[ARVADOS] updated: 2.1.0-2514-gbcad695db
Git user
git at public.arvados.org
Wed May 18 18:01:52 UTC 2022
Summary of changes:
.licenseignore | 1 +
build/run-build-packages.sh | 4 +-
.../arvados-server}/arvados-health.service | 3 +-
cmd/arvados-server/cmd.go | 19 +++
.../arvados-server}/crunch-dispatch-slurm.service | 3 +-
doc/admin/config-urls.html.textile.liquid | 12 +-
doc/admin/upgrading.html.textile.liquid | 21 +++
.../install-dispatch.html.textile.liquid | 13 +-
doc/install/install-api-server.html.textile.liquid | 12 +-
doc/user/cwl/cwl-runner.html.textile.liquid | 24 +++-
lib/boot/supervisor.go | 2 +-
lib/config/config.default.yml | 3 +
lib/crunchrun/crunchrun.go | 7 +-
lib/crunchrun/crunchrun_test.go | 5 +-
lib/crunchrun/docker.go | 15 +-
lib/crunchrun/executor.go | 2 +-
lib/crunchrun/executor_test.go | 1 +
lib/crunchrun/integration_test.go | 2 +
lib/crunchrun/singularity.go | 17 ++-
lib/crunchrun/singularity_test.go | 2 +-
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 | 145 +++++++++++++++-----
sdk/cwl/test_with_arvbox.sh | 47 ++++---
.../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 | 21 ++-
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/go/arvados/config.go | 3 +
sdk/go/health/aggregator_test.go | 1 +
sdk/python/arvados/commands/keepdocker.py | 43 ++++--
sdk/python/tests/nginx.conf | 4 +
sdk/python/tests/test_arv_keepdocker.py | 8 +-
.../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 116 +++++-----------
.../crunch-dispatch-slurm_test.go | 65 +++++----
services/crunch-dispatch-slurm/node_type.go | 2 +-
services/crunch-dispatch-slurm/priority.go | 2 +-
services/crunch-dispatch-slurm/priority_test.go | 2 +-
services/crunch-dispatch-slurm/script.go | 2 +-
services/crunch-dispatch-slurm/script_test.go | 2 +-
services/crunch-dispatch-slurm/slurm.go | 2 +-
services/crunch-dispatch-slurm/squeue.go | 2 +-
services/crunch-dispatch-slurm/squeue_test.go | 2 +-
services/crunch-dispatch-slurm/usage.go | 2 +-
services/health/main.go | 39 ------
tools/arvbox/lib/arvbox/docker/Dockerfile.base | 11 +-
.../arvbox/docker/service/workbench2/run-service | 10 +-
.../aws/pillars/nginx_controller_configuration.sls | 4 +
.../pillars/nginx_controller_configuration.sls | 4 +
.../pillars/nginx_controller_configuration.sls | 4 +
63 files changed, 830 insertions(+), 324 deletions(-)
rename {services/health => cmd/arvados-server}/arvados-health.service (92%)
rename {services/crunch-dispatch-slurm => cmd/arvados-server}/crunch-dispatch-slurm.service (88%)
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
delete mode 100644 services/health/main.go
via bcad695db9a1c3aac5807faa153086e653107f51 (commit)
via 8b70a18b37ae6f5d081d469af6bcdc8ec3507e2b (commit)
via c50f13e8fca1039403ba1a0adb7aa54737989569 (commit)
via 1ef0acd580ddf41ed67f34152eadad0e60413008 (commit)
via 1849c576e1bad5e28b577bbd25994265dde03b5f (commit)
via 1161c9460bfdce3a81872866ccc2cd200b8de2de (commit)
via a654a04cc89e3920a84fe2979f910fe210972303 (commit)
via f42ee7c19b794e25db30051b1dfc4bee83929bcd (commit)
via 663f3742a80b1b236d727d2d27068d03a37b4469 (commit)
via bb1ef9ff8e1e5f9fb55738ec64e187f82c44b3de (commit)
via 844ff7cc1dc1c93a29b7ad8eca2987b987cf89e6 (commit)
via a3a51578bb709f35b57ab5c35790dcd9e4e7affc (commit)
via f7954ab0a45cbc302aa07fa60697363895395dde (commit)
via 03a0562aedc85d2f5fd3ded8830e8948051c0331 (commit)
via 7ce1178d95fa5feeb0efef46332e62abd54d7c28 (commit)
via aa03bc3e2a1122e02bb305bda7fadb96c68706b1 (commit)
via ead34cd306205a1f477a3d72df3293f48d5da3eb (commit)
via 1f92b08e21c19dfa0c6d2260fe2fd8b24529e9e3 (commit)
via f6a29cc714dd3409f865ceb799a886dd0b5d8152 (commit)
via d904fbcd2e67054784954c0af54ef8758a37f5ea (commit)
via 7865723dc5eee129e7ac269f3495274a13ff70ae (commit)
via 91dc80d9060c5aeb04228f0f280ecc3db182ff94 (commit)
via b4a0205b95c4ba9cf2c9aba4314ddd6867edc158 (commit)
via a89fbc8b4f2d8db8654175428bd1f041eed6f109 (commit)
via 93380e6aec7e11607019cdce88419b6f708327d7 (commit)
via f076c4497f2fce89f8fef9ccd601fcf316901993 (commit)
via 10d497fe4eb9ab1dc10171ba90c0c1b148108a35 (commit)
via 09963d2b633769549eea8739be3b541835839462 (commit)
via e3363715769a2503fdcbbb1274d7d04c6852c9c3 (commit)
via 1a6cf8e65c86a0002f0cf0c3a2d4092b67f9b57b (commit)
via 45e2ea82d68e74774bf61f6966e3777973e61845 (commit)
via 58ebceb34531be92f74f593d532276368a87a6de (commit)
via 9ca1b9f63b0fdaac45d04393e413cbc0b7f16d88 (commit)
via dec2837a7cb9d6c0538e7a4b699fd08435e8353a (commit)
via 7d01c644639aa75500c8cfb2a2b7bfd83941eac3 (commit)
via a4d6d061cb30cc2f77d4d64283ee998bb3e3a97b (commit)
via 4af2a63dcd4460b11c8f9f05a51caf1954972c95 (commit)
via 2b0fad4e2c099ebe42ae7cdb20615d9e0da2afc9 (commit)
via b5d0e0ad775eb822b9ab4bed5b57c2e9072f4c0b (commit)
via be6d658dd95d3a0d63bb3441e50877a4916a5b8e (commit)
via 9bbb935dc521f16b2b2b3d7c99653fa20914d90d (commit)
via 12e0b04c56f0e1ba9dd0f0450d9e96ceee04f1b7 (commit)
via 58241cc5b82c39270b1d0425a0a1fec4aae8f45e (commit)
via 8e43dcf899a3322e66c709b149ce557f5255bf18 (commit)
via 162d5c17961b6e5939f46f8c43dd1d854efc76c0 (commit)
via 66ef73b96e38c87a84ae64bd19385d5d5e9e07ed (commit)
via 217aba73f6366cf1af30683baa6d0d5d1e3407a9 (commit)
via 6b1a602cf1de1b6488c7d6b55e8d99ca8f707160 (commit)
from 731c5e81f5aedc82d03786670610bde68bba27c7 (commit)
Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit bcad695db9a1c3aac5807faa153086e653107f51
Merge: 731c5e81f 8b70a18b3
Author: Tom Clegg <tom at curii.com>
Date: Wed May 18 14:01:21 2022 -0400
15370: Merge branch 'main' into 15370-loopback-dispatchcloud
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom at curii.com>
-----------------------------------------------------------------------
hooks/post-receive
--
More information about the arvados-commits
mailing list