[med-svn] [python-pysam] branch debian/jessie-backports updated (ffc27b1 -> 07c538d)

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

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

      from  ffc27b1   Correct default branch for Jessie backports.
      adds  de94e82   Add version constraints to d/control
      adds  ccd78f8   Add changelog entry for next release
      adds  96729e6   Drom ds suffix versioning
      adds  f8c3dc9   Prepare for next version to drop ds version suffix
      adds  bb7aa1f   Update changelog for new release
      adds  18e4903   Imported Upstream version 0.8.4+ds
      adds  b8581f9   Merge tag 'upstream/0.8.4+ds'
      adds  7eb7048   Remove patches applied upstream
      adds  21aac6c   Refresh existing patches
      adds  29b0822   Use pre-defined variables from dpkg rather than manually scraping changelog
      adds  90b30c3   Remove unnecessary rule override in d/rules
      adds  37c466d   Set Vcs-Browser to point to cgit rather than gitweb
      adds  b892e0d   Reduce dependencies in autopktest dependencies
      adds  eeec80e   Replace patch for network-dependent tests
      adds  496e384   Add more lintian overrides
      adds  50cc7a0   Refine testing in d/rules
      adds  96af80c   python-pysam (0.8.4+ds-1) unstable; urgency=medium
       new  f81b198   Merge branch 'master' into debian/jessie-backports
       new  07c538d   python-pysam (0.8.4+ds-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
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 README.rst                                         |    5 +-
 benchmark/AlignedSegment_bench.py                  |   43 +
 debian/changelog                                   |   21 +
 debian/control                                     |    2 +-
 debian/patches/adding-include-hts-dirs             |    2 +-
 .../change-htslib-statement-to-link-to-debian      |    4 +-
 debian/patches/correct-spelling-errors.patch       |  115 -
 debian/patches/cython23.patch                      |   39 -
 .../patches/disable-tests-requiring-network.patch  |   42 +
 debian/patches/ignore-htslib-dir.patch             |    6 +-
 debian/patches/improve-python3-compatibility.patch |   27 -
 debian/patches/sam_mpileup.patch                   |   28 -
 debian/patches/series                              |    6 +-
 debian/patches/strip_online_tests.patch            |   82 -
 debian/python-pysam.lintian-overrides              |    2 +
 debian/python3-pysam.lintian-overrides             |    2 +
 debian/rules                                       |   19 +-
 debian/tests/control                               |    4 +-
 debian/watch                                       |    2 +-
 doc/api.rst                                        |   15 +-
 doc/conf.py                                        |   20 +-
 doc/faq.rst                                        |   26 +-
 doc/glossary.rst                                   |   34 +-
 doc/release.rst                                    |   86 +
 doc/usage.rst                                      |   22 +-
 pysam/TabProxies.pxd                               |   94 -
 pysam/__init__.py                                  |   64 +-
 pysam/calignedsegment.pxd                          |   94 +
 pysam/calignedsegment.pyx                          | 2277 +++++++
 pysam/calignmentfile.pxd                           |   71 +-
 pysam/calignmentfile.pyx                           | 3595 +++--------
 pysam/cbcf.pxd                                     |    2 +-
 pysam/cbcf.pyx                                     |  694 ++-
 pysam/cfaidx.pxd                                   |   54 +-
 pysam/cfaidx.pyx                                   |  470 +-
 pysam/chtslib.pxd                                  |   43 +-
 pysam/chtslib.pyx                                  |   97 +-
 pysam/csamfile.pxd                                 |    4 +-
 pysam/csamfile.pyx                                 |    2 +-
 pysam/csamtools.pxd                                |   13 +-
 pysam/csamtools.pyx                                |   63 +-
 pysam/ctabix.pxd                                   |   39 +-
 pysam/ctabix.pyx                                   |  312 +-
 pysam/ctabixproxies.pxd                            |   59 +
 pysam/{TabProxies.pyx => ctabixproxies.pyx}        |  176 +-
 pysam/cutils.pxd                                   |   27 +
 pysam/cutils.pyx                                   |  214 +
 pysam/cvcf.pxd                                     |   40 -
 pysam/cvcf.pyx                                     |  152 +-
 pysam/htslib_util.h                                |    3 -
 pysam/pysam_util.c                                 |    2 +-
 pysam/tabix_util.c                                 |    5 +-
 pysam/version.py                                   |    2 +-
 requires.txt => requirements.txt                   |    0
 save/pysam_test2.6.py                              |    2 +-
 setup.py                                           |  228 +-
 tests/AlignedSegment_test.py                       |  236 +-
 tests/AlignmentFile_test.py                        |  314 +-
 tests/SamFile_test.py                              |   74 +-
 tests/TestUtils.py                                 |    6 +-
 tests/faidx_test.py                                |   99 +-
 tests/pysam_data/Makefile                          |    2 +-
 tests/pysam_data/faidx_ex1.fa                      | 6540 ++++++++++++++++++++
 tests/pysam_data/{ex1.fq => faidx_ex1.fq}          |    0
 tests/samtools_test.py                             |   93 +-
 tests/tabix_test.py                                |   46 +-
 66 files changed, 12622 insertions(+), 4340 deletions(-)
 create mode 100644 benchmark/AlignedSegment_bench.py
 delete mode 100644 debian/patches/correct-spelling-errors.patch
 delete mode 100644 debian/patches/cython23.patch
 create mode 100644 debian/patches/disable-tests-requiring-network.patch
 delete mode 100644 debian/patches/improve-python3-compatibility.patch
 delete mode 100644 debian/patches/sam_mpileup.patch
 delete mode 100644 debian/patches/strip_online_tests.patch
 delete mode 100644 pysam/TabProxies.pxd
 create mode 100644 pysam/calignedsegment.pxd
 create mode 100644 pysam/calignedsegment.pyx
 create mode 100644 pysam/ctabixproxies.pxd
 rename pysam/{TabProxies.pyx => ctabixproxies.pyx} (87%)
 create mode 100644 pysam/cutils.pxd
 create mode 100644 pysam/cutils.pyx
 rename requires.txt => requirements.txt (100%)
 create mode 100644 tests/pysam_data/faidx_ex1.fa
 rename tests/pysam_data/{ex1.fq => faidx_ex1.fq} (100%)

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