Merge pull request #3066 from jessica-mitchell/doc-indexpage

Modify doc index page
nest · Mar 4, 2024 · ffce3b3 · ffce3b3
2 parents a69a12e + d64d2eb
commit ffce3b3
Show file tree

Hide file tree

Showing 24 changed files with 32,987 additions and 1,037 deletions.
diff --git a/doc/htmldoc/attribution-list.rst b/doc/htmldoc/attribution-list.rst
@@ -1,28 +1,46 @@
-:orphan: 
+:orphan:
+
+Attribution for images, icons, diagrams
+=======================================
+
+Custom images
+-------------
+
+The following images were created by  *A. Fischer - INM-6 Forschungszentrum Juelich GmBH*
+
+* neuron.svg
+* synapse.svg
+* networkbrainlight.svg
+* stimulatelight.svg
+* recordinglight.svg
+
+For use in Forschungszentrum Juelich GmBH. Cite the author of the work if using.
 
 Icons provided by Flaticon
 --------------------------
 
 
-<a href="https://www.flaticon.com/free-icons/neuron" title="neuron icons">Neuron icons created by Nadiinko - Flaticon</a>
-<a href="https://www.flaticon.com/free-icons/neuron" title="neuron icons">Neuron icons created by Freepik - Flaticon</a>
-<a href="https://www.flaticon.com/free-icons/monitor" title="monitor icons">Monitor icons created by Icongeek26 - Flaticon</a>
-<a href="https://www.flaticon.com/free-icons/dictionary" title="dictionary icons">Dictionary icons created by Freepik - Flaticon</a>
-<a href="https://www.flaticon.com/free-icons/neuron" title="neuron icons">Neuron icons created by Freepik - Flaticon</a>
-<a href="https://www.flaticon.com/free-icons/chat" title="chat icons">Chat icons created by Freepik - Flaticon</a>
-<a href="https://www.flaticon.com/free-icons/user" title="user icons">User icons created by Freepik - Flaticon</a>
-<a href="https://www.flaticon.com/free-icons/data-science" title="data science icons">Data science icons created by Eucalyp - Flaticon</a>
-<a href="https://www.flaticon.com/free-icons/brain" title="brain icons">Brain icons created by Freepik - Flaticon</a>
-<a href="https://www.flaticon.com/free-icons/teacher" title="teacher icons">Teacher icons created by Good Ware - Flaticon</a>
-<a href="https://www.flaticon.com/free-icons/math" title="math icons">Math icons created by Freepik - Flaticon</a>
-<a href="https://www.flaticon.com/free-icons/data-storage" title="data storage icons">Data storage icons created by IconLauk - Flaticon</a> 
-<a href="https://www.flaticon.com/free-icons/version" title="version icons">Version icons created by Ahmad Roaayala - Flaticon</a>
-<a href="https://www.flaticon.com/free-icons/developer" title="developer icons">Developer icons created by Freepik - Flaticon</a>
-<a href="https://www.flaticon.com/free-icons/cloud-computing" title="cloud computing icons">Cloud computing icons created by Prosymbols Premium - Flaticon</a>
-<a href="https://www.flaticon.com/free-icons/teacher" title="teacher icons">Teacher icons created by Freepik - Flaticon</a>
-<a href="https://www.flaticon.com/free-icons/launch" title="launch icons">Launch icons created by Freepik - Flaticon</a>
-<a href="https://www.flaticon.com/free-icons/conversation" title="conversation icons">Conversation icons created by Freepik - Flaticon</a>
-<a href="https://www.flaticon.com/free-icons/quotation-marks" title="quotation marks icons">Quotation marks icons created by Retinaicons - Flaticon</a>
-<a href="https://www.flaticon.com/free-icons/quote" title="quote icons">Quote icons created by DinosoftLabs - Flaticon</a>
-<a href="https://www.flaticon.com/free-icons/mail" title="mail icons">Mail icons created by Freepik - Flaticon</a>
-<a href="https://www.flaticon.com/free-icons/external-link" title="external link icons">External link icons created by Bharat Icons - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/neuron" title="neuron icons">Neuron icons created by Nadiinko - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/neuron" title="neuron icons">Neuron icons created by Freepik - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/monitor" title="monitor icons">Monitor icons created by Icongeek26 - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/dictionary" title="dictionary icons">Dictionary icons created by Freepik - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/neuron" title="neuron icons">Neuron icons created by Freepik - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/chat" title="chat icons">Chat icons created by Freepik - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/user" title="user icons">User icons created by Freepik - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/data-science" title="data science icons">Data science icons created by Eucalyp - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/brain" title="brain icons">Brain icons created by Freepik - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/teacher" title="teacher icons">Teacher icons created by Good Ware - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/math" title="math icons">Math icons created by Freepik - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/data-storage" title="data storage icons">Data storage icons created by IconLauk - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/version" title="version icons">Version icons created by Ahmad Roaayala - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/developer" title="developer icons">Developer icons created by Freepik - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/cloud-computing" title="cloud computing icons">Cloud computing icons created by Prosymbols Premium - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/teacher" title="teacher icons">Teacher icons created by Freepik - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/launch" title="launch icons">Launch icons created by Freepik - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/conversation" title="conversation icons">Conversation icons created by Freepik - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/quotation-marks" title="quotation marks icons">Quotation marks icons created by Retinaicons - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/quote" title="quote icons">Quote icons created by DinosoftLabs - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/mail" title="mail icons">Mail icons created by Freepik - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/external-link" title="external link icons">External link icons created by Bharat Icons - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/checklist" title="checklist icons">Checklist icons created by juicy_fish - Flaticon</a>
+* <a href="https://www.flaticon.com/free-icons/scientist" title="scientist icons">Scientist icons created by Victoruler - Flaticon</a>
diff --git a/doc/htmldoc/conf.py b/doc/htmldoc/conf.py
@@ -53,26 +53,27 @@
     "sphinx.ext.intersphinx",
     "sphinxcontrib.mermaid",
     "sphinx.ext.mathjax",
+    "sphinx_carousel.carousel",
     "sphinxcontrib.plantuml",
     "add_button_notebook",
     "IPython.sphinxext.ipython_console_highlighting",
     "nbsphinx",
     "extract_api_functions",
     "sphinx_design",
-    "HoverXTooltip",
     "VersionSyncRole",
+    "HoverXTooltip",
     "sphinx_copybutton",
     "notfound.extension",
 ]
 
 autodoc_mock_imports = ["nest.pynestkernel", "nest.ll_api"]
 mathjax_path = "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"
-panels_add_bootstrap_css = False
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["templates"]
 
 # To run plantuml locally see the user documentation workflow
 plantuml = "java -jar /tmp/plantuml.jar"
+plantuml_output_format = "svg_img"
 sphinx_gallery_conf = {
     # path to your examples scripts
     "examples_dirs": "../../pynest/examples",
@@ -124,9 +125,6 @@
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = "manni"
 
-# If true, `todo` and `todoList` produce output, else they produce nothing.
-todo_include_todos = False
-
 # add numbered figure link
 numfig = True
 
@@ -160,13 +158,11 @@
     "color_primary": "orange",
     "color_accent": "white",
     "theme_color": "ff6633",
-    "master_doc": True,
+    "master_doc": False,
     # Set the repo location to get a badge with stats
     "repo_url": "https://github.com/nest/nest-simulator/",
     "repo_name": "NEST Simulator",
-    # "nav_links": [
-    #     {"href": "index", "internal": True, "title": "NEST docs home"}
-    #     ],
+    "nav_links": [{"href": "index", "internal": True, "title": "NEST docs home"}],
     # Visible levels of the global TOC; -1 means unlimited
     "globaltoc_depth": 1,
     # If False, expand all TOC entries
@@ -177,7 +173,15 @@
 }
 
 html_static_path = ["static"]
-html_additional_pages = {"index": "index.html"}
+
+html_css_files = [
+    "css/custom.css",
+    "css/pygments.css",
+]
+
+html_js_files = [
+    "js/custom.js",
+]
 html_sidebars = {"**": ["logo-text.html", "globaltoc.html", "localtoc.html", "searchbox.html"]}
 
 html_favicon = "static/img/nest_favicon.ico"
@@ -230,9 +234,6 @@ def setup(app):
     # for events see
     # https://www.sphinx-doc.org/en/master/extdev/appapi.html#sphinx-core-events
     app.connect("source-read", toc_customizer)
-    app.add_css_file("css/custom.css")
-    app.add_css_file("css/pygments.css")
-    app.add_js_file("js/custom.js")
     app.connect("config-inited", config_inited_handler)
 
 

diff --git a/doc/htmldoc/get-started_index.rst b/doc/htmldoc/get-started_index.rst
@@ -1,28 +1,31 @@
-Tutorials and examples
-======================
+.. _tutorials_guides:
+
+Tutorials and guides
+====================
 
 .. toctree::
    :maxdepth: 1
    :hidden:
 
    tutorials/index
-   PyNEST example scripts <examples/index>
-   understand_index
 
 .. grid:: 1 1 2 2
     :gutter: 1
 
-    .. grid-item-card:: |nav| Tutorials
+    .. grid-item-card:: |nav| Tutorials: Introduction to PyNEST
        :class-title: sd-d-flex-row sd-align-minor-center
        :link: tutorials
        :link-type: ref
 
-    .. grid-item-card:: |example| PyNEST example scripts
+    .. grid-item-card:: |example| Topical guides
        :class-title: sd-d-flex-row sd-align-minor-center
-       :link: pynest_examples
+       :link: guides
        :link-type: ref
 
+.. toctree::
+   :hidden:
 
+   understand_index
 
 .. |nav| image:: static/img/GPS-Settings-256_nest.svg
 .. |example| image::  static/img/Documents-02-256_nest.svg
diff --git a/doc/htmldoc/index.rst b/doc/htmldoc/index.rst
@@ -1,16 +1,111 @@
-NEST Simulator documentaiton
-============================
+Welcome to the NEST Simulator documentation
+===========================================
+
+
+
+
+.. grid::
+
+  .. grid-item::
+
+    NEST is used in computational neuroscience to model and study behavior of large networks of neurons.
+
+    The models describe single neuron and synapse behavior and their connections.
+    Different mechanisms of plasticity can be used to investigate artificial learning
+    and help to shed light on the fundamental principles of how the brain works.
+
+    NEST offers convenient and efficient commands to define and connect large networks,
+    ranging from algorithmically determined connections to data-driven connectivity.
+    Create connections between neurons using numerous synapse models from STDP to gap junctions.
+
+    .. button-ref:: tutorials_guides
+       :ref-type: ref
+       :shadow:
+       :color: primary
+
+       Get started with NEST
+
+  .. grid-item::
+
+     .. grid:: 1 1 1 1
+       :gutter: 2
+
+       .. grid-item-card::
+
+          .. carousel::
+              :show_indicators:
+              :show_fade:
+              :show_dark:
+              :data-bs-ride: carousel
+
+                .. figure:: static/img/network_model_sketch_mesocircuit.png
+
+
+                  Create spatially structured networks
+
+
+                .. figure:: static/img/astrocyte_interaction.png
+
+
+                  Investigate neuron and astrocyte interactions
+
+
+                .. figure:: static/img/hpc_benchmark_connectivity.svg
+
+
+                  Test perfomance and benchmarks
+
+                .. figure:: static/img/pong_sim.gif
+
+
+                  Play PONG with NEST
+
+                .. figure:: static/img/gapjunctions.png
+
+
+                  Explore synapse types like gap junctions
+
+       .. grid-item::
+
+          .. button-ref:: pynest_examples
+             :ref-type: ref
+             :color: info
+             :align: center
+             :shadow:
+
+             Discover all our examples!
+
 
 .. toctree::
-   :maxdepth: 1
+   :caption: USAGE
    :hidden:
+   :glob:
+
+   Install <installation/index>
+   Tutorials and Guides <get-started_index>
+   Examples <examples/index>
+   Models <models/index>
+   Python API <ref_material/pynest_api/index>
+   ref_material/glossary
+   Cite NEST <citing-nest>
+   License <license>
 
-   Installation <installation/index>
-   Tutorials and examples <get-started_index>
-   Understand how NEST works <understand_index>
-   PyNEST API <ref_material/pynest_api/index>
-   Available models <models/index>
+
+.. toctree::
+   :caption: COMMUNITY
+   :hidden:
+   :glob:
+
+   Contact us <community>
    Contribute <developer_space/index>
    What's new? <whats_new/index>
-   Community <community>
-   license
+   NEST Homepage <https://nest-simulator.org>
+   Acknowledgments <https://github.com/nest/nest-simulator/blob/master/ACKNOWLEDGMENTS.md>
+
+.. toctree::
+   :caption: RELATED PROJECTS
+   :hidden:
+
+   NEST Desktop <https://nest-desktop.readthedocs.io/en/latest/>
+   NESTML <https://nestml.readthedocs.io/en/latest/>
+   NESTGPU <https://nest-gpu.readthedocs.io/en/latest/>