[ARVADOS] updated: efb3422f119be36e133ffbd14519c5d6c74addc8

[Git user]

Summary of changes:
 build/run-build-packages.sh                        |   7 +-
 doc/_config.yml                                    |  10 +-
 doc/_includes/_register_cwl_workflow.liquid        |  21 ---
 doc/user/cwl/cwl-extensions.html.textile.liquid    |  56 ++++++
 .../cwl/cwl-run-options.html.textile.liquid}       |  44 ++++-
 doc/user/cwl/cwl-runner.html.textile.liquid        | 206 +++++++--------------
 doc/user/cwl/cwl-style.html.textile.liquid         |   2 +
 .../examples/crunch-examples.html.textile.liquid   |   2 +
 .../getting_started/workbench.html.textile.liquid  |   2 +-
 .../reference/job-pipeline-ref.html.textile.liquid |   2 +
 doc/user/topics/arv-docker.html.textile.liquid     |  12 +-
 doc/user/topics/run-command.html.textile.liquid    |   2 +
 ...nning-pipeline-command-line.html.textile.liquid |   2 +-
 ...nning-workflow-command-line.html.textile.liquid |  17 --
 .../running-external-program.html.textile.liquid   |   2 +-
 .../tutorial-submit-job.html.textile.liquid        |   2 +-
 .../writing-cwl-workflow.html.textile.liquid       | 186 ++++++++++++++++++-
 sdk/cwl/arvados_cwl/__init__.py                    |  28 ++-
 sdk/cwl/arvados_cwl/arvcontainer.py                | 102 ++++++----
 sdk/cwl/arvados_cwl/arvjob.py                      |   6 -
 sdk/cwl/arvados_cwl/fsaccess.py                    |  84 +++++++++
 sdk/cwl/arvados_cwl/pathmapper.py                  |   2 +
 sdk/cwl/arvados_cwl/runner.py                      |  12 +-
 sdk/cwl/setup.py                                   |   7 +-
 sdk/cwl/tests/test_job.py                          |   6 +
 sdk/cwl/tests/test_submit.py                       | 203 ++++++++++++++++++--
 sdk/cwl/tests/test_urljoin.py                      |  56 ++++++
 sdk/cwl/tests/wf/expect_arvworkflow.cwl            |  24 +++
 sdk/cwl/tests/wf/expect_packed.cwl                 |   2 +-
 .../wf/{submit_wf.cwl => submit_keepref_wf.cwl}    |  13 +-
 30 files changed, 824 insertions(+), 296 deletions(-)
 delete mode 100644 doc/_includes/_register_cwl_workflow.liquid
 create mode 100644 doc/user/cwl/cwl-extensions.html.textile.liquid
 rename doc/{_includes/_arvados_cwl_runner.liquid => user/cwl/cwl-run-options.html.textile.liquid} (51%)
 delete mode 100644 doc/user/topics/running-workflow-command-line.html.textile.liquid
 create mode 100644 sdk/cwl/tests/test_urljoin.py
 create mode 100644 sdk/cwl/tests/wf/expect_arvworkflow.cwl
 copy sdk/cwl/tests/wf/{submit_wf.cwl => submit_keepref_wf.cwl} (70%)

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commit efb3422f119be36e133ffbd14519c5d6c74addc8
Merge: d070d1e c668e74
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed Dec 14 10:01:50 2016 -0500

    Merge branch '10576-cwl-keep-fetcher' closes #10576


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