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

[Kevin Murray]

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

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

commit 189bb92ebc6f11c6952114c8e4246d90838f2ec4
Merge: 2343b29 a51fb0f
Author: Kevin Murray <kdmfoss at gmail.com>
Date:   Wed Dec 7 09:02:03 2016 +1100

    Merge branch 'upstream'

 CHANGELOG.md                                       |  15 ++
 biglogo.pdf                                        | Bin 0 -> 3806 bytes
 biglogo.png                                        | Bin 0 -> 17334 bytes
 biglogo.svg                                        | 141 +++++++++++
 bitbucket-pipelines.yml                            |   1 -
 environment.yml                                    |   4 +
 setup.py                                           |  12 +-
 snakemake/__init__.py                              |  47 +++-
 snakemake/common.py                                |  10 +
 snakemake/conda.py                                 |  50 ++++
 snakemake/dag.py                                   |  22 +-
 snakemake/exceptions.py                            |   8 +
 snakemake/executors.py                             | 131 ++++++----
 snakemake/futures.py                               |  36 ---
 snakemake/io.py                                    |  98 ++++++--
 snakemake/jobs.py                                  |  56 ++++-
 snakemake/logging.py                               |  53 ++--
 snakemake/parser.py                                | 110 ++++----
 snakemake/persistence.py                           |  20 +-
 snakemake/remote/HTTP.py                           |  14 +-
 snakemake/remote/__init__.py                       |   4 +-
 snakemake/report.py                                |  46 ++--
 snakemake/rules.py                                 |  53 +++-
 snakemake/scheduler.py                             |  18 +-
 snakemake/script.py                                | 160 +++++++-----
 snakemake/shell.py                                 |   8 +-
 snakemake/version.py                               |   4 +-
 snakemake/workflow.py                              |  45 +++-
 snakemake/wrapper.py                               |  38 ++-
 tests/test01/Snakefile                             |   2 +-
 tests/test05/Snakefile                             |   4 +
 tests/test09/Snakefile                             |   3 +
 tests/test13/Snakefile                             |   4 +
 tests/test14/Snakefile.nonstandard                 |   4 +
 tests/test_ancient/Snakefile                       |  28 +++
 tests/test_ancient/expected-results/A              |   0
 tests/test_ancient/expected-results/B              |   0
 tests/test_ancient/expected-results/C              |   1 +
 tests/test_ancient/expected-results/D              |   1 +
 tests/test_conda/Snakefile                         |  11 +
 tests/test_conda/expected-results/test0.out        | 279 +++++++++++++++++++++
 tests/test_conda/expected-results/test1.out        | 279 +++++++++++++++++++++
 tests/test_conda/expected-results/test2.out        | 279 +++++++++++++++++++++
 tests/test_conda/test-env.yaml                     |   4 +
 tests/test_delete_output/Snakefile                 |  52 +++-
 tests/test_delete_output/nosuchfile                |   0
 tests/test_get_log_both/test.out                   |   2 -
 tests/test_get_log_complex/test.out                |   2 -
 tests/test_get_log_stderr/test.out                 |   2 -
 tests/test_get_log_stdout/test.out                 |   2 -
 tests/test_issue381/Snakefile                      |  21 ++
 tests/test_issue381/a.in                           |   0
 tests/test_issue381/expected-results/b.out         |   0
 tests/test_persistent_dict/Snakefile               |  44 ++--
 tests/test_rule_defined_in_for_loop/Snakefile      |  12 +
 .../expected-results/iteration-01.txt              |   0
 .../expected-results/iteration-02.txt              |   0
 .../test_rule_defined_in_for_loop/iteration-01.txt |   0
 tests/test_wrapper/Snakefile                       |   7 +
 tests/test_wrapper/expected-results/test.vcf.gz    | Bin 0 -> 438 bytes
 tests/test_wrapper/test.vcf                        |  15 ++
 tests/tests.py                                     |  44 +++-
 62 files changed, 1915 insertions(+), 391 deletions(-)

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