[med-svn] [snakemake] branch master updated (e650711 -> 0370bc2)

[Kevin Murray]

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

      from  e650711   Update changelog
       new  14aba72   Imported Upstream version 3.5.5
       new  3e50d34   Merge tag 'upstream/3.5.5'
       new  0370bc2   New upstream release in d/ch

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Summary of changes:
 debian/changelog                                   |   6 +
 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 ++
 31 files changed, 363 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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