TypeError - code that used to work

[paulrbuckley-kcl]

Hi,

Last week, on a CYX image, I was able to get the code below to process the external image:

steinbock="singularity run -B /X/$FOLDER:/data --env STEINBOCK_MASK_DTYPE=uint32 docker://ghcr.io/bodenmillergroup/steinbock:0.16.1 where $FOLDER has been defined previously. then the following code is generates the issue: $steinbock preprocess external images --img /data/external --imgout /data/images --infoout /data/images/images.csv

Now, when I run the same code on the same image, I receive the following error. I'm not sure if this is a steinbock issue or a singularity issue. Wondering if you could point me in the right direction? Thanks

Traceback (most recent call last): File "/usr/lib/python3.8/runpy.py", line 194, in _run_module_as_main return _run_code(code, main_globals, None, File "/usr/lib/python3.8/runpy.py", line 87, in _run_code exec(code, run_globals) File "/app/steinbock/steinbock/main.py", line 5, in from ._cli import steinbock_cmd_group File "/app/steinbock/steinbock/_cli/init.py", line 1, in from ._cli import steinbock_cmd_group File "/app/steinbock/steinbock/_cli/_cli.py", line 12, in from .visualization import view_cmd File "/app/steinbock/steinbock/_cli/visualization.py", line 9, in from ..visualization import view File "/app/steinbock/steinbock/visualization.py", line 14, in ) -> Optional[napari.Viewer]: File "/opt/steinbock-venv/lib/python3.8/site-packages/napari/_lazy.py", line 48, in getattr submod = import_module( File "/usr/lib/python3.8/importlib/init.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "/opt/steinbock-venv/lib/python3.8/site-packages/napari/viewer.py", line 8, in from .components.viewer_model import ViewerModel File "/opt/steinbock-venv/lib/python3.8/site-packages/napari/components/init.py", line 18, in from .dims import Dims File "/opt/steinbock-venv/lib/python3.8/site-packages/napari/components/dims.py", line 12, in class Dims(EventedModel): File "/opt/steinbock-venv/lib/python3.8/site-packages/napari/utils/events/evented_model.py", line 82, in new cls = super().new(mcs, name, bases, namespace, **kwargs) File "pydantic/main.py", line 197, in pydantic.main.ModelMetaclass.new File "pydantic/fields.py", line 506, in pydantic.fields.ModelField.infer File "pydantic/fields.py", line 436, in pydantic.fields.ModelField.init File "pydantic/fields.py", line 552, in pydantic.fields.ModelField.prepare File "pydantic/fields.py", line 668, in pydantic.fields.ModelField._type_analysis File "/usr/lib/python3.8/typing.py", line 774, in subclasscheck return issubclass(cls, self.origin) TypeError: issubclass() arg 1 must be a class