Unverified Commit e65fbe1c authored by Daiki Nishikawa's avatar Daiki Nishikawa Committed by GitHub
Browse files

Merge pull request #2145 from nd-02110114/update-data-2 

Refactor save.py and utils/__init__.py
parents cb785956 20220a90

deepchem/data/data_loader.py

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@@ -13,7 +13,7 @@ import pandas as pd 
import numpy as np



from deepchem.utils.typing import OneOrMany

from deepchem.utils.save import load_image_files, load_csv_files, load_json_files, load_sdf_files

from deepchem.utils.data_utils import load_image_files, load_csv_files, load_json_files, load_sdf_files

from deepchem.utils.genomics_utils import encode_bio_sequence

from deepchem.feat import UserDefinedFeaturizer, Featurizer

from deepchem.data import Dataset, DiskDataset, NumpyDataset, ImageDataset

deepchem/data/datasets.py

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@@ -18,7 +18,7 @@ import pandas as pd 


import deepchem as dc

from deepchem.utils.typing import OneOrMany, Shape

from deepchem.utils.save import save_to_disk, load_from_disk, load_image_files

from deepchem.utils.data_utils import save_to_disk, load_from_disk, load_image_files



Batch = Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]

deepchem/data/tests/test_reload.py

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@@ -23,7 +23,7 @@ class TestReload(unittest.TestCase): 
    # Load MUV dataset

    logger.info("About to featurize compounds")

    featurizer = dc.feat.CircularFingerprint(size=1024)

    raw_dataset = dc.utils.save.load_from_disk(dataset_file)

    raw_dataset = dc.utils.data_utils.load_from_disk(dataset_file)

    MUV_tasks = [

        'MUV-692', 'MUV-689', 'MUV-846', 'MUV-859', 'MUV-644', 'MUV-548',

        'MUV-852', 'MUV-600', 'MUV-810', 'MUV-712', 'MUV-737', 'MUV-858',

deepchem/dock/pose_generation.py

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@@ -12,7 +12,7 @@ from subprocess import check_output 
from typing import List, Optional, Tuple, Union



from deepchem.dock.binding_pocket import BindingPocketFinder

from deepchem.utils import download_url, get_data_dir

from deepchem.utils.data_utils import download_url, get_data_dir

from deepchem.utils.typing import RDKitMol

from deepchem.utils.geometry_utils import compute_centroid, compute_protein_range

from deepchem.utils.rdkit_utils import load_molecule, write_molecule

deepchem/feat/atomic_coordinates.py

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@@ -5,7 +5,7 @@ import logging 
import numpy as np

from deepchem.feat import Featurizer

from deepchem.feat import ComplexFeaturizer

from deepchem.utils import pad_array

from deepchem.utils.data_utils import pad_array

from deepchem.utils.rdkit_utils import MoleculeLoadException, get_xyz_from_mol, \

  load_molecule, merge_molecules_xyz, merge_molecules

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