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 del WorkflowController 251125-04:03:36,119 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 ... 251125-04:03:36,127 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/tmprr74jilo) ________________________________________________________________________________ [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/tmprr74jilo) ____________________________________________________________________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/tmprr74jilo) ________________________________________________________________________________ [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/tmprr74jilo) ____________________________________________________________________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/tmprr74jilo) [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/tmprr74jilo)... ________________________________________________________________________________ [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/tmpq1hrf11o) ________________________________________________________________________________ [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/tmpq1hrf11o) ________________________________________________________________________________ [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/tmpq1hrf11o) 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: machin: {'i': '/home_local/a-sac-ns-brainvisa/tmp/tmp9j4paow0/test_memory.py', 'l': ['/home_local/a-sac-ns-brainvisa/tmp/tmp9j4paow0/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/tmpb0s7fbqr) ________________________________________________________________________________ [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/tmpb0s7fbqr) ________________________________________________________________________________ [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/tmpb0s7fbqr) ________________________________________________________________________________ [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/tmpbnjy4y84) ________________________________________________________________________________ [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/tmpbnjy4y84) ________________________________________________________________________________ [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/tmpbnjy4y84) soma-workflow starting in light mode Workflow controller initialised execution started WARNING: The file or directory /home_local/a-sac-ns-brainvisa/tmp/tmpg97jprey/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/tmpg97jprey/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/tmpg97jprey/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/tmpg97jprey/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-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 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 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 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.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._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.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 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 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( connection = sqlite3.connect( ^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^ soma_workflow.errors.DatabaseError: On database file /home_local/a-sac-ns-brainvisa/tmp/tmpg97jprey/soma-workflow.db: : unable to open database file soma_workflow.errors.DatabaseError: On database file /home_local/a-sac-ns-brainvisa/tmp/tmpg97jprey/soma-workflow.db: : 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_fslxytcs7l3/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 133.484s OK (skipped=1) WARNING: The file or directory /home_local/a-sac-ns-brainvisa/tmp/tmpg97jprey/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/tmpg97jprey/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/tmpg97jprey/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/tmpg97jprey/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/tmpmva3yum0/file_out2.nii from: node3.output changes to input. transfered output path: /home_local/a-sac-ns-brainvisa/tmp/tmpcii0wxyl/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 WARNING: The file or directory /home_local/a-sac-ns-brainvisa/tmp/tmp3xusk8t9/file_in.nii.minf doesn't exist on the client machine. execution started WARNING: The file or directory /home_local/a-sac-ns-brainvisa/tmp/tmpg97jprey/transfered_files/a-sac-ns-brainvisa_1/2_dir/file_out1.nii doesn't exist on the computing resource side. WARNING: The file or directory /home_local/a-sac-ns-brainvisa/tmp/tmpg97jprey/transfered_files/a-sac-ns-brainvisa_1/2_dir/file_out1.nii.minf doesn't exist on the computing resource side. WARNING: The file or directory /home_local/a-sac-ns-brainvisa/tmp/tmpg97jprey/transfered_files/a-sac-ns-brainvisa_1/2_dir/file_out2.nii doesn't exist on the computing resource side. WARNING: The file or directory /home_local/a-sac-ns-brainvisa/tmp/tmpg97jprey/transfered_files/a-sac-ns-brainvisa_1/2_dir/file_out2.nii.minf doesn't exist on the computing resource side. WARNING: The file or directory /home_local/a-sac-ns-brainvisa/tmp/tmpg97jprey/transfered_files/a-sac-ns-brainvisa_1/2_dir/file_out3.nii doesn't exist on the computing resource side. WARNING: The file or directory /home_local/a-sac-ns-brainvisa/tmp/tmpg97jprey/transfered_files/a-sac-ns-brainvisa_1/2_dir/file_out3.nii.minf doesn't exist on the computing resource side. 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/tmp_flstox0capsul_input.txt -> /home_local/a-sac-ns-brainvisa/tmp/tmpobmt3374capsul DummyProcess : /home_local/a-sac-ns-brainvisa/tmp/tmp_flstox0capsul_input.txt -> /home_local/a-sac-ns-brainvisa/tmp/tmpyzoh6hwfcapsul DummyProcess : /home_local/a-sac-ns-brainvisa/tmp/tmp_flstox0capsul_input.txt -> /home_local/a-sac-ns-brainvisa/tmp/tmpx0xps77ncapsul cat ['/home_local/a-sac-ns-brainvisa/tmp/tmpobmt3374capsul', '/home_local/a-sac-ns-brainvisa/tmp/tmpyzoh6hwfcapsul', '/home_local/a-sac-ns-brainvisa/tmp/tmpx0xps77ncapsul'] to: /home_local/a-sac-ns-brainvisa/tmp/tmpth70jrkacapsul_output.txt DummyProcess : /home_local/a-sac-ns-brainvisa/tmp/tmpo2zew9dvcapsul_input.txt -> /home_local/a-sac-ns-brainvisa/tmp/tmp435xy22rcapsul DummyProcess : /home_local/a-sac-ns-brainvisa/tmp/tmp435xy22rcapsul -> /home_local/a-sac-ns-brainvisa/tmp/tmpn8jd_odlcapsul_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_pipelinedohjwm88.py /home_local/a-sac-ns-brainvisa/tmp/__pycache__/test_pipelinedohjwm88.cpython-311.pyc run: /home_local/a-sac-ns-brainvisa/tmp/capsul_tests4r3z1ry/toto -> define output_image: /home_local/a-sac-ns-brainvisa/tmp/capsul_tests4r3z1ry/toto-5.0-3.0 run: /home_local/a-sac-ns-brainvisa/tmp/capsul_tests4r3z1ry/tutu -> define output_image: /home_local/a-sac-ns-brainvisa/tmp/capsul_tests4r3z1ry/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