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ruff linting
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sophiamaedler committed Nov 30, 2024
1 parent 221960f commit b051095
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Showing 3 changed files with 5 additions and 3 deletions.
1 change: 1 addition & 0 deletions src/scportrait/pipeline/featurization.py
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from scportrait.tools.ml.datasets import HDF5SingleCellDataset
from scportrait.tools.ml.plmodels import MultilabelSupervisedModel


class _FeaturizationBase(ProcessingStep):
PRETRAINED_MODEL_NAMES = [
"autophagy_classifier",
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5 changes: 3 additions & 2 deletions src/scportrait/pipeline/project.py
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Expand Up @@ -4,6 +4,7 @@
import tempfile
import warnings
from time import time
from typing import Literal

import dask.array as darray
import datatree
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remap_region_annotation_table,
)

from typing import Literal

class Project(Logable):
CLEAN_LOG = True

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def featurize(
self,
n_cells: int = 0,
data_type: Literal["complete", "partial", "filtered"] ="complete",
data_type: Literal["complete", "partial", "filtered"] = "complete",
partial_seed: None | int = None,
overwrite: bool | None = None,
):
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2 changes: 1 addition & 1 deletion tests/e2e_tests/segmentation_workflow.py
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Expand Up @@ -6,8 +6,8 @@
import pandas as pd

from scportrait.pipeline._utils.segmentation import numba_mask_centroid
from scportrait.pipeline.featurization import CellFeaturizer
from scportrait.pipeline.extraction import HDF5CellExtraction
from scportrait.pipeline.featurization import CellFeaturizer
from scportrait.pipeline.project import Project
from scportrait.pipeline.segmentation.workflows import CytosolSegmentationCellpose, ShardedCytosolSegmentationCellpose

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