revamp tutorial structure

docs/source/_static/custom.css

@@ -1,40 +1,12 @@
-/* Hero section */
-.hero {
-  text-align: center;
-  padding: 3rem 0;
-}
-.hero img {
-  max-width: 320px;
-}
-.hero .tagline {
-  font-size: 1.25rem;
-  color: var(--pst-color-text-muted);
-  margin: 1rem 0 2rem;
-}
-
-/* Feature cards — subtle lift on hover */
-.sd-card {
-  transition: transform 0.2s ease, box-shadow 0.2s ease;
-}
-.sd-card:hover {
-  transform: translateY(-2px);
-  box-shadow: 0 4px 12px rgba(0,0,0,0.1);
-}
-
-/* Card links — no underline */
-.sd-card a {
-  text-decoration: none;
+/* Keep the navigation consistent with the main PINA documentation. */
+.nav-link.nav-external::after {
+  display: none;
 }
 
-/* Hero buttons — always white text */
-.hero .btn {
-  color: #fff !important;
-}
-.hero .btn:hover {
-  color: #fff !important;
+.bd-content .toctree-wrapper > ul {
+  padding-left: 1.25rem;
 }
 
-/* Hide external-link icons in navigation tabs only. */
-.nav-link.nav-external::after {
-  display: none;
+.bd-content .toctree-wrapper li {
+  margin: 0.5rem 0;
 }

docs/source/_templates/external-nav.html

@@ -0,0 +1,7 @@
+<nav aria-label="{{ _('PINA links') }}">
+  <ul class="navbar-nav">
+    {% for link in theme_external_links %}
+    <li class="nav-item"><a class="nav-link nav-external" href="{{ link.url }}">{{ link.name }}</a></li>
+    {% endfor %}
+  </ul>
+</nav>

docs/source/_templates/global-sidebar-nav.html

@@ -0,0 +1,14 @@
+<nav class="bd-docs-nav bd-links" aria-label="{{ _('Tutorial navigation') }}">
+  <p class="bd-links__title" role="heading" aria-level="1">{{ _('Tutorial navigation') }}</p>
+  <div class="bd-toc-item navbar-nav">
+    {{ generate_toctree_html(
+      "sidebar",
+      startdepth=0,
+      show_nav_level=theme_show_nav_level | int,
+      maxdepth=theme_navigation_depth | int,
+      collapse=theme_collapse_navigation | tobool,
+      includehidden=theme_sidebar_includehidden | tobool,
+      titles_only=True
+    ) }}
+  </div>
+</nav>

docs/source/conf.py

@@ -36,13 +36,15 @@
     "sphinx.ext.coverage",
     "sphinx.ext.viewcode",
     "sphinx.ext.mathjax",
-    "sphinx.ext.intersphinx",
+    "sphinx_design",
+    "nbsphinx",
+    "nbsphinx_link",
 ]
 
 # 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", "**/.gitkeep"]
+exclude_patterns = ["build", "docstrings", "nextgen", "Thumbs.db", ".DS_Store", "**/.gitkeep", "guides/*/index.rst"]
 
 # The reST default role (used for this markup: `text`) to use for all documents.
 default_role = "literal"
@@ -66,7 +68,10 @@
 templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
-source_suffix = ".rst"
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.ipynb': 'jupyter_notebook',
+}
 
 # The master toctree document.
 master_doc = "index"
@@ -165,8 +170,13 @@
             "type": "fontawesome",
         },
     ],
-    "show_prev_next": False,
+    "show_prev_next": True,
+    "collapse_navigation": False,
+    "navigation_depth": 2,
+    "show_nav_level": 1,
+    "sidebar_includehidden": True,
     "navbar_start": ["navbar-logo"],
+    "navbar_center": ["external-nav"],
     "navbar_end": ["navbar-icon-links"],
     "header_links_before_dropdown": 5,
 }
@@ -191,16 +201,13 @@
 # Output file base name for HTML help builder.
 htmlhelp_basename = "pinatutorialsdoc"
 
-# Link to external html files
-html_extra_path = ["tutorials"]
+# Tutorial pages are Sphinx sources, not files to copy verbatim.
+html_extra_path = []
 
 html_static_path = ["_static"]
 html_css_files = ["custom.css"]
 
-# Avoid side bar for html files
-html_sidebars = {
-    "index": [],
-}
+html_sidebars = {"**": ["sidebar-collapse", "global-sidebar-nav"]}
 
 # -- Options for LaTeX output ---------------------------------------------
 
@@ -257,3 +264,14 @@
 
 # Do consider meth ending with _ (needed for in-place methods of torch)
 strip_signature_backslash = True
+
+# -- nbsphinx configuration ------------------------------------------------
+
+# Render outputs already saved in the notebooks without executing them.
+nbsphinx_execute = "never"
+
+# Custom CSS for notebooks
+nbsphinx_codecell_lexer = "python3"
+
+# Show link to source notebook
+nbsphinx_show_notebook_link = True

docs/source/guides/getting-started/index.rst

@@ -0,0 +1,15 @@
+Getting Started with PINA
+=========================
+
+Learn the core components of PINA.
+
+.. toctree::
+   :maxdepth: 1
+
+   tutorial17
+   tutorial16
+   tutorial18
+   tutorial11
+   tutorial19
+   tutorial6
+   tutorial12

docs/source/guides/getting-started/tutorial11.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/00-getting-started/tutorial11/tutorial.ipynb"}

docs/source/guides/getting-started/tutorial12.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/00-getting-started/tutorial12/tutorial.ipynb"}

docs/source/guides/getting-started/tutorial16.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/00-getting-started/tutorial16/tutorial.ipynb"}

docs/source/guides/getting-started/tutorial17.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/00-getting-started/tutorial17/tutorial.ipynb"}

docs/source/guides/getting-started/tutorial18.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/00-getting-started/tutorial18/tutorial.ipynb"}

docs/source/guides/getting-started/tutorial19.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/00-getting-started/tutorial19/tutorial.ipynb"}

docs/source/guides/getting-started/tutorial6.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/00-getting-started/tutorial6/tutorial.ipynb"}

docs/source/guides/neural-operators/index.rst

@@ -0,0 +1,12 @@
+Neural Operator Learning
+========================
+
+Learn mappings between function spaces with neural operators.
+
+.. toctree::
+   :maxdepth: 1
+
+   tutorial21
+   tutorial5
+   tutorial10
+   tutorial24

docs/source/guides/neural-operators/tutorial10.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/02-neural-operators/tutorial10/tutorial.ipynb", "extra-media":["../../../../tutorials/02-neural-operators/tutorial10/data"]}

docs/source/guides/neural-operators/tutorial21.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/02-neural-operators/tutorial21/tutorial.ipynb"}

docs/source/guides/neural-operators/tutorial24.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/02-neural-operators/tutorial24/tutorial.ipynb", "extra-media":["../../../../tutorials/02-neural-operators/tutorial24/data"]}

docs/source/guides/neural-operators/tutorial5.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/02-neural-operators/tutorial5/tutorial.ipynb", "extra-media":["../../../../tutorials/02-neural-operators/tutorial5/Data_Darcy.mat"]}

docs/source/guides/pinns/index.rst

@@ -0,0 +1,15 @@
+Physics Informed Neural Networks
+================================
+
+Solve forward and inverse problems with physics-informed neural networks.
+
+.. toctree::
+   :maxdepth: 1
+
+   tutorial1
+   tutorial2
+   tutorial3
+   tutorial9
+   tutorial7
+   tutorial13
+   tutorial14

docs/source/guides/pinns/tutorial1.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/01-pinns/tutorial1/tutorial.ipynb"}

docs/source/guides/pinns/tutorial13.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/01-pinns/tutorial13/tutorial.ipynb"}

docs/source/guides/pinns/tutorial14.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/01-pinns/tutorial14/tutorial.ipynb"}

docs/source/guides/pinns/tutorial2.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/01-pinns/tutorial2/tutorial.ipynb"}

docs/source/guides/pinns/tutorial3.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/01-pinns/tutorial3/tutorial.ipynb"}

docs/source/guides/pinns/tutorial7.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/01-pinns/tutorial7/tutorial.ipynb", "extra-media":["../../../../tutorials/01-pinns/tutorial7/data"]}

docs/source/guides/pinns/tutorial9.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/01-pinns/tutorial9/tutorial.ipynb"}

docs/source/guides/supervised-learning/index.rst

@@ -0,0 +1,14 @@
+Supervised Learning
+===================
+
+Explore data-driven models and reduced-order modeling.
+
+.. toctree::
+   :maxdepth: 1
+
+   tutorial20
+   tutorial15
+   tutorial22
+   tutorial23
+   tutorial4
+   tutorial8

docs/source/guides/supervised-learning/tutorial15.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/03-supervised-learning/tutorial15/tutorial.ipynb"}

docs/source/guides/supervised-learning/tutorial20.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/03-supervised-learning/tutorial20/tutorial.ipynb"}

docs/source/guides/supervised-learning/tutorial22.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/03-supervised-learning/tutorial22/tutorial.ipynb", "extra-media":["../../../../tutorials/03-supervised-learning/tutorial22/holed_poisson.pt"]}

docs/source/guides/supervised-learning/tutorial23.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/03-supervised-learning/tutorial23/tutorial.ipynb"}

docs/source/guides/supervised-learning/tutorial4.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/03-supervised-learning/tutorial4/tutorial.ipynb"}

docs/source/guides/supervised-learning/tutorial8.nblink

@@ -0,0 +1 @@
+{"path":"../../../../tutorials/03-supervised-learning/tutorial8/tutorial.ipynb"}

docs/source/index.rst

@@ -1,54 +1,50 @@
-Welcome to the PINA Tutorials
-========================================
-
-This site collects step-by-step tutorials to help you understand the principles and potential of **PINA**.
-Whether you are just getting started or looking to deepen your understanding, these resources will guide you.
-
-For installation instructions and API documentation, visit the
-`PINA documentation <https://PINA-org.github.io/PINA/>`_.
-
-Getting started with PINA
-----------------------------------------
-
-- `Introductory Tutorial: A Beginner's Guide to PINA <https://PINA-org.github.io/PINA-Tutorials/tutorial17/tutorial.html>`_
-- `How to build a Problem in PINA <https://PINA-org.github.io/PINA-Tutorials/tutorial16/tutorial.html>`_
-- `Introduction to Solver classes <https://PINA-org.github.io/PINA-Tutorials/tutorial18/tutorial.html>`_
-- `Introduction to Trainer class <https://PINA-org.github.io/PINA-Tutorials/tutorial11/tutorial.html>`_
-- `Data structure for SciML: Tensor, LabelTensor, Data and Graph <https://PINA-org.github.io/PINA-Tutorials/tutorial19/tutorial.html>`_
-- `Building domains with PINA's BaseDomain class <https://PINA-org.github.io/PINA-Tutorials/tutorial6/tutorial.html>`_
-- `Introduction to PINA Equation class <https://PINA-org.github.io/PINA-Tutorials/tutorial12/tutorial.html>`_
-
-Physics Informed Neural Networks
---------------------------------
-
-- `Introductory Tutorial: Physics Informed Neural Networks with PINA <https://PINA-org.github.io/PINA-Tutorials/tutorial1/tutorial.html>`_
-- `Enhancing PINNs with Extra Features to solve the Poisson Problem <https://PINA-org.github.io/PINA-Tutorials/tutorial2/tutorial.html>`_
-- `Applying Hard Constraints in PINNs to solve the Wave Problem <https://PINA-org.github.io/PINA-Tutorials/tutorial3/tutorial.html>`_
-- `Applying Periodic Boundary Conditions in PINNs to solve the Helmholtz Problem <https://PINA-org.github.io/PINA-Tutorials/tutorial9/tutorial.html>`_
-- `Inverse Problem Solving with Physics-Informed Neural Network <https://PINA-org.github.io/PINA-Tutorials/tutorial7/tutorial.html>`_
-- `Learning Multiscale PDEs Using Fourier Feature Networks <https://PINA-org.github.io/PINA-Tutorials/tutorial13/tutorial.html>`_
-- `Learning Bifurcating PDE Solutions with Physics-Informed Deep Ensembles <https://PINA-org.github.io/PINA-Tutorials/tutorial14/tutorial.html>`_
-
-Neural Operator Learning
-----------------------------------------
-
-- `Introductory Tutorial: Neural Operator Learning with PINA <https://PINA-org.github.io/PINA-Tutorials/tutorial21/tutorial.html>`_
-- `Modeling 2D Darcy Flow with the Fourier Neural Operator <https://PINA-org.github.io/PINA-Tutorials/tutorial5/tutorial.html>`_
-- `Solving the Kuramoto-Sivashinsky Equation with Averaging Neural Operator <https://PINA-org.github.io/PINA-Tutorials/tutorial10/tutorial.html>`_
-- `Advection Equation with data driven DeepONet <https://PINA-org.github.io/PINA-Tutorials/tutorial24/tutorial.html>`_
-
-Supervised Learning
--------------------
-
-- `Introductory Tutorial: Supervised Learning with PINA <https://PINA-org.github.io/PINA-Tutorials/tutorial20/tutorial.html>`_
-- `Chemical Properties Prediction with Graph Neural Networks <https://PINA-org.github.io/PINA-Tutorials/tutorial15/tutorial.html>`_
-- `Reduced Order Model with Graph Neural Networks for Unstructured Domains <https://PINA-org.github.io/PINA-Tutorials/tutorial22/tutorial.html>`_
-- `Data-driven System Identification with SINDy <https://PINA-org.github.io/PINA-Tutorials/tutorial23/tutorial.html>`_
-- `Unstructured Convolutional Autoencoders with Continuous Convolution <https://PINA-org.github.io/PINA-Tutorials/tutorial4/tutorial.html>`_
-- `Reduced Order Modeling with POD-RBF and POD-NN Approaches for Fluid Dynamics <https://PINA-org.github.io/PINA-Tutorials/tutorial8/tutorial.html>`_
-
-See Also
---------
-
-- `Quickstart guide <https://PINA-org.github.io/PINA/_quickstart.html>`_
-- `API Reference <https://PINA-org.github.io/PINA/_rst/_code.html>`_
+PINA Tutorials
+==============
+
+Explore scientific machine learning with PINA, from the fundamentals to
+physics-informed neural networks, neural operators, and data-driven models.
+For installation and API reference, visit the `PINA documentation <https://pina-org.github.io/PINA/>`_.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Getting Started with PINA
+
+   guides/getting-started/tutorial17
+   guides/getting-started/tutorial16
+   guides/getting-started/tutorial18
+   guides/getting-started/tutorial11
+   guides/getting-started/tutorial19
+   guides/getting-started/tutorial6
+   guides/getting-started/tutorial12
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Physics Informed Neural Networks
+
+   guides/pinns/tutorial1
+   guides/pinns/tutorial2
+   guides/pinns/tutorial3
+   guides/pinns/tutorial9
+   guides/pinns/tutorial7
+   guides/pinns/tutorial13
+   guides/pinns/tutorial14
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Neural Operator Learning
+
+   guides/neural-operators/tutorial21
+   guides/neural-operators/tutorial5
+   guides/neural-operators/tutorial10
+   guides/neural-operators/tutorial24
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Supervised Learning
+
+   guides/supervised-learning/tutorial20
+   guides/supervised-learning/tutorial15
+   guides/supervised-learning/tutorial22
+   guides/supervised-learning/tutorial23
+   guides/supervised-learning/tutorial4
+   guides/supervised-learning/tutorial8