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Multiprocessing #486

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Commits on Oct 9, 2024

  1. Correct typo in comment

    @nkrah
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  2. Implement DynamicGateObject.reassign_subset_of_dynamic_params()

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  3. Add attribute process_index to SimulationEngine (not used yet)

    @nkrah
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  4. First steps towards multi processing

    @nkrah
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  5. Add test080_multiprocessing_1.py

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  6. Add test030_dose_motion_dynamic_param_multiproc.py

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  7. [pre-commit.ci] Automatic python and c++ formatting

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Commits on Oct 13, 2024

  1. Implement MultiProcessingHandler classes

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  2. create test080_multiprocessing_handler.py

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  3. Implement import_data_from_actor_output()

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  4. Implement import_user_output_from_actor()

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  5. Implement import_user_output_from_actor in ActorBase

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  6. Change local variable name in reassign_dynamic_params_for_process()

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  7. Implement FinalizeSimulation() in VoxelDepositActor

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  8. Add simulation_id to SimulationOutput

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  9. Implement SimulationOutput.store_output_from_simulation_engine()

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  10. Simplify code in run_engine()

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  11. Implement SimulationMetaData class

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  12. Use SimulationMetaData in Simulation

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  13. Update MultiProcessingHandlerBase class

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  14. Remove obsolete generate_run_timing_interval_map() method

    @nkrah
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  15. Update imports in managers.py

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  16. Update run_in_process()

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  17. Store number_of_sub_processes and start_new_process in simulation_met… 

    …a_data
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  18. Introduce avoid_write_to_disk_in_subprocess kwarg in Simulation.run()

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  19. Use multi_proc_handler in Simulation.run()

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  20. Trigger import_user_output_from_actor() after multi_proc run

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  21. store meta_data after run

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  22. Get parameters from sources after multiproc run

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  23. Remove obsolete code

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  24. Trigger FinalizeSimulation() at the end of a run

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  25. remove obsolete code

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  26. Add test008_dose_actor_multiproc.py

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  27. Update test080_multiprocessing_1.py

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  28. Update GateObject to rename property 'warnings' in Simulation

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  29. Update run_engine to use Simulation.meta_data

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  30. [pre-commit.ci] Automatic python and c++ formatting

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  31. Rename FinalizeSimulation() to EndOfMultiProcessAction()

    @nkrah
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Commits on Oct 14, 2024

  1. Implement explicit inplace_merge_with in ItkImageDataItem

    @nkrah
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  2. Adapt merge_data to try to accelerate it (WIP)

    @nkrah
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  3. Implement sum_itk_images based on SimpleITK (workaround)

    @nkrah
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  4. remove debug prints and clean code

    @nkrah
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  5. In BaseUserInterfaceToActorOutput.__getstate__: always use return_dic… 

    …t = self.__dict__.copy()
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  6. Implement reset_user_output() and reset_data()

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  7. remove debug print

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  8. Update comment

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  9. Update test008_dose_actor_multiproc.py

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  10. Update test009_voxels_dynamic.py (not relevant for test result)

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  11. [pre-commit.ci] Automatic python and c++ formatting

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Commits on Oct 24, 2024

  1. Correct typo in comment

    @nkrah
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  2. Implement DynamicGateObject.reassign_subset_of_dynamic_params()

    @nkrah
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  3. Add attribute process_index to SimulationEngine (not used yet)

    @nkrah
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  4. First steps towards multi processing

    @nkrah
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  5. Add test080_multiprocessing_1.py

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  6. Add test030_dose_motion_dynamic_param_multiproc.py

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  7. [pre-commit.ci] Automatic python and c++ formatting

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  8. Implement MultiProcessingHandler classes

    @nkrah
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  9. create test080_multiprocessing_handler.py

    @nkrah
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  10. Implement import_data_from_actor_output()

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  11. Implement import_user_output_from_actor()

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  12. Implement import_user_output_from_actor in ActorBase

    @nkrah
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  13. Change local variable name in reassign_dynamic_params_for_process()

    @nkrah
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  14. Implement FinalizeSimulation() in VoxelDepositActor

    @nkrah
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  15. Add simulation_id to SimulationOutput

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  16. Implement SimulationOutput.store_output_from_simulation_engine()

    @nkrah
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  17. Simplify code in run_engine()

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  18. Implement SimulationMetaData class

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  19. Use SimulationMetaData in Simulation

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  20. Update MultiProcessingHandlerBase class

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  21. Remove obsolete generate_run_timing_interval_map() method

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  22. Update imports in managers.py

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  23. Update run_in_process()

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  24. Store number_of_sub_processes and start_new_process in simulation_met… 

    …a_data
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  25. Introduce avoid_write_to_disk_in_subprocess kwarg in Simulation.run()

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  26. Use multi_proc_handler in Simulation.run()

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  27. Trigger import_user_output_from_actor() after multi_proc run

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  28. store meta_data after run

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  29. Get parameters from sources after multiproc run

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  30. Remove obsolete code

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  31. Trigger FinalizeSimulation() at the end of a run

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  32. remove obsolete code

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  33. Add test008_dose_actor_multiproc.py

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  34. Update test080_multiprocessing_1.py

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  35. Update GateObject to rename property 'warnings' in Simulation

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  36. Update run_engine to use Simulation.meta_data

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  37. [pre-commit.ci] Automatic python and c++ formatting

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  38. Rename FinalizeSimulation() to EndOfMultiProcessAction()

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  39. Implement explicit inplace_merge_with in ItkImageDataItem

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  40. Adapt merge_data to try to accelerate it (WIP)

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  41. Implement sum_itk_images based on SimpleITK (workaround)

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  42. remove debug prints and clean code

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  43. In BaseUserInterfaceToActorOutput.__getstate__: always use return_dic… 

    …t = self.__dict__.copy()
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  44. Implement reset_user_output() and reset_data()

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  45. remove debug print

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  46. Update comment

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  47. Update test008_dose_actor_multiproc.py

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  48. Update test009_voxels_dynamic.py (not relevant for test result)

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  49. Increment random_seed in run_in_process

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  50. Extend inplace_merge_with() to accept *other, i.e. an unpackaged list

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  51. Fix ItkImageDataItem.inplace_merge_with()

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  52. Fix typo in error message

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  53. Update test008_dose_actor_multiproc.py

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  54. Deprecate unused kwarg 'stat' in assert_images()

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  55. Update multiproc logic in Simulation class

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  56. Merge remote-tracking branch 'origin/multiproc' into multiproc 

    # Conflicts:
#	opengate/actors/base.py
#	opengate/actors/dataitems.py
#	opengate/image.py
#	opengate/managers.py
#	opengate/tests/src/test008_dose_actor_multiproc.py
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  57. [pre-commit.ci] Automatic python and c++ formatting

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  58. Implement reset_data() in DataItem base class

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  59. update imports in dataitems.py

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  60. Implement StatisticsDataItem

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  61. Implement StatisticsItemContainer

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  62. Let SimulationStatisticsActor use new ActorOutputStatisticsActor

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  63. Implement ActorOutputStatisticsActor

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  64. Implement UserInterfaceToActorOutputStatisticsActor

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Commits on Oct 25, 2024

  1. let default_suffix be an instance attribute of the ActorOutput classe… 

    …s rather than a class attribute.
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  2. Implement ActorOutputUsingDataItemContainer.reset_data()

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  3. Add process_cls(ActorOutputStatisticsActor) 

    in actoroutput.py
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  4. Remove unused store_output_data() method

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  5. Update test008_dose_actor_multiproc.py

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Commits on Oct 28, 2024

  1. Update physics and sources documentation 

    Updated the user guide for physics and sources to use new method names for accessing physics settings and organizing content. Introduced subheadings for better structure and improved clarity. Corrected minor grammatical issues.
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  2. Add test080_multiprocessing_1.py

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  4. Implement MultiProcessingHandler classes

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  5. create test080_multiprocessing_handler.py

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  6. Implement FinalizeSimulation() in VoxelDepositActor

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  7. Add test008_dose_actor_multiproc.py

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  9. Rename FinalizeSimulation() to EndOfMultiProcessAction()

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  10. Update test008_dose_actor_multiproc.py

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  12. Merge remote-tracking branch 'origin/master' into multiproc

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  14. rename test080 on multi processing to test082_xxx

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  15. Add merge_root to processing.py

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  16. rename import_data_from_actor_output to merge_data_from_actor_output

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  17. Extend signature of import_user_output_from_actor by **kwargs

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  18. Add process_index attribute to SimulationEngine and SimulationOutput

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  19. Implement clear_output_dir_before_run 

    option in sim.run()
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  20. Implement sub_process_registry

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  21. Make multi_proc_handler an instance attribute

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  22. Add output_dir as argument to run_in_process()

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  23. Let each process store a json in the subfolder

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  24. Capsulate code into merge_simulations_from_multiprocessing()

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  25. check global variable __spec__ in run() to avoid breaking when runnin… 

    …g multiproc in interactive session
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  26. Remove merge_root() and unicity(): now in ActorOutputRoot class

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  27. Implement ActorOutputRootmerge_data_from_actor_output()

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  28. Add test019_phsp_actor_multiproc.py

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  29. [pre-commit.ci] Automatic python and c++ formatting

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  30. Remove obsolete imports in processing.py

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Commits on Oct 29, 2024

  1. Add property counts to SimulationStatisticsActor

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  2. remove obsolete UserInterfaceToActorOutputStatisticsActor

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  3. Extend DataItem.__getattr__ to get attributes from self.data if possible

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  4. Adapt read_stat_file_legacy() to updated stats actor

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  5. Adapt assert_stats() and assert_stats_json() to updated stats actor

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Commits on Oct 30, 2024

  1. Merge sim_start_time and sim_stop_time via min/max

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  2. Adapt assert_stats_json() to updated StatsActor

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  3. Improve handling of start_time and stop_time in StatisticsDataItem

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  4. Update GateSimulationStatisticsActor::GetCounts()

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  5. In GateSimulationStatisticsActor: save start_time and stop_time as ep… 

    …och time rather than date time str
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Commits on Oct 31, 2024

  1. adapt read_stat_file_json() to updated StatsActor

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  2. remove redundant code in test008_dose_actor_multiproc.py

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  3. Merge remote-tracking branch 'origin/master' into multiproc

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  4. [pre-commit.ci] Automatic python and c++ formatting

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  5. activate ssh session on github

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  6. update test082_multiprocessing_1.py

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  7. pick up simulation_id as meta_data after a simulation

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  8. add explicit process_cls() for MultiProcessHandler classes

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  9. Update file names in test081_simulation_optigan_with_random_seed.py

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  10. Adapt test006_runs.py to updated StatsActorOutput

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