[med-svn] [snakemake] branch upstream updated (8111782 -> 91fdd01)

[Kevin Murray]

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

      from  8111782   New upstream version 3.9.1
      adds  91fdd01   New upstream version 3.10.0

No new revisions were added by this update.

Summary of changes:
 CHANGELOG.md                                       |  14 ++-
 docs/index.rst                                     |   2 +-
 docs/project_info/faq.rst                          |   4 +-
 docs/snakefiles/rules.rst                          |  41 +++++++
 docs/tutorial/welcome.rst                          |   2 +-
 snakemake/__init__.py                              |  22 +++-
 snakemake/common.py                                |  24 ++++
 snakemake/conda.py                                 | 121 +++++++++++++++++----
 snakemake/dag.py                                   |  99 ++++++++++++++++-
 snakemake/executors.py                             |  15 ++-
 snakemake/io.py                                    |  32 +++++-
 snakemake/jobs.py                                  |  65 ++++++++---
 snakemake/logging.py                               |  72 ++++++------
 snakemake/persistence.py                           |   4 +-
 snakemake/remote/HTTP.py                           |   3 +
 snakemake/rules.py                                 |  57 +++++++---
 snakemake/script.py                                |  13 ++-
 snakemake/version.py                               |   2 +-
 snakemake/workflow.py                              |  11 +-
 tests/test_parser/Snakefile                        |   3 +-
 tests/test_unpack_dict/Snakefile                   |  27 +++++
 .../expected-results/prefix.out1.txt}              |   0
 .../expected-results/prefix.out2.txt}              |   0
 .../foo.1.in => test_unpack_dict/prefix.in1.txt}   |   0
 .../foo.2.in => test_unpack_dict/prefix.in2.txt}   |   0
 tests/test_unpack_list/Snakefile                   |  27 +++++
 .../expected-results/prefix.out1.txt}              |   0
 .../expected-results/prefix.out2.txt}              |   0
 .../foo.1.in => test_unpack_list/prefix.in1.txt}   |   0
 .../foo.2.in => test_unpack_list/prefix.in2.txt}   |   0
 tests/tests.py                                     |   8 ++
 31 files changed, 545 insertions(+), 123 deletions(-)
 create mode 100644 tests/test_unpack_dict/Snakefile
 copy tests/{test_input_generator/foo.1.in => test_unpack_dict/expected-results/prefix.out1.txt} (100%)
 copy tests/{test_input_generator/foo.2.in => test_unpack_dict/expected-results/prefix.out2.txt} (100%)
 copy tests/{test_input_generator/foo.1.in => test_unpack_dict/prefix.in1.txt} (100%)
 copy tests/{test_input_generator/foo.2.in => test_unpack_dict/prefix.in2.txt} (100%)
 create mode 100644 tests/test_unpack_list/Snakefile
 copy tests/{test_input_generator/foo.1.in => test_unpack_list/expected-results/prefix.out1.txt} (100%)
 copy tests/{test_input_generator/foo.2.in => test_unpack_list/expected-results/prefix.out2.txt} (100%)
 copy tests/{test_input_generator/foo.1.in => test_unpack_list/prefix.in1.txt} (100%)
 copy tests/{test_input_generator/foo.2.in => test_unpack_list/prefix.in2.txt} (100%)

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