[med-svn] [snakemake] branch master updated (c7005f1 -> 602a820)

[Kevin Murray]

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

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

      from  c7005f1   Add ca-certificates as a build-dep
       new  d977f15   Imported Upstream version 3.4.2
       new  7f1a10b   Merge tag 'upstream/3.4.2'
       new  ca204c0   Misc changes for 3.4.2
       new  602a820   Combine patches for local JS use

The 4 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:
 .gitignore                                         |   3 +-
 conda/build.sh                                     |  12 --
 conda/snakemake/bld.bat                            |   8 -
 conda/snakemake/build.sh                           |   9 -
 conda/snakemake/meta.yaml                          |  22 ---
 debian/changelog                                   |   2 +-
 debian/copyright                                   |   3 +-
 ...2-Use-local-javascript-css-as-appropriate.patch |  27 ---
 .../0003-Use-debian-s-mathjax-package.patch        |  30 ++-
 debian/patches/series                              |   1 -
 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 +-
 40 files changed, 508 insertions(+), 323 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 debian/patches/0002-Use-local-javascript-css-as-appropriate.patch
 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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