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remove chebi version param from base data class
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  • chebai/preprocessing/datasets

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chebai/preprocessing/datasets/base.py

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@@ -36,7 +36,6 @@ class XYBaseDataModule(LightningDataModule):
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label_filter (Optional[int]): The index of the label to filter. Default is None.
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balance_after_filter (Optional[float]): The ratio of negative samples to positive samples after filtering. Default is None.
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num_workers (int): The number of worker processes for data loading. Default is 1.
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chebi_version (int): The version of ChEBI to use. Default is 200.
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inner_k_folds (int): The number of folds for inner cross-validation. Use -1 to disable inner cross-validation. Default is -1.
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fold_index (Optional[int]): The index of the fold to use for training and validation. Default is None.
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base_dir (Optional[str]): The base directory for storing processed and raw data. Default is None.
@@ -52,7 +51,6 @@ class XYBaseDataModule(LightningDataModule):
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label_filter (Optional[int]): The index of the label to filter.
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balance_after_filter (Optional[float]): The ratio of negative samples to positive samples after filtering.
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num_workers (int): The number of worker processes for data loading.
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chebi_version (int): The version of ChEBI to use.
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inner_k_folds (int): The number of folds for inner cross-validation. If it is less than to, no cross-validation will be performed.
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fold_index (Optional[int]): The index of the fold to use for training and validation (only relevant for cross-validation).
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_base_dir (Optional[str]): The base directory for storing processed and raw data.
@@ -75,7 +73,6 @@ def __init__(
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label_filter: Optional[int] = None,
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balance_after_filter: Optional[float] = None,
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num_workers: int = 1,
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chebi_version: int = 200,
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inner_k_folds: int = -1, # use inner cross-validation if > 1
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fold_index: Optional[int] = None,
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base_dir: Optional[str] = None,
@@ -95,7 +92,6 @@ def __init__(
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), "Filter balancing requires a filter"
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self.balance_after_filter = balance_after_filter
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self.num_workers = num_workers
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self.chebi_version = chebi_version
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assert type(inner_k_folds) is int
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self.inner_k_folds = inner_k_folds
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self.use_inner_cross_validation = (

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