diff --git a/src/scportrait/pipeline/featurization.py b/src/scportrait/pipeline/featurization.py index 5363277c..12cadbfe 100644 --- a/src/scportrait/pipeline/featurization.py +++ b/src/scportrait/pipeline/featurization.py @@ -17,6 +17,7 @@ from scportrait.tools.ml.datasets import HDF5SingleCellDataset from scportrait.tools.ml.plmodels import MultilabelSupervisedModel + class _FeaturizationBase(ProcessingStep): PRETRAINED_MODEL_NAMES = [ "autophagy_classifier", diff --git a/src/scportrait/pipeline/project.py b/src/scportrait/pipeline/project.py index 76e26c55..230842d9 100644 --- a/src/scportrait/pipeline/project.py +++ b/src/scportrait/pipeline/project.py @@ -4,6 +4,7 @@ import tempfile import warnings from time import time +from typing import Literal import dask.array as darray import datatree @@ -33,7 +34,7 @@ remap_region_annotation_table, ) -from typing import Literal + class Project(Logable): CLEAN_LOG = True @@ -1039,7 +1040,7 @@ def extract(self, partial=False, n_cells=None, overwrite: bool | None = None): 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, ): diff --git a/tests/e2e_tests/segmentation_workflow.py b/tests/e2e_tests/segmentation_workflow.py index fba12b6e..54d29157 100644 --- a/tests/e2e_tests/segmentation_workflow.py +++ b/tests/e2e_tests/segmentation_workflow.py @@ -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