Started
Running as brainvisa
================================================================================
----------------------------------------
$ /usr/bin/python3 /volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-master-5.3/src/development/casa-distro/master/bin/casa_distro run name=brainvisa-5.1-5.3-userimage env=BRAINVISA_TEST_RUN_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test,BRAINVISA_TEST_REF_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/ref -- sh -c '/casa/install/bin/bv_env_test "timeout" "-k" "10" "1000.000000" "python" "-m" "capsul.test" "--verbose"'
----------------------------------------
test_completion (capsul.attributes.test.test_attributed_process.TestCompletion) ... ok
test_iteration (capsul.attributes.test.test_attributed_process.TestCompletion) ... ok
test_list_completion (capsul.attributes.test.test_attributed_process.TestCompletion) ... ok
test_run_iteraton_sequential (capsul.attributes.test.test_attributed_process.TestCompletion) ... ok
test_run_iteraton_swf (capsul.attributes.test.test_attributed_process.TestCompletion) ... soma-workflow starting in light mode
<frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
ok
test_completion (capsul.attributes.test.test_fom_process.TestCompletion) ... Workflow controller initialised
del WorkflowController
ok
test_iteration (capsul.attributes.test.test_fom_process.TestCompletion) ... ok
test_list_completion (capsul.attributes.test.test_fom_process.TestCompletion) ... ok
test_run_iteraton_sequential (capsul.attributes.test.test_fom_process.TestCompletion) ... ok
test_run_iteraton_swf (capsul.attributes.test.test_fom_process.TestCompletion) ... ok
test_engine_settings (capsul.engine.test.test_capsul_engine.TestCapsulEngine) ... ok
test_fsl_config (capsul.engine.test.test_capsul_engine.TestCapsulEngine) ... ['/tmp/capsul_fsl62qonjdj/bin/fsl5.0-bet', 'nothing', 'nothing_else']
ok
test_matlab_config (capsul.engine.test.test_capsul_engine.TestCapsulEngine) ... ok
test_nipype_spm_config (capsul.engine.test.test_capsul_engine.TestCapsulEngine) ... /usr/local/lib/python3.10/dist-packages/nibabel/openers.py:16: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
from distutils.version import StrictVersion
<frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
<frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
<frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
<frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
stty: 'standard input': Inappropriate ioctl for device
ok
test_python_config (capsul.engine.test.test_capsul_engine.TestCapsulEngine) ... ok
test_full_desactivation (capsul.pipeline.test.test_activation.TestPipeline) ... ok
test_partial_desactivation (capsul.pipeline.test.test_activation.TestPipeline) ... ok
test_activations (capsul.pipeline.test.test_complex_pipeline_activations.TestComplexPipeline) ... <frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
ok
test_custom_nodes (capsul.pipeline.test.test_custom_nodes.TestCustomNodes) ... ok
test_custom_nodes_json_io (capsul.pipeline.test.test_custom_nodes.TestCustomNodes) ... ok
test_custom_nodes_py_io (capsul.pipeline.test.test_custom_nodes.TestCustomNodes) ... ok
test_custom_nodes_workflow (capsul.pipeline.test.test_custom_nodes.TestCustomNodes) ... ok
test_custom_nodes_xml_io (capsul.pipeline.test.test_custom_nodes.TestCustomNodes) ... ok
test_cv_json_io (capsul.pipeline.test.test_custom_nodes.TestCustomNodes) ... assign parameter subject :
The 'subject' trait of a ProcessIteration instance must be a list of items which are a string, but a value of 'subject0' <class 'str'> was specified.
assign parameter out1 :
The 'out1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '' <class 'str'> was specified.
assign parameter in1 :
The 'in1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '/tmp/swf_custom5dbrby_e/file0' <class 'str'> was specified.
assign parameter subject :
The 'subject' trait of a ProcessIteration instance must be a list of items which are a string, but a value of 'subject1' <class 'str'> was specified.
assign parameter out1 :
The 'out1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '' <class 'str'> was specified.
assign parameter in1 :
The 'in1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '/tmp/swf_custom5dbrby_e/file1' <class 'str'> was specified.
assign parameter subject :
The 'subject' trait of a ProcessIteration instance must be a list of items which are a string, but a value of 'subject2' <class 'str'> was specified.
assign parameter out1 :
The 'out1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '' <class 'str'> was specified.
assign parameter in1 :
The 'in1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '/tmp/swf_custom5dbrby_e/file2' <class 'str'> was specified.
assign parameter subject :
The 'subject' trait of a ProcessIteration instance must be a list of items which are a string, but a value of 'subject3' <class 'str'> was specified.
assign parameter out1 :
The 'out1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '' <class 'str'> was specified.
assign parameter in1 :
The 'in1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '/tmp/swf_custom5dbrby_e/file3' <class 'str'> was specified.
ok
test_cv_py_io (capsul.pipeline.test.test_custom_nodes.TestCustomNodes) ... assign parameter subject :
The 'subject' trait of a ProcessIteration instance must be a list of items which are a string, but a value of 'subject0' <class 'str'> was specified.
assign parameter out1 :
The 'out1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '' <class 'str'> was specified.
assign parameter in1 :
The 'in1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '/tmp/swf_customl1l8rejx/file0' <class 'str'> was specified.
assign parameter subject :
The 'subject' trait of a ProcessIteration instance must be a list of items which are a string, but a value of 'subject1' <class 'str'> was specified.
assign parameter out1 :
The 'out1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '' <class 'str'> was specified.
assign parameter in1 :
The 'in1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '/tmp/swf_customl1l8rejx/file1' <class 'str'> was specified.
assign parameter subject :
The 'subject' trait of a ProcessIteration instance must be a list of items which are a string, but a value of 'subject2' <class 'str'> was specified.
assign parameter out1 :
The 'out1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '' <class 'str'> was specified.
assign parameter in1 :
The 'in1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '/tmp/swf_customl1l8rejx/file2' <class 'str'> was specified.
assign parameter subject :
The 'subject' trait of a ProcessIteration instance must be a list of items which are a string, but a value of 'subject3' <class 'str'> was specified.
assign parameter out1 :
The 'out1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '' <class 'str'> was specified.
assign parameter in1 :
The 'in1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '/tmp/swf_customl1l8rejx/file3' <class 'str'> was specified.
ok
test_cv_xml_io (capsul.pipeline.test.test_custom_nodes.TestCustomNodes) ... assign parameter subject :
The 'subject' trait of a ProcessIteration instance must be a list of items which are a string, but a value of 'subject0' <class 'str'> was specified.
assign parameter out1 :
The 'out1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '' <class 'str'> was specified.
assign parameter in1 :
The 'in1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '/tmp/swf_customip7eo8oj/file0' <class 'str'> was specified.
assign parameter subject :
The 'subject' trait of a ProcessIteration instance must be a list of items which are a string, but a value of 'subject1' <class 'str'> was specified.
assign parameter out1 :
The 'out1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '' <class 'str'> was specified.
assign parameter in1 :
The 'in1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '/tmp/swf_customip7eo8oj/file1' <class 'str'> was specified.
assign parameter subject :
The 'subject' trait of a ProcessIteration instance must be a list of items which are a string, but a value of 'subject2' <class 'str'> was specified.
assign parameter out1 :
The 'out1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '' <class 'str'> was specified.
assign parameter in1 :
The 'in1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '/tmp/swf_customip7eo8oj/file2' <class 'str'> was specified.
assign parameter subject :
The 'subject' trait of a ProcessIteration instance must be a list of items which are a string, but a value of 'subject3' <class 'str'> was specified.
assign parameter out1 :
The 'out1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '' <class 'str'> was specified.
assign parameter in1 :
The 'in1' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '/tmp/swf_customip7eo8oj/file3' <class 'str'> was specified.
ok
test_leave_one_out_pipeline (capsul.pipeline.test.test_custom_nodes.TestCustomNodes) ... ok
test_loo_json_io (capsul.pipeline.test.test_custom_nodes.TestCustomNodes) ... ok
test_loo_py_io (capsul.pipeline.test.test_custom_nodes.TestCustomNodes) ... ok
test_loo_xml_io (capsul.pipeline.test.test_custom_nodes.TestCustomNodes) ... ok
test_mapreduce (capsul.pipeline.test.test_custom_nodes.TestCustomNodes) ... ok
test_way1 (capsul.pipeline.test.test_double_switch.TestDoubleSwitchPipeline) ... ok
test_way2 (capsul.pipeline.test.test_double_switch.TestDoubleSwitchPipeline) ... ok
test_iterative_big_pipeline_workflow (capsul.pipeline.test.test_iterative_process.TestPipeline) ... assign parameter input_image :
The 'input_image' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of 'tutu' <class 'str'> was specified.
assign parameter other_output :
The 'other_output' trait of a ProcessIteration instance must be a list of items which are a float, but a value of 2.1 <class 'float'> was specified.
assign parameter output_image :
The 'output_image' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '/tmp/capsul_testtll3tgw9/tutu_out' <class 'str'> was specified.
assign parameter dynamic_parameter :
The 'dynamic_parameter' trait of a ProcessIteration instance must be a list of items which are a float, but a value of 2.0 <class 'float'> was specified.
assign parameter input_image :
The 'input_image' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of 'tete' <class 'str'> was specified.
assign parameter other_output :
The 'other_output' trait of a ProcessIteration instance must be a list of items which are a float, but a value of 5.1 <class 'float'> was specified.
assign parameter output_image :
The 'output_image' trait of a ProcessIteration instance must be a list of items which are a string or os.PathLike object, but a value of '/tmp/capsul_testtll3tgw9/tete_out' <class 'str'> was specified.
assign parameter dynamic_parameter :
The 'dynamic_parameter' trait of a ProcessIteration instance must be a list of items which are a float, but a value of 5.0 <class 'float'> was specified.
ok
test_iterative_pipeline_connection (capsul.pipeline.test.test_iterative_process.TestPipeline)
Test if an iterative process works correctly ... ok
test_iterative_pipeline_workflow (capsul.pipeline.test.test_iterative_process.TestPipeline) ... ok
test_iterative_pipeline_workflow_run (capsul.pipeline.test.test_iterative_process.TestPipeline) ... ok
test_json (capsul.pipeline.test.test_optional_output_switch.TestPipeline) ... <frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
ok
test_way1 (capsul.pipeline.test.test_optional_output_switch.TestPipeline) ... ok
test_way2 (capsul.pipeline.test.test_optional_output_switch.TestPipeline) ... ok
test_xml (capsul.pipeline.test.test_optional_output_switch.TestPipeline) ... ok
test_constant (capsul.pipeline.test.test_pipeline.TestPipeline) ... ok
test_enabled (capsul.pipeline.test.test_pipeline.TestPipeline) ... ok
test_pipeline_io_py (capsul.pipeline.test.test_pipeline.TestPipeline) ... ok
test_pipeline_json (capsul.pipeline.test.test_pipeline.TestPipeline) ... ok
test_pipeline_xml (capsul.pipeline.test.test_pipeline.TestPipeline) ... ok
test_run_pipeline (capsul.pipeline.test.test_pipeline.TestPipeline) ... ok
test_date_time (capsul.pipeline.test.test_pipeline_parameters.TestPipelineMethods) ... /casa/install/python/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)
/casa/install/python/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)
/casa/install/python/capsul/pipeline/pipeline_tools.py:1275: 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(pipeline, trait_name, None)
/casa/install/python/capsul/pipeline/pipeline_tools.py:1275: 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(pipeline, trait_name, None)
ok
test_file (capsul.pipeline.test.test_pipeline_parameters.TestPipelineMethods) ... ok
test_float (capsul.pipeline.test.test_pipeline_parameters.TestPipelineMethods) ... ok
test_int (capsul.pipeline.test.test_pipeline_parameters.TestPipelineMethods) ... ok
test_list_file (capsul.pipeline.test.test_pipeline_parameters.TestPipelineMethods) ... ok
test_list_float (capsul.pipeline.test.test_pipeline_parameters.TestPipelineMethods) ... ok
test_list_int (capsul.pipeline.test.test_pipeline_parameters.TestPipelineMethods) ... ok
test_list_list (capsul.pipeline.test.test_pipeline_parameters.TestPipelineMethods) ... ok
test_list_string (capsul.pipeline.test.test_pipeline_parameters.TestPipelineMethods) ... ok
test_string (capsul.pipeline.test.test_pipeline_parameters.TestPipelineMethods) ... ok
test_iterative_pipeline_with_temp (capsul.pipeline.test.test_pipeline_with_temp.TestPipelineWithTemp) ... ok
test_pipeline_with_temp (capsul.pipeline.test.test_pipeline_with_temp.TestPipelineWithTemp) ... ok
test_full_wf (capsul.pipeline.test.test_pipeline_workflow.TestPipelineWorkflow) ... ok
test_iter_workflow (capsul.pipeline.test.test_pipeline_workflow.TestPipelineWorkflow) ... ok
test_iter_workflow_without_temp (capsul.pipeline.test.test_pipeline_workflow.TestPipelineWorkflow) ... ok
test_partial_wf1 (capsul.pipeline.test.test_pipeline_workflow.TestPipelineWorkflow) ... ok
test_partial_wf2 (capsul.pipeline.test.test_pipeline_workflow.TestPipelineWorkflow) ... ok
test_partial_wf3_fail (capsul.pipeline.test.test_pipeline_workflow.TestPipelineWorkflow) ... ok
test_requirements (capsul.pipeline.test.test_pipeline_workflow.TestPipelineWorkflow) ... ok
test_wf_run (capsul.pipeline.test.test_pipeline_workflow.TestPipelineWorkflow) ... ok
test_direct_run (capsul.pipeline.test.test_proc_with_outputs.TestPipelineContainingProcessWithOutputs) ... Exception in thread Thread-9:
Traceback (most recent call last):
File "/casa/install/python/soma_workflow/database_server.py", line 619, 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 "/usr/lib/python3.10/threading.py", line 1016, in _bootstrap_inner
self.run()
File "/casa/install/python/soma_workflow/engine.py", line 102, in run
self.engine_loop.start_loop(self.time_interval)
File "/casa/install/python/soma_workflow/engine.py", line 269, in start_loop
= self._database_server.jobs_to_delete_and_kill(
File "/casa/install/python/soma_workflow/database_server.py", line 3752, in jobs_to_delete_and_kill
connection = self._connect()
File "/casa/install/python/soma_workflow/database_server.py", line 629, in _connect
six.reraise(DatabaseError,
File "/usr/lib/python3/dist-packages/six.py", line 718, in reraise
raise value.with_traceback(tb)
File "/casa/install/python/soma_workflow/database_server.py", line 619, in _connect
connection = sqlite3.connect(
soma_workflow.errors.DatabaseError: On database file /tmp/tmpjtciw5wn/soma-workflow.db: <class 'sqlite3.OperationalError'>: unable to open database file
Exception in thread Thread-8:
Traceback (most recent call last):
File "/casa/install/python/soma_workflow/database_server.py", line 619, 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 "/usr/lib/python3.10/threading.py", line 1016, in _bootstrap_inner
self.run()
File "/casa/install/python/soma_workflow/engine.py", line 102, in run
self.engine_loop.start_loop(self.time_interval)
File "/casa/install/python/soma_workflow/engine.py", line 269, in start_loop
= self._database_server.jobs_to_delete_and_kill(
File "/casa/install/python/soma_workflow/database_server.py", line 3752, in jobs_to_delete_and_kill
connection = self._connect()
File "/casa/install/python/soma_workflow/database_server.py", line 629, in _connect
six.reraise(DatabaseError,
File "/usr/lib/python3/dist-packages/six.py", line 718, in reraise
raise value.with_traceback(tb)
File "/casa/install/python/soma_workflow/database_server.py", line 619, in _connect
connection = sqlite3.connect(
soma_workflow.errors.DatabaseError: On database file /tmp/tmpjtciw5wn/soma-workflow.db: <class 'sqlite3.OperationalError'>: unable to open database file
ok
test_direct_run_sub_iter (capsul.pipeline.test.test_proc_with_outputs.TestPipelineContainingProcessWithOutputs) ... ok
test_direct_run_subpipeline (capsul.pipeline.test.test_proc_with_outputs.TestPipelineContainingProcessWithOutputs) ... ok
test_direct_run_switch (capsul.pipeline.test.test_proc_with_outputs.TestPipelineContainingProcessWithOutputs) ... ok
test_full_wf (capsul.pipeline.test.test_proc_with_outputs.TestPipelineContainingProcessWithOutputs) ... ok
test_full_wf_switch (capsul.pipeline.test.test_proc_with_outputs.TestPipelineContainingProcessWithOutputs) ... ok
test_iterative_pipeline_connection (capsul.pipeline.test.test_process_iteration.TestPipeline)
Method to test if an iterative node and built in iterative ... ok
test_qc_active (capsul.pipeline.test.test_qc_nodes.TestQCNodes)
Method to test if the run qc option works properly. ... ok
test_qc_inactive (capsul.pipeline.test.test_qc_nodes.TestQCNodes)
Method to test if the run qc option works properly. ... ok
test_way1 (capsul.pipeline.test.test_switch_optional_output.TestPipeline) ... ok
test_way2 (capsul.pipeline.test.test_switch_optional_output.TestPipeline) ... ok
test_hard (capsul.pipeline.test.test_switch_pipeline.TestSwitchPipeline) ... ok
test_io (capsul.pipeline.test.test_switch_pipeline.TestSwitchPipeline) ... <frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
ok
test_parameter_propagation (capsul.pipeline.test.test_switch_pipeline.TestSwitchPipeline) ... ok
test_way1 (capsul.pipeline.test.test_switch_pipeline.TestSwitchPipeline) ... ok
test_way2 (capsul.pipeline.test.test_switch_pipeline.TestSwitchPipeline) ... ok
test_way3 (capsul.pipeline.test.test_switch_pipeline.TestSwitchPipeline) ... ok
test_weak_off (capsul.pipeline.test.test_switch_pipeline.TestSwitchPipeline) ... ok
test_weak_on (capsul.pipeline.test.test_switch_pipeline.TestSwitchPipeline) ... ok
test_self_state (capsul.pipeline.test.test_switch_subpipeline.TestSwitchPipeline) ... ok
test_switch_value (capsul.pipeline.test.test_switch_subpipeline.TestSwitchPipeline) ... ok
test_direct_run (capsul.pipeline.test.test_temporary.TestTemporary) ... ok
test_full_wf (capsul.pipeline.test.test_temporary.TestTemporary) ... ok
test_structure (capsul.pipeline.test.test_temporary.TestTemporary) ... ok
test_named_outputs (capsul.process.test.test_load_from_description.TestLoadFromDescription) ... ok
test_pipeline_warping (capsul.process.test.test_load_from_description.TestLoadFromDescription)
Method to test the xml description to pipeline on the fly warping. ... <frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
ok
test_pipeline_writing (capsul.process.test.test_load_from_description.TestLoadFromDescription)
Method to test the xml description saving and reloading ... ok
test_process_warping (capsul.process.test.test_load_from_description.TestLoadFromDescription)
Method to test the function to process on the fly warping. ... ok
test_return_list (capsul.process.test.test_load_from_description.TestLoadFromDescription) ... ok
test_return_string (capsul.process.test.test_load_from_description.TestLoadFromDescription) ... ok
test_process_wrap (capsul.process.test.test_load_from_description.TestProcessWrap)
Method to test if the process has been wrapped properly. ... ok
test_nipype_automatic_wrap (capsul.process.test.test_nipype_wrap.TestNipypeWrap)
Method to test if the automatic nipype interfaces wrap work ... ok
test_nipype_monkey_patching (capsul.process.test.test_nipype_wrap.TestNipypeWrap)
Method to test the monkey patching used to work in user ... ok
test_help (capsul.process.test.test_runprocess.TestRunProcess) ... ok
test_python_m_capsul (capsul.process.test.test_runprocess.TestRunProcess) ... ok
test_run_dummy_process (capsul.process.test.test_runprocess.TestRunProcess) ... ok
test_run_dummy_process_wrong_args (capsul.process.test.test_runprocess.TestRunProcess) ... ok
test_run_process_help (capsul.process.test.test_runprocess.TestRunProcess) ... ok
test_class_user_parameters (capsul.process.test.test_traits.TestProcessUserTrait)
Method to test if class user parameters are not shared at ... ok
test_pipeline_doc (capsul.sphinxext.test.test_process_pipeline_doc.TestSphinxExt)
Method to test the pipeline rst documentation. ... ok
test_process_doc (capsul.sphinxext.test.test_process_pipeline_doc.TestSphinxExt)
Method to test the process rst documentation. ... ok
test_use_cases_doc (capsul.sphinxext.test.test_usercases_doc.TestUseCases)
Method to test the use cases rst documentation. ... ok
test_study_config_fsl (capsul.study_config.test.test_fsl_config.TestFSL) ... WARNING: Skip FSL test because it cannot be configured automatically: FSL command "bet" cannot be found in PATH
ok
test_proxy_process_copy (capsul.study_config.test.test_memory.TestMemory)
Test memory with copy. ... ok
test_proxy_process_with_cache (capsul.study_config.test.test_memory.TestMemory)
Test the proxy process behaviours with cache. ... ok
test_proxy_process_without_cache (capsul.study_config.test.test_memory.TestMemory)
Test the proxy process behaviours without cache. ... ok
test_execution_with_cache (capsul.study_config.test.test_run_in_study_config.TestRunProcess)
Execute a process with cache. ... ok
test_execution_without_cache (capsul.study_config.test.test_run_in_study_config.TestRunProcess)
Execute a process without cache. ... ok
test_execution_with_cache (capsul.study_config.test.test_run_process.TestRunProcess)
Execute a process with cache. ... soma-workflow starting in light mode
Workflow controller initialised
del WorkflowController
soma-workflow starting in light mode
Workflow controller initialised
del WorkflowController
soma-workflow starting in light mode
Workflow controller initialised
del WorkflowController
soma-workflow starting in light mode
Workflow controller initialised
del WorkflowController
run: /tmp/capsul_testeiufwsb1/toto ->
define output_image: /tmp/capsul_testeiufwsb1/toto-5.0-3.0
run: /tmp/capsul_testeiufwsb1/tutu -> <undefined>
define output_image: /tmp/capsul_testeiufwsb1/tutu-5.0-1.0
* running pipeline...
soma-workflow starting in light mode
Workflow controller initialised
* finished.
cache_dir: /tmp/__pycache__
added py tmpfile: /tmp/test_pipelinewpjf_1mo.py /tmp/__pycache__/test_pipelinewpjf_1mo.cpython-310.pyc
DummyProcess : /tmp/tmp0kwqh955capsul_input.txt -> /tmp/tmp9f12h9aqcapsul
DummyProcess : /tmp/tmp0kwqh955capsul_input.txt -> /tmp/tmp5f0bbs2ncapsul
DummyProcess : /tmp/tmp0kwqh955capsul_input.txt -> /tmp/tmp_469wlv9capsul
cat ['/tmp/tmp9f12h9aqcapsul', '/tmp/tmp5f0bbs2ncapsul', '/tmp/tmp_469wlv9capsul'] to: /tmp/tmpy0z3vcspcapsul_output.txt
DummyProcess : /tmp/tmptx0ovt0dcapsul_input.txt -> /tmp/tmpr6wvns8ocapsul
DummyProcess : /tmp/tmpr6wvns8ocapsul -> /tmp/tmpoxbbf5p9capsul_output.txt
soma-workflow starting in light mode
Workflow controller initialised
execution started
WARNING: The file or directory /tmp/tmpjtciw5wn/transfered_files/a-sac-ns-brainvisa_1/file_out1 doesn't exist on the computing resource side.
WARNING: The file or directory /tmp/tmpjtciw5wn/transfered_files/a-sac-ns-brainvisa_1/file_out1.minf doesn't exist on the computing resource side.
WARNING: The file or directory /tmp/tmpjtciw5wn/transfered_files/a-sac-ns-brainvisa_1/file_out2 doesn't exist on the computing resource side.
WARNING: The file or directory /tmp/tmpjtciw5wn/transfered_files/a-sac-ns-brainvisa_1/file_out2.minf doesn't exist on the computing resource side.
WARNING: The file or directory /tmp/tmpjtciw5wn/transfered_files/a-sac-ns-brainvisa_1/file_out3 doesn't exist on the computing resource side.
WARNING: The file or directory /tmp/tmpjtciw5wn/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 /tmp/tmpjtciw5wn/transfered_files/a-sac-ns-brainvisa_1/1_dir/file_out doesn't exist on the computing resource side.
WARNING: The file or directory /tmp/tmpjtciw5wn/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: /tmp/tmpenty1iwf/file_out2.nii from: node3.output changes to input.
transfered output path: /tmp/tmpkd9cvz30/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
soma-workflow starting in light mode
Workflow controller initialised
soma-workflow starting in light mode
Workflow controller initialised
del WorkflowController
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=/casa/install/python/capsul/study_config/test/test_memory.py, l=['/casa/install/python/capsul/study_config/test/test_memory.py'])
____________________________________________________________________0.0s, 0.0min
proxy_process: <class 'capsul.study_config.memory.UnMemorizedProcess'>
machin: {'i': '/tmp/tmpl7ml0mpb/test_memory.py', 'l': ['/tmp/tmpl7ml0mpb/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_in_study_config.DummyProcess...
capsul.study_config.test.test_run_in_study_config.DummyProcess(f1=1.0, f2=2.3, output_directory=/tmp/tmp83zq18oz)
________________________________________________________________________________
[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=/tmp/tmp83zq18oz)
____________________________________________________________________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=/tmp/tmp83zq18oz)
________________________________________________________________________________
[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=/tmp/tmp83zq18oz)
____________________________________________________________________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=/tmp/tmp83zq18oz)
[Memory]: Loading capsul.study_config.test.test_run_in_study_config.DummyProcess(f1=1.0, f2=2.3, output_directory=/tmp/tmp83zq18oz)...
________________________________________________________________________________
[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=/tmp/tmpzd82rhr9)
________________________________________________________________________________
[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=/tmp/tmpzd82rhr9)
________________________________________________________________________________
[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=/tmp/tmpzd82rhr9)
ok
test_execution_without_cache (capsul.study_config.test.test_run_process.TestRunProcess)
Execute a process without cache. ... ok
test_missing_parameters (capsul.study_config.test.test_run_process.TestRunProcess)
Test if missing mandatory parameters raise the appropriate error ... ok
test_atomic_dependencies (capsul.study_config.test.test_soma_workflow.TestSomaWorkflow) ... ok
test_atomic_execution (capsul.study_config.test.test_soma_workflow.TestSomaWorkflow) ... ok
test_composite_dependencies (capsul.study_config.test.test_soma_workflow.TestSomaWorkflow) ... ok
test_composite_execution (capsul.study_config.test.test_soma_workflow.TestSomaWorkflow) ... ok
test_atomic_dependencies (capsul.study_config.test.test_soma_workflow_with_kw.TestSomaWorkflow) ... ok
test_atomic_execution (capsul.study_config.test.test_soma_workflow_with_kw.TestSomaWorkflow) ... ok
test_atomic_execution_kwparams (capsul.study_config.test.test_soma_workflow_with_kw.TestSomaWorkflow) ... ok
test_composite_dependencies (capsul.study_config.test.test_soma_workflow_with_kw.TestSomaWorkflow) ... ok
test_composite_execution (capsul.study_config.test.test_soma_workflow_with_kw.TestSomaWorkflow) ... ok
test_study_config_configuration (capsul.study_config.test.test_study_config_configuration.TestStudyConfigConfiguration) ... ok
test_study_config_fom (capsul.study_config.test.test_study_config_fom.TestStudyConfigFOM) ... ok
test_capsul_import (capsul.test.test_capsul_modules_import.TestCapsulModulesImport) ... ok
test_capsul_pipeline_import (capsul.test.test_capsul_modules_import.TestCapsulModulesImport) ... ok
test_capsul_pipeline_pipeline_workflow_import (capsul.test.test_capsul_modules_import.TestCapsulModulesImport) ... ok
test_capsul_process_import (capsul.test.test_capsul_modules_import.TestCapsulModulesImport) ... ok
test_capsul_studyconfig_import (capsul.test.test_capsul_modules_import.TestCapsulModulesImport) ... ok
test_capsul_utils_import (capsul.test.test_capsul_modules_import.TestCapsulModulesImport) ... ok
test_version_interfaces (capsul.utils.test.test_utils.TestUtils)
Method to test if we can get the nipype interfaces versions. ... ok
test_version_python (capsul.utils.test.test_utils.TestUtils)
Method to test if we can get a python module version from ... <frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
ok
----------------------------------------------------------------------
Ran 137 tests in 216.692s
OK
________________________________________________________________________________
[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=/tmp/tmpdii0rujg)
________________________________________________________________________________
[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=/tmp/tmpdii0rujg)
________________________________________________________________________________
[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=/tmp/tmpdii0rujg)
________________________________________________________________________________
[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=/tmp/tmpuef9brss)
________________________________________________________________________________
[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=/tmp/tmpuef9brss)
________________________________________________________________________________
[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=/tmp/tmpuef9brss)
soma-workflow starting in light mode
Workflow controller initialised
soma-workflow starting in light mode
del WorkflowController
del WorkflowController
del WorkflowController
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
del WorkflowController
del WorkflowController
del WorkflowController
del WorkflowController
================================================================================
SUCCESS (exit code 0)
Finished: SUCCESS
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