Skip to content

Cannot use MicroSimulation.initialize() with macro_data anymore #248

@steffenger

Description

@steffenger

When using version 0.9.0 of the MM i cannot use macro_data anymore in the initialize() function of the MicroSimulation() class

def initialize(self, macro_data):
Traceback (most recent call last):
  File "/home/USADR/ac135212/spack/var/spack/environments/coupled-liver-models/.spack-env/view/bin/micro-manager-precice", line 8, in <module>
    sys.exit(main())
             ~~~~^^
  File "/home/USADR/ac135212/spack/var/spack/environments/coupled-liver-models/.spack-env/._view/l2dgjuhlncvihibtp2wrckc2owloskmv/lib/python3.13/site-packages/micro_manager/__init__.py", line 123, in main
    manager.initialize()
    ~~~~~~~~~~~~~~~~~~^^
  File "/home/USADR/ac135212/spack/var/spack/environments/coupled-liver-models/.spack-env/._view/l2dgjuhlncvihibtp2wrckc2owloskmv/lib/python3.13/site-packages/micro_manager/micro_manager.py", line 728, in initialize
    initial_micro_output = self._micro_sims[first_id].initialize()
  File "/home/USADR/ac135212/spack/var/spack/environments/coupled-liver-models/.spack-env/._view/l2dgjuhlncvihibtp2wrckc2owloskmv/lib/python3.13/site-packages/micro_manager/micro_simulation.py", line 358, in initialize
    return self._impl.initialize(*args, **kwargs)
           ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
  File "/home/USADR/ac135212/spack/var/spack/environments/coupled-liver-models/.spack-env/._view/l2dgjuhlncvihibtp2wrckc2owloskmv/lib/python3.13/site-packages/micro_manager/micro_simulation.py", line 211, in initialize
    return self._instance.initialize(*args, **kwargs)
           ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
  File "<string>", line 24, in initialize
TypeError: MicroSimulation.initialize() missing 1 required positional argument: 'macro_data'
(3) 15:18:12 [impl::ParticipantImpl]:168 in ~ParticipantImpl: Implicitly finalizing in destructor
(3) 15:18:12 [impl::ParticipantImpl]:1832 in closeCommunicationChannels: Close communication channels
Traceback (most recent call last):
  File "/home/USADR/ac135212/spack/var/spack/environments/coupled-liver-models/.spack-env/view/bin/micro-manager-precice", line 8, in <module>
    sys.exit(main())
             ~~~~^^
  File "/home/USADR/ac135212/spack/var/spack/environments/coupled-liver-models/.spack-env/._view/l2dgjuhlncvihibtp2wrckc2owloskmv/lib/python3.13/site-packages/micro_manager/__init__.py", line 123, in main
    manager.initialize()
    ~~~~~~~~~~~~~~~~~~^^
  File "/home/USADR/ac135212/spack/var/spack/environments/coupled-liver-models/.spack-env/._view/l2dgjuhlncvihibtp2wrckc2owloskmv/lib/python3.13/site-packages/micro_manager/micro_manager.py", line 728, in initialize
    initial_micro_output = self._micro_sims[first_id].initialize()
  File "/home/USADR/ac135212/spack/var/spack/environments/coupled-liver-models/.spack-env/._view/l2dgjuhlncvihibtp2wrckc2owloskmv/lib/python3.13/site-packages/micro_manager/micro_simulation.py", line 358, in initialize
    return self._impl.initialize(*args, **kwargs)
           ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
  File "/home/USADR/ac135212/spack/var/spack/environments/coupled-liver-models/.spack-env/._view/l2dgjuhlncvihibtp2wrckc2owloskmv/lib/python3.13/site-packages/micro_manager/micro_simulation.py", line 211, in initialize
    return self._instance.initialize(*args, **kwargs)
           ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
  File "<string>", line 24, in initialize
TypeError: MicroSimulation.initialize() missing 1 required positional argument: 'macro_data'

Metadata

Metadata

Assignees

Labels

bugSomething isn't working

Type

No type
No fields configured for issues without a type.

Projects

No projects

Milestone

No milestone

Relationships

None yet

Development

No branches or pull requests

Issue actions