[med-svn] [snakemake] 02/06: Update upstream source from tag 'upstream/4.3.0'

[chrysn]

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

commit 26639721e5d07c9cb8f849290d525a296c5fe8e3
Merge: afcb2de 06602fe
Author: chrysn <chrysn at fsfe.org>
Date:   Fri Nov 3 11:33:23 2017 +0100

    Update upstream source from tag 'upstream/4.3.0'
    
    Update to upstream version '4.3.0'
    with Debian dir e1aef2daa842e41818d93e1cebfc2917b6f66a12

 CHANGELOG.md                                       |  51 ++
 Dockerfile                                         |  14 +-
 docs/_static/sphinx-argparse.css                   |   6 +
 docs/conf.py                                       |   6 +-
 docs/executable.rst                                | 123 +++-
 docs/getting_started/installation.rst              |   4 +-
 docs/index.rst                                     |  26 +-
 docs/project_info/faq.rst                          |   6 +-
 docs/project_info/more_resources.rst               |   6 +-
 docs/requirements.txt                              |   1 +
 docs/snakefiles/deployment.rst                     |  29 +
 docs/snakefiles/modularization.rst                 |   8 +-
 docs/snakefiles/remote_files.rst                   | 108 +++-
 docs/snakefiles/rules.rst                          |  34 +-
 docs/tutorial/tutorial.rst                         |   2 +-
 environment.yml                                    |  15 +-
 setup.py                                           |  16 +-
 snakemake/__init__.py                              | 359 ++++++++++--
 snakemake/common.py                                |   9 +
 snakemake/conda.py                                 |  23 +-
 snakemake/dag.py                                   | 162 ++++--
 snakemake/exceptions.py                            |   4 +
 snakemake/executors.py                             | 619 +++++++++++++++++----
 snakemake/io.py                                    | 100 +++-
 snakemake/jobs.py                                  |  44 +-
 snakemake/logging.py                               |  53 +-
 snakemake/parser.py                                |  28 +-
 snakemake/persistence.py                           | 222 ++++----
 snakemake/remote/FTP.py                            |   3 +
 snakemake/remote/GS.py                             | 128 ++++-
 snakemake/remote/HTTP.py                           |   3 +
 snakemake/remote/NCBI.py                           |   6 +-
 snakemake/remote/S3.py                             | 225 ++------
 snakemake/remote/S3Mocked.py                       |  13 +-
 snakemake/remote/__init__.py                       |  38 +-
 snakemake/remote/dropbox.py                        |   2 +-
 snakemake/remote/gfal.py                           | 137 +++++
 snakemake/remote/gridftp.py                        |  71 +++
 snakemake/remote/webdav.py                         | 167 ++++++
 snakemake/rules.py                                 | 104 ++--
 snakemake/scheduler.py                             | 167 ++++--
 snakemake/script.py                                |  12 +-
 snakemake/shell.py                                 |  18 +-
 snakemake/singularity.py                           |  73 +++
 snakemake/version.py                               |   4 +-
 snakemake/workflow.py                              | 123 +++-
 snakemake/wrapper.py                               |  20 +-
 test-environment.yml                               |  19 +-
 tests/test_issue612/Snakefile                      |  11 +
 .../expected-results/.gitignore}                   |   0
 tests/test_kubernetes/README.md                    |  11 +
 tests/test_kubernetes/Snakefile                    |  29 +
 tests/test_kubernetes/envs/gzip.yaml               |   4 +
 tests/test_profile/Snakefile                       |   3 +
 tests/test_profile/Snakefile.internal              |   5 +
 tests/test_profile/config.yaml                     |   1 +
 .../expected-results/test.out}                     |   0
 tests/test_profile/workflow-config.yaml            |   1 +
 tests/test_remote_gs/Snakefile                     |  15 +
 .../expected-results/landsat-data.txt              | 218 ++++++++
 tests/test_remote_gs/landsat-data.txt              | 218 ++++++++
 tests/test_remote_log/Snakefile                    |  17 +
 tests/test_remote_log/expected-results/motoState.p | Bin 0 -> 848 bytes
 .../.done => test_remote_log/test.txt}             |   0
 tests/test_remote_ncbi/Snakefile                   |   5 +-
 tests/test_remote_ncbi/expected-results/sizes.txt  |   8 +-
 tests/test_remote_ncbi_simple/Snakefile            |   4 +-
 .../expected-results/sizes.txt                     |   2 +-
 tests/test_restartable_job_cmd_exit_1/Snakefile    |  27 +-
 .../expected-results/.done                         |   1 +
 tests/test_script/expected-results/test.html       |  85 +--
 tests/test_singularity/Snakefile                   |   7 +
 tests/test_singularity/expected-results/test.out   |   2 +
 tests/test_static_remote/S3MockedForStaticTest.py  |   7 +-
 tests/test_wrapper/Snakefile                       |   2 +-
 tests/tests.py                                     | 103 ++--
 wercker.yml                                        |   6 +-
 77 files changed, 3359 insertions(+), 844 deletions(-)

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