[med-svn] [snakemake] branch upstream updated (300fdf5 -> 14aba72)

[Kevin Murray]

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

      from  300fdf5   Imported Upstream version 3.5.4+dfsg
       new  14aba72   Imported Upstream version 3.5.5

The 1 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
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Summary of changes:
 docker/Dockerfile                                  |   7 --
 snakemake/__init__.py                              |  26 ++++-
 snakemake/dag.py                                   |  75 ++++++++++++-
 snakemake/executors.py                             |  11 +-
 snakemake/jobs.py                                  |  10 +-
 snakemake/parser.py                                |  14 ++-
 snakemake/remote/FTP.py                            |   2 +-
 snakemake/remote/GS.py                             |   1 +
 snakemake/remote/HTTP.py                           |   2 +-
 snakemake/remote/SFTP.py                           |   2 +-
 snakemake/remote/dropbox.py                        |   2 +-
 snakemake/script.py                                | 122 +++++++++++----------
 snakemake/shell.py                                 |   2 +-
 snakemake/version.py                               |   2 +-
 snakemake/workflow.py                              |  28 ++++-
 snakemake/wrapper.py                               |  22 ++++
 tests/test_omitfrom/Snakefile                      |  54 +++++++++
 .../test_omitfrom/expected-results/independent.txt |   0
 .../test_omitfrom/expected-results/levelone.txt    |   0
 .../expected-results/leveltwo_first.txt            |   0
 .../expected-results/leveltwo_second.txt           |   0
 .../test_omitfrom/expected-results/test1.second    |   0
 .../test_omitfrom/expected-results/test2.second    |   0
 tests/test_until/Snakefile                         |  54 +++++++++
 .../test_until/expected-results/levelone.txt       |   0
 .../test_until/expected-results/leveltwo_first.txt |   0
 .../expected-results/leveltwo_second.txt           |   0
 .../test_until/expected-results/test1.second       |   0
 .../test_until/expected-results/test2.second       |   0
 tests/tests.py                                     |  11 ++
 30 files changed, 357 insertions(+), 90 deletions(-)
 delete mode 100644 docker/Dockerfile
 create mode 100644 snakemake/wrapper.py
 create mode 100644 tests/test_omitfrom/Snakefile
 copy examples/cufflinks/hg19.fa => tests/test_omitfrom/expected-results/independent.txt (100%)
 copy examples/cufflinks/hg19.fa => tests/test_omitfrom/expected-results/levelone.txt (100%)
 copy examples/cufflinks/hg19.fa => tests/test_omitfrom/expected-results/leveltwo_first.txt (100%)
 copy examples/cufflinks/hg19.fa => tests/test_omitfrom/expected-results/leveltwo_second.txt (100%)
 copy examples/cufflinks/hg19.fa => tests/test_omitfrom/expected-results/test1.second (100%)
 copy examples/cufflinks/hg19.fa => tests/test_omitfrom/expected-results/test2.second (100%)
 create mode 100644 tests/test_until/Snakefile
 copy examples/cufflinks/hg19.fa => tests/test_until/expected-results/levelone.txt (100%)
 copy examples/cufflinks/hg19.fa => tests/test_until/expected-results/leveltwo_first.txt (100%)
 copy examples/cufflinks/hg19.fa => tests/test_until/expected-results/leveltwo_second.txt (100%)
 copy examples/cufflinks/hg19.fa => tests/test_until/expected-results/test1.second (100%)
 copy examples/cufflinks/hg19.fa => tests/test_until/expected-results/test2.second (100%)

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