Started
Running as brainvisa
================================================================================
----------------------------------------
$ /usr/bin/python3 /home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0/src/brainvisa-cmake/bin/bv_run_pixi_env.py run name=brainvisa-sf-6.0_user env=BRAINVISA_TEST_RUN_DATA_DIR=/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/tests/test,BRAINVISA_TEST_REF_DATA_DIR=/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/tests/ref -- sh -c 'timeout -k 10 1000.000000 python -m capsul.test --verbose'
----------------------------------------
test_completion (capsul.attributes.test.test_attributed_process.TestCompletion.test_completion) ... ok
test_iteration (capsul.attributes.test.test_attributed_process.TestCompletion.test_iteration) ... ok
test_list_completion (capsul.attributes.test.test_attributed_process.TestCompletion.test_list_completion) ... ok
test_run_iteraton_sequential (capsul.attributes.test.test_attributed_process.TestCompletion.test_run_iteraton_sequential) ... ok
test_run_iteraton_swf (capsul.attributes.test.test_attributed_process.TestCompletion.test_run_iteraton_swf) ... soma-workflow starting in light mode
ok
test_completion (capsul.attributes.test.test_fom_process.TestCompletion.test_completion) ... Workflow controller initialised
del WorkflowController
ok
test_iteration (capsul.attributes.test.test_fom_process.TestCompletion.test_iteration) ... ok
test_list_completion (capsul.attributes.test.test_fom_process.TestCompletion.test_list_completion) ... ok
test_run_iteraton_sequential (capsul.attributes.test.test_fom_process.TestCompletion.test_run_iteraton_sequential) ... ok
test_run_iteraton_swf (capsul.attributes.test.test_fom_process.TestCompletion.test_run_iteraton_swf) ... ok
test_capsul_import (capsul.test.test_capsul_modules_import.TestCapsulModulesImport.test_capsul_import) ... ok
test_capsul_pipeline_import (capsul.test.test_capsul_modules_import.TestCapsulModulesImport.test_capsul_pipeline_import) ... ok
test_capsul_pipeline_pipeline_workflow_import (capsul.test.test_capsul_modules_import.TestCapsulModulesImport.test_capsul_pipeline_pipeline_workflow_import) ... ok
test_capsul_process_import (capsul.test.test_capsul_modules_import.TestCapsulModulesImport.test_capsul_process_import) ... ok
test_capsul_studyconfig_import (capsul.test.test_capsul_modules_import.TestCapsulModulesImport.test_capsul_studyconfig_import) ... ok
test_capsul_utils_import (capsul.test.test_capsul_modules_import.TestCapsulModulesImport.test_capsul_utils_import) ... ok
test_class_user_parameters (capsul.process.test.test_traits.TestProcessUserTrait.test_class_user_parameters)
Method to test if class user parameters are not shared at ... ok
test_nipype_automatic_wrap (capsul.process.test.test_nipype_wrap.TestNipypeWrap.test_nipype_automatic_wrap)
Method to test if the automatic nipype interfaces wrap work ... soma-workflow starting in light mode
Workflow controller initialised
250917-04:02:43,556 nipype.interface WARNING:
FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING:nipype.interface:FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
ok
test_nipype_monkey_patching (capsul.process.test.test_nipype_wrap.TestNipypeWrap.test_nipype_monkey_patching)
Method to test the monkey patching used to work in user ... 250917-04:02:43,565 nipype.interface WARNING:
FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING:nipype.interface:FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
ok
test_help (capsul.process.test.test_runprocess.TestRunProcess.test_help) ... ok
test_python_m_capsul (capsul.process.test.test_runprocess.TestRunProcess.test_python_m_capsul) ... ok
test_run_dummy_process (capsul.process.test.test_runprocess.TestRunProcess.test_run_dummy_process) ... ok
test_run_dummy_process_wrong_args (capsul.process.test.test_runprocess.TestRunProcess.test_run_dummy_process_wrong_args) ... ok
test_run_process_help (capsul.process.test.test_runprocess.TestRunProcess.test_run_process_help) ... ok
test_named_outputs (capsul.process.test.test_load_from_description.TestLoadFromDescription.test_named_outputs) ... ok
test_pipeline_warping (capsul.process.test.test_load_from_description.TestLoadFromDescription.test_pipeline_warping)
Method to test the xml description to pipeline on the fly warping. ... ok
test_pipeline_writing (capsul.process.test.test_load_from_description.TestLoadFromDescription.test_pipeline_writing)
Method to test the xml description saving and reloading ... ok
test_process_warping (capsul.process.test.test_load_from_description.TestLoadFromDescription.test_process_warping)
Method to test the function to process on the fly warping. ... ok
test_return_list (capsul.process.test.test_load_from_description.TestLoadFromDescription.test_return_list) ... ok
test_return_string (capsul.process.test.test_load_from_description.TestLoadFromDescription.test_return_string) ... ok
test_process_wrap (capsul.process.test.test_load_from_description.TestProcessWrap.test_process_wrap)
Method to test if the process has been wrapped properly. ... ok
test_version_interfaces (capsul.utils.test.test_utils.TestUtils.test_version_interfaces)
Method to test if we can get the nipype interfaces versions. ... ok
test_version_python (capsul.utils.test.test_utils.TestUtils.test_version_python)
Method to test if we can get a python module version from ... ok
test_study_config_fsl (capsul.study_config.test.test_fsl_config.TestFSL.test_study_config_fsl) ... WARNING: Skip FSL test because it cannot be configured automatically: FSL command "bet" cannot be found in PATH
ok
test_study_config_fom (capsul.study_config.test.test_study_config_fom.TestStudyConfigFOM.test_study_config_fom) ... ok
test_execution_with_cache (capsul.study_config.test.test_run_in_study_config.TestRunProcess.test_execution_with_cache)
Execute a process with cache. ... ok
test_execution_without_cache (capsul.study_config.test.test_run_in_study_config.TestRunProcess.test_execution_without_cache)
Execute a process without cache. ... ok
test_atomic_dependencies (capsul.study_config.test.test_soma_workflow.TestSomaWorkflow.test_atomic_dependencies) ... ok
test_atomic_execution (capsul.study_config.test.test_soma_workflow.TestSomaWorkflow.test_atomic_execution) ... ok
test_composite_dependencies (capsul.study_config.test.test_soma_workflow.TestSomaWorkflow.test_composite_dependencies) ... ok
test_composite_execution (capsul.study_config.test.test_soma_workflow.TestSomaWorkflow.test_composite_execution) ... ok
test_atomic_dependencies (capsul.study_config.test.test_soma_workflow_with_kw.TestSomaWorkflow.test_atomic_dependencies) ... ok
test_atomic_execution (capsul.study_config.test.test_soma_workflow_with_kw.TestSomaWorkflow.test_atomic_execution) ... ok
test_atomic_execution_kwparams (capsul.study_config.test.test_soma_workflow_with_kw.TestSomaWorkflow.test_atomic_execution_kwparams) ... ok
test_composite_dependencies (capsul.study_config.test.test_soma_workflow_with_kw.TestSomaWorkflow.test_composite_dependencies) ... ok
test_composite_execution (capsul.study_config.test.test_soma_workflow_with_kw.TestSomaWorkflow.test_composite_execution) ... ok
test_proxy_process_copy (capsul.study_config.test.test_memory.TestMemory.test_proxy_process_copy)
Test memory with copy. ... ok
test_proxy_process_with_cache (capsul.study_config.test.test_memory.TestMemory.test_proxy_process_with_cache)
Test the proxy process behaviours with cache. ... ok
test_proxy_process_without_cache (capsul.study_config.test.test_memory.TestMemory.test_proxy_process_without_cache)
Test the proxy process behaviours without cache. ... ok
test_study_config_configuration (capsul.study_config.test.test_study_config_configuration.TestStudyConfigConfiguration.test_study_config_configuration) ... ok
test_execution_with_cache (capsul.study_config.test.test_run_process.TestRunProcess.test_execution_with_cache)
Execute a process with cache. ... ok
test_execution_without_cache (capsul.study_config.test.test_run_process.TestRunProcess.test_execution_without_cache)
Execute a process without cache. ... ok
test_missing_parameters (capsul.study_config.test.test_run_process.TestRunProcess.test_missing_parameters)
Test if missing mandatory parameters raise the appropriate error ... ok
test_use_cases_doc (capsul.sphinxext.test.test_usercases_doc.TestUseCases.test_use_cases_doc)
Method to test the use cases rst documentation. ... ok
test_pipeline_doc (capsul.sphinxext.test.test_process_pipeline_doc.TestSphinxExt.test_pipeline_doc)
Method to test the pipeline rst documentation. ... ok
test_process_doc (capsul.sphinxext.test.test_process_pipeline_doc.TestSphinxExt.test_process_doc)
Method to test the process rst documentation. ... ok
test_way1 (capsul.pipeline.test.test_switch_optional_output.TestPipeline.test_way1) ... ok
test_way2 (capsul.pipeline.test.test_switch_optional_output.TestPipeline.test_way2) ... ok
test_self_state (capsul.pipeline.test.test_switch_subpipeline.TestSwitchPipeline.test_self_state) ... ok
test_switch_value (capsul.pipeline.test.test_switch_subpipeline.TestSwitchPipeline.test_switch_value) ... ok
test_full_pipeline_wf (capsul.pipeline.test.test_pipeline_workflow.TestPipelineWorkflow.test_full_pipeline_wf) ... ok
test_iter_workflow (capsul.pipeline.test.test_pipeline_workflow.TestPipelineWorkflow.test_iter_workflow) ... ________________________________________________________________________________
[Process] Calling capsul.study_config.test.test_run_in_study_config.DummyProcess...
capsul.study_config.test.test_run_in_study_config.DummyProcess(f1=1.0, f2=2.3, output_directory=/home_local/a-sac-ns-brainvisa/tmp/tmpopd4ciwe)
________________________________________________________________________________
[Memory] Calling capsul.study_config.test.test_run_in_study_config.DummyProcess...
capsul.study_config.test.test_run_in_study_config.DummyProcess(f1=1.0, f2=2.3, output_directory=/home_local/a-sac-ns-brainvisa/tmp/tmpopd4ciwe)
____________________________________________________________________0.0s, 0.0min
________________________________________________________________________________
[Process] Calling capsul.study_config.test.test_run_in_study_config.DummyProcess...
capsul.study_config.test.test_run_in_study_config.DummyProcess(f1=2.0, f2=2.0, output_directory=/home_local/a-sac-ns-brainvisa/tmp/tmpopd4ciwe)
________________________________________________________________________________
[Memory] Calling capsul.study_config.test.test_run_in_study_config.DummyProcess...
capsul.study_config.test.test_run_in_study_config.DummyProcess(f1=2.0, f2=2.0, output_directory=/home_local/a-sac-ns-brainvisa/tmp/tmpopd4ciwe)
____________________________________________________________________0.0s, 0.0min
________________________________________________________________________________
[Process] Calling capsul.study_config.test.test_run_in_study_config.DummyProcess...
capsul.study_config.test.test_run_in_study_config.DummyProcess(f1=1.0, f2=2.3, output_directory=/home_local/a-sac-ns-brainvisa/tmp/tmpopd4ciwe)
[Memory]: Loading capsul.study_config.test.test_run_in_study_config.DummyProcess(f1=1.0, f2=2.3, output_directory=/home_local/a-sac-ns-brainvisa/tmp/tmpopd4ciwe)...
________________________________________________________________________________
[Process] Calling capsul.study_config.test.test_run_in_study_config.DummyProcess...
capsul.study_config.test.test_run_in_study_config.DummyProcess(f1=1.0, f2=2.3, output_directory=/home_local/a-sac-ns-brainvisa/tmp/tmpxyo2q9mf)
________________________________________________________________________________
[Process] Calling capsul.study_config.test.test_run_in_study_config.DummyProcess...
capsul.study_config.test.test_run_in_study_config.DummyProcess(f1=2.0, f2=2.0, output_directory=/home_local/a-sac-ns-brainvisa/tmp/tmpxyo2q9mf)
________________________________________________________________________________
[Process] Calling capsul.study_config.test.test_run_in_study_config.DummyProcess...
capsul.study_config.test.test_run_in_study_config.DummyProcess(f1=1.0, f2=2.3, output_directory=/home_local/a-sac-ns-brainvisa/tmp/tmpxyo2q9mf)
del WorkflowController
soma-workflow starting in light mode
Workflow controller initialised
soma-workflow starting in light mode
Workflow controller initialised
soma-workflow starting in light mode
Workflow controller initialised
soma-workflow starting in light mode
Workflow controller initialised
soma-workflow starting in light mode
Workflow controller initialised
________________________________________________________________________________
[Process] Calling capsul.study_config.test.test_memory.DummyCopyProcess...
capsul.study_config.test.test_memory.DummyCopyProcess(f=2.5, i=/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/capsul/study_config/test/test_memory.py, l=['/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/capsul/study_config/test/test_memory.py'])
____________________________________________________________________0.0s, 0.0min
proxy_process: <class 'capsul.study_config.memory.UnMemorizedProcess'>
machin: {'i': '/home_local/a-sac-ns-brainvisa/tmp/tmp3f1zlf8f/test_memory.py', 'l': ['/home_local/a-sac-ns-brainvisa/tmp/tmp3f1zlf8f/test_memory.py'], 'f': 2.5}
________________________________________________________________________________
[Memory] Calling capsul.study_config.test.test_memory.DummyProcess...
capsul.study_config.test.test_memory.DummyProcess(f=1.0, ff=2.3)
____________________________________________________________________0.0s, 0.0min
________________________________________________________________________________
[Memory] Calling capsul.study_config.test.test_memory.DummyProcess...
capsul.study_config.test.test_memory.DummyProcess(f=2.0, ff=2.0)
____________________________________________________________________0.0s, 0.0min
[Memory]: Loading capsul.study_config.test.test_memory.DummyProcess(f=1.0, ff=2.3)...
________________________________________________________________________________
[Process] Calling capsul.study_config.test.test_memory.DummyProcess...
capsul.study_config.test.test_memory.DummyProcess(f=1.0, ff=2.3)
____________________________________________________________________0.0s, 0.0min
________________________________________________________________________________
[Process] Calling capsul.study_config.test.test_memory.DummyProcess...
capsul.study_config.test.test_memory.DummyProcess(f=2.0, ff=2.0)
____________________________________________________________________0.0s, 0.0min
________________________________________________________________________________
[Process] Calling capsul.study_config.test.test_memory.DummyProcess...
capsul.study_config.test.test_memory.DummyProcess(f=1.0, ff=2.3)
____________________________________________________________________0.0s, 0.0min
________________________________________________________________________________
[Process] Calling capsul.study_config.test.test_run_process.DummyProcess...
capsul.study_config.test.test_run_process.DummyProcess(f1=0.0, f2=0.0, output_directory=/home_local/a-sac-ns-brainvisa/tmp/tmp2ljsnciv)
________________________________________________________________________________
[Process] Calling capsul.study_config.test.test_run_process.DummyProcess...
capsul.study_config.test.test_run_process.DummyProcess(f1=1.0, f2=2.3, output_directory=/home_local/a-sac-ns-brainvisa/tmp/tmp2ljsnciv)
________________________________________________________________________________
[Process] Calling capsul.study_config.test.test_run_process.DummyProcess...
capsul.study_config.test.test_run_process.DummyProcess(f1=2.0, f2=2.0, output_directory=/home_local/a-sac-ns-brainvisa/tmp/tmp2ljsnciv)
________________________________________________________________________________
[Process] Calling capsul.study_config.test.test_run_process.DummyProcess...
capsul.study_config.test.test_run_process.DummyProcess(f1=0.0, f2=0.0, output_directory=/home_local/a-sac-ns-brainvisa/tmp/tmpy1kbsp_a)
________________________________________________________________________________
[Process] Calling capsul.study_config.test.test_run_process.DummyProcess...
capsul.study_config.test.test_run_process.DummyProcess(f1=1.0, f2=2.3, output_directory=/home_local/a-sac-ns-brainvisa/tmp/tmpy1kbsp_a)
________________________________________________________________________________
[Process] Calling capsul.study_config.test.test_run_process.DummyProcess...
capsul.study_config.test.test_run_process.DummyProcess(f1=2.0, f2=2.0, output_directory=/home_local/a-sac-ns-brainvisa/tmp/tmpy1kbsp_a)
soma-workflow starting in light mode
Workflow controller initialised
execution started
WARNING: The file or directory /home_local/a-sac-ns-brainvisa/tmp/tmptamf2cze/transfered_files/a-sac-ns-brainvisa_1/file_out1 doesn't exist on the computing resource side.
WARNING: The file or directory /home_local/a-sac-ns-brainvisa/tmp/tmptamf2cze/transfered_files/a-sac-ns-brainvisa_1/file_out1.minf doesn't exist on the computing resource side.
WARNING: The file or directory /home_local/a-sac-ns-brainvisa/tmp/tmptamf2cze/transfered_files/a-sac-ns-brainvisa_1/file_out2 doesn't exist on the computing resource side.
WARNING: The file or directory /home_local/a-sac-ns-brainvisa/tmp/tmptamf2cze/transfered_files/a-sac-ns-brainvisa_1/file_out2.minf doesn't exist on the computing resource side.
ok
test_iter_workflow_without_temp (capsul.pipeline.test.test_pipeline_workflow.TestPipelineWorkflow.test_iter_workflow_without_temp) ... ok
test_partial_wf1 (capsul.pipeline.test.test_pipeline_workflow.TestPipelineWorkflow.test_partial_wf1) ... ok
test_partial_wf2 (capsul.pipeline.test.test_pipeline_workflow.TestPipelineWorkflow.test_partial_wf2) ... ok
test_partial_wf3_fail (capsul.pipeline.test.test_pipeline_workflow.TestPipelineWorkflow.test_partial_wf3_fail) ... ok
test_requirements (capsul.pipeline.test.test_pipeline_workflow.TestPipelineWorkflow.test_requirements) ... ok
test_wf_run (capsul.pipeline.test.test_pipeline_workflow.TestPipelineWorkflow.test_wf_run) ... ok
test_full_desactivation (capsul.pipeline.test.test_activation.TestPipeline.test_full_desactivation) ... ok
test_partial_desactivation (capsul.pipeline.test.test_activation.TestPipeline.test_partial_desactivation) ... ok
test_activations (capsul.pipeline.test.test_complex_pipeline_activations.TestComplexPipeline.test_activations) ... Exception in thread Thread-10:
Traceback (most recent call last):
File "/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/soma_workflow/database_server.py", line 642, in _connect
connection = sqlite3.connect(
^^^^^^^^^^^^^^^^
sqlite3.OperationalError: unable to open database file
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/threading.py", line 1038, in _bootstrap_inner
self.run()
File "/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/soma_workflow/engine.py", line 97, in run
Exception in thread Thread-9:
Traceback (most recent call last):
File "/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/soma_workflow/database_server.py", line 642, in _connect
self.engine_loop.start_loop(self.time_interval)
File "/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/soma_workflow/engine.py", line 264, in start_loop
connection = sqlite3.connect(
^^^^^^^^^^^^^^^^
sqlite3.OperationalError: unable to open database file
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/threading.py", line 1038, in _bootstrap_inner
= self._database_server.jobs_to_delete_and_kill(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/soma_workflow/database_server.py", line 3762, in jobs_to_delete_and_kill
self.run()
File "/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/soma_workflow/engine.py", line 97, in run
self.engine_loop.start_loop(self.time_interval)
File "/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/soma_workflow/engine.py", line 264, in start_loop
= self._database_server.jobs_to_delete_and_kill(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/soma_workflow/database_server.py", line 3762, in jobs_to_delete_and_kill
connection = self._connect()
^^^^^^^^^^^^^^^
File "/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/soma_workflow/database_server.py", line 652, in _connect
raise DatabaseError('On database file %s: %s: %s \n'
File "/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/soma_workflow/database_server.py", line 642, in _connect
connection = sqlite3.connect(
^^^^^^^^^^^^^^^^
soma_workflow.errors.DatabaseError: On database file /home_local/a-sac-ns-brainvisa/tmp/tmptamf2cze/soma-workflow.db: <class 'sqlite3.OperationalError'>: unable to open database file
connection = self._connect()
^^^^^^^^^^^^^^^
File "/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/soma_workflow/database_server.py", line 652, in _connect
raise DatabaseError('On database file %s: %s: %s \n'
File "/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/soma_workflow/database_server.py", line 642, in _connect
connection = sqlite3.connect(
^^^^^^^^^^^^^^^^
soma_workflow.errors.DatabaseError: On database file /home_local/a-sac-ns-brainvisa/tmp/tmptamf2cze/soma-workflow.db: <class 'sqlite3.OperationalError'>: unable to open database file
ok
test_direct_run (capsul.pipeline.test.test_temporary.TestTemporary.test_direct_run) ... ok
test_full_wf (capsul.pipeline.test.test_temporary.TestTemporary.test_full_wf) ... ok
test_structure (capsul.pipeline.test.test_temporary.TestTemporary.test_structure) ... ok
test_date_time (capsul.pipeline.test.test_pipeline_parameters.TestPipelineMethods.test_date_time) ... /home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/soma/controller/controller.py:330: DeprecationWarning: In the future, None will no longer be accepted by this trait type. To allow None and silence this warning, use Date(allow_none=True).
setattr(self, name, value)
/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/soma/controller/controller.py:330: DeprecationWarning: In the future, None will no longer be accepted by this trait type. To allow None and silence this warning, use Time(allow_none=True).
setattr(self, name, value)
ok
test_file (capsul.pipeline.test.test_pipeline_parameters.TestPipelineMethods.test_file) ... ok
test_float (capsul.pipeline.test.test_pipeline_parameters.TestPipelineMethods.test_float) ... ok
test_int (capsul.pipeline.test.test_pipeline_parameters.TestPipelineMethods.test_int) ... ok
test_list_file (capsul.pipeline.test.test_pipeline_parameters.TestPipelineMethods.test_list_file) ... ok
test_list_float (capsul.pipeline.test.test_pipeline_parameters.TestPipelineMethods.test_list_float) ... ok
test_list_int (capsul.pipeline.test.test_pipeline_parameters.TestPipelineMethods.test_list_int) ... ok
test_list_list (capsul.pipeline.test.test_pipeline_parameters.TestPipelineMethods.test_list_list) ... ok
test_list_string (capsul.pipeline.test.test_pipeline_parameters.TestPipelineMethods.test_list_string) ... ok
test_string (capsul.pipeline.test.test_pipeline_parameters.TestPipelineMethods.test_string) ... ok
test_json (capsul.pipeline.test.test_optional_output_switch.TestPipeline.test_json) ... ok
test_way1 (capsul.pipeline.test.test_optional_output_switch.TestPipeline.test_way1) ... ok
test_way2 (capsul.pipeline.test.test_optional_output_switch.TestPipeline.test_way2) ... ok
test_xml (capsul.pipeline.test.test_optional_output_switch.TestPipeline.test_xml) ... ok
test_iterative_pipeline_with_temp (capsul.pipeline.test.test_pipeline_with_temp.TestPipelineWithTemp.test_iterative_pipeline_with_temp) ... ok
test_pipeline_with_temp (capsul.pipeline.test.test_pipeline_with_temp.TestPipelineWithTemp.test_pipeline_with_temp) ... ok
test_direct_run (capsul.pipeline.test.test_proc_with_outputs.TestPipelineContainingProcessWithOutputs.test_direct_run) ... ok
test_direct_run_sub_iter (capsul.pipeline.test.test_proc_with_outputs.TestPipelineContainingProcessWithOutputs.test_direct_run_sub_iter) ... ok
test_direct_run_subpipeline (capsul.pipeline.test.test_proc_with_outputs.TestPipelineContainingProcessWithOutputs.test_direct_run_subpipeline) ... ok
test_direct_run_switch (capsul.pipeline.test.test_proc_with_outputs.TestPipelineContainingProcessWithOutputs.test_direct_run_switch) ... ok
test_full_wf (capsul.pipeline.test.test_proc_with_outputs.TestPipelineContainingProcessWithOutputs.test_full_wf) ... ok
test_full_wf_switch (capsul.pipeline.test.test_proc_with_outputs.TestPipelineContainingProcessWithOutputs.test_full_wf_switch) ... ok
test_constant (capsul.pipeline.test.test_pipeline.TestPipeline.test_constant) ... ok
test_enabled (capsul.pipeline.test.test_pipeline.TestPipeline.test_enabled) ... ok
test_pipeline_io_py (capsul.pipeline.test.test_pipeline.TestPipeline.test_pipeline_io_py) ... ok
test_pipeline_json (capsul.pipeline.test.test_pipeline.TestPipeline.test_pipeline_json) ... ok
test_pipeline_xml (capsul.pipeline.test.test_pipeline.TestPipeline.test_pipeline_xml) ... ok
test_run_pipeline (capsul.pipeline.test.test_pipeline.TestPipeline.test_run_pipeline) ... ok
test_hard (capsul.pipeline.test.test_switch_pipeline.TestSwitchPipeline.test_hard) ... ok
test_io (capsul.pipeline.test.test_switch_pipeline.TestSwitchPipeline.test_io) ... ok
test_parameter_propagation (capsul.pipeline.test.test_switch_pipeline.TestSwitchPipeline.test_parameter_propagation) ... ok
test_way1 (capsul.pipeline.test.test_switch_pipeline.TestSwitchPipeline.test_way1) ... ok
test_way2 (capsul.pipeline.test.test_switch_pipeline.TestSwitchPipeline.test_way2) ... ok
test_way3 (capsul.pipeline.test.test_switch_pipeline.TestSwitchPipeline.test_way3) ... ok
test_weak_off (capsul.pipeline.test.test_switch_pipeline.TestSwitchPipeline.test_weak_off) ... ok
test_weak_on (capsul.pipeline.test.test_switch_pipeline.TestSwitchPipeline.test_weak_on) ... ok
test_iterative_big_pipeline_workflow (capsul.pipeline.test.test_iterative_process.TestPipeline.test_iterative_big_pipeline_workflow) ... ok
test_iterative_pipeline_connection (capsul.pipeline.test.test_iterative_process.TestPipeline.test_iterative_pipeline_connection)
Test if an iterative process works correctly ... ok
test_iterative_pipeline_workflow (capsul.pipeline.test.test_iterative_process.TestPipeline.test_iterative_pipeline_workflow) ... ok
test_iterative_pipeline_workflow_run (capsul.pipeline.test.test_iterative_process.TestPipeline.test_iterative_pipeline_workflow_run) ... ok
test_custom_nodes (capsul.pipeline.test.test_custom_nodes.TestCustomNodes.test_custom_nodes) ... ok
test_custom_nodes_json_io (capsul.pipeline.test.test_custom_nodes.TestCustomNodes.test_custom_nodes_json_io) ... ok
test_custom_nodes_py_io (capsul.pipeline.test.test_custom_nodes.TestCustomNodes.test_custom_nodes_py_io) ... ok
test_custom_nodes_workflow (capsul.pipeline.test.test_custom_nodes.TestCustomNodes.test_custom_nodes_workflow) ... ok
test_custom_nodes_xml_io (capsul.pipeline.test.test_custom_nodes.TestCustomNodes.test_custom_nodes_xml_io) ... ok
test_cv_json_io (capsul.pipeline.test.test_custom_nodes.TestCustomNodes.test_cv_json_io) ... ok
test_cv_py_io (capsul.pipeline.test.test_custom_nodes.TestCustomNodes.test_cv_py_io) ... ok
test_cv_xml_io (capsul.pipeline.test.test_custom_nodes.TestCustomNodes.test_cv_xml_io) ... ok
test_leave_one_out_pipeline (capsul.pipeline.test.test_custom_nodes.TestCustomNodes.test_leave_one_out_pipeline) ... ok
test_loo_json_io (capsul.pipeline.test.test_custom_nodes.TestCustomNodes.test_loo_json_io) ... ok
test_loo_py_io (capsul.pipeline.test.test_custom_nodes.TestCustomNodes.test_loo_py_io) ... ok
test_loo_xml_io (capsul.pipeline.test.test_custom_nodes.TestCustomNodes.test_loo_xml_io) ... ok
test_mapreduce (capsul.pipeline.test.test_custom_nodes.TestCustomNodes.test_mapreduce) ... ok
test_qc_active (capsul.pipeline.test.test_qc_nodes.TestQCNodes.test_qc_active)
Method to test if the run qc option works properly. ... ok
test_qc_inactive (capsul.pipeline.test.test_qc_nodes.TestQCNodes.test_qc_inactive)
Method to test if the run qc option works properly. ... ok
test_way1 (capsul.pipeline.test.test_double_switch.TestDoubleSwitchPipeline.test_way1) ... ok
test_way2 (capsul.pipeline.test.test_double_switch.TestDoubleSwitchPipeline.test_way2) ... ok
test_iterative_pipeline_connection (capsul.pipeline.test.test_process_iteration.TestPipeline.test_iterative_pipeline_connection)
Method to test if an iterative node and built in iterative ... ok
test_engine_settings (capsul.engine.test.test_capsul_engine.TestCapsulEngine.test_engine_settings) ... ok
test_fsl_config (capsul.engine.test.test_capsul_engine.TestCapsulEngine.test_fsl_config) ... ['/home_local/a-sac-ns-brainvisa/tmp/capsul_fsl9eg12ngq/bin/fsl5.0-bet', 'nothing', 'nothing_else']
ok
test_matlab_config (capsul.engine.test.test_capsul_engine.TestCapsulEngine.test_matlab_config) ... ok
test_nipype_spm_config (capsul.engine.test.test_capsul_engine.TestCapsulEngine.test_nipype_spm_config) ... skipped 'SPM12 standalone or nipype are not found'
test_python_config (capsul.engine.test.test_capsul_engine.TestCapsulEngine.test_python_config) ... ok
----------------------------------------------------------------------
Ran 137 tests in 125.777s
OK (skipped=1)
WARNING: The file or directory /home_local/a-sac-ns-brainvisa/tmp/tmptamf2cze/transfered_files/a-sac-ns-brainvisa_1/file_out3 doesn't exist on the computing resource side.
WARNING: The file or directory /home_local/a-sac-ns-brainvisa/tmp/tmptamf2cze/transfered_files/a-sac-ns-brainvisa_1/file_out3.minf doesn't exist on the computing resource side.
finished: workflow_done
soma-workflow starting in light mode
Workflow controller initialised
execution started
WARNING: The file or directory /home_local/a-sac-ns-brainvisa/tmp/tmptamf2cze/transfered_files/a-sac-ns-brainvisa_1/1_dir/file_out doesn't exist on the computing resource side.
WARNING: The file or directory /home_local/a-sac-ns-brainvisa/tmp/tmptamf2cze/transfered_files/a-sac-ns-brainvisa_1/1_dir/file_out.minf doesn't exist on the computing resource side.
finished: workflow_done
transfered output path: /home_local/a-sac-ns-brainvisa/tmp/tmp90k_e4dw/file_out2.nii from: node3.output changes to input.
transfered output path: /home_local/a-sac-ns-brainvisa/tmp/tmppli3mwtn/file_out1.nii from: node2.output changes to input.
temp path in: node1.output will not be produced.
soma-workflow starting in light mode
Workflow controller initialised
execution started
finished: workflow_done
del WorkflowController
del WorkflowController
del WorkflowController
del WorkflowController
del WorkflowController
del WorkflowController
del WorkflowController
del WorkflowController
soma-workflow starting in light mode
Workflow controller initialised
del WorkflowController
DummyProcess : /home_local/a-sac-ns-brainvisa/tmp/tmp6k03lii4capsul_input.txt -> /home_local/a-sac-ns-brainvisa/tmp/tmpscv7wr_wcapsul
DummyProcess : /home_local/a-sac-ns-brainvisa/tmp/tmp6k03lii4capsul_input.txt -> /home_local/a-sac-ns-brainvisa/tmp/tmpd09o3lbacapsul
DummyProcess : /home_local/a-sac-ns-brainvisa/tmp/tmp6k03lii4capsul_input.txt -> /home_local/a-sac-ns-brainvisa/tmp/tmpbcq8x9h2capsul
cat ['/home_local/a-sac-ns-brainvisa/tmp/tmpscv7wr_wcapsul', '/home_local/a-sac-ns-brainvisa/tmp/tmpd09o3lbacapsul', '/home_local/a-sac-ns-brainvisa/tmp/tmpbcq8x9h2capsul'] to: /home_local/a-sac-ns-brainvisa/tmp/tmpacl3oxydcapsul_output.txt
DummyProcess : /home_local/a-sac-ns-brainvisa/tmp/tmptll1ticscapsul_input.txt -> /home_local/a-sac-ns-brainvisa/tmp/tmppqj0nh0ycapsul
DummyProcess : /home_local/a-sac-ns-brainvisa/tmp/tmppqj0nh0ycapsul -> /home_local/a-sac-ns-brainvisa/tmp/tmpd7jszbjgcapsul_output.txt
soma-workflow starting in light mode
Workflow controller initialised
soma-workflow starting in light mode
Workflow controller initialised
cache_dir: /home_local/a-sac-ns-brainvisa/tmp/__pycache__
added py tmpfile: /home_local/a-sac-ns-brainvisa/tmp/test_pipelineo11dkjfj.py /home_local/a-sac-ns-brainvisa/tmp/__pycache__/test_pipelineo11dkjfj.cpython-311.pyc
run: /home_local/a-sac-ns-brainvisa/tmp/capsul_testl8t0wtwo/toto ->
define output_image: /home_local/a-sac-ns-brainvisa/tmp/capsul_testl8t0wtwo/toto-5.0-3.0
run: /home_local/a-sac-ns-brainvisa/tmp/capsul_testl8t0wtwo/tutu -> <undefined>
define output_image: /home_local/a-sac-ns-brainvisa/tmp/capsul_testl8t0wtwo/tutu-5.0-1.0
* running pipeline...
soma-workflow starting in light mode
Workflow controller initialised
* finished.
del WorkflowController
del WorkflowController
del WorkflowController
soma-workflow starting in light mode
Workflow controller initialised
del WorkflowController
soma-workflow starting in light mode
Workflow controller initialised
del WorkflowController
================================================================================
SUCCESS (exit code 0)
Finished: SUCCESS
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