[med-svn] [circlator] 01/02: Merge tag 'debian/1.3.0-1' into debian/jessie-backports

[Afif Elghraoui]

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

afif pushed a commit to branch debian/jessie-backports
in repository circlator.

commit dd4cc0455843d3e593688a37d2a3d747f7aa3abf
Merge: fc94339 461ff2e
Author: Afif Elghraoui <afif at debian.org>
Date:   Mon Aug 22 00:38:01 2016 -0700

    Merge tag 'debian/1.3.0-1' into debian/jessie-backports
    
    tagging package circlator version debian/1.3.0-1

 .travis.yml                                        |   4 -
 circlator/__init__.py                              |   2 +-
 circlator/external_progs.py                        |  45 +-
 circlator/fixstart.py                              |  55 --
 circlator/program.py                               |  55 +-
 circlator/start_fixer.py                           | 337 +++++++++
 circlator/tasks/all.py                             |   5 +-
 circlator/tasks/fixstart.py                        |   6 +-
 circlator/tasks/progcheck.py                       |   6 +-
 ...tart_fixer_find_circular_using_prodigal.ctgs.fa | 109 +++
 ...art_fixer_find_circular_using_promer.contigs.fa | 168 +++++
 .../start_fixer_find_circular_using_promer.refs.fa |  75 ++
 circlator/tests/data/start_fixer_init_contigs.fa   |   4 +
 circlator/tests/data/start_fixer_init_dnaA.fa      |   2 +
 circlator/tests/data/start_fixer_init_ignore_ids   |   2 +
 .../data/start_fixer_max_length_from_fasta_file.fa |   6 +
 .../data/start_fixer_rearrange_contigs.expect.fa   | 776 +++++++++++++++++++++
 .../data/start_fixer_rearrange_contigs.expect.log  |   8 +
 .../tests/data/start_fixer_rearrange_contigs.in.fa | 776 +++++++++++++++++++++
 .../data/start_fixer_rearrange_contigs.refs.fa     |  50 ++
 .../data/start_fixer_run_bit_of_everything.ctg.fa  | 282 ++++++++
 .../start_fixer_run_bit_of_everything.expect.fa    | 282 ++++++++
 .../data/start_fixer_run_bit_of_everything.ignore  |   1 +
 .../data/start_fixer_run_bit_of_everything.ref.fa  |  25 +
 .../data/start_fixer_run_ignore_all.expect.fa      |   2 +
 circlator/tests/data/start_fixer_run_ignore_all.fa |   2 +
 .../data/start_fixer_run_ignore_all.to_ignore      |   1 +
 .../data/start_fixer_run_none_for_prodigal.ctg.fa  |  91 +++
 .../start_fixer_run_none_for_prodigal.expect.fa    |  91 +++
 .../data/start_fixer_run_none_for_prodigal.ref.fa  |  25 +
 ..._fixer_write_fasta_plus_circularized_ends.in.fa |   8 +
 ...fixer_write_fasta_plus_circularized_ends.out.fa |  12 +
 ...rite_fasta_plus_circularized_ends.out.ignore.fa |   6 +
 .../data/start_fixer_write_renamed_contigs.fa      |   4 +
 circlator/tests/start_fixer_test.py                | 225 ++++++
 circlator/versions.py                              |   7 +-
 debian/README.source                               |  24 -
 debian/changelog                                   |   9 +
 debian/control                                     |   1 +
 debian/man/bio-assembly-refinement.1               |  27 -
 debian/man/contig_break_finder.1                   |   1 -
 debian/man/contig_cleaner.1                        |   1 -
 debian/man/contig_overlap_trimmer.1                |   1 -
 debian/man/pacbio_post_process.1                   |   1 -
 debian/patches/bundle-bioassemblyref.patch         |  23 -
 debian/patches/pysam-maxversion.patch              |  17 -
 debian/patches/series                              |   3 -
 debian/patches/spades-call.patch                   |  18 -
 debian/rules                                       |  11 -
 debian/watch                                       |   8 +-
 install_dependencies.sh                            |   2 +-
 setup.py                                           |   5 +-
 52 files changed, 3462 insertions(+), 245 deletions(-)

diff --cc debian/changelog
index a74c5e8,f538835..877f520
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,12 +1,18 @@@
+ circlator (1.3.0-1) unstable; urgency=medium
+ 
+   * Remove second tarball and supporting code
+   * Imported Upstream version 1.3.0
+   * Drop all patches
+   * Build-depend on prodigal to run test suite
+ 
+  -- Afif Elghraoui <afif at debian.org>  Mon, 15 Aug 2016 23:31:57 -0700
+ 
 +circlator (1.2.1-1~bpo8+1) jessie-backports; urgency=medium
 +
 +  * Rebuild for jessie-backports.
 +
 + -- Afif Elghraoui <afif at debian.org>  Sun, 08 May 2016 01:07:27 -0700
 +
  circlator (1.2.1-1) unstable; urgency=medium
  
    * Fix typo in d/upstream/metadata

-- 
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