docs: adding sphinx

.gitignore

@@ -212,4 +212,5 @@ docs/source/_autosummary/*
 # End of https://www.toptal.com/developers/gitignore/api/python,visualstudiocode,c++,cmake
 #ignore automatically generated doc files
 docs/source/_autosummary 
-
+docs/source/_auto_examples/*
+docs/source/_auto_examples

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/API.rst

@@ -0,0 +1,10 @@
+API
+---
+
+.. autosummary::
+   :caption: API
+   :toctree: _autosummary
+   :template: custom-module-template.rst
+   :recursive:
+
+   map2loop

docs/source/_templates/custom-class-template.rst

@@ -0,0 +1,32 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:                                   
+   :show-inheritance:                           
+   :inherited-members:                          
+
+   {% block methods %}
+   .. automethod:: __init__
+
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
+
+   .. autosummary::
+   {% for item in methods %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}

docs/source/_templates/custom-module-template.rst

@@ -0,0 +1,68 @@
+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Module Attributes
+
+   .. autosummary::
+      :toctree:                                          
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+      :toctree:
+      :recursive:
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+      :toctree:                                          
+      :template: custom-class-template.rst
+      :recursive:              
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+      :toctree:                                          
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+{% block modules %}
+{% if modules %}
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :template: custom-module-template.rst                 
+   :recursive:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}

docs/source/_templates/custom.css

@@ -0,0 +1,12 @@
+.toggle .header {
+    display: block;
+    clear: both;
+}
+
+.toggle .header:after {
+    content: " ▶";
+}
+
+.toggle .header.open:after {
+    content: " ▼";
+}

docs/source/_templates/page.html

@@ -0,0 +1,12 @@
+{% extends "!page.html" %} {% block footer %}
+<script type="text/javascript">
+  $(document).ready(function () {
+    $(".toggle > *").hide();
+    $(".toggle .header").show();
+    $(".toggle .header").click(function () {
+      $(this).parent().children().not(".header").toggle(400);
+      $(this).parent().children(".header").toggleClass("open");
+    });
+  });
+</script>
+{% endblock %}

docs/source/conf.py

@@ -0,0 +1,121 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# 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.
+#
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("."))
+
+
+# -- Project information -----------------------------------------------------
+import map2loop
+
+project = "map2loop"
+copyright = "2024, Loop development team"
+author = "Roy Thomson, Mark Jessell, Lachlan Grose, and others"
+
+# The full version, including alpha/beta/rc tags
+release = map2loop.__version__
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+autoclass_content = "both"  # include both class docstring and __init__
+autodoc_default_flags = [
+    # Make sure that any autodoc declarations show the right members
+    "members",
+    "inherited-members",
+    "private-members",
+    "show-inheritance",
+]
+autosummary_generate = True  # Make _autosummary files and include them
+napoleon_numpy_docstring = True  # False  # Force consistency, leave only Google
+napoleon_use_rtype = False  # More legible
+autosummary_imported_members = True
+autosummary_ignore_module_all = False
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    # Need the autodoc and autosummary packages to generate our docs.
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    # The Napoleon extension allows for nicer argument formatting.
+    "sphinx.ext.napoleon",
+    # add sphinx gallery
+    "sphinx_gallery.gen_gallery",
+    # citations
+]
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# 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 = []
+
+
+# -- Options for HTML output -------------------------------------------------
+html_theme_options = {
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/loop3d/map2loop",
+            "icon": "fab fa-github-square",
+        },
+        {
+            "name": "Twitter",
+            "url": "https://twitter.com/loop3d",
+            "icon": "fab fa-twitter-square",
+        },
+    ],
+    #     "navbar_start": ["navbar-logo", "navbar-version"],
+    #     "use_edit_page_button": True,
+    "collapse_navigation": True,
+    "external_links": [
+        {"name": "Loop3d", "url": "https://www.loop3d.org"},
+    ],
+}
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "pydata_sphinx_theme"
+
+# 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".
+# 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".
+html_static_path = ["_static"]
+autosummary_mock_imports = [
+    "LoopStructural.interpolators._cython",
+]
+# Sphinx gallery examples
+from LoopStructural.visualisation.sphinx_scraper import Scraper as LoopScraper
+from sphinx_gallery.sorting import ExampleTitleSortKey
+
+sphinx_gallery_conf = {
+    "examples_dirs": ["../../examples/"],
+    "gallery_dirs": [
+        "_auto_examples/"
+    ],  # path to where to save gallery generated output
+    "image_scrapers": ("matplotlib", LoopScraper()),
+    "within_subsection_order": ExampleTitleSortKey,
+    "reference_url": {"LoopStructural": None},
+}
+
+# def setup(app):
+#     app.add_stylesheet('custom.css')

docs/source/index.rst

@@ -0,0 +1,26 @@
+.. map2loop documentation master file, created by
+   sphinx-quickstart on Wed Jan 17 15:48:56 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to map2loop's documentation!
+====================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+.. toctree::
+   :caption: map2loop API
+   :hidden:
+
+   API

docs/source/sg_execution_times.rst

@@ -0,0 +1,37 @@
+
+:orphan:
+
+.. _sphx_glr_sg_execution_times:
+
+
+Computation times
+=================
+**00:00.000** total execution time for 0 files **from all galleries**:
+
+.. container::
+
+  .. raw:: html
+
+    <style scoped>
+    <link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/5.3.0/css/bootstrap.min.css" rel="stylesheet" />
+    <link href="https://cdn.datatables.net/1.13.6/css/dataTables.bootstrap5.min.css" rel="stylesheet" />
+    </style>
+    <script src="https://code.jquery.com/jquery-3.7.0.js"></script>
+    <script src="https://cdn.datatables.net/1.13.6/js/jquery.dataTables.min.js"></script>
+    <script src="https://cdn.datatables.net/1.13.6/js/dataTables.bootstrap5.min.js"></script>
+    <script type="text/javascript" class="init">
+    $(document).ready( function () {
+        $('table.sg-datatable').DataTable({order: [[1, 'desc']]});
+    } );
+    </script>
+
+  .. list-table::
+   :header-rows: 1
+   :class: table table-striped sg-datatable
+
+   * - Example
+     - Time
+     - Mem (MB)
+   * - N/A
+     - N/A
+     - N/A

examples/README.rst

@@ -0,0 +1,2 @@
+Examples
+========