Loading deepchem/data/data_loader.py +2 −1 Original line number Original line Diff line number Diff line Loading @@ -976,7 +976,8 @@ class InMemoryLoader(DataLoader): Parameters Parameters ---------- ---------- inputs: Sequence[Any] inputs: Sequence[Any] List of inputs to process. Entries can be filenames or arbitrary objects. List of inputs to process. Entries can be arbitrary objects so long as they are understood by `self.featurizer` data_dir: str, optional data_dir: str, optional Directory to store featurized dataset. Directory to store featurized dataset. shard_size: int, optional shard_size: int, optional Loading deepchem/data/datasets.py +6 −1 Original line number Original line Diff line number Diff line Loading @@ -1943,7 +1943,12 @@ class ImageDataset(Dataset): self._X_shape = self._find_array_shape(X) self._X_shape = self._find_array_shape(X) self._y_shape = self._find_array_shape(y) self._y_shape = self._find_array_shape(y) if w is None: if w is None: if len(self._y_shape) == 1: if len(self._y_shape) == 0: # Case n_samples should be 1 if n_samples != 1: raise ValueError("y can only be a scalar if n_samples == 1") w = np.ones_like(y) elif len(self._y_shape) == 1: w = np.ones(self._y_shape[0], np.float32) w = np.ones(self._y_shape[0], np.float32) else: else: w = np.ones((self._y_shape[0], 1), np.float32) w = np.ones((self._y_shape[0], 1), np.float32) Loading deepchem/utils/save.py +10 −6 Original line number Original line Diff line number Diff line Loading @@ -11,7 +11,7 @@ import os import deepchem import deepchem import warnings import warnings import logging import logging from typing import List, Optional, Iterator from typing import List, Optional, Iterator, Any from deepchem.utils.genomics import encode_bio_sequence as encode_sequence, encode_fasta_sequence as fasta_sequence, seq_one_hot_encode as seq_one_hotencode from deepchem.utils.genomics import encode_bio_sequence as encode_sequence, encode_fasta_sequence as fasta_sequence, seq_one_hot_encode as seq_one_hotencode logger = logging.getLogger(__name__) logger = logging.getLogger(__name__) Loading Loading @@ -45,7 +45,8 @@ def get_input_type(input_file): raise ValueError("Unrecognized extension %s" % file_extension) raise ValueError("Unrecognized extension %s" % file_extension) def load_data(input_files, shard_size=None): def load_data(input_files: List[str], shard_size: Optional[int] = None) -> Iterator[Any]: """Loads data from disk. """Loads data from disk. For CSV files, supports sharded loading for large files. For CSV files, supports sharded loading for large files. Loading Loading @@ -77,7 +78,9 @@ def load_data(input_files, shard_size=None): yield load_pickle_from_disk(input_file) yield load_pickle_from_disk(input_file) def load_sdf_files(input_files, clean_mols, tasks=[]): def load_sdf_files(input_files: List[str], clean_mols: bool = True, tasks: List[str] = []) -> List[pd.DataFrame]: """Load SDF file into dataframe. """Load SDF file into dataframe. Parameters Parameters Loading @@ -99,7 +102,7 @@ def load_sdf_files(input_files, clean_mols, tasks=[]): ------- ------- dataframes: list dataframes: list This function returns a list of pandas dataframes. Each dataframe will This function returns a list of pandas dataframes. Each dataframe will columns `('mol_id', 'smiles', 'mol')`. contain columns `('mol_id', 'smiles', 'mol')`. """ """ from rdkit import Chem from rdkit import Chem dataframes = [] dataframes = [] Loading Loading @@ -130,12 +133,13 @@ def load_sdf_files(input_files, clean_mols, tasks=[]): return dataframes return dataframes def load_csv_files(filenames, shard_size=None): def load_csv_files(filenames: List[str], shard_size: Optional[int] = None) -> Iterator[pd.DataFrame]: """Load data as pandas dataframe. """Load data as pandas dataframe. Parameters Parameters ---------- ---------- input_files: list[str] filenames: list[str] List of filenames List of filenames shard_size: int, optional (default None) shard_size: int, optional (default None) The shard size to yield at one time. The shard size to yield at one time. Loading Loading
deepchem/data/data_loader.py +2 −1 Original line number Original line Diff line number Diff line Loading @@ -976,7 +976,8 @@ class InMemoryLoader(DataLoader): Parameters Parameters ---------- ---------- inputs: Sequence[Any] inputs: Sequence[Any] List of inputs to process. Entries can be filenames or arbitrary objects. List of inputs to process. Entries can be arbitrary objects so long as they are understood by `self.featurizer` data_dir: str, optional data_dir: str, optional Directory to store featurized dataset. Directory to store featurized dataset. shard_size: int, optional shard_size: int, optional Loading
deepchem/data/datasets.py +6 −1 Original line number Original line Diff line number Diff line Loading @@ -1943,7 +1943,12 @@ class ImageDataset(Dataset): self._X_shape = self._find_array_shape(X) self._X_shape = self._find_array_shape(X) self._y_shape = self._find_array_shape(y) self._y_shape = self._find_array_shape(y) if w is None: if w is None: if len(self._y_shape) == 1: if len(self._y_shape) == 0: # Case n_samples should be 1 if n_samples != 1: raise ValueError("y can only be a scalar if n_samples == 1") w = np.ones_like(y) elif len(self._y_shape) == 1: w = np.ones(self._y_shape[0], np.float32) w = np.ones(self._y_shape[0], np.float32) else: else: w = np.ones((self._y_shape[0], 1), np.float32) w = np.ones((self._y_shape[0], 1), np.float32) Loading
deepchem/utils/save.py +10 −6 Original line number Original line Diff line number Diff line Loading @@ -11,7 +11,7 @@ import os import deepchem import deepchem import warnings import warnings import logging import logging from typing import List, Optional, Iterator from typing import List, Optional, Iterator, Any from deepchem.utils.genomics import encode_bio_sequence as encode_sequence, encode_fasta_sequence as fasta_sequence, seq_one_hot_encode as seq_one_hotencode from deepchem.utils.genomics import encode_bio_sequence as encode_sequence, encode_fasta_sequence as fasta_sequence, seq_one_hot_encode as seq_one_hotencode logger = logging.getLogger(__name__) logger = logging.getLogger(__name__) Loading Loading @@ -45,7 +45,8 @@ def get_input_type(input_file): raise ValueError("Unrecognized extension %s" % file_extension) raise ValueError("Unrecognized extension %s" % file_extension) def load_data(input_files, shard_size=None): def load_data(input_files: List[str], shard_size: Optional[int] = None) -> Iterator[Any]: """Loads data from disk. """Loads data from disk. For CSV files, supports sharded loading for large files. For CSV files, supports sharded loading for large files. Loading Loading @@ -77,7 +78,9 @@ def load_data(input_files, shard_size=None): yield load_pickle_from_disk(input_file) yield load_pickle_from_disk(input_file) def load_sdf_files(input_files, clean_mols, tasks=[]): def load_sdf_files(input_files: List[str], clean_mols: bool = True, tasks: List[str] = []) -> List[pd.DataFrame]: """Load SDF file into dataframe. """Load SDF file into dataframe. Parameters Parameters Loading @@ -99,7 +102,7 @@ def load_sdf_files(input_files, clean_mols, tasks=[]): ------- ------- dataframes: list dataframes: list This function returns a list of pandas dataframes. Each dataframe will This function returns a list of pandas dataframes. Each dataframe will columns `('mol_id', 'smiles', 'mol')`. contain columns `('mol_id', 'smiles', 'mol')`. """ """ from rdkit import Chem from rdkit import Chem dataframes = [] dataframes = [] Loading Loading @@ -130,12 +133,13 @@ def load_sdf_files(input_files, clean_mols, tasks=[]): return dataframes return dataframes def load_csv_files(filenames, shard_size=None): def load_csv_files(filenames: List[str], shard_size: Optional[int] = None) -> Iterator[pd.DataFrame]: """Load data as pandas dataframe. """Load data as pandas dataframe. Parameters Parameters ---------- ---------- input_files: list[str] filenames: list[str] List of filenames List of filenames shard_size: int, optional (default None) shard_size: int, optional (default None) The shard size to yield at one time. The shard size to yield at one time. Loading
