[med-svn] [snakemake] branch upstream updated (14aba72 -> 9445144)

[Kevin Murray]

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

      from  14aba72   Imported Upstream version 3.5.5
      adds  fa7a4fd   Imported Upstream version 3.6.1+dfsg
       new  9445144   Imported Upstream version 3.7.1+dfsg

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:
 CHANGELOG.md                                       |  85 ++++++++++++++
 LICENSE => LICENSE.md                              |   2 +-
 README => README.md                                |   2 +-
 environment.yml                                    |  15 +++
 misc/vim/syntax/snakemake.vim                      |   6 +-
 setup.py                                           |   4 +-
 snakemake-tutorial.html                            |   2 +-
 snakemake/__init__.py                              |  57 +++++----
 snakemake/common.py                                |   1 +
 snakemake/dag.py                                   | 130 ++++++++++++---------
 snakemake/exceptions.py                            |  18 +--
 snakemake/executors.py                             |  66 ++++++++---
 snakemake/io.py                                    | 113 +++++++++++-------
 snakemake/jobs.py                                  |  99 +++++++++-------
 snakemake/logging.py                               |  32 +++--
 snakemake/output_index.py                          |   8 +-
 snakemake/parser.py                                |   8 +-
 snakemake/persistence.py                           |   2 +
 snakemake/remote/FTP.py                            |  12 +-
 snakemake/remote/HTTP.py                           |  14 ++-
 snakemake/remote/dropbox.py                        |  33 ++++--
 snakemake/rules.py                                 |  55 ++++-----
 snakemake/scheduler.py                             |   7 +-
 snakemake/script.py                                |  22 +++-
 snakemake/shell.py                                 |   2 +-
 snakemake/utils.py                                 |  24 ++++
 snakemake/version.py                               |   2 +-
 snakemake/workflow.py                              |  19 ++-
 tests/test01/Snakefile                             |   5 +
 tests/test_input_generator/Snakefile               |  33 ++++++
 .../test_input_generator/expected-results/foo.out1 |   3 +
 .../test_input_generator/expected-results/foo.out2 |   3 +
 .../test_input_generator/expected-results/foo.out3 |   3 +
 tests/test_input_generator/foo.1.in                |   1 +
 tests/test_input_generator/foo.2.in                |   1 +
 tests/test_input_generator/foo.3.in                |   1 +
 tests/test_script/Snakefile                        |   5 +
 tests/test_script/config.yaml                      |   1 +
 tests/test_script/scripts/test.R                   |   6 +
 tests/testapi.py                                   |  13 +++
 tests/tests.py                                     |   3 +
 41 files changed, 650 insertions(+), 268 deletions(-)
 create mode 100644 CHANGELOG.md
 rename LICENSE => LICENSE.md (94%)
 rename README => README.md (88%)
 create mode 100644 environment.yml
 create mode 100644 snakemake/common.py
 create mode 100644 tests/test_input_generator/Snakefile
 create mode 100644 tests/test_input_generator/expected-results/foo.out1
 create mode 100644 tests/test_input_generator/expected-results/foo.out2
 create mode 100644 tests/test_input_generator/expected-results/foo.out3
 create mode 100644 tests/test_input_generator/foo.1.in
 create mode 100644 tests/test_input_generator/foo.2.in
 create mode 100644 tests/test_input_generator/foo.3.in
 create mode 100644 tests/test_script/config.yaml
 create mode 100644 tests/testapi.py

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