[med-svn] [python-pysam] branch master updated (ccd78f8 -> 37c466d)

[Afif Elghraoui]

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

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

      from  ccd78f8   Add changelog entry for next release
       new  96729e6   Drom ds suffix versioning
       new  f8c3dc9   Prepare for next version to drop ds version suffix
       new  bb7aa1f   Update changelog for new release
       new  18e4903   Imported Upstream version 0.8.4+ds
       new  b8581f9   Merge tag 'upstream/0.8.4+ds'
       new  7eb7048   Remove patches applied upstream
       new  21aac6c   Refresh existing patches
       new  29b0822   Use pre-defined variables from dpkg rather than manually scraping changelog
       new  90b30c3   Remove unnecessary rule override in d/rules
       new  37c466d   Set Vcs-Browser to point to cgit rather than gitweb

The 10 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                                   |    5 +-
 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 -
 debian/patches/ignore-htslib-dir.patch             |    6 +-
 debian/patches/improve-python3-compatibility.patch |   27 -
 debian/patches/sam_mpileup.patch                   |   28 -
 debian/patches/series                              |    4 -
 debian/rules                                       |   12 +-
 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 +-
 61 files changed, 12555 insertions(+), 4250 deletions(-)
 create mode 100644 benchmark/AlignedSegment_bench.py
 delete mode 100644 debian/patches/correct-spelling-errors.patch
 delete mode 100644 debian/patches/cython23.patch
 delete mode 100644 debian/patches/improve-python3-compatibility.patch
 delete mode 100644 debian/patches/sam_mpileup.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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