[med-svn] [python-pbcore] branch debian/jessie-backports updated (2c0f431 -> bdd3a09)

[Afif Elghraoui]

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afif-guest pushed a change to branch debian/jessie-backports
in repository python-pbcore.

      from  2c0f431   python-pbcore (1.2.6+dfsg-1~bpo8+1) jessie-backports; urgency=medium
      adds  41d7f1c   Revert "Set watch file to point to pypi rather than github"
      adds  b924872   Imported Upstream version 1.2.7+dfsg
      adds  79f6474   Merge tag 'upstream/1.2.7+dfsg'
      adds  a540761   Drop patch applied upstream
      adds  280aa3c   Refresh existing patches
      adds  3c1a87c   Prevent requirements.txt from triggering download of unnecessary dependency
      adds  8eb7941   Fix license name format
      adds  a61daa3   python-pbcore (1.2.7+dfsg-1) unstable; urgency=medium
       new  6ad6a99   Merge branch 'master' into debian/jessie-backports
       new  bdd3a09   python-pbcore (1.2.7+dfsg-1~bpo8+1) jessie-backports; urgency=medium

The 2 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:
 .circleci/installHDF5.sh                           |   14 +
 .gitignore                                         |   13 +
 CHANGELOG.org                                      |    8 +
 PKG-INFO                                           |   69 -
 circle.yml                                         |    1 +
 debian/changelog                                   |   15 +
 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, 4183 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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