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fix the scimilarity_gred error. #2

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fix the scimilarity_gred error. #2

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2 changes: 1 addition & 1 deletion build/lib/cellm/data/data_scimilarity.py
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import torch
from lightning import LightningDataModule
from scimilarity_gred.tiledb_sample_data_models import SampleCellsDataModule_disease, scDataset_disease
from scimilarity.tiledb_sample_data_models import SampleCellsDataModule_disease, scDataset_disease
from torch.utils.data import Dataset, DataLoader

# from cellm.data.data_structures import CellSample
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2 changes: 1 addition & 1 deletion build/lib/pascient/data/data_scimilarity.py
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import torch
from lightning import LightningDataModule
from scimilarity_gred.tiledb_sample_data_models import SampleCellsDataModule_disease, scDataset_disease
from scimilarity.tiledb_sample_data_models import SampleCellsDataModule_disease, scDataset_disease
from torch.utils.data import Dataset, DataLoader

# from cellm.data.data_structures import CellSample
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2 changes: 1 addition & 1 deletion cellm/data/data_scimilarity.py
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Expand Up @@ -3,7 +3,7 @@

import torch
from lightning import LightningDataModule
from scimilarity_gred.tiledb_sample_data_models import SampleCellsDataModule_disease, scDataset_disease
from scimilarity.tiledb_sample_data_models import SampleCellsDataModule_disease, scDataset_disease
from torch.utils.data import Dataset, DataLoader

# from cellm.data.data_structures import CellSample
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2 changes: 1 addition & 1 deletion cellm/data/data_scimilarity_gred.py
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Expand Up @@ -17,7 +17,7 @@
from imblearn.over_sampling import RandomOverSampler ,SVMSMOTE
from imblearn.under_sampling import RandomUnderSampler

from scimilarity_gred.tiledb_sample_data_models import query_tiledb_df, import_cell_ontology, get_id_mapper, scDataset
from scimilarity.tiledb_sample_data_models import query_tiledb_df, import_cell_ontology, get_id_mapper, scDataset


# Turn off multithreading to allow multiple pytorch dataloader workers
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4 changes: 1 addition & 3 deletions relevant_install.sh
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@@ -1,7 +1,5 @@
#!/bin/bash
git clone https://github.com/Genentech/scimilarity.git
cd scimilarity
pip install .
cd ../
cd scimilarity_gred
pip install .
cd ../
2 changes: 1 addition & 1 deletion reproduce/supp_figures_part3.ipynb
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"\n",
"import torch\n",
"from lightning import LightningDataModule\n",
"from scimilarity_gred.tiledb_sample_data_models import SampleCellsDataModule_disease, scDataset_disease\n",
"from scimilarity.tiledb_sample_data_models import SampleCellsDataModule_disease, scDataset_disease\n",
"from torch.utils.data import Dataset, DataLoader\n",
"\n",
"# from cellm.data.data_structures import CellSample\n",
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