[med-svn] [python-pbcore] branch master updated (71606f7 -> a61daa3)

[Afif Elghraoui]

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

      from  71606f7   python-pbcore (1.2.6+dfsg-1) unstable; urgency=medium
       new  41d7f1c   Revert "Set watch file to point to pypi rather than github"
       new  b924872   Imported Upstream version 1.2.7+dfsg
       new  79f6474   Merge tag 'upstream/1.2.7+dfsg'
       new  a540761   Drop patch applied upstream
       new  280aa3c   Refresh existing patches
       new  3c1a87c   Prevent requirements.txt from triggering download of unnecessary dependency
       new  8eb7941   Fix license name format
       new  a61daa3   python-pbcore (1.2.7+dfsg-1) unstable; urgency=medium

The 8 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
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Summary of changes:
 .circleci/installHDF5.sh                           |   14 +
 .gitignore                                         |   13 +
 CHANGELOG.org                                      |    8 +
 PKG-INFO                                           |   69 -
 circle.yml                                         |    1 +
 debian/changelog                                   |    9 +
 debian/copyright                                   |    2 +-
 debian/patches/enable-build-time-testing.patch     |    9 +-
 debian/patches/fix-pysam-compatibility.patch       |   36 -
 debian/patches/remove-unnecessary-cython-dep.patch |   14 +
 debian/patches/series                              |    2 +-
 debian/watch                                       |    5 +-
 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 +-
 50 files changed, 4177 insertions(+), 7251 deletions(-)
 create mode 100644 .circleci/installHDF5.sh
 create mode 100644 .gitignore
 delete mode 100644 PKG-INFO
 delete mode 100644 debian/patches/fix-pysam-compatibility.patch
 create mode 100644 debian/patches/remove-unnecessary-cython-dep.patch
 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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