[med-svn] [snakemake] 02/05: Updated version 3.13.3 from 'upstream/3.13.3'

[Kevin Murray]

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

commit 4cce424a8bb76e90e8afbedfa6b4a9f8beb5b287
Merge: 54f4469 955a326
Author: Kevin Murray <kdmfoss at gmail.com>
Date:   Tue Jul 18 10:08:51 2017 +1000

    Updated version 3.13.3 from 'upstream/3.13.3'
    
    with Debian dir 20b11a77378f0a5f6b91f57c85ec368005a18b0b

 CHANGELOG.md                                       |  65 +++
 Dockerfile                                         |  17 +-
 README.md                                          |  13 +-
 docs/getting_started/examples.rst                  |   5 +-
 docs/getting_started/installation.rst              |  35 +-
 docs/index.rst                                     |  34 +-
 docs/project_info/authors.rst                      |   1 +
 docs/project_info/citations.rst                    |   4 +-
 docs/project_info/contributing.rst                 |   4 +-
 docs/project_info/faq.rst                          |  25 +
 docs/project_info/more_resources.rst               |   4 +
 docs/snakefiles/configuration.rst                  |  32 ++
 docs/snakefiles/deployment.rst                     |  38 +-
 docs/snakefiles/modularization.rst                 |  79 ++-
 docs/snakefiles/remote_files.rst                   | 119 ++++-
 docs/snakefiles/rules.rst                          | 190 ++++++-
 docs/tutorial/additional_features.rst              | 120 ++++-
 docs/tutorial/advanced.rst                         |  51 +-
 docs/tutorial/basics.rst                           | 100 +++-
 docs/tutorial/{welcome.rst => setup.rst}           |  46 +-
 docs/tutorial/tutorial.rst                         |  37 ++
 environment.yml                                    |  12 +-
 examples/c/src/Snakefile                           |   2 +-
 misc/vim/syntax/snakemake.vim                      |   2 +-
 setup.py                                           |   6 +-
 snakemake/__init__.py                              | 116 ++++-
 snakemake/benchmark.py                             | 259 ++++++++++
 snakemake/common.py                                |   6 +
 snakemake/conda.py                                 | 262 ++++++----
 snakemake/dag.py                                   | 118 +++--
 snakemake/exceptions.py                            |  20 +-
 snakemake/executors.py                             | 203 +++++---
 snakemake/io.py                                    |  32 +-
 snakemake/jobs.py                                  |  60 ++-
 snakemake/logging.py                               |  16 +-
 snakemake/parser.py                                |   9 +-
 snakemake/persistence.py                           |  13 +-
 snakemake/remote/FTP.py                            |  89 +++-
 snakemake/remote/GS.py                             |  23 +-
 snakemake/remote/HTTP.py                           |  65 ++-
 snakemake/remote/NCBI.py                           | 574 +++++++++++++++++++++
 snakemake/remote/S3.py                             |  52 +-
 .../test_remote => snakemake/remote}/S3Mocked.py   |  14 +-
 snakemake/remote/SFTP.py                           |  28 +-
 snakemake/remote/XRootD.py                         | 197 +++++++
 snakemake/remote/__init__.py                       | 114 ++--
 snakemake/remote/dropbox.py                        |  47 +-
 snakemake/report.py                                |   4 +-
 snakemake/rules.py                                 |  38 +-
 snakemake/scheduler.py                             |  39 +-
 snakemake/script.py                                |  55 +-
 snakemake/shell.py                                 |  12 +-
 snakemake/utils.py                                 |   9 +
 snakemake/version.py                               |   2 +-
 snakemake/workflow.py                              |  43 +-
 snakemake/wrapper.py                               |  10 +-
 environment.yml => test-environment.yml            |  11 +-
 tests/test_benchmark/Snakefile                     |  30 +-
 .../{test.benchmark.txt => test.benchmark_run.txt} |   0
 .../expected-results/test.benchmark_run_shell.txt} |   0
 ...est.benchmark.txt => test.benchmark_script.txt} |   0
 ...test.benchmark.txt => test.benchmark_shell.txt} |   0
 tests/test_benchmark/script.py                     |   7 +
 tests/test_conda/Snakefile                         |   4 +-
 tests/test_conda_custom_prefix/Snakefile           |  12 +
 .../expected-results/test0.out                     |   1 +
 .../expected-results/test1.out                     |   1 +
 .../expected-results/test2.out                     |   1 +
 tests/test_conda_custom_prefix/test-env.yaml       |   4 +
 tests/test_default_remote/Snakefile                |  40 ++
 .../expected-results/.gitignore}                   |   0
 tests/test_default_remote/test.txt                 |   1 +
 tests/test_dynamic_temp/Snakefile                  |  30 ++
 .../expected-results/out.txt}                      |   0
 tests/test_dynamic_temp/test1.txt                  |   8 +
 tests/test_dynamic_temp/test2.txt                  |   8 +
 tests/test_ftp_immediate_close/Snakefile           |  11 +
 .../expected-results/size.txt                      |   1 +
 tests/test_get_log_none/Snakefile                  |   2 +-
 tests/test_issue260/Snakefile                      |  32 ++
 .../test_issue260/expected-results/output/done.txt |   1 +
 .../expected-results/output/result.n1              |   1 +
 .../expected-results/output/result.n2              |   1 +
 .../expected-results/output/result.n3              |   1 +
 tests/test_remote/Snakefile                        |  21 +-
 tests/test_remote_ncbi/Snakefile                   |  26 +
 tests/test_remote_ncbi/expected-results/sizes.txt  |   4 +
 tests/test_remote_ncbi_simple/Snakefile            |  14 +
 .../expected-results/sizes.txt                     |   1 +
 tests/test_run_namedlist/Snakefile                 |   5 +
 .../expected-results/file.txt}                     |   0
 tests/test_script/Snakefile                        |  13 +
 tests/test_script/expected-results/test.html       | 234 +++++++++
 tests/test_script/scripts/test.Rmd                 |  22 +
 tests/test_subworkflows/Snakefile                  |   7 +-
 tests/test_symlink_time_handling/Snakefile         |  22 +-
 tests/test_xrootd/Snakefile                        |  27 +
 tests/tests.py                                     |  56 +-
 wercker.yml                                        |   4 +
 99 files changed, 3563 insertions(+), 671 deletions(-)

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