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Error with Cellassign workflow - NameError: name 'configs' is not defined #18

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Mdack1 opened this issue Dec 12, 2024 · 0 comments
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@Mdack1
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Mdack1 commented Dec 12, 2024

from enact.pipeline import ENACT
import yaml

configs_path = "/content/drive/MyDrive/Visium data/Configs.yaml" # Change this to the location of the configs.yaml file that you just edited
with open(configs_path, "r") as stream:
    configs = yaml.safe_load(stream)

so_hd = ENACT(configs_dict=configs)
so_hd.run_enact()

NameError Traceback (most recent call last)
in <cell line: 9>()
7
8 so_hd = ENACT(configs_dict=configs)
----> 9 so_hd.run_enact()

2 frames
/usr/local/lib/python3.10/dist-packages/enact/pipeline.py in run_enact(self)
1037 # Run cell type annotation
1038 if self.cell_type_annotation:
-> 1039 self.run_cell_type_annotation()
1040 self.package_results()
1041

/usr/local/lib/python3.10/dist-packages/enact/pipeline.py in run_cell_type_annotation(self)
933 from .cellassign import CellAssignPipeline
934
--> 935 cellassign_obj = CellAssignPipeline(**self.kwargs)
936 cellassign_obj.format_markers_to_df()
937 cellassign_obj.run_cell_assign()

/usr/local/lib/python3.10/dist-packages/enact/cellassign.py in init(self, **kwargs)
22 def init(self, **kwargs):
23 super().init(**kwargs)
---> 24 self.configs = configs
25
26 def format_markers_to_df(self):

NameError: name 'configs' is not defined

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