[med-svn] [snakemake] 02/03: Merge tag 'upstream/3.5.4+dfsg'

[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 2426771a4f64d4ddef9355ba4668ddc260e0d55a
Merge: c734010 300fdf5
Author: Kevin Murray <spam at kdmurray.id.au>
Date:   Thu Dec 17 21:08:03 2015 +1100

    Merge tag 'upstream/3.5.4+dfsg'
    
    Upstream version 3.5.4+dfsg

 README                                             |   7 +-
 docker/Dockerfile                                  |   7 +
 docs/index.rst                                     |   2 +-
 misc/vim/README.md                                 |  13 +
 misc/{ => vim/syntax}/snakemake.vim                |   0
 setup.py                                           |  22 +-
 snakemake-tutorial.html                            | 605 +++++++++++++++++++++
 snakemake/__init__.py                              |  52 +-
 snakemake/dag.py                                   |  90 ++-
 snakemake/decorators.py                            |  17 +
 snakemake/exceptions.py                            |  36 +-
 snakemake/executors.py                             |  65 ++-
 snakemake/io.py                                    | 155 +++++-
 snakemake/jobs.py                                  | 210 ++++++-
 snakemake/output_index.py                          |   5 +-
 snakemake/parser.py                                |  82 ++-
 snakemake/persistence.py                           |  10 +-
 snakemake/remote/FTP.py                            | 126 +++++
 snakemake/remote/GS.py                             |  21 +
 snakemake/remote/HTTP.py                           | 143 +++++
 snakemake/remote/S3.py                             | 443 +++++++++++++++
 snakemake/remote/SFTP.py                           | 112 ++++
 snakemake/remote/__init__.py                       | 159 ++++++
 snakemake/remote/dropbox.py                        | 110 ++++
 snakemake/rules.py                                 |  86 ++-
 snakemake/scheduler.py                             | 116 ++--
 snakemake/script.py                                | 139 +++++
 snakemake/shell.py                                 |  13 +-
 snakemake/utils.py                                 |  25 +-
 snakemake/version.py                               |   2 +-
 snakemake/workflow.py                              |  37 +-
 tests/test_empty_include/Snakefile                 |   1 +
 .../test_empty_include/expected-results/.gitignore |   0
 tests/test_empty_include/include.rules             |   0
 tests/test_nonstr_params/Snakefile                 |   8 +
 tests/test_nonstr_params/expected-results/test.out |   0
 tests/test_remote/S3Mocked.py                      | 125 +++++
 tests/test_remote/Snakefile                        |  86 +++
 tests/test_remote/__init__.py                      |   0
 tests/test_remote/expected-results/out.txt         |   4 +
 tests/test_remote/test.txt                         |   4 +
 tests/test_script/Snakefile                        |  14 +
 tests/test_script/expected-results/test.in         |   1 +
 tests/test_script/expected-results/test.out        |   1 +
 tests/test_script/scripts/test.R                   |   8 +
 tests/test_script/scripts/test.py                  |   2 +
 tests/test_shadow/Snakefile                        |  26 +
 tests/test_shadow/expected-results/simple_full.out |   2 +
 .../expected-results/simple_shallow.out            |   2 +
 tests/test_shadow/test.in                          |   1 +
 tests/test_url_include/Snakefile                   |   2 +-
 tests/tests.py                                     |  34 +-
 52 files changed, 2977 insertions(+), 254 deletions(-)

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snakemake.git