[med-svn] [snakemake] 02/04: Merge tag 'upstream/3.4.2'

[Kevin Murray]

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

commit 7f1a10b3414762f855ece00fc74cb4358969d99c
Merge: c7005f1 d977f15
Author: Kevin Murray <spam at kdmurray.id.au>
Date:   Tue Sep 15 23:48:27 2015 +1000

    Merge tag 'upstream/3.4.2'
    
    Upstream version 3.4.2

 .gitignore                                         |   3 +-
 conda/build.sh                                     |  12 --
 conda/snakemake/bld.bat                            |   8 -
 conda/snakemake/build.sh                           |   9 -
 conda/snakemake/meta.yaml                          |  22 ---
 docker/Dockerfile                                  |   7 -
 setup.py                                           |  24 ++-
 snakemake/__init__.py                              | 213 ++++++++++++---------
 snakemake/exceptions.py                            |  13 +-
 snakemake/executors.py                             | 211 +++++++++++---------
 snakemake/io.py                                    |  43 ++++-
 snakemake/jobs.py                                  |   2 +-
 snakemake/logging.py                               |   5 +
 snakemake/persistence.py                           |   7 +-
 snakemake/report.css                               |  25 ++-
 snakemake/report.py                                |  17 +-
 snakemake/scheduler.py                             |   4 +-
 snakemake/shell.py                                 |   2 +
 snakemake/utils.py                                 |  24 +++
 snakemake/version.py                               |   2 +-
 snakemake/workflow.py                              |  15 +-
 tests/test_benchmark/Snakefile                     |   4 +-
 .../{test.benchmark.json => test.benchmark.txt}    |   0
 tests/test_report/Snakefile                        |  11 +-
 tests/test_symlink_temp/Snakefile                  |  22 +++
 .../test.benchmark.json => test_symlink_temp/a}    |   0
 .../test.benchmark.json => test_symlink_temp/b}    |   0
 .../expected-results/.gitignore}                   |   0
 tests/test_update_config/Snakefile                 |  14 ++
 tests/test_update_config/cp.rule                   |  16 ++
 tests/test_update_config/echo.rule                 |   7 +
 tests/test_update_config/echo.yaml                 |   2 +
 .../expected-results/config.yaml                   |   4 +
 tests/test_update_config/test.yaml                 |   4 +
 tests/tests.py                                     |  16 +-
 35 files changed, 480 insertions(+), 288 deletions(-)

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