +-
 pbcore/io/dataset/DataSetIO.py                     |  649 ++++--
 pbcore/io/dataset/DataSetMembers.py                |  720 ++++---
 pbcore/io/dataset/DataSetReader.py                 |   60 +-
 pbcore/io/dataset/DataSetValidator.py              |    7 +-
 pbcore/io/dataset/DataSetWriter.py                 |  111 +-
 pbcore/io/dataset/pyxb/DataSetXsd.py               | 2148 ++++++++++++++++++++
 pbcore/io/dataset/pyxb/__init__.py                 |    0
 pbcore/io/dataset/{ => pyxb}/_pbbase.py            | 1983 +++++++++++-------
 pbcore/io/dataset/{DataSetXsd.py => pyxb/_pbds.py} |  908 +++++----
 pbcore/io/dataset/{ => pyxb}/_pbmeta.py            | 1087 ++++++----
 pbcore/io/dataset/pyxb/_pbpn.py                    |  941 +++++++++
 pbcore/io/dataset/{ => pyxb}/_pbrk.py              |  414 ++--
 pbcore/io/dataset/{ => pyxb}/_pbsample.py          |  318 +--
 pbcore/io/dataset/utils.py                         |  321 +--
 pbcore/io/opener.py                                |    2 +-
 pbcore/io/rangeQueries.py                          |   17 +-
 pbcore/util/__init__.py                            |    4 +
 requirements-dev.txt                               |    4 +-
 requirements.txt                                   |    1 -
 setup.py                                           |    2 +-
 tests/test_pbcore_extract_bam_sequence.py          |    5 +-
 tests/test_pbcore_io_AlnFileReaders.py             |   23 +-
 tests/test_pbcore_io_VcfIO.py                      |   64 +
 tests/test_pbcore_io_lossless_bam.py               |    5 +-
 tests/test_pbdataset.py                            |  577 +++++-
 tests/test_pbdataset_filters.py                    |  274 ++-
 tests/test_pbdataset_metadata.py                   |   59 +-
 tests/test_pbdataset_split.py                      |  348 +++-
 tests/test_pbdataset_subtypes.py                   |  108 +-
 tests/test_pbdataset_utils.py                      |   75 +-
 tests/utils.py                                     |   22 +-
 61 files changed, 8981 insertions(+), 2941 deletions(-)
 create mode 100644 .pylintrc
 create mode 100755 bamboo_build.sh
 delete mode 100755 bin/dataset.py
 delete mode 100644 debian/patches/deprecate-dataset.patch
 create mode 100644 pbcore/data/chemistry.xml
 create mode 100644 pbcore/io/VcfIO.py
 create mode 100644 pbcore/io/dataset/pyxb/DataSetXsd.py
 create mode 100644 pbcore/io/dataset/pyxb/__init__.py
 rename pbcore/io/dataset/{ => pyxb}/_pbbase.py (72%)
 rename pbcore/io/dataset/{DataSetXsd.py => pyxb/_pbds.py} (81%)
 rename pbcore/io/dataset/{ => pyxb}/_pbmeta.py (61%)
 create mode 100644 pbcore/io/dataset/pyxb/_pbpn.py
 rename pbcore/io/dataset/{ => pyxb}/_pbrk.py (74%)
 rename pbcore/io/dataset/{ => pyxb}/_pbsample.py (62%)
 create mode 100644 tests/test_pbcore_io_VcfIO.py

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