Updated the design and the logo in documentation

docs/source/_rst/_code.rst

@@ -93,6 +93,7 @@ Problem
     SpatialProblem <problem/spatialproblem.rst>
     TimeDependentProblem <problem/timedepproblem.rst>
     ParametricProblem <problem/parametricproblem.rst>
+    InverseProblem <problem/invproblem.rst>
 
 Geometries
 -----------------

docs/source/_rst/geometry/cartesian.rst

@@ -7,4 +7,3 @@ CartesianDomain
 .. autoclass:: CartesianDomain
     :members:
     :show-inheritance:
-    :noindex:

docs/source/_rst/geometry/ellipsoid.rst

@@ -7,4 +7,3 @@ EllipsoidDomain
 .. autoclass:: EllipsoidDomain
     :members:
     :show-inheritance:
-    :noindex:

docs/source/_rst/geometry/simplex.rst

@@ -7,4 +7,3 @@ SimplexDomain
 .. autoclass:: SimplexDomain
     :members:
     :show-inheritance:
-    :noindex:

docs/source/_rst/problem/invproblem.rst

@@ -0,0 +1,9 @@
+InverseProblem
+================
+.. currentmodule:: pina.problem.inverse_problem
+
+.. automodule:: pina.problem.inverse_problem
+
+.. autoclass:: InverseProblem
+    :members:
+    :show-inheritance:

docs/source/conf.py

@@ -15,13 +15,16 @@
 import sys
 import os
 import sphinx_rtd_theme
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0, os.path.abspath('../..'))
 import pina
 
+# -- Project information -----------------------------------------------------
+
+project = pina.__project__
+copyright = pina.__copyright__
+author = pina.__author__
+version = release ='1.0.0' 
+
+
 sys.path.insert(0, os.path.abspath('../sphinx_extensions')) # extension to remove paramref link from lightinig
 
 # -- General configuration ------------------------------------------------
@@ -51,6 +54,21 @@
     'sphinx_copybutton', 
 ]
 
+# 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']
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+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),
     # 'numpy': ('http://docs.scipy.org/doc/numpy/', None),
@@ -68,7 +86,6 @@
     ('py:func', 'torch.inference_mode'),
     ('py:func', 'torch.no_grad'),
     ('py:class', 'torch.utils.data.DistributedSampler'),
-    ('py:class', 'CartesianDomain'), # TO FIX
     ('py:class', 'pina.model.layers.convolution.BaseContinuousConv'),
     ('py:class', 'Module'),
     ('py:class', 'torch.nn.modules.loss._Loss'), # TO FIX
@@ -162,7 +179,7 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = "sphinx_rtd_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
@@ -181,12 +198,32 @@
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-html_logo = "index_files/pina_logo.png"
+html_logo = "index_files/pina_logo_pina.png"
 html_theme_options = {
-    'logo_only': True,
-    'display_version': True,
-    'prev_next_buttons_location': 'bottom',
-
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/mathLab/PINA",
+            "icon": "fab fa-github",
+            "type": "fontawesome",
+        },
+        {
+            "name": "StackOverflow",
+            "url": "https://github.com/mathLab/PINA",
+            "icon": "fab fa-stack-overflow",
+            "type": "fontawesome",
+        },
+        {
+            "name": "Twitter",
+            "url": "http://twitter.com/rozzagroup",
+            "icon": "fab fa-twitter",
+            "type": "fontawesome",
+        },
+    ],
+    "show_prev_next": False,
+    "navbar_start": ["navbar-logo"],
+    "navbar_end": ["navbar-icon-links"],
+    "header_links_before_dropdown": 8,
 }
 
 # The name of an image file (within the static path) to use as favicon of the
@@ -195,8 +232,7 @@
 # html_favicon = None
 
 # Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
+# relative to this directory. They are copied after the builtin static files,# so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
 
 # Add any extra paths that contain custom files (such as robots.txt or
@@ -342,4 +378,4 @@
 
 # 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'

docs/source/index.rst

@@ -1,6 +1,11 @@
 Welcome to PINA's documentation!
 ===================================================
 
+.. figure:: index_files/API_color.png
+    :alt: PINA application program interface
+    :align: center
+    :width: 700
+
 Physics Informed Neural network for Advanced modeling (**PINA**) is
 an open-source Python library providing an intuitive interface for
 solving differential equations using PINNs, NOs or both together.
@@ -19,32 +24,6 @@ underlying code.
 The high-level structure of the package is depicted in our API. The pipeline to solve differential equations
 with PINA follows just five steps: problem definition, model selection, data generation, solver selection, and training.
 
-.. figure:: index_files/API_color.png
-    :alt: PINA application program interface
-    :align: center
-    :width: 600
-
-|
-
-Physics-informed neural network
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-`PINN <https://www.sciencedirect.com/science/article/abs/pii/S0021999118307125>`_ is a novel approach that
-involves neural networks to solve differential equations in an unsupervised manner, while respecting
-any given law of physics described by general differential equations. Proposed in "*Physics-informed neural
-networks: A deep learning framework for solving forward and inverse problems
-involving nonlinear partial differential equations*", such framework aims to
-solve problems in a continuous and nonlinear settings. 
-
-Neural operator learning
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-`Neural Operators <https://www.jmlr.org/papers/v24/21-1524.html>`_ is a novel approach involving neural networks
-to learn differential operators using supervised learning strategies. By learning the differential operator, the
-neural network is able to generalize across different instances of the differential equations (e.g. different forcing
-terms), without the need of re-training. 
-
-
 
 .. toctree::
    :maxdepth: 1
@@ -70,4 +49,4 @@ terms), without the need of re-training.
     Team & Foundings <_team.rst>
     Contributing <_rst/_contributing>
     License <_LICENSE.rst>
-    Cite PINA <_cite.rst>
+    Cite PINA <_cite.rst>

pina/condition.py

@@ -14,7 +14,7 @@ class Condition:
     """
     The class ``Condition`` is used to represent the constraints (physical
     equations, boundary conditions, etc.) that should be satisfied in the
-    problem at hand. Condition objects are used to formulate the PINA :obj:`pina.problem.abstract_problem.AbstractProblem` object.
+    problem at hand. Condition objects are used to formulate the PINA :class:`~pina.problem.abstract_problem.AbstractProblem` object.
     Conditions can be specified in three ways:
 
         1. By specifying the input and output points of the condition; in such a

pina/geometry/cartesian.py

@@ -39,9 +39,9 @@ def variables(self):
         return list(self.fixed_.keys()) + list(self.range_.keys())
 
     def update(self, new_domain):
-        """Adding new dimensions on the ``CartesianDomain``
+        """Adding new dimensions on the :class:`~pina.geometry.cartesian.CartesianDomain`
 
-        :param CartesianDomain new_domain: A new ``CartesianDomain`` object to merge
+        :param CartesianDomain new_domain: A new :class:`~pina.geometry.cartesian.CartesianDomain` object to merge
 
         :Example:
             >>> spatial_domain = CartesianDomain({'x': [0, 1], 'y': [0, 1]})
@@ -103,7 +103,7 @@ def sample(self, n, mode="random", variables="all"):
         :type mode: str
         :param variables: pinn variable to be sampled, defaults to ``all``.
         :type variables: str | list[str]
-        :return: Returns ``LabelTensor`` of n sampled points.
+        :return: Returns :class:`~pina.label_tensor.LabelTensor` of n sampled points.
         :rtype: LabelTensor
 
         .. note::

pina/geometry/difference_domain.py

@@ -20,7 +20,7 @@ def __init__(self, geometries):
         the dimension of the geometry space.
 
         :param list geometries: A list of geometries from ``pina.geometry``
-            such as ``EllipsoidDomain`` or ``CartesianDomain``. The first
+            such as :class:`~pina.geometry.ellipsoid.EllipsoidDomain` or :class:`~pina.geometry.cartesian.CartesianDomain`. The first
             geometry in the list is the geometry from which points are
             sampled. The rest of the geometries are the geometries that
             are excluded from the first geometry to find the difference.
@@ -36,7 +36,7 @@ def __init__(self, geometries):
 
     def is_inside(self, point, check_border=False):
         """
-        Check if a point is inside the ``Difference`` domain.
+        Check if a point is inside the :class:`~pina.geometry.difference_domain.Difference` domain.
 
         :param point: Point to be checked.
         :type point: torch.Tensor
@@ -51,13 +51,13 @@ def is_inside(self, point, check_border=False):
 
     def sample(self, n, mode="random", variables="all"):
         """
-        Sample routine for ``Difference`` domain.
+        Sample routine for :class:`~pina.geometry.difference_domain.Difference` domain.
 
         :param int n: Number of points to sample in the shape.
         :param str mode: Mode for sampling, defaults to ``random``. Available modes include: ``random``.
         :param variables: Variables to be sampled, defaults to ``all``.
         :type variables: str | list[str]
-        :return: Returns ``LabelTensor`` of n sampled points.
+        :return: Returns :class:`~pina.label_tensor.LabelTensor` of n sampled points.
         :rtype: LabelTensor
 
         :Example:

pina/geometry/ellipsoid.py

@@ -202,7 +202,7 @@ def sample(self, n, mode="random", variables="all"):
         :param str mode: Mode for sampling, defaults to ``random``. Available modes include: ``random``.
         :param variables: Variables to be sampled, defaults to ``all``.
         :type variables: str | list[str]
-        :return: Returns ``LabelTensor`` of n sampled points.
+        :return: Returns :class:`~pina.label_tensor.LabelTensor` of n sampled points.
         :rtype: LabelTensor
 
         :Example:

pina/geometry/exclusion_domain.py

@@ -21,7 +21,7 @@ def __init__(self, geometries):
         the dimension of the geometry space.
 
         :param list geometries: A list of geometries from ``pina.geometry``
-            such as ``EllipsoidDomain`` or ``CartesianDomain``.
+            such as :class:`~pina.geometry.ellipsoid.EllipsoidDomain` or :class:`~pina.geometry.cartesian.CartesianDomain`.
 
         :Example:
             >>> # Create two ellipsoid domains
@@ -34,7 +34,7 @@ def __init__(self, geometries):
 
     def is_inside(self, point, check_border=False):
         """
-        Check if a point is inside the ``Exclusion`` domain.
+        Check if a point is inside the :class:`~pina.geometry.exclusion_domain.Exclusion` domain.
 
         :param point: Point to be checked.
         :type point: torch.Tensor
@@ -50,13 +50,13 @@ def is_inside(self, point, check_border=False):
 
     def sample(self, n, mode="random", variables="all"):
         """
-        Sample routine for ``Exclusion`` domain.
+        Sample routine for :class:`~pina.geometry.exclusion_domain.Exclusion` domain.
 
         :param int n: Number of points to sample in the shape.
         :param str mode: Mode for sampling, defaults to ``random``. Available modes include: ``random``.
         :param variables: Variables to be sampled, defaults to ``all``.
         :type variables: str | list[str]
-        :return: Returns ``LabelTensor`` of n sampled points.
+        :return: Returns :class:`~pina.label_tensor.LabelTensor` of n sampled points.
         :rtype: LabelTensor
 
         :Example:

pina/geometry/intersection_domain.py

@@ -21,7 +21,7 @@ def __init__(self, geometries):
         the dimension of the geometry space.
 
         :param list geometries: A list of geometries from ``pina.geometry``
-            such as ``EllipsoidDomain`` or ``CartesianDomain``. The intersection
+            such as :class:`~pina.geometry.ellipsoid.EllipsoidDomain` or :class:`~pina.geometry.cartesian.CartesianDomain`. The intersection
             will be taken between all the geometries in the list. The resulting
             geometry will be the intersection of all the geometries in the list.
 
@@ -36,7 +36,7 @@ def __init__(self, geometries):
 
     def is_inside(self, point, check_border=False):
         """
-        Check if a point is inside the ``Intersection`` domain.
+        Check if a point is inside the :class:`~pina.geometry.intersection_domain.Intersection` domain.
 
         :param point: Point to be checked.
         :type point: torch.Tensor
@@ -52,13 +52,13 @@ def is_inside(self, point, check_border=False):
 
     def sample(self, n, mode="random", variables="all"):
         """
-        Sample routine for ``Intersection`` domain.
+        Sample routine for :class:`~pina.geometry.intersection_domain.Intersection` domain.
 
         :param int n: Number of points to sample in the shape.
         :param str mode: Mode for sampling, defaults to ``random``. Available modes include: ``random``.
         :param variables: Variables to be sampled, defaults to ``all``.
         :type variables: str | list[str]
-        :return: Returns ``LabelTensor`` of n sampled points.
+        :return: Returns :class:`~pina.label_tensor.LabelTensor` of n sampled points.
         :rtype: LabelTensor
 
         :Example:

pina/geometry/operation_interface.py

@@ -12,7 +12,7 @@ def __init__(self, geometries):
         Abstract set operation class. Any geometry operation entity must inherit from this class.
 
         :param list geometries: A list of geometries from ``pina.geometry``
-            such as ``EllipsoidDomain`` or ``CartesianDomain``.
+            such as :class:`~pina.geometry.ellipsoid.EllipsoidDomain` or :class:`~pina.geometry.cartesian.CartesianDomain`.
         """
         # check consistency geometries
         check_consistency(geometries, Location)

pina/geometry/simplex.py

@@ -222,7 +222,7 @@ def sample(self, n, mode="random", variables="all"):
         :param str mode: Mode for sampling, defaults to ``random``. Available modes include: ``random``.
         :param variables: Variables to be sampled, defaults to ``all``.
         :type variables: str | list[str]
-        :return: Returns ``LabelTensor`` of n sampled points.
+        :return: Returns :class:`~pina.label_tensor.LabelTensor` of n sampled points.
         :rtype: LabelTensor
 
         .. warning::

pina/geometry/union_domain.py

@@ -21,7 +21,7 @@ def __init__(self, geometries):
         the dimension of the geometry space.
 
         :param list geometries: A list of geometries from ``pina.geometry``
-            such as ``EllipsoidDomain`` or ``CartesianDomain``.
+            such as :class:`~pina.geometry.ellipsoid.EllipsoidDomain` or :class:`~pina.geometry.cartesian.CartesianDomain`.
 
         :Example:
             >>> # Create two ellipsoid domains
@@ -35,7 +35,7 @@ def __init__(self, geometries):
 
     def is_inside(self, point, check_border=False):
         """
-        Check if a point is inside the ``Union`` domain.
+        Check if a point is inside the :class:`~pina.geometry.union_domain.Union` domain.
 
         :param point: Point to be checked.
         :type point: LabelTensor
@@ -52,13 +52,13 @@ def is_inside(self, point, check_border=False):
 
     def sample(self, n, mode="random", variables="all"):
         """
-        Sample routine for ``Union`` domain.
+        Sample routine for :class:`~pina.geometry.union_domain.Union` domain.
 
         :param int n: Number of points to sample in the shape.
         :param str mode: Mode for sampling, defaults to ``random``. Available modes include: ``random``.
         :param variables: Variables to be sampled, defaults to ``all``.
         :type variables: str | list[str]
-        :return: Returns ``LabelTensor`` of n sampled points.
+        :return: Returns :class:`~pina.label_tensor.LabelTensor` of n sampled points.
         :rtype: LabelTensor
 
         :Example: