[med-svn] [snakemake] branch upstream updated (955a326 -> 06602fe)

[chrysn]

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

      from  955a326   New upstream version 3.13.3
       new  06602fe   New upstream version 4.3.0

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
been added to this reference.


Summary of changes:
 CHANGELOG.md                                       |  51 ++
 Dockerfile                                         |  14 +-
 docs/_static/sphinx-argparse.css                   |   6 +
 docs/conf.py                                       |   6 +-
 docs/executable.rst                                | 123 +++-
 docs/getting_started/installation.rst              |   4 +-
 docs/index.rst                                     |  26 +-
 docs/project_info/faq.rst                          |   6 +-
 docs/project_info/more_resources.rst               |   6 +-
 docs/requirements.txt                              |   1 +
 docs/snakefiles/deployment.rst                     |  29 +
 docs/snakefiles/modularization.rst                 |   8 +-
 docs/snakefiles/remote_files.rst                   | 108 +++-
 docs/snakefiles/rules.rst                          |  34 +-
 docs/tutorial/tutorial.rst                         |   2 +-
 environment.yml                                    |  15 +-
 setup.py                                           |  16 +-
 snakemake/__init__.py                              | 359 ++++++++++--
 snakemake/common.py                                |   9 +
 snakemake/conda.py                                 |  23 +-
 snakemake/dag.py                                   | 162 ++++--
 snakemake/exceptions.py                            |   4 +
 snakemake/executors.py                             | 619 +++++++++++++++++----
 snakemake/io.py                                    | 100 +++-
 snakemake/jobs.py                                  |  44 +-
 snakemake/logging.py                               |  53 +-
 snakemake/parser.py                                |  28 +-
 snakemake/persistence.py                           | 222 ++++----
 snakemake/remote/FTP.py                            |   3 +
 snakemake/remote/GS.py                             | 128 ++++-
 snakemake/remote/HTTP.py                           |   3 +
 snakemake/remote/NCBI.py                           |   6 +-
 snakemake/remote/S3.py                             | 225 ++------
 snakemake/remote/S3Mocked.py                       |  13 +-
 snakemake/remote/__init__.py                       |  38 +-
 snakemake/remote/dropbox.py                        |   2 +-
 snakemake/remote/gfal.py                           | 137 +++++
 snakemake/remote/gridftp.py                        |  71 +++
 snakemake/remote/webdav.py                         | 167 ++++++
 snakemake/rules.py                                 | 104 ++--
 snakemake/scheduler.py                             | 167 ++++--
 snakemake/script.py                                |  12 +-
 snakemake/shell.py                                 |  18 +-
 snakemake/singularity.py                           |  73 +++
 snakemake/version.py                               |   4 +-
 snakemake/workflow.py                              | 123 +++-
 snakemake/wrapper.py                               |  20 +-
 test-environment.yml                               |  19 +-
 tests/test_issue612/Snakefile                      |  11 +
 .../expected-results/.gitignore                    |   0
 tests/test_kubernetes/README.md                    |  11 +
 tests/test_kubernetes/Snakefile                    |  29 +
 tests/test_kubernetes/envs/gzip.yaml               |   4 +
 tests/test_profile/Snakefile                       |   3 +
 tests/test_profile/Snakefile.internal              |   5 +
 tests/test_profile/config.yaml                     |   1 +
 .../expected-results/test.out                      |   0
 tests/test_profile/workflow-config.yaml            |   1 +
 tests/test_remote_gs/Snakefile                     |  15 +
 .../expected-results/landsat-data.txt              | 218 ++++++++
 tests/test_remote_gs/landsat-data.txt              | 218 ++++++++
 tests/test_remote_log/Snakefile                    |  17 +
 tests/test_remote_log/expected-results/motoState.p | Bin 0 -> 848 bytes
 AUTHORS.rst => tests/test_remote_log/test.txt      |   0
 tests/test_remote_ncbi/Snakefile                   |   5 +-
 tests/test_remote_ncbi/expected-results/sizes.txt  |   8 +-
 tests/test_remote_ncbi_simple/Snakefile            |   4 +-
 .../expected-results/sizes.txt                     |   2 +-
 tests/test_restartable_job_cmd_exit_1/Snakefile    |  27 +-
 .../expected-results/.done                         |   1 +
 tests/test_script/expected-results/test.html       |  85 +--
 tests/test_singularity/Snakefile                   |   7 +
 tests/test_singularity/expected-results/test.out   |   2 +
 tests/test_static_remote/S3MockedForStaticTest.py  |   7 +-
 tests/test_wrapper/Snakefile                       |   2 +-
 tests/tests.py                                     | 103 ++--
 wercker.yml                                        |   6 +-
 77 files changed, 3359 insertions(+), 844 deletions(-)
 create mode 100644 docs/_static/sphinx-argparse.css
 create mode 100644 snakemake/remote/gfal.py
 create mode 100644 snakemake/remote/gridftp.py
 create mode 100644 snakemake/remote/webdav.py
 create mode 100644 snakemake/singularity.py
 create mode 100644 tests/test_issue612/Snakefile
 copy tests/{test09 => test_issue612}/expected-results/.gitignore (100%)
 create mode 100644 tests/test_kubernetes/README.md
 create mode 100644 tests/test_kubernetes/Snakefile
 create mode 100644 tests/test_kubernetes/envs/gzip.yaml
 create mode 100644 tests/test_profile/Snakefile
 create mode 100644 tests/test_profile/Snakefile.internal
 create mode 100644 tests/test_profile/config.yaml
 copy tests/{test_conditional => test_profile}/expected-results/test.out (100%)
 create mode 100644 tests/test_profile/workflow-config.yaml
 create mode 100644 tests/test_remote_gs/Snakefile
 create mode 100644 tests/test_remote_gs/expected-results/landsat-data.txt
 create mode 100644 tests/test_remote_gs/landsat-data.txt
 create mode 100644 tests/test_remote_log/Snakefile
 create mode 100644 tests/test_remote_log/expected-results/motoState.p
 copy AUTHORS.rst => tests/test_remote_log/test.txt (100%)
 create mode 100644 tests/test_singularity/Snakefile
 create mode 100644 tests/test_singularity/expected-results/test.out

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