[med-svn] [snakemake] branch master updated (c734010 -> e650711)

[Kevin Murray]

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

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

      from  c734010   Fix URL to upstream in d/copyright
       new  300fdf5   Imported Upstream version 3.5.4+dfsg
       new  2426771   Merge tag 'upstream/3.5.4+dfsg'
       new  e650711   Update changelog

The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 README                                             |   7 +-
 debian/changelog                                   |   6 +
 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 +
 .../expected-results/.gitignore                    |   0
 .../test_empty_include/include.rules               |   0
 tests/test_nonstr_params/Snakefile                 |   8 +
 .../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 +-
 53 files changed, 2983 insertions(+), 254 deletions(-)
 create mode 100644 docker/Dockerfile
 create mode 100644 misc/vim/README.md
 rename misc/{ => vim/syntax}/snakemake.vim (100%)
 create mode 100644 snakemake-tutorial.html
 create mode 100644 snakemake/decorators.py
 create mode 100644 snakemake/remote/FTP.py
 create mode 100644 snakemake/remote/GS.py
 create mode 100644 snakemake/remote/HTTP.py
 create mode 100644 snakemake/remote/S3.py
 create mode 100644 snakemake/remote/SFTP.py
 create mode 100644 snakemake/remote/__init__.py
 create mode 100644 snakemake/remote/dropbox.py
 create mode 100644 snakemake/script.py
 create mode 100644 tests/test_empty_include/Snakefile
 copy tests/{test09 => test_empty_include}/expected-results/.gitignore (100%)
 copy examples/cufflinks/hg19.fa => tests/test_empty_include/include.rules (100%)
 create mode 100644 tests/test_nonstr_params/Snakefile
 copy tests/{test_conditional => test_nonstr_params}/expected-results/test.out (100%)
 create mode 100644 tests/test_remote/S3Mocked.py
 create mode 100644 tests/test_remote/Snakefile
 copy tests/{ => test_remote}/__init__.py (100%)
 create mode 100644 tests/test_remote/expected-results/out.txt
 create mode 100644 tests/test_remote/test.txt
 create mode 100644 tests/test_script/Snakefile
 create mode 100644 tests/test_script/expected-results/test.in
 create mode 100644 tests/test_script/expected-results/test.out
 create mode 100644 tests/test_script/scripts/test.R
 create mode 100644 tests/test_script/scripts/test.py
 create mode 100644 tests/test_shadow/Snakefile
 create mode 100644 tests/test_shadow/expected-results/simple_full.out
 create mode 100644 tests/test_shadow/expected-results/simple_shallow.out
 create mode 100644 tests/test_shadow/test.in

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