docs: fix Sphinx build issues, mambular to deeptab rename

Co-authored-by: Copilot <copilot@github.com>

Author: mkumar73

deeptab/utils/docstring_generator.py

@@ -1,3 +1,6 @@
+import inspect
+import textwrap
+
 from pretab.preprocessor import Preprocessor
 
 
@@ -6,27 +9,34 @@ def generate_docstring(config, model_description, examples):
 
     The `Parameters` tag is stripped from the Preprocessor docstring to avoid duplication.
     """
-    config_doc = config.__doc__ or "No documentation for DefaultFTTransformerConfig."
-    preprocessor_doc = Preprocessor.__doc__ or "No documentation for Preprocessor."
-
-    # Remove "Parameters" section header from the Preprocessor docstring
-    preprocessor_doc_cleaned = preprocessor_doc.split("Parameters\n    ----------\n", 1)[-1].strip()
-
+    # inspect.cleandoc is the correct tool for Python docstrings: it strips
+    # leading blank lines, then removes the common indentation from lines 2+
+    # (the class-body indent).  textwrap.dedent cannot do this because Python
+    # stores line 1 without any leading whitespace, making the common indent 0.
+    config_doc = inspect.cleandoc(config.__doc__ or "No documentation.")
+    preprocessor_doc = inspect.cleandoc(Preprocessor.__doc__ or "No documentation.")
+
+    # After cleandoc the section header is at column 0: "Parameters\n----------\n"
+    preprocessor_doc_cleaned = preprocessor_doc.split("Parameters\n----------\n", 1)[-1].strip()
     preprocessor_doc_cleaned = preprocessor_doc_cleaned.split("Attributes")[0].strip()
 
-    config_doc += preprocessor_doc_cleaned
+    # Combine config doc + preprocessor params, then re-indent uniformly at 4 spaces.
+    config_doc_indented = textwrap.indent(config_doc + "\n\n" + preprocessor_doc_cleaned, "    ")
+
+    description_indented = textwrap.indent(textwrap.dedent(model_description).strip(), "    ")
+    examples_indented = textwrap.indent(textwrap.dedent(examples).strip(), "    ")
 
     return f"""
-    {model_description.strip()}
+{description_indented}
 
     Notes
     -----
     The parameters for this class include the attributes from the config
     dataclass as well as preprocessing arguments handled by the base class.
 
-    {config_doc}
+{config_doc_indented}
 
     Examples
     --------
-    {examples.strip()}
+{examples_indented}
     """

docs/api/base_models/BaseModels.rst

@@ -1,29 +1,25 @@
 deeptab.base_models
 =======================
 
-.. autoclass:: deeptab.base_models.BaseModel
-    :members:
-    :no-inherited-members:
-
-.. autoclass:: deeptab.base_models.TaskModel
-    :members:
-    :no-inherited-members:
-
 .. autoclass:: deeptab.base_models.Mambular
     :members:
     :no-inherited-members:
+    :exclude-members: forward
 
 .. autoclass:: deeptab.base_models.MLP
     :members:
     :no-inherited-members:
+    :exclude-members: forward
 
 .. autoclass:: deeptab.base_models.ResNet
     :members:
     :no-inherited-members:
+    :exclude-members: forward
 
 .. autoclass:: deeptab.base_models.FTTransformer
     :members:
     :no-inherited-members:
+    :exclude-members: forward
 
 .. autoclass:: deeptab.base_models.TabTransformer
     :members:
@@ -33,22 +29,52 @@ deeptab.base_models
     :members:
     :no-inherited-members:
 
-.. autoclass:: mambular.base_models.MambAttention
+.. autoclass:: deeptab.base_models.MambAttention
+    :members:
+    :no-inherited-members:
+    :exclude-members: forward
+
+.. autoclass:: deeptab.base_models.MambaTab
+    :members:
+    :no-inherited-members:
+    :exclude-members: forward
+
+.. autoclass:: deeptab.base_models.TabM
+    :members:
+    :no-inherited-members:
+
+.. autoclass:: deeptab.base_models.NODE
+    :members:
+    :no-inherited-members:
+    :exclude-members: forward
+
+.. autoclass:: deeptab.base_models.NDTF
+    :members:
+    :no-inherited-members:
+    :exclude-members: forward, penalty_forward
+
+.. autoclass:: deeptab.base_models.SAINT
+    :members:
+    :no-inherited-members:
+    :exclude-members: forward
+
+.. autoclass:: deeptab.base_models.AutoInt
     :members:
     :no-inherited-members:
 
-.. autoclass:: mambular.base_models.TabM
+.. autoclass:: deeptab.base_models.ENODE
     :members:
     :no-inherited-members:
+    :exclude-members: forward
 
-.. autoclass:: mambular.base_models.NODE
+.. autoclass:: deeptab.base_models.ModernNCA
     :members:
     :no-inherited-members:
 
-.. autoclass:: mambular.base_models.NDTF
+.. autoclass:: deeptab.base_models.Tangos
     :members:
     :no-inherited-members:
 
-.. autoclass:: mambular.base_models.SAINT
+.. autoclass:: deeptab.base_models.Trompt
     :members:
     :no-inherited-members:

docs/api/base_models/index.rst

@@ -1,17 +1,15 @@
 .. -*- mode: rst -*-
 
-.. currentmodule:: mambular.base_models
+.. currentmodule:: deeptab.base_models
 
 BaseModels
 ==========
 
-This module provides foundational classes and architectures for Mambular models, including various neural network architectures tailored for tabular data.
+This module provides foundational classes and architectures for deeptab models, including various neural network architectures tailored for tabular data.
 
 =========================================    =======================================================================================================
 Modules                                       Description
 =========================================    =======================================================================================================
-:class:`BaseModel`                            Abstract base class defining the core structure and initialization logic for Mambular models.
-:class:`TaskModel`                            PyTorch Lightning module for managing model training, validation, and testing workflows.
 :class:`Mambular`                             Flexible neural network model leveraging the Mamba architecture with configurable normalization techniques for tabular data.
 :class:`MLP`                                  Multi-layer perceptron (MLP) model designed for tabular tasks, initialized with a custom configuration.
 :class:`ResNet`                               Deep residual network (ResNet) model optimized for structured/tabular datasets.
@@ -22,7 +20,13 @@ Modules                                       Description
 :class:`NDTF`                                 Neural Decision Tree Forest (NDTF) model for tabular tasks, blending decision tree concepts with neural networks.
 :class:`TabulaRNN`                            Recurrent neural network (RNN) model, including LSTM and GRU architectures, tailored for sequential or time-series tabular data.
 :class:`MambAttention`                        Attention-based architecture for tabular tasks, combining feature importance weighting with advanced normalization techniques.
-:class:`SAINT`                                SAINT model. Transformer based model using row and column attetion.
+:class:`SAINT`                                SAINT model. Transformer based model using row and column attention.
+:class:`MambaTab`                             Tabular model using a Mamba-Block on a joint input representation.
+:class:`AutoInt`                              Automatic Feature Interaction model for tabular data.
+:class:`ENODE`                                Embedding Neural Oblivious Decision Ensembles for tabular tasks.
+:class:`ModernNCA`                            Modern Nearest Centroid Approach for tabular deep learning.
+:class:`Tangos`                               Tangos model for tabular data.
+:class:`Trompt`                               Trompt model for tabular data.
 =========================================    =======================================================================================================
 
 

docs/api/configs/Configurations.rst

@@ -1,50 +1,70 @@
 Configurations
 ===============
 
-.. autoclass:: mambular.configs.DefaultMambularConfig
+.. autoclass:: deeptab.configs.DefaultMambularConfig
    :members:
    :undoc-members:
 
-.. autoclass:: mambular.configs.DefaultFTTransformerConfig
+.. autoclass:: deeptab.configs.DefaultFTTransformerConfig
    :members:
    :undoc-members:
 
-.. autoclass:: mambular.configs.DefaultResNetConfig
+.. autoclass:: deeptab.configs.DefaultResNetConfig
    :members:
    :undoc-members:
 
-.. autoclass:: mambular.configs.DefaultMLPConfig
+.. autoclass:: deeptab.configs.DefaultMLPConfig
    :members:
    :undoc-members:
 
-.. autoclass:: mambular.configs.DefaultTabTransformerConfig
+.. autoclass:: deeptab.configs.DefaultTabTransformerConfig
    :members:
    :undoc-members:
 
-.. autoclass:: mambular.configs.DefaultMambaTabConfig
+.. autoclass:: deeptab.configs.DefaultMambaTabConfig
    :members:
    :undoc-members:
 
-.. autoclass:: mambular.configs.DefaultTabulaRNNConfig
+.. autoclass:: deeptab.configs.DefaultTabulaRNNConfig
    :members:
    :undoc-members:
 
-.. autoclass:: mambular.configs.DefaultMambAttentionConfig
+.. autoclass:: deeptab.configs.DefaultMambAttentionConfig
    :members:
    :undoc-members:
 
-.. autoclass:: mambular.configs.DefaultNDTFConfig
+.. autoclass:: deeptab.configs.DefaultNDTFConfig
    :members:
    :undoc-members:
 
-.. autoclass:: mambular.configs.DefaultNODEConfig
+.. autoclass:: deeptab.configs.DefaultNODEConfig
    :members:
    :undoc-members:
 
-.. autoclass:: mambular.configs.DefaultTabMConfig
+.. autoclass:: deeptab.configs.DefaultTabMConfig
    :members:
    :undoc-members:
 
-.. autoclass:: mambular.configs.DefaultSAINTConfig
+.. autoclass:: deeptab.configs.DefaultSAINTConfig
+   :members:
+   :undoc-members:
+
+.. autoclass:: deeptab.configs.DefaultAutoIntConfig
+   :members:
+   :undoc-members:
+
+.. autoclass:: deeptab.configs.DefaultENODEConfig
+   :members:
+   :undoc-members:
+
+.. autoclass:: deeptab.configs.DefaultModernNCAConfig
+   :members:
+   :undoc-members:
+
+.. autoclass:: deeptab.configs.DefaultTangosConfig
+   :members:
+   :undoc-members:
+
+.. autoclass:: deeptab.configs.DefaultTromptConfig
    :members:
    :undoc-members: