[med-svn] [snakemake] 02/03: Merge tag 'upstream/3.5.5'

[Kevin Murray]

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daube-guest pushed a commit to branch master
in repository snakemake.

commit 3e50d342d35353347645ac2fad6e3ae65f292f82
Merge: e650711 14aba72
Author: Kevin Murray <spam at kdmurray.id.au>
Date:   Fri Jan 29 17:17:38 2016 +0200

    Merge tag 'upstream/3.5.5'
    
    Upstream version 3.5.5

 docker/Dockerfile                                  |   7 --
 snakemake/__init__.py                              |  26 ++++-
 snakemake/dag.py                                   |  75 ++++++++++++-
 snakemake/executors.py                             |  11 +-
 snakemake/jobs.py                                  |  10 +-
 snakemake/parser.py                                |  14 ++-
 snakemake/remote/FTP.py                            |   2 +-
 snakemake/remote/GS.py                             |   1 +
 snakemake/remote/HTTP.py                           |   2 +-
 snakemake/remote/SFTP.py                           |   2 +-
 snakemake/remote/dropbox.py                        |   2 +-
 snakemake/script.py                                | 122 +++++++++++----------
 snakemake/shell.py                                 |   2 +-
 snakemake/version.py                               |   2 +-
 snakemake/workflow.py                              |  28 ++++-
 snakemake/wrapper.py                               |  22 ++++
 tests/test_omitfrom/Snakefile                      |  54 +++++++++
 .../test_omitfrom/expected-results/independent.txt |   0
 tests/test_omitfrom/expected-results/levelone.txt  |   0
 .../expected-results/leveltwo_first.txt            |   0
 .../expected-results/leveltwo_second.txt           |   0
 tests/test_omitfrom/expected-results/test1.second  |   0
 tests/test_omitfrom/expected-results/test2.second  |   0
 tests/test_until/Snakefile                         |  54 +++++++++
 tests/test_until/expected-results/levelone.txt     |   0
 .../test_until/expected-results/leveltwo_first.txt |   0
 .../expected-results/leveltwo_second.txt           |   0
 tests/test_until/expected-results/test1.second     |   0
 tests/test_until/expected-results/test2.second     |   0
 tests/tests.py                                     |  11 ++
 30 files changed, 357 insertions(+), 90 deletions(-)

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