Started
Running as brainvisa
----------------------------------------
$ /usr/bin/python3 /volatile/a-sac-ns-brainvisa/bbi_nightly/cea-master-5.3/src/development/casa-distro/master/bin/casa_distro bv_maker name=cea-master-5.3 -- sources
----------------------------------------
Updating git repository /casa/host/src/aims/aims-free/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
Updating git repository /casa/host/src/aims/aims-gpl/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
Updating git repository /casa/host/src/anatomist/anatomist-free/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
Updating git repository /casa/host/src/anatomist/anatomist-gpl/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
Updating git repository /casa/host/src/axon/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
Updating git repository /casa/host/src/brainrat/bioprocessing/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
Using BioProj credentials stored in svn.secret (username 'brainvisa-admin')
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
Updating git repository /casa/host/src/brainrat/brainrat-gpl/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
Using BioProj credentials stored in svn.secret (username 'brainvisa-admin')
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
Updating git repository /casa/host/src/brainrat/brainrat-private/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
Using BioProj credentials stored in svn.secret (username 'brainvisa-admin')
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
Updating git repository /casa/host/src/brainrat/primatologist-gpl/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
Using BioProj credentials stored in svn.secret (username 'brainvisa-admin')
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
Updating git repository /casa/host/src/brainvisa-share/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
Updating git repository /casa/host/src/brainvisa-spm/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
Updating git repository /casa/host/src/capsul/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
$ pre-commit install
pre-commit installed at .git/hooks/pre-commit
Updating git repository /casa/host/src/constellation/constellation-gpl/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
Updating git repository /casa/host/src/constellation/constellation-nonfree/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
Updating git repository /casa/host/src/cortical_surface/brainvisa_freesurfer/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
Updating git repository /casa/host/src/cortical_surface/cortical_surface-gpl/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
Updating git repository /casa/host/src/cortical_surface/cortical_surface-nonfree/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
Updating git repository /casa/host/src/development/brainvisa-cmake/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
$ pre-commit install
pre-commit installed at .git/hooks/pre-commit
Updating git repository /casa/host/src/development/casa-distro/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
$ pre-commit install
pre-commit installed at .git/hooks/pre-commit
Updating git repository /casa/host/src/development/neuro-forge/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/main
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
Updating git repository /casa/host/src/disco/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
Using BioProj credentials stored in svn.secret (username 'brainvisa-admin')
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
$ pre-commit install
pre-commit installed at .git/hooks/pre-commit
Updating git repository /casa/host/src/highres-cortex/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
$ pre-commit install
pre-commit installed at .git/hooks/pre-commit
Updating git repository /casa/host/src/morphologist/morpho-deepsulci/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
Updating git repository /casa/host/src/morphologist/morphologist-gpl/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
Updating git repository /casa/host/src/morphologist/morphologist-nonfree/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
Updating git repository /casa/host/src/morphologist/morphologist-ui/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
Updating git repository /casa/host/src/morphologist/sulci-nonfree/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
Updating git repository /casa/host/src/populse/populse_db/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
From https://github.com/populse/populse_db
f271e95..698334b master -> origin/master
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Updating f271e95..698334b
Fast-forward
.pre-commit-config.yaml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
$ pre-commit install
pre-commit installed at .git/hooks/pre-commit
Updating git repository /casa/host/src/soma/soma-base/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
$ pre-commit install
pre-commit installed at .git/hooks/pre-commit
Updating git repository /casa/host/src/soma/soma-io/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Already up to date.
Updating git repository /casa/host/src/soma/soma-workflow/master
$ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*'
From https://github.com/populse/soma-workflow
9086676..c9a57a9 gh-pages -> origin/gh-pages
b83186e..7afea86 master -> origin/master
$ git update-ref --no-deref refs/bv_head refs/remotes/origin/master
$ git -c remote.origin.skipDefaultUpdate remote update
$ git merge --ff-only refs/bv_head
Updating b83186e..7afea86
Fast-forward
.pre-commit-config.yaml | 2 +-
bin/soma_delete_all_workflows | 1 -
bin/soma_kill_servers | 2 -
bin/soma_restart_workflow | 1 -
bin/soma_stop_workflow | 1 -
bin/soma_submit_workflow | 1 -
bin/soma_workflow_gui | 1 -
doc/source/conf.py | 22 +-
doc/source/conf_github.py | 22 +-
python/soma_workflow/MPI_workflow_runner.py | 7 +-
python/soma_workflow/check_requirement/__main__.py | 3 -
python/soma_workflow/check_requirement/drmaa.py | 3 -
python/soma_workflow/clean_server.py | 4 -
python/soma_workflow/configuration.py | 29 +--
python/soma_workflow/connection.py | 26 +--
python/soma_workflow/constants.py | 2 -
python/soma_workflow/custom_jobs.py | 17 +-
python/soma_workflow/database_server.py | 244 ++++++++++-----------
python/soma_workflow/engine_types.py | 40 ++--
python/soma_workflow/errors.py | 1 -
python/soma_workflow/gui/workflowGui.py | 146 ++++++------
python/soma_workflow/info.py | 4 +-
python/soma_workflow/observer.py | 8 +-
python/soma_workflow/param_link_functions.py | 5 -
python/soma_workflow/scheduler.py | 8 +-
.../soma_workflow/schedulers/drmaa2_scheduler.py | 2 -
python/soma_workflow/schedulers/drmaa_scheduler.py | 21 +-
python/soma_workflow/schedulers/local_scheduler.py | 18 +-
python/soma_workflow/schedulers/mpi_scheduler.py | 8 +-
.../soma_workflow/schedulers/pbspro_scheduler.py | 38 ++--
python/soma_workflow/setup_client2server.py | 41 ++--
python/soma_workflow/setup_server.py | 24 +-
python/soma_workflow/sro.py | 11 +-
python/soma_workflow/start_database_server.py | 4 -
python/soma_workflow/start_workflow_engine.py | 18 +-
python/soma_workflow/subprocess.py | 3 -
python/soma_workflow/test/__main__.py | 4 -
python/soma_workflow/test/data/TestDrmaaCTypes.py | 9 +-
.../data/jobExamples/complete/exception_job.py | 2 -
.../test/data/jobExamples/complete/job1.py | 4 -
.../test/data/jobExamples/complete/job2.py | 5 -
.../test/data/jobExamples/complete/job3.py | 5 -
.../test/data/jobExamples/complete/job4.py | 5 -
.../test/data/jobExamples/complete/job5.py | 4 -
.../test/data/jobExamples/complete/job6.py | 4 -
.../test/data/jobExamples/complete/job7.py | 5 -
.../test/data/jobExamples/complete/job8.py | 4 -
.../test/data/jobExamples/complete/job9.py | 4 -
.../data/jobExamples/complete/job_with_outputs1.py | 5 -
.../test/data/jobExamples/complete/sleep_job.py | 2 -
.../data/jobExamples/complete/special_command.py | 4 -
.../jobExamples/special_transfers/dir_contents.py | 2 -
.../special_transfers/multiple_file_format.py | 2 -
.../test/data/workflow_examples/create_file.py | 2 -
.../test/data/workflow_examples/file_transfer.py | 3 -
.../test/data/workflow_examples/simple_example.py | 2 -
.../data/workflow_examples/simple_example_group.py | 3 -
.../test/data/workflow_examples/simple_transfer.py | 2 -
.../test/data/workflow_examples/srp_example.py | 2 -
.../data/workflow_examples/working_dir_transfer.py | 4 -
python/soma_workflow/test/job_tests/__init__.py | 1 -
.../soma_workflow/test/job_tests/job_examples.py | 7 +-
python/soma_workflow/test/job_tests/job_tests.py | 13 +-
.../test/job_tests/test_MPI_parallel_job.py | 1 -
.../test/job_tests/test_disconnection.py | 1 -
.../test/job_tests/test_ended_job_with_transfer.py | 6 +-
.../test/job_tests/test_exception_job.py | 1 -
.../job_tests/test_job_pipeline_with_transfer.py | 1 -
.../test/job_tests/test_local_custom_submission.py | 1 -
.../test/job_tests/test_local_submission.py | 1 -
.../job_tests/test_submission_with_transfer.py | 1 -
.../test/job_tests/test_workflow_api.py | 7 +-
python/soma_workflow/test/test_serialization.py | 5 +-
python/soma_workflow/test/utils.py | 2 -
.../soma_workflow/test/workflow_tests/__init__.py | 2 -
.../test/workflow_tests/test_barrier_jobs.py | 3 -
.../test/workflow_tests/test_exception1.py | 3 -
.../test/workflow_tests/test_exception2.py | 4 -
.../test/workflow_tests/test_fake_pipeline.py | 3 -
.../test/workflow_tests/test_multiple.py | 3 -
.../test/workflow_tests/test_native_spec.py | 3 -
.../test/workflow_tests/test_njobs.py | 3 -
.../workflow_tests/test_njobs_with_dependencies.py | 3 -
.../test/workflow_tests/test_serial_jobs.py | 3 -
.../test/workflow_tests/test_simple.py | 8 +-
.../test/workflow_tests/test_special_command.py | 3 -
.../test/workflow_tests/test_special_transfer.py | 3 -
.../test/workflow_tests/test_workflow_config.py | 3 -
.../test/workflow_tests/test_workflow_env.py | 3 -
.../test/workflow_tests/test_wrong_native_spec.py | 6 +-
.../workflow_tests/workflow_examples/__init__.py | 1 -
.../workflow_examples/workflow_examples.py | 10 +-
.../workflow_examples/workflow_local.py | 7 +-
.../workflow_examples/workflow_shared.py | 4 -
.../workflow_examples/workflow_shared_transfer.py | 4 -
.../workflow_examples/workflow_transfer.py | 4 -
.../test/workflow_tests/workflow_test.py | 18 +-
python/soma_workflow/test/zro_tests/sro.py | 11 +-
.../soma_workflow/test/zro_tests/sro_testClient.py | 4 -
.../soma_workflow/test/zro_tests/sro_testServer.py | 5 +-
.../soma_workflow/test/zro_tests/zro_testClient.py | 4 -
.../soma_workflow/test/zro_tests/zro_testServer.py | 5 +-
python/soma_workflow/transfer.py | 135 ++++++------
python/soma_workflow/utils.py | 13 +-
python/soma_workflow/version.py | 3 -
python/soma_workflow/zro.py | 31 ++-
python/somadrmaa/__init__.py | 6 +-
python/somadrmaa/const.py | 7 +-
python/somadrmaa/errors.py | 6 +-
python/somadrmaa/helpers.py | 34 ++-
python/somadrmaa/nt.py | 11 +-
python/somadrmaa/wrappers.py | 2 -
python/somadrmaa2/__init__.py | 2 -
python/somadrmaa2/wrappers.py | 7 +-
setup.py | 2 -
115 files changed, 472 insertions(+), 844 deletions(-)
$ pre-commit install
pre-commit installed at .git/hooks/pre-commit
Summary of Git repositories in /casa/host/src
=============================================
┌───── * uncommitted working tree changes
│┌──── + uncommitted index changes
││┌─── $ stash present
│││┌── % untracked files
││││ ┌ HEAD
││││ │ ┌ update status
││││ │ │ ┌ bv_maker upstream state
││││ │ │ │ ┌ Git upstream state
││││ │ │ │ │┌ Directory
master (5bfc5e14) ✓ U= aims/aims-free/master
master (87e39e9) ✓ U= aims/aims-gpl/master
master (e414bea7) ✓ U= anatomist/anatomist-free/master
% master (fa70746) ✓ U= anatomist/anatomist-gpl/master
master (f997fc8a) ✓ U= axon/master
master (bb16881) ✓ U= brainrat/bioprocessing/master
master (9a3882e) ✓ U= brainrat/brainrat-gpl/master
master (e9670b4) ✓ U= brainrat/brainrat-private/master
master (f30acde) ✓ U= brainrat/primatologist-gpl/master
master (869819a) ✓ U= brainvisa-share/master
master (273f2ca) ✓ U= brainvisa-spm/master
master (3fd2e485) ✓ U= capsul/master
master (ea5df9f) ✓ U= constellation/constellation-gpl/master
master (ccb3558) ✓ U= constellation/constellation-nonfree/master
master (a40875d) ✓ U= cortical_surface/brainvisa_freesurfer/master
master (04f5e7e) ✓ U= cortical_surface/cortical_surface-gpl/master
master (c20dd90) ✓ U= cortical_surface/cortical_surface-nonfree/master
master (914be65) ✓ U= development/brainvisa-cmake/master
master (69ef51d) ✓ U= development/casa-distro/master
main (016fe62) ✓ U= development/neuro-forge/master
master (186f84c) ✓ U= disco/master
master (a2d6a7d) ✓ U= highres-cortex/master
master (e72510d) ✓ U= morphologist/morpho-deepsulci/master
master (4333dbf9) ✓ U= morphologist/morphologist-gpl/master
master (c8cf86b) ✓ U= morphologist/morphologist-nonfree/master
master (c22bab8) ✓ U= morphologist/morphologist-ui/master
master (cb2e0eb) ✓ U= morphologist/sulci-nonfree/master
master (698334b) ✓ U= populse/populse_db/master
master (f6a92dc) ✓ U= soma/soma-base/master
master (9a978e0) ✓ U= soma/soma-io/master
master (7afea86) ✓ U= soma/soma-workflow/master
bv_maker summary:
OK step sources: /casa/host/src, started: 2025/08/27 04:59, stopped: 2025/08/27 04:59
All went good.
Finished: SUCCESS