[med-svn] [python-htseq] branch master updated (3a7e70e -> 13b926e)

[Diane Trout]

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diane-guest pushed a change to branch master
in repository python-htseq.

      from  3a7e70e   Add bug closing
       new  1965301   Imported Upstream version 0.6.1p1
       new  36c4d8d   Imported Upstream version 0.6.1p1
       new  ae4a1b4   Merge tag 'upstream/0.6.1p1'
       new  0d6b97f   Add get-orig-source to download from upstream svn. (upstream's release process deletes source files)
       new  63425f9   Imported Upstream version 0.6.1p1
       new  7e64908   Imported Upstream version 0.6.1p1
       new  86cfafe   Merge tag 'upstream/0.6.1p1'
       new  c4eae79   New upstream release.
       new  1f420b7   Use upstream scripts to build and clean.
       new  0c72d1d   Try to delete generated test data and setup generated files.
       new  a48a249   Use dh_numpy to detect numpy abi version. (Closes: #742921)
       new  a3d464c   remove DH_VERBOSE=1, defaulting to verbose is against policy
       new  fbc4e1b   add set-matplotlib-backend.patch to avoid a missing _TkAgg matplotlib backend.
       new  99c284a   Add build dependency on python-matplotlib and python-pysam (for testing)
       new  13b926e   Run upstream tests.

The 15 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:
 HTSeq/__init__.py                                  |    173 +-
 HTSeq/_version.py                                  |      1 -
 HTSeq/scripts/count.py                             |    135 +-
 PKG-INFO                                           |     19 -
 VERSION                                            |      2 +-
 debian/changelog                                   |     15 +
 debian/control                                     |      4 +-
 debian/patches/series                              |      1 +
 debian/patches/set-matplotlib-backend.patch        |     29 +
 debian/rules                                       |     40 +-
 doc/GenomicArrayOfSets.svg                         |    309 +
 doc/alignments.rst                                 |     32 +-
 doc/cigar.png                                      |    Bin 0 -> 13104 bytes
 doc/count.rst                                      |    184 +-
 doc/counting.rst                                   |    303 +
 doc/features.rst                                   |    106 -
 doc/genomic.rst                                    |      2 +-
 doc/history.rst                                    |     47 +-
 doc/index.rst                                      |      2 +
 doc/install.rst                                    |      2 +-
 doc/make_it                                        |      3 -
 doc/otherparsers.rst                               |    173 +
 doc/overview.rst                                   |     20 +
 doc/tour.rst                                       |    222 +-
 example_data/Homo_sapiens.GRCh37.56_chrom1.gtf     | 197895 ++++++++++++++++++
 example_data/SRR001432_head.bam                    |    Bin 0 -> 12849262 bytes
 example_data/SRR001432_head_sorted.bam             |    Bin 0 -> 11925267 bytes
 example_data/SRR001432_head_sorted.bam.bai         |    Bin 0 -> 2873888 bytes
 .../Saccharomyces_cerevisiae.SGD1.01.56.gtf.gz     |    Bin 0 -> 373439 bytes
 example_data/fastaEx.fa                            |      6 +
 example_data/feature_list.txt                      |      3 +
 example_data/yeast_RNASeq_excerpt.sam              |  25019 +++
 example_data/yeast_RNASeq_excerpt_sequence.txt     |  99996 +++++++++
 setup.cfg                                          |      5 -
 setup.py                                           |      2 +-
 src/HTSeq/_HTSeq.pyx                               |     45 +-
 test/test.py                                       |     36 +
 test/tss_test.py                                   |     35 +
 todo.txt                                           |      8 +
 39 files changed, 324492 insertions(+), 382 deletions(-)
 delete mode 100644 HTSeq/_version.py
 delete mode 100644 PKG-INFO
 create mode 100644 debian/patches/set-matplotlib-backend.patch
 create mode 100644 doc/GenomicArrayOfSets.svg
 create mode 100644 doc/cigar.png
 create mode 100644 doc/counting.rst
 delete mode 100644 doc/make_it
 create mode 100644 doc/otherparsers.rst
 create mode 100644 example_data/Homo_sapiens.GRCh37.56_chrom1.gtf
 create mode 100644 example_data/SRR001432_head.bam
 create mode 100644 example_data/SRR001432_head_sorted.bam
 create mode 100644 example_data/SRR001432_head_sorted.bam.bai
 create mode 100644 example_data/Saccharomyces_cerevisiae.SGD1.01.56.gtf.gz
 create mode 100644 example_data/fastaEx.fa
 create mode 100644 example_data/feature_list.txt
 create mode 100644 example_data/yeast_RNASeq_excerpt.sam
 create mode 100644 example_data/yeast_RNASeq_excerpt_sequence.txt
 delete mode 100644 setup.cfg
 create mode 100644 test/test.py
 create mode 100644 test/tss_test.py
 create mode 100644 todo.txt

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