[ARVADOS] updated: 2.1.0-2474-ga89fbc8b4

[Git user]

Summary of changes:
 .licenseignore                                     |   1 +
 doc/admin/upgrading.html.textile.liquid            |   4 +
 doc/user/cwl/cwl-runner.html.textile.liquid        |  24 +++-
 sdk/cwl/arvados_cwl/__init__.py                    |   6 +-
 sdk/cwl/arvados_cwl/arvcontainer.py                |  23 ++--
 sdk/cwl/arvados_cwl/arvdocker.py                   |  47 +++++--
 sdk/cwl/arvados_cwl/arvworkflow.py                 |  20 ++-
 sdk/cwl/arvados_cwl/context.py                     |   1 +
 sdk/cwl/arvados_cwl/executor.py                    |  46 +++++--
 sdk/cwl/arvados_cwl/runner.py                      | 143 ++++++++++++++-----
 .../example3.cwl => 19070-copy-deps.cwl}           |  13 +-
 sdk/cwl/tests/19109-upload-secondary.cwl           |  42 ++++++
 sdk/cwl/tests/19109-upload-secondary.yml           |  10 ++
 sdk/cwl/tests/19109-upload-secondary/file1.txt     |   1 +
 sdk/cwl/tests/19109-upload-secondary/file1.txt.tbi |   1 +
 sdk/cwl/tests/19109-upload-secondary/file2.txt     |   1 +
 sdk/cwl/tests/19109-upload-secondary/file2.txt.tbi |   1 +
 sdk/cwl/tests/arvados-tests.sh                     |   9 ++
 sdk/cwl/tests/arvados-tests.yml                    |  20 +++
 sdk/cwl/tests/cat2.cwl                             |  17 +++
 sdk/cwl/tests/scripts/download_all_data.sh         |   4 +-
 sdk/cwl/tests/test_copy_deps.py                    | 152 +++++++++++++++++++++
 sdk/cwl/tests/test_submit.py                       |  38 +++++-
 sdk/python/arvados/commands/keepdocker.py          |  43 ++++--
 sdk/python/tests/test_arv_keepdocker.py            |   8 +-
 25 files changed, 560 insertions(+), 115 deletions(-)
 copy sdk/cwl/tests/{secondaryFiles/example3.cwl => 19070-copy-deps.cwl} (62%)
 create mode 100644 sdk/cwl/tests/19109-upload-secondary.cwl
 create mode 100644 sdk/cwl/tests/19109-upload-secondary.yml
 create mode 100644 sdk/cwl/tests/19109-upload-secondary/file1.txt
 create mode 100644 sdk/cwl/tests/19109-upload-secondary/file1.txt.tbi
 create mode 100644 sdk/cwl/tests/19109-upload-secondary/file2.txt
 create mode 100644 sdk/cwl/tests/19109-upload-secondary/file2.txt.tbi
 create mode 100644 sdk/cwl/tests/cat2.cwl
 create mode 100644 sdk/cwl/tests/test_copy_deps.py

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commit a89fbc8b4f2d8db8654175428bd1f041eed6f109
Merge: 93380e6ae 1a6cf8e65
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Fri May 13 11:08:31 2022 -0400

    Merge branch '19109-upload-secondary' refs #19109
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>


commit 93380e6aec7e11607019cdce88419b6f708327d7
Merge: 57b2caac6 45e2ea82d
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Fri May 13 11:08:08 2022 -0400

    Merge branch '19070-update-workflow-deps' refs #19070
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>


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