update rsts

docs/source/_rst/_code.rst

@@ -12,22 +12,39 @@ The high-level structure of the package is depicted in our API.
 The pipeline to solve differential equations with PINA follows just five steps:
 
     1. Define the `Problem`_ the user aim to solve
-    2. Generate data using built in `Geometries`_, or load high level simulation results as :doc:`LabelTensor <label_tensor>`
+    2. Generate data using built in `Domains`_, or load high level simulation results as :doc:`LabelTensor <label_tensor>`
     3. Choose or build one or more `Models`_ to solve the problem
     4. Choose a solver across PINA available `Solvers`_, or build one using the :doc:`SolverInterface <solvers/solver_interface>`
-    5. Train the model with the PINA :doc:`Trainer <solvers/solver_interface>`, enhance the train with `Callbacks`_
+    5. Train the model with the PINA :doc:`Trainer <solvers/solver_interface>`, enhance the train with `Callback`_
 
-PINA Features
---------------
+
+Training and Datamodules
+-------------------------
+.. toctree::
+    :titlesonly:
+
+    Trainer <trainer.rst>
+
+Data Types
+------------
 .. toctree::
     :titlesonly:
 
     LabelTensor <label_tensor.rst>
-    Condition <condition.rst>
-    Trainer <trainer.rst>
-    Plotter <plotter.rst>
 
 
+Conditions
+-------------
+.. toctree::
+    :titlesonly:
+
+    ConditionInterface <condition/condition_interface.rst>
+    Condition <condition/condition.rst>
+    DataCondition <condition/data_condition.rst>
+    DomainEquationCondition <condition/domain_equation_condition.rst>
+    InputEquationCondition <condition/input_equation_condition.rst>
+    InputTargetCondition <condition/input_target_condition.rst>
+
 Solvers
 --------------
 
@@ -91,19 +108,19 @@ Adaptive Activation Functions
 .. toctree::
     :titlesonly:
 
-    Adaptive Function Interface <adaptive_functions/AdaptiveFunctionInterface.rst>
-    Adaptive ReLU <adaptive_functions/AdaptiveReLU.rst>
-    Adaptive Sigmoid <adaptive_functions/AdaptiveSigmoid.rst>
-    Adaptive Tanh <adaptive_functions/AdaptiveTanh.rst>
-    Adaptive SiLU <adaptive_functions/AdaptiveSiLU.rst>
-    Adaptive Mish <adaptive_functions/AdaptiveMish.rst>
-    Adaptive ELU <adaptive_functions/AdaptiveELU.rst>
-    Adaptive CELU <adaptive_functions/AdaptiveCELU.rst>
-    Adaptive GELU <adaptive_functions/AdaptiveGELU.rst>
-    Adaptive Softmin <adaptive_functions/AdaptiveSoftmin.rst>
-    Adaptive Softmax <adaptive_functions/AdaptiveSoftmax.rst>
-    Adaptive SIREN <adaptive_functions/AdaptiveSIREN.rst>
-    Adaptive Exp <adaptive_functions/AdaptiveExp.rst>
+    Adaptive Function Interface <adaptive_function/AdaptiveFunctionInterface.rst>
+    Adaptive ReLU <adaptive_function/AdaptiveReLU.rst>
+    Adaptive Sigmoid <adaptive_function/AdaptiveSigmoid.rst>
+    Adaptive Tanh <adaptive_function/AdaptiveTanh.rst>
+    Adaptive SiLU <adaptive_function/AdaptiveSiLU.rst>
+    Adaptive Mish <adaptive_function/AdaptiveMish.rst>
+    Adaptive ELU <adaptive_function/AdaptiveELU.rst>
+    Adaptive CELU <adaptive_function/AdaptiveCELU.rst>
+    Adaptive GELU <adaptive_function/AdaptiveGELU.rst>
+    Adaptive Softmin <adaptive_function/AdaptiveSoftmin.rst>
+    Adaptive Softmax <adaptive_function/AdaptiveSoftmax.rst>
+    Adaptive SIREN <adaptive_function/AdaptiveSIREN.rst>
+    Adaptive Exp <adaptive_function/AdaptiveExp.rst>
 
 
 Equations and Operators
@@ -127,38 +144,39 @@ Problem
     TimeDependentProblem <problem/timedepproblem.rst>
     ParametricProblem <problem/parametricproblem.rst>
 
-Geometries
+Domains
 -----------------
 
 .. toctree::
     :titlesonly:
 
-    Location <geometry/location.rst>
-    CartesianDomain <geometry/cartesian.rst>
-    EllipsoidDomain <geometry/ellipsoid.rst>
-    SimplexDomain <geometry/simplex.rst>
+    Domain <domain/domain.rst>
+    CartesianDomain <domain/cartesian.rst>
+    EllipsoidDomain <domain/ellipsoid.rst>
+    SimplexDomain <domain/simplex.rst>
 
-Geometry set operations
+domain set operations
 ------------------------
 
 .. toctree::
     :titlesonly:
 
-    OperationInterface <geometry/operation_interface.rst>
-    Union <geometry/union_domain.rst>
-    Intersection <geometry/intersection_domain.rst>
-    Difference <geometry/difference_domain.rst>
-    Exclusion <geometry/exclusion_domain.rst>
+    OperationInterface <domain/operation_interface.rst>
+    Union <domain/union_domain.rst>
+    Intersection <domain/intersection_domain.rst>
+    Difference <domain/difference_domain.rst>
+    Exclusion <domain/exclusion_domain.rst>
 
-Callbacks
+Callback
 --------------------
 
 .. toctree::
     :titlesonly:
 
-    Processing Callbacks <callbacks/processing_callbacks.rst>
-    Optimizer Callbacks <callbacks/optimizer_callbacks.rst>
-    Adaptive Refinment Callback <callbacks/adaptive_refinment_callbacks.rst>
+    Processing callback <callback/processing_callback.rst>
+    Optimizer callback <callback/optimizer_callback.rst>
+    Refinment callback <callback/adaptive_refinment_callback.rst>
+    Weighting callback <callback/linear_weight_update_callback.rst>
 
 Metrics and Losses
 --------------------

docs/source/_rst/adaptive_functions/AdaptiveCELU.rst

@@ -1,9 +0,0 @@
-AdaptiveCELU
-============
-
-.. currentmodule:: pina.adaptive_functions.adaptive_func
-
-.. autoclass:: AdaptiveCELU
-    :members:
-    :show-inheritance:
-    :inherited-members: AdaptiveActivationFunctionInterface

docs/source/_rst/adaptive_functions/AdaptiveELU.rst

@@ -1,9 +0,0 @@
-AdaptiveELU
-===========
-
-.. currentmodule:: pina.adaptive_functions.adaptive_func
-
-.. autoclass:: AdaptiveELU
-    :members:
-    :show-inheritance:
-    :inherited-members: AdaptiveActivationFunctionInterface

docs/source/_rst/adaptive_functions/AdaptiveExp.rst

@@ -1,9 +0,0 @@
-AdaptiveExp
-===========
-
-.. currentmodule:: pina.adaptive_functions.adaptive_func
-
-.. autoclass:: AdaptiveExp
-    :members:
-    :show-inheritance:
-    :inherited-members: AdaptiveActivationFunctionInterface

docs/source/_rst/adaptive_functions/AdaptiveFunctionInterface.rst

@@ -1,8 +0,0 @@
-AdaptiveActivationFunctionInterface
-=======================================
-
-.. currentmodule:: pina.adaptive_functions.adaptive_func_interface
-
-.. automodule:: pina.adaptive_functions.adaptive_func_interface
-    :members:
-    :show-inheritance:

docs/source/_rst/adaptive_functions/AdaptiveGELU.rst

@@ -1,9 +0,0 @@
-AdaptiveGELU
-============
-
-.. currentmodule:: pina.adaptive_functions.adaptive_func
-
-.. autoclass:: AdaptiveGELU
-    :members:
-    :show-inheritance:
-    :inherited-members: AdaptiveActivationFunctionInterface

docs/source/_rst/adaptive_functions/AdaptiveMish.rst

@@ -1,9 +0,0 @@
-AdaptiveMish
-============
-
-.. currentmodule:: pina.adaptive_functions.adaptive_func
-
-.. autoclass:: AdaptiveMish
-    :members:
-    :show-inheritance:
-    :inherited-members: AdaptiveActivationFunctionInterface

docs/source/_rst/adaptive_functions/AdaptiveReLU.rst

@@ -1,9 +0,0 @@
-AdaptiveReLU
-============
-
-.. currentmodule:: pina.adaptive_functions.adaptive_func
-
-.. autoclass:: AdaptiveReLU
-    :members:
-    :show-inheritance:
-    :inherited-members: AdaptiveActivationFunctionInterface

docs/source/_rst/adaptive_functions/AdaptiveSIREN.rst

@@ -1,9 +0,0 @@
-AdaptiveSIREN
-=============
-
-.. currentmodule:: pina.adaptive_functions.adaptive_func
-
-.. autoclass:: AdaptiveSIREN
-    :members:
-    :show-inheritance:
-    :inherited-members: AdaptiveActivationFunctionInterface

docs/source/_rst/adaptive_functions/AdaptiveSiLU.rst

@@ -1,9 +0,0 @@
-AdaptiveSiLU
-============
-
-.. currentmodule:: pina.adaptive_functions.adaptive_func
-
-.. autoclass:: AdaptiveSiLU
-    :members:
-    :show-inheritance:
-    :inherited-members: AdaptiveActivationFunctionInterface

docs/source/_rst/adaptive_functions/AdaptiveSigmoid.rst

@@ -1,9 +0,0 @@
-AdaptiveSigmoid
-===============
-
-.. currentmodule:: pina.adaptive_functions.adaptive_func
-
-.. autoclass:: AdaptiveSigmoid
-    :members:
-    :show-inheritance:
-    :inherited-members: AdaptiveActivationFunctionInterface

docs/source/_rst/adaptive_functions/AdaptiveSoftmax.rst

@@ -1,9 +0,0 @@
-AdaptiveSoftmax
-===============
-
-.. currentmodule:: pina.adaptive_functions.adaptive_func
-
-.. autoclass:: AdaptiveSoftmax
-    :members:
-    :show-inheritance:
-    :inherited-members: AdaptiveActivationFunctionInterface

docs/source/_rst/adaptive_functions/AdaptiveSoftmin.rst

@@ -1,9 +0,0 @@
-AdaptiveSoftmin
-===============
-
-.. currentmodule:: pina.adaptive_functions.adaptive_func
-
-.. autoclass:: AdaptiveSoftmin
-    :members:
-    :show-inheritance:
-    :inherited-members: AdaptiveActivationFunctionInterface

docs/source/_rst/adaptive_functions/AdaptiveTanh.rst

@@ -1,9 +0,0 @@
-AdaptiveTanh
-============
-
-.. currentmodule:: pina.adaptive_functions.adaptive_func
-
-.. autoclass:: AdaptiveTanh
-    :members:
-    :show-inheritance:
-    :inherited-members: AdaptiveActivationFunctionInterface

docs/source/_rst/callback/adaptive_refinment_callbacks.rst

@@ -0,0 +1,7 @@
+Refinments callbacks
+=======================
+
+.. currentmodule:: pina.callback.adaptive_refinement_callback
+.. autoclass:: R3Refinement
+   :members:
+   :show-inheritance:

docs/source/_rst/callback/linear_weight_update_callback.rst

@@ -0,0 +1,7 @@
+Weighting callbacks
+========================
+
+.. currentmodule:: pina.callback.linear_weight_update_callback
+.. autoclass:: LinearWeightUpdate
+   :members:
+   :show-inheritance:

docs/source/_rst/callback/optimizer_callbacks.rst

@@ -1,7 +1,7 @@
 Optimizer callbacks
 =====================
 
-.. currentmodule:: pina.callbacks.optimizer_callbacks
+.. currentmodule:: pina.callback.optimizer_callback
 .. autoclass:: SwitchOptimizer
    :members:
    :show-inheritance:

docs/source/_rst/callback/processing_callbacks.rst

@@ -1,7 +1,7 @@
 Processing callbacks
 =======================
 
-.. currentmodule:: pina.callbacks.processing_callbacks
+.. currentmodule:: pina.callbacks.processing_callback
 .. autoclass:: MetricTracker
    :members:
    :show-inheritance:

docs/source/_rst/callbacks/adaptive_refinment_callbacks.rst

@@ -1,7 +0,0 @@
-Adaptive Refinments callbacks
-===============================
-
-.. currentmodule:: pina.callbacks.adaptive_refinment_callbacks
-.. autoclass:: R3Refinement
-   :members:
-   :show-inheritance:

docs/source/_rst/condition.rst

@@ -1,7 +0,0 @@
-Condition
-=========
-.. currentmodule:: pina.condition
-
-.. autoclass:: Condition
-    :members:
-    :show-inheritance:

docs/source/_rst/condition/condition.rst

@@ -0,0 +1,7 @@
+Conditions
+=============
+.. currentmodule:: pina.condition.condition
+
+.. autoclass:: Condition
+    :members:
+    :show-inheritance:

docs/source/_rst/condition/condition_interface.rst

@@ -0,0 +1,7 @@
+ConditionInterface
+======================
+.. currentmodule:: pina.condition.condition_interface
+
+.. autoclass:: ConditionInterface
+    :members:
+    :show-inheritance:

docs/source/_rst/condition/data_condition.rst

@@ -0,0 +1,15 @@
+Data Conditions
+==================
+.. currentmodule:: pina.condition.data_condition
+
+.. autoclass:: DataCondition
+    :members:
+    :show-inheritance:
+
+.. autoclass:: GraphDataCondition
+    :members:
+    :show-inheritance:
+
+.. autoclass:: TensorDataCondition
+    :members:
+    :show-inheritance:

docs/source/_rst/condition/domain_equation_condition.rst

@@ -0,0 +1,7 @@
+Domain Equation Condition
+===========================
+.. currentmodule:: pina.condition.domain_equation_condition
+
+.. autoclass:: DomainEquationCondition
+    :members:
+    :show-inheritance:

docs/source/_rst/condition/input_equation_condition.rst

@@ -0,0 +1,15 @@
+Input Equation Condition
+===========================
+.. currentmodule:: pina.condition.input_equation_condition
+
+.. autoclass:: InputEquationCondition
+    :members:
+    :show-inheritance:
+
+.. autoclass:: InputTensorEquationCondition
+    :members:
+    :show-inheritance:
+
+.. autoclass:: InputGraphEquationCondition
+    :members:
+    :show-inheritance:

docs/source/_rst/condition/input_target_condition.rst

@@ -0,0 +1,23 @@
+Input Target Condition
+===========================
+.. currentmodule:: pina.condition.input_target_condition
+
+.. autoclass:: InputTargetCondition
+    :members:
+    :show-inheritance:
+
+.. autoclass:: TensorInputTensorTargetCondition
+    :members:
+    :show-inheritance:
+
+.. autoclass:: TensorInputGraphTargetCondition
+    :members:
+    :show-inheritance:
+
+.. autoclass:: GraphInputTensorTargetCondition
+    :members:
+    :show-inheritance:
+
+.. autoclass:: GraphInputGraphTargetCondition
+    :members:
+    :show-inheritance:

docs/source/_rst/data/data_module.rst

@@ -0,0 +1,7 @@
+PinaDataModule
+======================
+.. currentmodule:: pina.data.data_module
+
+.. autoclass:: PinaDataModule
+    :members:
+    :show-inheritance:

docs/source/_rst/data/dataset.rst

@@ -0,0 +1,7 @@
+PinaDataset
+======================
+.. currentmodule:: pina.data.dataset
+
+.. autoclass:: PinaDataset
+    :members:
+    :show-inheritance:

docs/source/_rst/domain/cartesian.rst

@@ -1,8 +1,8 @@
 CartesianDomain
 ======================
-.. currentmodule:: pina.geometry.cartesian
+.. currentmodule:: pina.domain.cartesian
 
-.. automodule:: pina.geometry.cartesian
+.. automodule:: pina.domain.cartesian
 
 .. autoclass:: CartesianDomain
     :members:

docs/source/_rst/domain/difference_domain.rst

@@ -1,8 +1,8 @@
 Difference
 ======================
-.. currentmodule:: pina.geometry.difference_domain
+.. currentmodule:: pina.domain.difference_domain
 
-.. automodule:: pina.geometry.difference_domain
+.. automodule:: pina.domain.difference_domain
 
 .. autoclass:: Difference
     :members:

docs/source/_rst/domain/domain.rst

@@ -0,0 +1,9 @@
+Domain
+===========
+.. currentmodule:: pina.domain.domain_interface
+
+.. automodule:: pina.domain.domain_interface
+
+.. autoclass:: Domain
+    :members:
+    :show-inheritance:

docs/source/_rst/domain/ellipsoid.rst

@@ -1,8 +1,8 @@
 EllipsoidDomain
 ======================
-.. currentmodule:: pina.geometry.ellipsoid
+.. currentmodule:: pina.domain.ellipsoid
 
-.. automodule:: pina.geometry.ellipsoid
+.. automodule:: pina.domain.ellipsoid
 
 .. autoclass:: EllipsoidDomain
     :members:

docs/source/_rst/domain/exclusion_domain.rst

@@ -1,8 +1,8 @@
 Exclusion
 ======================
-.. currentmodule:: pina.geometry.exclusion_domain
+.. currentmodule:: pina.domain.exclusion_domain
 
-.. automodule:: pina.geometry.exclusion_domain
+.. automodule:: pina.domain.exclusion_domain
 
 .. autoclass:: Exclusion
     :members:

docs/source/_rst/domain/intersection_domain.rst

@@ -1,8 +1,8 @@
 Intersection
 ======================
-.. currentmodule:: pina.geometry.intersection_domain
+.. currentmodule:: pina.domain.intersection_domain
 
-.. automodule:: pina.geometry.intersection_domain
+.. automodule:: pina.domain.intersection_domain
 
 .. autoclass:: Intersection
     :members:

docs/source/_rst/domain/operation_interface.rst

@@ -1,8 +1,8 @@
 OperationInterface
 ======================
-.. currentmodule:: pina.geometry.operation_interface
+.. currentmodule:: pina.domain.operation_interface
 
-.. automodule:: pina.geometry.operation_interface
+.. automodule:: pina.domain.operation_interface
 
 .. autoclass:: OperationInterface
     :members:

docs/source/_rst/domain/simplex.rst

@@ -1,8 +1,8 @@
 SimplexDomain
 ======================
-.. currentmodule:: pina.geometry.simplex
+.. currentmodule:: pina.domain.simplex
 
-.. automodule:: pina.geometry.simplex
+.. automodule:: pina.domain.simplex
 
 .. autoclass:: SimplexDomain
     :members:

docs/source/_rst/domain/union_domain.rst

@@ -1,8 +1,8 @@
 Union
 ======================
-.. currentmodule:: pina.geometry.union_domain
+.. currentmodule:: pina.domain.union_domain
 
-.. automodule:: pina.geometry.union_domain
+.. automodule:: pina.domain.union_domain
 
 .. autoclass:: Union
     :members:

docs/source/_rst/geometry/location.rst

@@ -1,9 +0,0 @@
-Location
-====================
-.. currentmodule:: pina.geometry.location
-
-.. automodule:: pina.geometry.location
-
-.. autoclass:: Location
-    :members:
-    :show-inheritance:

docs/source/_tutorial.rst

@@ -9,10 +9,10 @@ Getting started with PINA
    :maxdepth: 3
    :titlesonly:
 
-   Introduction to PINA for Physics Informed Neural Networks training <tutorials/tutorial1/tutorial.rst>
-   Introduction to PINA Equation class <tutorials/tutorial12/tutorial.rst>
-   PINA and PyTorch Lightning, training tips and visualizations <tutorials/tutorial11/tutorial.rst>
-   Building custom geometries with PINA Location class <tutorials/tutorial6/tutorial.rst>
+   `Introduction to PINA for Physics Informed Neural Networks training <tutorials/tutorial1/tutorial.html>`_
+   `Introduction to PINA Equation class <tutorials/tutorial12/tutorial.html>`_
+   `PINA and PyTorch Lightning, training tips and visualizations <tutorials/tutorial11/tutorial.html>`_
+   `Building custom geometries with PINA Location class <tutorials/tutorial6/tutorial.html>`_
 
 
 Physics Informed Neural Networks
@@ -21,11 +21,11 @@ Physics Informed Neural Networks
    :maxdepth: 3
    :titlesonly:
 
-   Two dimensional Poisson problem using Extra Features Learning<tutorials/tutorial2/tutorial.rst>
-   Two dimensional Wave problem with hard constraint<tutorials/tutorial3/tutorial.rst>
-   Resolution of a 2D Poisson inverse problem<tutorials/tutorial7/tutorial.rst>
-   Periodic Boundary Conditions for Helmotz Equation<tutorials/tutorial9/tutorial.rst>
-   Multiscale PDE learning with Fourier Feature Network<tutorials/tutorial13/tutorial.rst>
+   `Two dimensional Poisson problem using Extra Features Learning <tutorials/tutorial2/tutorial.html>`_
+   `Two dimensional Wave problem with hard constraint <tutorials/tutorial3/tutorial.html>`_
+   `Resolution of a 2D Poisson inverse problem <tutorials/tutorial7/tutorial.html>`_
+   `Periodic Boundary Conditions for Helmotz Equation <tutorials/tutorial9/tutorial.html>`_
+   `Multiscale PDE learning with Fourier Feature Network <tutorials/tutorial13/tutorial.html>`_
 
 Neural Operator Learning
 ------------------------
@@ -33,8 +33,8 @@ Neural Operator Learning
    :maxdepth: 3
    :titlesonly:
 
-   Two dimensional Darcy flow using the Fourier Neural Operator<tutorials/tutorial5/tutorial.rst>
-   Time dependent Kuramoto Sivashinsky equation using the Averaging Neural Operator<tutorials/tutorial10/tutorial.rst>
+   `Two dimensional Darcy flow using the Fourier Neural Operator <tutorials/tutorial5/tutorial.html>`_
+   `Time dependent Kuramoto Sivashinsky equation using the Averaging Neural Operator <tutorials/tutorial10/tutorial.html>`_
 
 Supervised Learning
 -------------------
@@ -42,5 +42,5 @@ Supervised Learning
    :maxdepth: 3
    :titlesonly:
 
-   Unstructured convolutional autoencoder via continuous convolution<tutorials/tutorial4/tutorial.rst>
-   POD-RBF and POD-NN for reduced order modeling<tutorials/tutorial8/tutorial.rst>
+   `Unstructured convolutional autoencoder via continuous convolution <tutorials/tutorial4/tutorial.html>`_
+   `POD-RBF and POD-NN for reduced order modeling <tutorials/tutorial8/tutorial.html>`_