[med-svn] [snakemake] 02/04: Merge tag 'upstream/3.6.1+dfsg'

[Kevin Murray]

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

commit 568ba093fc52ad31bfa7e129199c3a42b94e4832
Merge: 08cd602 fa7a4fd
Author: Kevin Murray <spam at kdmurray.id.au>
Date:   Tue Apr 19 12:12:58 2016 +1000

    Merge tag 'upstream/3.6.1+dfsg'
    
    Upstream version 3.6.1+dfsg

 CHANGELOG.md                                       |  71 ++++++++++++
 LICENSE => LICENSE.md                              |   2 +-
 README => README.md                                |   2 +-
 misc/vim/syntax/snakemake.vim                      |   6 +-
 setup.py                                           |   2 +-
 snakemake-tutorial.html                            |   2 +-
 snakemake/__init__.py                              |  18 +--
 snakemake/dag.py                                   | 127 ++++++++++++---------
 snakemake/exceptions.py                            |  18 +--
 snakemake/executors.py                             |  26 +++--
 snakemake/io.py                                    | 106 ++++++++++-------
 snakemake/jobs.py                                  |  86 ++++++++------
 snakemake/logging.py                               |   5 +-
 snakemake/output_index.py                          |   8 +-
 snakemake/parser.py                                |   8 +-
 snakemake/persistence.py                           |   2 +
 snakemake/remote/FTP.py                            |  12 +-
 snakemake/remote/dropbox.py                        |  33 ++++--
 snakemake/rules.py                                 |  39 +++----
 snakemake/script.py                                |  22 +++-
 snakemake/shell.py                                 |   2 +-
 snakemake/version.py                               |   2 +-
 snakemake/workflow.py                              |   7 ++
 tests/test01/Snakefile                             |   5 +
 tests/test_input_generator/Snakefile               |  33 ++++++
 .../test_input_generator/expected-results/foo.out1 |   3 +
 .../test_input_generator/expected-results/foo.out2 |   3 +
 .../test_input_generator/expected-results/foo.out3 |   3 +
 tests/test_input_generator/foo.1.in                |   1 +
 tests/test_input_generator/foo.2.in                |   1 +
 tests/test_input_generator/foo.3.in                |   1 +
 tests/test_script/Snakefile                        |   5 +
 tests/test_script/config.yaml                      |   1 +
 tests/test_script/scripts/test.R                   |   6 +
 tests/testapi.py                                   |  13 +++
 tests/tests.py                                     |   3 +
 36 files changed, 469 insertions(+), 215 deletions(-)

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