update doc

docs/source/_rst/_code.rst

@@ -11,11 +11,11 @@ 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 `Domains`_, or load high level simulation results as :doc:`LabelTensor <label_tensor>`
+    1. Define the `Problems`_ the user aim to solve
+    2. Generate data using built in `Geometrical 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 <solver/solver_interface>`
-    5. Train the model with the PINA :doc:`Trainer <solver/solver_interface>`, enhance the train with `Callback`_
+    5. Train the model with the PINA :doc:`Trainer <solver/solver_interface>`, enhance the train with `Callbacks`_
 
 
 Trainer, Dataset and Datamodule
@@ -34,6 +34,7 @@ Data Types
 
     LabelTensor <label_tensor.rst>
     Graph <graph/graph.rst>
+    LabelBatch <graph/label_batch.rst>
 
 
 Graphs Structures
@@ -41,7 +42,6 @@ Graphs Structures
 .. toctree::
     :titlesonly:
 
-    Graph <graph/graph.rst>
     GraphBuilder <graph/graph_builder.rst>
     RadiusGraph <graph/radius_graph.rst>
     KNNGraph <graph/knn_graph.rst>
@@ -98,7 +98,8 @@ Models
     FNO <model/fourier_neural_operator.rst>
     AveragingNeuralOperator <model/average_neural_operator.rst>
     LowRankNeuralOperator <model/low_rank_neural_operator.rst>
-    GraphNeuralOperator <model/>
+    GraphNeuralOperator <model/graph_neural_operator.rst>
+    GraphNeuralKernel <model/graph_neural_operator_integral_kernel.rst>
 
 Blocks
 -------------
@@ -112,7 +113,10 @@ Blocks
     Fourier Block <model/block/fourier_block.rst>
     Averaging Block <model/block/average_neural_operator_block.rst>
     Low Rank Block <model/block/low_rank_block.rst>
+    Graph Neural Operator Block <model/block/gno_block.rst>
+    Continuous Convolution Interface <model/block/convolution_interface.rst>
     Continuous Convolution Block <model/block/convolution.rst>
+    Orthogonal Block <model/block/orthogonal.rst>
 
 
 Reduction and Embeddings
@@ -144,7 +148,7 @@ Adaptive Activation Functions
 .. toctree::
     :titlesonly:
 
-    Adaptive Function Interface <adaptive_function/AdaptiveFunctionInterface.rst>
+    Adaptive Function Interface <adaptive_function/AdaptiveActivationFunctionInterface.rst>
     Adaptive ReLU <adaptive_function/AdaptiveReLU.rst>
     Adaptive Sigmoid <adaptive_function/AdaptiveSigmoid.rst>
     Adaptive Tanh <adaptive_function/AdaptiveTanh.rst>
@@ -165,10 +169,10 @@ Equations and Differential Operators
 .. toctree::
     :titlesonly:
 
-    EquationInterface <equation.equation_interface.rst>
-    Equation <equation.equation.rst>
-    SystemEquation <equation.system_equation.rst>
-    Equation Factory <equation.equation_factory.rst>
+    EquationInterface <equation/equation_interface.rst>
+    Equation <equation/equation.rst>
+    SystemEquation <equation/system_equation.rst>
+    Equation Factory <equation/equation_factory.rst>
     Differential Operators <operator.rst>
 
 
@@ -200,7 +204,7 @@ Problems Zoo
 
 
 Geometrical Domains
----------------------
+--------------------
 
 .. toctree::
     :titlesonly:
@@ -222,8 +226,8 @@ Domain Operations
     Difference <domain/difference_domain.rst>
     Exclusion <domain/exclusion_domain.rst>
 
-Callback
---------------------
+Callbacks
+-----------
 
 .. toctree::
     :titlesonly:

docs/source/_rst/adaptive_function/AdaptiveActivationFunctionInterface.rst

@@ -3,6 +3,6 @@ AdaptiveActivationFunctionInterface
 
 .. currentmodule:: pina.adaptive_function.adaptive_function_interface
 
-.. automodule:: pina.adaptive_function.adaptive_functiontion_interface
+.. automodule:: pina.adaptive_function.adaptive_function_interface
     :members:
     :show-inheritance:

docs/source/_rst/callback/processing_callback.rst

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

docs/source/_rst/domain/domain.rst

@@ -4,6 +4,6 @@ Domain
 
 .. automodule:: pina.domain.domain_interface
 
-.. autoclass:: Domain
+.. autoclass:: DomainInterface
     :members:
     :show-inheritance:

docs/source/_rst/graph/label_batch.rst

@@ -0,0 +1,9 @@
+LabelBatch
+===========
+.. currentmodule:: pina.graph
+
+
+.. autoclass:: LabelBatch
+   :members:
+   :private-members:
+   :show-inheritance:

docs/source/_rst/model/block/convolution_interface.rst

@@ -0,0 +1,8 @@
+Continuous Convolution Interface
+==================================
+.. currentmodule:: pina.model.block.convolution
+
+.. autoclass:: BaseContinuousConv
+    :members:
+    :show-inheritance:
+    :noindex:

docs/source/_rst/model/fourier_integral_kernel.rst

@@ -1,6 +1,6 @@
 FourierIntegralKernel
 =========================
-.. currentmodule:: pina.model.fno
+.. currentmodule:: pina.model.fourier_neural_operator
 
 .. autoclass:: FourierIntegralKernel
    :members:

docs/source/_rst/model/graph_neural_operator_integral_kernel.rst

@@ -0,0 +1,7 @@
+GraphNeuralKernel
+=======================
+.. currentmodule:: pina.model.graph_neural_operator
+
+.. autoclass:: GraphNeuralKernel
+   :members:
+   :show-inheritance:

docs/source/_rst/solver/physic_informed_solver/causal_pinn.rst

@@ -1,6 +1,6 @@
 CausalPINN
 ==============
-.. currentmodule:: pina.solver.physic_informed_solver.causalpinn
+.. currentmodule:: pina.solver.physic_informed_solver.causal_pinn
 
 .. autoclass:: CausalPINN
    :members:

docs/source/_rst/solver/physic_informed_solver/rba_pinn.rst

@@ -1,6 +1,6 @@
 RBAPINN
 ========
-.. currentmodule:: pina.solver.physic_informed_solver.rbapinn
+.. currentmodule:: pina.solver.physic_informed_solver.rba_pinn
 
 .. autoclass:: RBAPINN
    :members:

docs/source/_tutorial.rst

@@ -1,46 +1,35 @@
 PINA Tutorials
-==============
+======================
+
 
 In this folder we collect useful tutorials in order to understand the principles and the potential of **PINA**.
 
 Getting started with PINA
 -------------------------
-.. toctree::
-   :maxdepth: 3
-   :titlesonly:
 
-   `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>`_
+- `Introduction to PINA for Physics Informed Neural Networks training <tutorial1/tutorial.html>`_
+- `Introduction to PINA Equation class <tutorial12/tutorial.html>`_
+- `PINA and PyTorch Lightning, training tips and visualizations <tutorial11/tutorial.html>`_
+- `Building custom geometries with PINA Location class <tutorial6/tutorial.html>`_
 
 
 Physics Informed Neural Networks
 --------------------------------
-.. toctree::
-   :maxdepth: 3
-   :titlesonly:
 
-   `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>`_
+- `Two dimensional Poisson problem using Extra Features Learning <tutorial2/tutorial.html>`_
+- `Two dimensional Wave problem with hard constraint <tutorial3/tutorial.html>`_
+- `Resolution of a 2D Poisson inverse problem <tutorial7/tutorial.html>`_
+- `Periodic Boundary Conditions for Helmotz Equation <tutorial9/tutorial.html>`_
+- `Multiscale PDE learning with Fourier Feature Network <tutorial13/tutorial.html>`_
 
 Neural Operator Learning
 ------------------------
-.. toctree::
-   :maxdepth: 3
-   :titlesonly:
 
-   `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>`_
+- `Two dimensional Darcy flow using the Fourier Neural Operator <tutorial5/tutorial.html>`_
+- `Time dependent Kuramoto Sivashinsky equation using the Averaging Neural Operator <tutorial10/tutorial.html>`_
 
 Supervised Learning
 -------------------
-.. toctree::
-   :maxdepth: 3
-   :titlesonly:
 
-   `Unstructured convolutional autoencoder via continuous convolution <tutorials/tutorial4/tutorial.html>`_
-   `POD-RBF and POD-NN for reduced order modeling <tutorials/tutorial8/tutorial.html>`_
+- `Unstructured convolutional autoencoder via continuous convolution <tutorial4/tutorial.html>`_
+- `POD-RBF and POD-NN for reduced order modeling <tutorial8/tutorial.html>`_

docs/source/conf.py

@@ -19,84 +19,84 @@ import importlib.metadata
 
 
 # -- Project information -----------------------------------------------------
-_DISTRIBUTION_METADATA = importlib.metadata.metadata('pina-mathlab')
-project = _DISTRIBUTION_METADATA['Name']
-copyright = _DISTRIBUTION_METADATA['License-File']
-author = "PINA contributors"
-version = _DISTRIBUTION_METADATA['Version']
+_DISTRIBUTION_METADATA = importlib.metadata.metadata("pina-mathlab")
+project = _DISTRIBUTION_METADATA["Name"]
+copyright = _DISTRIBUTION_METADATA["License-File"]
+author = "PINA Contributors"
+version = _DISTRIBUTION_METADATA["Version"]
 
 
-sys.path.insert(0, os.path.abspath('../sphinx_extensions')) # extension to remove paramref link from lightinig
+sys.path.insert(
+    0, os.path.abspath("../sphinx_extensions")
+)
 
 # -- General configuration ------------------------------------------------
 
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.doctest',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.todo',
-    'sphinx.ext.coverage',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.intersphinx',
-    'paramref_extension',    # this extension is made to remove paramref links from lightining doc
-    'sphinx_copybutton', 
-    'sphinx_design'
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.doctest",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.intersphinx",
+    "paramref_extension",  # this extension is made to remove paramref links from lightining doc
+    "sphinx_copybutton",
+    "sphinx_design",
 ]
 
-# The root document.
-root_doc = 'index'
-
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'docstrings', 'nextgen', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["build", "docstrings", "nextgen", "Thumbs.db", ".DS_Store"]
 
 # The reST default role (used for this markup: `text`) to use for all documents.
-#default_role = 'literal'
+# default_role = 'literal'
 
 # Generate the API documentation when building
 autosummary_generate = True
 numpydoc_show_class_members = False
 
 intersphinx_mapping = {
-    'python': ('http://docs.python.org/3', None),
-    'matplotlib': ('https://matplotlib.org/stable', None),
-    'torch': ('https://pytorch.org/docs/stable/', None), 
-    'lightning.pytorch': ("https://lightning.ai/docs/pytorch/stable/", None),
-    }
+    "python": ("http://docs.python.org/3", None),
+    "matplotlib": ("https://matplotlib.org/stable", None),
+    "torch": ("https://pytorch.org/docs/stable/", None),
+    "lightning.pytorch": ("https://lightning.ai/docs/pytorch/stable/", None),
+    "torch_geometric": (
+        "https://pytorch-geometric.readthedocs.io/en/latest/",
+        None,
+    ),
+}
 
-nitpicky = True
-nitpick_ignore = [
-    # ('py:meth', 'lightning.pytorch.core.module.LightningModule.log'),
-    # ('py:meth', 'lightning.pytorch.core.module.LightningModule.log_dict'),
-    # ('py:exc', 'MisconfigurationException'),
-    # ('py:func', 'torch.inference_mode'),
-    # ('py:func', 'torch.no_grad'),
-    # ('py:class', 'torch.utils.data.DistributedSampler'),
-    # ('py:class', 'pina.model.layers.convolution.BaseContinuousConv'),
-    # ('py:class', 'Module'),
-    # ('py:class', 'torch.nn.modules.loss._Loss'), # TO FIX
-    # ('py:class', 'torch.optim.LRScheduler'), # TO FIX 
-
-    ]
+# nitpicky = True
+# nitpick_ignore = [
+#     ("py:meth", "lightning.pytorch.core.module.LightningModule.log"),
+#     ("py:meth", "lightning.pytorch.core.module.LightningModule.log_dict"),
+#     ("py:exc", "MisconfigurationException"),
+#     ("py:func", "torch.inference_mode"),
+#     ("py:func", "torch.no_grad"),
+#     ("py:class", "torch.utils.data.DistributedSampler"),
+#     ("py:class", "pina.model.layers.convolution.BaseContinuousConv"),
+#     ("py:class", "Module"),
+#     ("py:class", "torch.nn.modules.loss._Loss"),  # TO FIX
+#     ("py:class", "torch.optim.LRScheduler"),  # TO FIX
+# ]
 
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-# source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # autoclass
-autoclass_content = 'both'
+autoclass_content = "both"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -108,7 +108,7 @@ release = version
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = 'en'
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -122,7 +122,7 @@ add_function_parentheses = True
 add_module_names = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sortins as "systems = False
 
@@ -143,7 +143,7 @@ viewcode_import = True
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'pydata_sphinx_theme'
+html_theme = "pydata_sphinx_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -151,7 +151,7 @@ html_theme = 'pydata_sphinx_theme'
 # html_theme_options = {}
 
 # Add any paths that contain custom themes here, relative to this directory.
-html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+# html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
@@ -162,7 +162,7 @@ html_theme_options = {
             "name": "GitHub",
             "url": "https://github.com/mathLab/PINA",
             "icon": "fab fa-github",
-            "type": "fontawesome",    
+            "type": "fontawesome",
         },
         {
             "name": "Twitter",
@@ -172,7 +172,7 @@ html_theme_options = {
         },
         {
             "name": "Email",
-            "url": "mailto:pina.mathlab@gmail.com",  
+            "url": "mailto:pina.mathlab@gmail.com",
             "icon": "fas fa-envelope",
             "type": "fontawesome",
         },
@@ -185,7 +185,7 @@ html_theme_options = {
 
 # If not ''i, a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
-html_last_updated_fmt = '%b %d, %Y'
+html_last_updated_fmt = "%b %d, %Y"
 
 # If false, no index is generated.
 html_use_index = True
@@ -197,40 +197,52 @@ html_show_sourcelink = True
 html_show_copyright = True
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'pinadoc'
+htmlhelp_basename = "pinadoc"
+
+# Link to external html files
+html_extra_path = ["tutorials"]
+
+# Avoid side bar for html files
+html_sidebars = {
+    "_tutorial": [],
+    "_team": [],
+    "_cite": [],
+    "_contributing": [],
+    "_installation": [],
+    "_LICENSE": [],
+}
 
 # -- Options for LaTeX output ---------------------------------------------
 
 latex_elements = {
     # The paper size ('letterpaper' or 'a4paper').
-    'papersize': 'a4paper',
-
+    "papersize": "a4paper",
     # The font size ('10pt', '11pt' or '12pt').
-    'pointsize': '20pt',
-
+    "pointsize": "20pt",
     # Additional stuff for the LaTeX preamble.
-    'preamble': '',
-
+    "preamble": "",
     # Latex figure (float) alignment
-    'figure_align': 'htbp',
+    "figure_align": "htbp",
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-  (master_doc, 'pina.tex', u'PINA Documentation',
-   u'PINA contributors', 'manual'),
+    (
+        master_doc,
+        "pina.tex",
+        "PINA Documentation",
+        "PINA contributors",
+        "manual",
+    ),
 ]
 
 # -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'pina', u'PINA Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "pina", "PINA Documentation", [author], 1)]
 
 # -- Options for Texinfo output -------------------------------------------
 
@@ -238,11 +250,20 @@ man_pages = [
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  (master_doc, 'pina', u'PINA Documentation',
-   author, 'pina', 'One line description of project.',
-   'Miscellaneous'),
+    (
+        master_doc,
+        "pina",
+        "PINA Documentation",
+        author,
+        "pina",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
 
 # If true, do not generate a @detailmenu in the "Top" node's menu.
 # texinfo_no_detailmenu = False
-autodoc_member_order = 'bysource'
+autodoc_member_order = "bysource"
+
+# Do consider meth ending with _ (needed for in-place methods of torch)
+strip_signature_backslash = True

docs/source/index.rst

@@ -9,32 +9,32 @@ Welcome to PINA’s documentation!
   .. grid-item::
 
       .. image:: index_files/tutorial_13_3.png
-        :target: tutorials/tutorial2/tutorial.html
+        :target: tutorial2/tutorial.html
 
   .. grid-item::
 
       .. image:: index_files/tutorial_32_0.png
-        :target: tutorials/tutorial4/tutorial.html
+        :target: tutorial4/tutorial.html
 
   .. grid-item::
 
       .. image:: index_files/tutorial_13_01.png
-        :target: tutorials/tutorial9/tutorial.html
+        :target: tutorial9/tutorial.html
 
   .. grid-item::
 
       .. image:: index_files/tutorial_36_0.png
-        :target: tutorials/tutorial6/tutorial.html
+        :target: tutorial6/tutorial.html
 
   .. grid-item::
 
       .. image:: index_files/tutorial_15_0.png
-        :target: tutorials/tutorial13/tutorial.html
+        :target: tutorial13/tutorial.html
 
   .. grid-item::
 
       .. image:: index_files/tutorial_5_0.png
-        :target: tutorials/tutorial10/tutorial.html
+        :target: tutorial10/tutorial.html
 
 .. grid:: 1 1 3 3
 
@@ -45,7 +45,7 @@ Welcome to PINA’s documentation!
     an open-source Python library providing an intuitive interface for
     solving differential equations using PINNs, NOs or both together.
 
-    Based on `PyTorch <https://pytorch.org/>`_ and `PyTorchLightning <https://lightning.ai/docs/pytorch/stable/>`_, **PINA** offers a simple and intuitive way to formalize a specific (differential) problem
+    Based on `PyTorch <https://pytorch.org/>`_, `PyTorchLightning <https://lightning.ai/docs/pytorch/stable/>`_, and `PyG <https://pytorch-geometric.readthedocs.io/en/latest/>`_, **PINA** offers a simple and intuitive way to formalize a specific (differential) problem
     and solve it using neural networks . The approximated solution of a differential equation
     can be implemented using PINA in a few lines of code thanks to the intuitive and user-friendly  interface.        
 
@@ -63,9 +63,9 @@ Welcome to PINA’s documentation!
     .. toctree::
       :maxdepth: 1
 
-      Installing <_installation>
-      Tutorial <_tutorial>
       API <_rst/_code>
+      Tutorial <_tutorial>
+      Installing <_installation>
       Team & Foundings <_team.rst>
       Contributing <_contributing>
       License <_LICENSE.rst>

docs/sphinx_extensions/paramref_extension.py

@@ -1,11 +1,12 @@
 from docutils import nodes
 from docutils.parsers.rst.roles import register_local_role
 
+
 def paramref_role(name, rawtext, text, lineno, inliner, options={}, content=[]):
     # Simply replace :paramref: with :param:
     new_role = nodes.literal(text=text[1:])
     return [new_role], []
 
-def setup(app):
-    register_local_role('paramref', paramref_role)
 
+def setup(app):
+    register_local_role("paramref", paramref_role)