[arvados] updated: 2.5.0-150-gaece35d20

Fri Feb 10 19:26:47 UTC 2023

Summary of changes:
 build/build-dev-docker-jobs-image.sh               |  22 +-
 sdk/cwl/arvados_cwl/__init__.py                    |   9 +-
 sdk/cwl/arvados_cwl/arvcontainer.py                |  25 +-
 sdk/cwl/arvados_cwl/arvdocker.py                   |  32 +-
 sdk/cwl/arvados_cwl/arvworkflow.py                 | 392 +++++++++++++++++++--
 sdk/cwl/arvados_cwl/context.py                     |   1 +
 sdk/cwl/arvados_cwl/executor.py                    |  98 ++++--
 sdk/cwl/arvados_cwl/fsaccess.py                    |  10 +-
 sdk/cwl/arvados_cwl/runner.py                      | 192 +++++-----
 sdk/cwl/setup.py                                   |   4 +-
 sdk/cwl/tests/arvados-tests.yml                    |   2 +-
 .../dmel_r6.16/WholeGenome/genome.dict             |   0
 .../dmel_r6.16/WholeGenome/genome.fa.fai           |   0
 .../Homo_sapiens/GRCh38.p2/WholeGenome/genome.dict |   0
 .../GRCh38.p2/WholeGenome/genome.fa.fai            |   0
 .../collection_per_tool/collection_per_tool.cwl    |   4 +-
 .../collection_per_tool_wrapper.cwl                |   2 +-
 sdk/cwl/tests/test_container.py                    |  19 +-
 sdk/cwl/tests/test_copy_deps.py                    |  72 ++--
 sdk/cwl/tests/test_submit.py                       | 257 +++++---------
 sdk/cwl/tests/wf/expect_upload_wrapper.cwl         |   5 +-
 sdk/cwl/tests/wf/expect_upload_wrapper_altname.cwl |   5 +-
 sdk/cwl/tests/wf/runin-reqs-wf.cwl                 |   3 +-
 sdk/cwl/tests/wf/runin-reqs-wf2.cwl                |   3 +-
 sdk/cwl/tests/wf/runin-reqs-wf3.cwl                |   3 +-
 sdk/cwl/tests/wf/runin-reqs-wf4.cwl                |   3 +-
 sdk/cwl/tests/wf/runin-reqs-wf5.cwl                |   3 +-
 sdk/cwl/tests/wf/secret_wf.cwl                     |   2 +-
 sdk/cwl/tests/wf/submit_wf.cwl                     |   2 +-
 sdk/cwl/tests/wf/submit_wf_no_reuse.cwl            |   4 +-
 sdk/cwl/tests/wf/submit_wf_process_properties.cwl  |   2 +-
 sdk/cwl/tests/wf/submit_wf_runner_resources.cwl    |   2 +-
 ...ct_upload_wrapper.cwl => submit_wf_wrapper.cwl} |  30 +-
 sdk/dev-jobs.dockerfile                            |   3 +
 sdk/python/arvados/util.py                         |  17 +
 35 files changed, 755 insertions(+), 473 deletions(-)
 copy apps/workbench/app/mailers/.gitkeep => sdk/cwl/tests/chipseq/data/Genomes/Drosophila_melanogaster/dmel_r6.16/WholeGenome/genome.dict (100%)
 copy apps/workbench/app/mailers/.gitkeep => sdk/cwl/tests/chipseq/data/Genomes/Drosophila_melanogaster/dmel_r6.16/WholeGenome/genome.fa.fai (100%)
 copy apps/workbench/app/mailers/.gitkeep => sdk/cwl/tests/chipseq/data/Genomes/Homo_sapiens/GRCh38.p2/WholeGenome/genome.dict (100%)
 copy apps/workbench/app/mailers/.gitkeep => sdk/cwl/tests/chipseq/data/Genomes/Homo_sapiens/GRCh38.p2/WholeGenome/genome.fa.fai (100%)
 copy sdk/cwl/tests/wf/{expect_upload_wrapper.cwl => submit_wf_wrapper.cwl} (54%)

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commit aece35d20c892aa7b3df29b15ac0a8a167b0b3ab
Merge: 952458464 083b86a4e
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Fri Feb 10 14:26:27 2023 -0500

    Merge branch '19385-cwl-fast-pack' refs #19385

    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

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