[med-svn] [snakemake] branch upstream updated (47de406 -> d977f15)

[Kevin Murray]

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

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

      from  47de406   Imported Upstream version 3.4
      adds  d977f15   Imported Upstream version 3.4.2

No new revisions were added by this update.

Summary of changes:
 .gitignore                                         |   3 +-
 conda/build.sh                                     |  12 --
 conda/snakemake/bld.bat                            |   8 -
 conda/snakemake/build.sh                           |   9 -
 conda/snakemake/meta.yaml                          |  22 ---
 docker/Dockerfile                                  |   7 -
 setup.py                                           |  24 ++-
 snakemake/__init__.py                              | 213 ++++++++++++---------
 snakemake/exceptions.py                            |  13 +-
 snakemake/executors.py                             | 211 +++++++++++---------
 snakemake/io.py                                    |  43 ++++-
 snakemake/jobs.py                                  |   2 +-
 snakemake/logging.py                               |   5 +
 snakemake/persistence.py                           |   7 +-
 snakemake/report.css                               |  25 ++-
 snakemake/report.py                                |  17 +-
 snakemake/scheduler.py                             |   4 +-
 snakemake/shell.py                                 |   2 +
 snakemake/utils.py                                 |  24 +++
 snakemake/version.py                               |   2 +-
 snakemake/workflow.py                              |  15 +-
 tests/test_benchmark/Snakefile                     |   4 +-
 .../{test.benchmark.json => test.benchmark.txt}    |   0
 tests/test_report/Snakefile                        |  11 +-
 tests/test_symlink_temp/Snakefile                  |  22 +++
 .../cufflinks/hg19.fa => tests/test_symlink_temp/a |   0
 .../cufflinks/hg19.fa => tests/test_symlink_temp/b |   0
 .../expected-results/.gitignore                    |   0
 tests/test_update_config/Snakefile                 |  14 ++
 tests/test_update_config/cp.rule                   |  16 ++
 tests/test_update_config/echo.rule                 |   7 +
 tests/test_update_config/echo.yaml                 |   2 +
 .../expected-results/config.yaml                   |   4 +
 tests/test_update_config/test.yaml                 |   4 +
 tests/tests.py                                     |  16 +-
 35 files changed, 480 insertions(+), 288 deletions(-)
 delete mode 100644 conda/build.sh
 delete mode 100644 conda/snakemake/bld.bat
 delete mode 100644 conda/snakemake/build.sh
 delete mode 100644 conda/snakemake/meta.yaml
 delete mode 100644 docker/Dockerfile
 rename tests/test_benchmark/expected-results/{test.benchmark.json => test.benchmark.txt} (100%)
 create mode 100644 tests/test_symlink_temp/Snakefile
 copy examples/cufflinks/hg19.fa => tests/test_symlink_temp/a (100%)
 copy examples/cufflinks/hg19.fa => tests/test_symlink_temp/b (100%)
 copy tests/{test09 => test_symlink_temp}/expected-results/.gitignore (100%)
 create mode 100644 tests/test_update_config/Snakefile
 create mode 100644 tests/test_update_config/cp.rule
 create mode 100644 tests/test_update_config/echo.rule
 create mode 100644 tests/test_update_config/echo.yaml
 create mode 100644 tests/test_update_config/expected-results/config.yaml
 create mode 100644 tests/test_update_config/test.yaml

-- 
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