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Update documentation index page and navigation structure #2969

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f42a109
setup new index
jessica-mitchell Aug 30, 2023
bb97a6f
fix up conf, modify css style
jessica-mitchell Sep 1, 2023
ff1494c
add brain network image, add dropdowns
jessica-mitchell Sep 1, 2023
8da8990
add popup css js
jessica-mitchell Sep 1, 2023
581fd33
add logos white and black
jessica-mitchell Sep 1, 2023
4c18df5
update toc
jessica-mitchell Sep 6, 2023
7698962
fix up sidebar and svg
jessica-mitchell Sep 11, 2023
31edd53
change toc structure, remove dropdowns
jessica-mitchell Sep 22, 2023
c89f088
move all guides and tutorials under one page
jessica-mitchell Sep 22, 2023
0791691
split contribute section to separte page, reorganize developer index
jessica-mitchell Sep 22, 2023
66887d5
add toc page for model details
jessica-mitchell Sep 22, 2023
17b5c33
add icons
jessica-mitchell Sep 22, 2023
6fa2043
add pynest tut index
jessica-mitchell Sep 22, 2023
f8874af
update css
jessica-mitchell Sep 22, 2023
528650c
Merge branch 'master' into new-index-page
jessica-mitchell Sep 22, 2023
23777c8
remove script from index
jessica-mitchell Sep 22, 2023
cf03e9c
fix link
jessica-mitchell Sep 22, 2023
6c9270e
modify guides index page, add toc for ssn
jessica-mitchell Sep 26, 2023
defa303
Merge branch 'master' into new-index-page
jessica-mitchell Sep 26, 2023
9925e07
update developer space
jessica-mitchell Sep 26, 2023
c78adc8
modify index and getting started pages
jessica-mitchell Sep 26, 2023
b7faf63
add arows and new icon
jessica-mitchell Sep 26, 2023
eae7d5c
add css button, arrows
jessica-mitchell Sep 26, 2023
f379d74
minor adjusts, change to technical docs
jessica-mitchell Sep 26, 2023
7aeb7be
modify index page
jessica-mitchell Sep 29, 2023
25ab53b
rm extra js
jessica-mitchell Oct 5, 2023
c8a2fc6
add toc
jessica-mitchell Oct 5, 2023
07f91da
add jquery to template
jessica-mitchell Oct 5, 2023
8dc52f2
remove page
jessica-mitchell Oct 5, 2023
f153794
remove and update images css
jessica-mitchell Oct 5, 2023
f32525d
update links to neurons, synapses, devices
jessica-mitchell Oct 5, 2023
0db3f32
Merge branch 'master' into new-index-page
jessica-mitchell Oct 5, 2023
730e293
remove implementations
jessica-mitchell Oct 5, 2023
8cbba4d
Merge branch 'master' into new-index-page
jessica-mitchell Oct 5, 2023
8e5af1d
Merge branch 'new-index-page' of github.com:jessica-mitchell/nest-sim…
jessica-mitchell Oct 5, 2023
fafaa58
try various hover mechanisms
jessica-mitchell Oct 11, 2023
941c3ce
get hoverxref working
jessica-mitchell Oct 12, 2023
0c90e54
modify install pages
jessica-mitchell Oct 18, 2023
82e120c
update nest desktop /ml and icon
jessica-mitchell Oct 18, 2023
012b127
modify links in get started, css
jessica-mitchell Oct 18, 2023
f9876b4
Merge branch 'master' into new-index-page
jessica-mitchell Nov 14, 2023
8fd949f
add svgs
jessica-mitchell Nov 14, 2023
981f073
modify mermaid, css
jessica-mitchell Nov 17, 2023
9d170f2
rm size hoverxref
jessica-mitchell Nov 23, 2023
1a54681
add svgs
jessica-mitchell Nov 28, 2023
ce07bfc
add plantuml diagram
jessica-mitchell Nov 30, 2023
573e427
Merge branch 'master' into new-index-page
jessica-mitchell Dec 5, 2023
7db39b7
add windows options
jessica-mitchell Dec 5, 2023
1f7dc7d
remove hover
jessica-mitchell Dec 13, 2023
b811a83
update diagram and links
jessica-mitchell Dec 13, 2023
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2 changes: 2 additions & 0 deletions doc/htmldoc/attribution-list.rst
Original file line number Diff line number Diff line change
Expand Up @@ -26,3 +26,5 @@ Icons provided by Flaticon
<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/start-icon" title="start icon icons">Start icon icons created by Creative Squad - Flaticon</a>
<a href="https://www.flaticon.com/free-icons/source-code" title="source code icons">Source code icons created by Pixel perfect - Flaticon</a>
24 changes: 18 additions & 6 deletions doc/htmldoc/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,7 @@
source_suffix = ".rst"
master_doc = "index"
extensions = [
"hoverxref.extension",
"sphinx_gallery.gen_gallery",
"list_examples",
"sphinx.ext.autodoc",
Expand All @@ -53,26 +54,26 @@
"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",
"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",
Expand All @@ -82,6 +83,9 @@
"download_all_examples": False,
}

carousel_show_captions_below = True
# carousel_show_controls = True

# General information about the project.
project = "NEST Simulator user documentation"
copyright = "2004, nest-simulator"
Expand Down Expand Up @@ -177,7 +181,18 @@
}

html_static_path = ["static"]
html_additional_pages = {"index": "index.html"}

html_css_files = [
"css/custom.css",
"css/popup.css",
"css/pygments.css",
]

html_js_files = [
"js/custom.js",
"js/popup.js",
]
# html_additional_pages = {"index": "index.html"}
html_sidebars = {"**": ["logo-text.html", "globaltoc.html", "localtoc.html", "searchbox.html"]}

html_favicon = "static/img/nest_favicon.ico"
Expand Down Expand Up @@ -230,9 +245,6 @@ 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)


Expand Down
61 changes: 61 additions & 0 deletions doc/htmldoc/contribute.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,61 @@
.. _contribute:

Contribute to NEST
==================

NEST draws its strength from the many people that use and improve it. We
are happy to consider your contributions (e.g., new models, bug or
documentation fixes) for addition to the official version of NEST.

Please familiarize yourself with our guides and workflows:



.. grid:: 1 1 2 2

.. grid-item-card:: Mailing list

Have a question or problem about NEST? Get help from the NEST community:
use our :ref:`mailing list <mail_guidelines>`.

.. grid-item-card:: Create a GitHub issue

If you have a feature request, bug report or other issue, create
an issue on GitHub using `the templates <https://github.com/nest/nest-simulator/issues/new/choose>`_
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Suggested change
an issue on GitHub using `the templates <https://github.com/nest/nest-simulator/issues/new/choose>`_
an issue on GitHub using `the templates <https://github.com/nest/nest-simulator/issues/new/choose>`_.



.. admonition:: First time contributors

In order to make sure that the NEST Initiative can manage the NEST code base in the long term,
we ask that you fill in the :download:`NEST Contributor Agreement <https://nest-simulator.readthedocs.io/en/latest/_downloads/9b65adbdacba6bfed66e68c62af4e308/NEST_Contributor_Agreement.pdf>`
form to transfer your copyright to the NEST initiative and send it to *info [at] nest-initiative.org*.
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suggest to turn this into a link, writing @ as [at] probably isn't going to stop any spambots and it's a bit of an inconvenience

Suggested change
form to transfer your copyright to the NEST initiative and send it to *info [at] nest-initiative.org*.
form to transfer your copyright to the NEST initiative and send it to *info@nest-initiative.org*.





.. grid:: 1 1 2 2

.. grid-item-card:: Contribute code

* New to git or need a refresher? See our :ref:`NEST git workflow <git_workflow>`
* Follow the :ref:`C++ coding style guidelines <code_style_cpp>`
* Review the :ref:`naming conventions for NEST <naming_conventions>`
* Writing an extension to NEST? See :doc:`extmod:index`
* :ref:`required_dev_tools` to ensure correct formatting

.. grid-item-card:: Contribute documentation

* See our documentation workflows for :ref:`user facing docs <userdoc_workflow>` and :ref:`technical docs <devdoc_workflow>`
* For making changes to the PyNEST APIs, see our :ref:`pyapi_template`
* If you have a Python example network to contribute, please refer to our
:ref:`pyexample_template`

.. admonition:: Adding models to NEST

If you are looking at creating a new model, please consider :doc:`NESTML <nestml:index>`:
a modeling language supporting neuron and synapse specification, based on the syntax of Python.


.. seealso::

You can find additional guides for technical documentation :ref:`here <developer_space>`
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ Why do we have a style guide?
-----------------------------

This style guide was created to provide a single reference point for content
creation in NEST. This helps ensure the NEST user-level documentation remains
creation in NEST. This helps ensure the NEST user facing documentation remains
clear and consistent. The style choices we make here are meant to follow the
major trends in technical writing for software.

Expand Down
75 changes: 13 additions & 62 deletions doc/htmldoc/developer_space/index.rst
Original file line number Diff line number Diff line change
@@ -1,14 +1,14 @@
.. _developer_space:

Developer space
===============
Technical documentation
=======================

Here is all documentation pertaining to the development of NEST.
It is documentation for anyone needing to touch the code or documentation.

.. grid:: 3
.. grid:: 3

.. grid-item-card::
.. grid-item-card::
:link-type: ref
:link: dev_install
:class-card: sd-bg-success sd-text-white
Expand All @@ -17,76 +17,27 @@ It is documentation for anyone needing to touch the code or documentation.



.. _contribute:
Guidelines and workflows for developing NEST
---------------------------------------------

Contribute to NEST
------------------

NEST draws its strength from the many people that use and improve it. We
are happy to consider your contributions (e.g., new models, bug or
documentation fixes) for addition to the official version of NEST.

Please familiarize yourself with our guides and workflows:
.. note::

Most of the guides and workflows for contributing to NEST can be found in our :ref:`contribute` guide.


.. grid:: 1 1 2 2

.. grid-item-card:: Mailing list

Have a question or problem about NEST? Get help from the NEST community:
use our :ref:`mailing list <mail_guidelines>`.

.. grid-item-card:: Create a GitHub issue

If you have a feature request, bug report or other issue, create
an issue on GitHub using `the templates <https://github.com/nest/nest-simulator/issues/new/choose>`_


.. grid:: 1 1 2 2

.. grid-item-card:: Contribute code

* New to git or need a refresher? See our :ref:`NEST git workflow <git_workflow>`
* Follow the :ref:`C++ coding style guidelines <code_style_cpp>`
* Review the :ref:`naming conventions for NEST <naming_conventions>`
* Writing an extension module? See :doc:`extmod:index`
* :ref:`required_dev_tools`

.. grid-item-card:: Contribute documentation

* Review the :ref:`documentation style guide <doc_styleguide>`
* For making changes to the PyNEST APIs, see our :ref:`pyapi_template`
* If you have a Python example network to contribute, please refer to our
:ref:`pyexample_template`
* Check that documentation renders properly: See the :ref:`build documentation <doc_workflow>` guide for developer and user documentation

.. note:: Adding models to NEST

If you are looking at creating a new model, please check out :doc:`NESTML <nestml:index>`:
a modeling language supporting neuron and synapse specification, based on the syntax of Python.

In order to make sure that the NEST Initiative can manage the NEST code base in the long term,
you need to send us a completed and signed
:download:`NEST Contributor Agreement <static/NEST_Contributor_Agreement.pdf>` to transfer your
copyright to the NEST Initiative before we can merge your pull request.

----

Developer guides
----------------

.. grid:: 1 1 2 2

.. grid-item-card:: Reviewer guidelines
.. grid-item-card:: Reviewer guidelines

If you are requested to review a pull request, please
check our :ref:`code_guidelines`
* If you are requested to review a pull request, please check our :ref:`code_guidelines`

.. grid-item-card:: CI Workflow

.. grid-item-card:: Continuous integration
* Here you can find details on our :ref:`CI workflow <cont_integration>`

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The "SLI documentation" button just below here is devoid of text. Could we add a little one-liner? "SLI is the internal scripting language of NEST. It is now deprecated and not recommended for new applications". Perhaps also on the sli_docs index page as well.

* Here you can find details on our :ref:`CI workflow <cont_integration>`

.. grid:: 1 1 2 2

Expand All @@ -112,7 +63,7 @@ Developer guides

.. toctree::
:maxdepth: 1
:hidden:
:hidden:
:glob:

workflows/*
Expand Down
Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
.. _devdoc_workflow:

Developer documentation workflow
################################
Techincal documentation workflow
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Techincal documentation workflow
Technical documentation workflow

================================

What you need to know
+++++++++++++++++++++
---------------------

For developer documentation, we use `Doxygen <http://doxygen.org/>`__
comments extensively throughout NEST.
Expand All @@ -15,12 +15,12 @@ generated in the ``doc`` folder in your source directory.

.. note::

This workflow shows you how to create **developer documentation**
for NEST. For the **user documentation**, please refer to our
:ref:`User documentation workflow <userdoc_workflow>`.
This workflow shows you how to create **technical documentation**
for NEST. For the **user facing documentation**, please refer to our
:ref:`User facing documentation workflow <userdoc_workflow>`.

Instructions
++++++++++++
------------

1. Install Doxygen and graphviz.

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,5 @@ Select the documentation workflow you would like to view:
.. toctree::
:maxdepth: 1

User-level documentation<user_documentation_workflow>
Developer documentation<developer_documentation_workflow>

User facing documentation<user_documentation_workflow>
Technical documentation<developer_documentation_workflow>
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
.. _userdoc_workflow:

User-level documentation workflow
=================================
User facing documentation workflow
==================================

Overview of workflow
--------------------
Expand Down Expand Up @@ -231,9 +231,9 @@ form to transfer your copyright to the NEST initiative and send it to *info [at]

.. seealso::

This workflow shows you how to create **user-level documentation**
for NEST. For the **developer documentation**, please refer to our
:ref:`Developer documentation workflow
This workflow shows you how to create **user facing documentation**
for NEST. For the **technical documentation**, please refer to our
:ref:`Technical documentation workflow
<devdoc_workflow>`.


Expand Down
23 changes: 21 additions & 2 deletions doc/htmldoc/devices/index.rst
Original file line number Diff line number Diff line change
@@ -1,10 +1,29 @@
.. _device_index:

All about devices in NEST
=========================
All about recording and stimulating networks in NEST
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Please add a link to this document under "More about devices" on get-started_index.html — or alternatively, delete devices/index.rst page as it contains very little content; just merge the links in to the "More about devices" box on get-started_index.html.

====================================================



.. grid:: 1 1 2 2

.. grid-item-card:: |device| All about devices
:class-title: sd-d-flex-row sd-align-minor-center

* :ref:`record_simulations`

* :ref:`stimulate_network`

.. grid-item-card:: |math| Device models
:class-title: sd-d-flex-row sd-align-minor-center

* :doc:`/models/index_device`

.. toctree::
:maxdepth: 1
:glob:
:hidden:

*
.. |math| image:: ../static/img/math_orange128.svg
.. |device| image:: ../static/img/device_orange128.svg
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