[med-svn] [python-pbcore] 01/03: Merge branch 'master' into debian/jessie-backports

[Afif Elghraoui]

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

commit 887a1abb59a4c45a5d7120b4533701db755a6710
Merge: 875e0f9 71606f7
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Wed Dec 2 21:17:44 2015 -0800

    Merge branch 'master' into debian/jessie-backports

 .circleci/installHDF5.sh                       |   14 -
 .gitignore                                     |   13 -
 CHANGELOG.org                                  |    7 +
 PKG-INFO                                       |   69 +
 debian/changelog                               |   10 +
 debian/control                                 |    2 +-
 debian/copyright                               |   21 +
 debian/patches/enable-build-time-testing.patch |    5 +-
 debian/patches/fix-pysam-compatibility.patch   |   36 +
 debian/patches/series                          |    1 +
 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/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 +-
 46 files changed, 4289 insertions(+), 2991 deletions(-)

diff --cc debian/changelog
index d8bcbce,416839f..3da5150
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,10 -1,13 +1,20 @@@
+ python-pbcore (1.2.6+dfsg-1) unstable; urgency=medium
+ 
+   * Set watch file to point to pypi rather than github
+   * Imported Upstream version 1.2.6+dfsg
+   * Refresh patches
+   * Fix compatibility with pysam 0.8.4 (Closes: #805687)
+   * Add license statement for a file added in-between releases
+ 
+  -- Afif Elghraoui <afif at ghraoui.name>  Fri, 27 Nov 2015 12:19:10 -0800
+ 
 +python-pbcore (1.2.4+dfsg-1~bpo8+1) jessie-backports; urgency=medium
 +
 +  * Rebuild for jessie-backports.
 +  * Explicitly add versioned Python dependencies to work around #791433.
 +
 + -- Afif Elghraoui <afif at ghraoui.name>  Sun, 01 Nov 2015 08:39:19 -0800
 +
  python-pbcore (1.2.4+dfsg-1) unstable; urgency=medium
  
    * Fix watch file after dropping the dfsg counting.

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