Fix doc data

pina/data/data_module.py

@@ -17,7 +17,7 @@ from ..collector import Collector
 
 class DummyDataloader:
     """
-    Dataloader used when batch size is ``None``. It returns the entire dataset
+    Dataloader used when batch size is `None`. It returns the entire dataset
     in a single batch.
     """
 
@@ -38,7 +38,7 @@ class DummyDataloader:
         :param dataset: The dataset object to be processed.
         :type dataset: PinaDataset
 
-        .. note:: This data loader is used when the batch size is ``None``.
+        .. note:: This data loader is used when the batch size is `None`.
         """
 
         if (
@@ -157,7 +157,7 @@ class Collator:
     def _collate_tensor_dataset(data_list):
         """
         Function used to collate the data when the dataset is a
-        :class:`PinaTensorDataset`.
+        :class:`pina.data.dataset.PinaTensorDataset`.
 
         :param data_list: Elements to be collated.
         :type data_list: list[torch.Tensor] | list[LabelTensor]
@@ -165,7 +165,7 @@ class Collator:
         :rtype: dict
 
         :raises RuntimeError: If the data is not a :class:`torch.Tensor` or a
-            :class:`LabelTensor`.
+            :class:`pina.label_tensor.LabelTensor`.
         """
 
         if isinstance(data_list[0], LabelTensor):
@@ -177,15 +177,15 @@ class Collator:
     def _collate_graph_dataset(self, data_list):
         """
         Function used to collate the data when the dataset is a
-        :class:`PinaGraphDataset`.
+        :class:`pina.data.dataset.PinaGraphDataset`.
 
         :param data_list: Elememts to be collated.
-        :type data_list: list[torch_geometric.data.Data] | list[Graph]
+        :type data_list: list[Data] | list[Graph]
         :return: Batch of data.
         :rtype: dict
 
         :raises RuntimeError: If the data is not a
-            :class:`torch_geometric.data.Data` or a :class:`Graph`.
+            :class:`~torch_geometric.data.Data` or a :class:`pina.graph.Graph`.
         """
 
         if isinstance(data_list[0], LabelTensor):
@@ -248,7 +248,7 @@ class PinaSampler:
 
 class PinaDataModule(LightningDataModule):
     """
-    This class extends :class:`pytorch_lightning.LightningDataModule`,
+    This class extends :class:`lightning.pytorch.LightningDataModule`,
     allowing proper creation and management of different types of datasets
     defined in PINA.
     """
@@ -536,8 +536,7 @@ class PinaDataModule(LightningDataModule):
         """
         Define the maximum length of the conditions.
 
-        :param split:  The splits of the dataset.
-        :type split: dict
+        :param dict split:  The splits of the dataset.
         :return: The maximum length of the conditions.
         :rtype: dict
         """
@@ -559,7 +558,7 @@ class PinaDataModule(LightningDataModule):
         Create the validation dataloader.
 
         :return: The validation dataloader
-        :rtype: DataLoader
+        :rtype: torch.utils.data.DataLoader
         """
         return self._create_dataloader("val", self.val_dataset)
 
@@ -568,7 +567,7 @@ class PinaDataModule(LightningDataModule):
         Create the training dataloader
 
         :return: The training dataloader
-        :rtype: DataLoader
+        :rtype: torch.utils.data.DataLoader
         """
         return self._create_dataloader("train", self.train_dataset)
 
@@ -577,7 +576,7 @@ class PinaDataModule(LightningDataModule):
         Create the testing dataloader
 
         :return: The testing dataloader
-        :rtype: DataLoader
+        :rtype: torch.utils.data.DataLoader
         """
         return self._create_dataloader("test", self.test_dataset)
 

pina/data/dataset.py

@@ -15,24 +15,26 @@ class PinaDatasetFactory:
     Depending on the type inside the conditions, it creates a different dataset
     object:
 
-    - :class:`PinaTensorDataset` for handling :class:`torch.Tensor` and
-        :class:`LabelTensor` data.
-    - :class:`PinaGraphDataset` for handling :class:`Graph` and :class:`Data`
-        data.
+    - :class:`pina.data.dataset.PinaTensorDataset` for handling
+        :class:`torch.Tensor` and :class:`pina.label_tensor.LabelTensor` data.
+    - :class:`pina.data.dataset.PinaGraphDataset` for handling
+        :class:`pina.graph.Graph` and :class:`~torch_geometric.data.Data` data.
     """
 
     def __new__(cls, conditions_dict, **kwargs):
         """
-        Instantiate the appropriate subclass of :class:`PinaDataset`.
+        Instantiate the appropriate subclass of
+        :class:`pina.data.dataset.PinaDataset`.
 
         If a graph is present in the conditions, returns a
-        :class:`PinaGraphDataset`,  otherwise returns a
-        :class:`PinaTensorDataset`.
+        :class:`pina.data.dataset.PinaGraphDataset`, otherwise returns a
+        :class:`pina.data.dataset.PinaTensorDataset`.
 
         :param dict conditions_dict: Dictionary containing all the conditions
             to be included in the dataset instance.
-        :return: A subclass of :class:`PinaDataset`.
-        :rtype: :class:`PinaTensorDataset` | :class:`PinaGraphDataset`
+        :return: A subclass of :class:`pina.data.dataset.PinaDataset`.
+        :rtype: :class:`pina.data.dataset.PinaTensorDataset` |
+            :class:`pina.data.dataset.PinaGraphDataset`
 
         :raises ValueError: If an empty dictionary is provided.
         """
@@ -73,25 +75,25 @@ class PinaDatasetFactory:
 class PinaDataset(Dataset, ABC):
     """
     Abstract class for the PINA dataset. It defines the common interface for
-    the :class:`PinaTensorDataset` and :class:`PinaGraphDataset` classes.
+    the :class:`pina.data.dataset.PinaTensorDataset` and
+    :class:`pina.data.dataset.PinaGraphDataset` classes.
     """
 
     def __init__(
         self, conditions_dict, max_conditions_lengths, automatic_batching
     ):
         """
-        Initialize a :class:`PinaDataset` instance by storing the provided
-        conditions dictionary, the maximum number of conditions to consider,
-        and the automatic batching flag.
+        Initialize a :class:`pina.data.dataset.PinaDataset` instance by storing
+        the providedconditions dictionary, the maximum number of conditions to
+        consider, and the automatic batching flag.
 
-        :param conditions_dict: Dictionary containing the conditions.
-        :type conditions_dict: dict
-        :param max_conditions_lengths: Specifies the maximum number of data
+        :param dict conditions_dict: Dictionary containing the conditions with
+            data.
+        :param dict max_conditions_lengths: Specifies the maximum number of data
             points to include in a single batch for each condition.
-        :type max_conditions_lengths: dict
-        :param automatic_batching: Indicates whether PyTorch automatic batching
-            is enabled in :class:`PinaDataModule`.
-        :type automatic_batching: bool
+        :param bool automatic_batching: Indicates whether PyTorch automatic
+            batching is enabled in
+            :class:`pina.data.data_module.PinaDataModule`.
         """
 
         # Store the conditions dictionary
@@ -134,8 +136,7 @@ class PinaDataset(Dataset, ABC):
         Return the index itself. This is used when automatic batching is
         disabled to postpone the data retrieval to the dataloader.
 
-        :param idx: Index.
-        :type idx: int
+        :param int idx: Index.
         :return: Index.
         :rtype: int
         """
@@ -174,8 +175,7 @@ class PinaDataset(Dataset, ABC):
         """
         Return data from the dataset given a list of indices.
 
-        :param idx: List of indices.
-        :type idx: list[int]
+        :param list[int] idx: List of indices.
         :return: A dictionary containing the data at the given indices.
         :rtype: dict
         """
@@ -205,7 +205,7 @@ class PinaDataset(Dataset, ABC):
 class PinaTensorDataset(PinaDataset):
     """
     Dataset class for the PINA dataset with :class:`torch.Tensor` and
-    :class:`LabelTensor` data.
+    :class:`pina.label_tensor.LabelTensor` data.
     """
 
     # Override _retrive_data method for torch.Tensor data
@@ -213,9 +213,9 @@ class PinaTensorDataset(PinaDataset):
         """
         Retrieve data from the dataset given a list of indices.
 
-        :param data: Dictionary containing the data
-            (only torch.Tensor/LableTensor).
-        :type data: dict
+        :param dict data: Dictionary containing the data
+            (only :class:`torch.Tensor` or
+            :class:`pina.label_tensor.LabelTensor`).
         :param list[int] idx_list: indices to retrieve.
         :return: Dictionary containing the data at the given indices.
         :rtype: dict
@@ -236,17 +236,17 @@ class PinaTensorDataset(PinaDataset):
 
 class PinaGraphDataset(PinaDataset):
     """
-    Dataset class for the PINA dataset with :class:`torch_geometric.data.Data`
-    and :class:`Graph` data.
+    Dataset class for the PINA dataset with :class:`~torch_geometric.data.Data`
+    and :class:`pina.graph.Graph` data.
     """
 
     def _create_graph_batch(self, data):
         """
         Create a LabelBatch object from a list of
-        :class:`torch_geometric.data.Data` objects.
+        :class:`~torch_geometric.data.Data` objects.
 
         :param data: List of items to collate in a single batch.
-        :type data: list[torch_geometric.data.Data] | list[Graph]
+        :type data: list[Data] | list[Graph]
         :return: LabelBatch object all the graph collated in a single batch
             disconnected graphs.
         :rtype: LabelBatch
@@ -256,13 +256,13 @@ class PinaGraphDataset(PinaDataset):
 
     def _create_tensor_batch(self, data):
         """
-        Reshape properly ``data`` tensor to be processed handle by the graph
+        Reshape properly `data` tensor to be processed handle by the graph
         based models.
 
         :param data: torch.Tensor object of shape (N, ...) where N is the
             number of data points.
         :type data: torch.Tensor | LabelTensor
-        :return: reshaped torch.Tensor or LabelTensor object.
+        :return: Reshaped tensor object.
         :rtype: torch.Tensor | LabelTensor
         """
         out = data.reshape(-1, *data.shape[2:])
@@ -270,11 +270,11 @@ class PinaGraphDataset(PinaDataset):
 
     def create_batch(self, data):
         """
-        Create a Batch object from a list of :class:`torch_geometric.data.Data`
+        Create a Batch object from a list of :class:`~torch_geometric.data.Data`
         objects.
 
         :param data: List of items to collate in a single batch.
-        :type data: list[torch_geometric.data.Data] | list[Graph]
+        :type data: list[Data] | list[Graph]
         :return: Batch object.
         :rtype: Batch | PinaBatch
         """