Fix documentation

docs/requirements.txt

@@ -1,11 +1,11 @@
-sphinx~=6.2.1
-sphinx-copybutton==0.5.1
+sphinx~=7.3.7
+sphinx-copybutton==0.5.2
 sphinx-autoapi==3.0.0
-sphinx-book-theme==1.0.1
+sphinx-book-theme==1.1.2
 sphinx-favicon==1.0.1
 sphinx-notfound-page==1.0.0
-myst-nb @ git+https://github.com/executablebooks/MyST-NB@59854c2
-nbconvert==7.7.1
+myst-nb==1.1.0
+nbconvert==7.16.4
 
 # notebook dependencies
 shapely

docs/source/_templates/autoapi/python/module.rst

@@ -0,0 +1,98 @@
+{% if not obj.display %}
+:orphan:
+
+{% endif %}
+:py:mod:`{{ obj.name }}`
+=========={{ "=" * obj.name|length }}
+
+.. py:module:: {{ obj.name }}
+
+{% if obj.docstring %}
+.. autoapi-nested-parse::
+
+   {{ obj.docstring|indent(3) }}
+
+{% endif %}
+
+{% block submodules %}
+{% set visible_submodules = obj.submodules|selectattr("display")|list %}
+{% if visible_submodules %}
+Submodules
+----------
+.. toctree::
+   :titlesonly:
+   :maxdepth: 1
+
+{% for submodule in visible_submodules %}
+   {{ submodule.short_name }}/index.rst
+{% endfor %}
+
+
+{% endif %}
+{% endblock %}
+{% block content %}
+{% if obj.all is not none %}
+{% set visible_children = obj.children|selectattr("short_name", "in", obj.all)|list %}
+{% elif obj.type is equalto("package") %}
+{% set visible_children = obj.children|selectattr("display")|list %}
+{% else %}
+{% set visible_children = obj.children|selectattr("display")|rejectattr("imported")|list %}
+{% endif %}
+{% if visible_children %}
+{{ obj.type|title }} Contents
+{{ "-" * obj.type|length }}---------
+
+{% set visible_classes = visible_children|selectattr("type", "equalto", "class")|list %}
+{% set visible_functions = visible_children|selectattr("type", "equalto", "function")|list %}
+{% set visible_attributes = visible_children|selectattr("type", "equalto", "data")|list %}
+{% if "show-module-summary" in autoapi_options and (visible_classes or visible_functions) %}
+{% block classes scoped %}
+{% if visible_classes %}
+Classes
+~~~~~~~
+
+.. autoapisummary::
+
+{% for klass in visible_classes %}
+   {{ klass.id }}
+{% endfor %}
+
+
+{% endif %}
+{% endblock %}
+
+{% block functions scoped %}
+{% if visible_functions %}
+Functions
+~~~~~~~~~
+
+.. autoapisummary::
+
+{% for function in visible_functions %}
+   {{ function.id }}
+{% endfor %}
+
+
+{% endif %}
+{% endblock %}
+
+{% block attributes scoped %}
+{% if visible_attributes %}
+Attributes
+~~~~~~~~~~
+
+.. autoapisummary::
+
+{% for attribute in visible_attributes %}
+   {{ attribute.id }}
+{% endfor %}
+
+
+{% endif %}
+{% endblock %}
+{% endif %}
+{% for obj_item in visible_children %}
+{{ obj_item.render()|indent(0) }}
+{% endfor %}
+{% endif %}
+{% endblock %}

docs/source/conf.py

@@ -54,25 +54,23 @@
     "members",
     "undoc-members",
     "show-inheritance",
+    "show-module-summary",
     "imported-members",
 ]
 autoapi_ignore = [
     "**/tests/**",
     "**/native/**",
     "**/internal/**",
-    "**/\\w.*.py",
 ]
-
-# autoapi_member_order = "groupwise"
-autodoc_typehints = "both"
-autoapi_python_class_content = "both"
-
-add_module_names = False
-
 autoapi_add_toctree_entry = False
+autoapi_python_class_content = "class"
+autoapi_template_dir = "_templates/autoapi"
+autoapi_member_order = "groupwise"
+autoapi_python_use_implicit_namespaces = True
 
+add_module_names = False
 
-def skip_submodules(app, what, name, obj, skip, options):
+def skip_rules(app, what, name, obj, skip, options):
     if what == "module":
         skip = True
     if what == "method":
@@ -86,8 +84,7 @@ def skip_submodules(app, what, name, obj, skip, options):
 
 
 def setup(sphinx):
-    sphinx.connect("autoapi-skip-member", skip_submodules)
-
+    sphinx.connect("autoapi-skip-member", skip_rules)
 
 # -- Automatic execution of jupyter notebooks --------------------------------
 nb_execution_excludepatterns = []

python_modules/jupedsim/jupedsim/__init__.py

@@ -15,11 +15,6 @@
     distribute_until_filled,
 )
 from jupedsim.geometry import Geometry
-from jupedsim.geometry_utils import (
-    _geometry_from_coordinates,
-    _geometry_from_shapely,
-    _geometry_from_wkt,
-)
 from jupedsim.internal.tracing import Trace
 from jupedsim.journey import JourneyDescription, Transition
 from jupedsim.library import (
@@ -64,10 +59,22 @@
 )
 
 __version__ = get_build_info().library_version
+"""
+The version of this module.
+"""
+
 __commit__ = get_build_info().git_commit_hash
+"""
+Commit id that was used to build this module.
+"""
+
 __compiler__ = (
     f"{get_build_info().compiler} ({get_build_info().compiler_version})"
 )
+"""
+Id of the compiler used to build the native portion of this module.
+"""
+
 
 __all__ = [
     "Agent",
@@ -113,9 +120,6 @@
     "distribute_in_circles_by_density",
     "distribute_in_circles_by_number",
     "distribute_until_filled",
-    "_geometry_from_coordinates",
-    "_geometry_from_shapely",
-    "_geometry_from_wkt",
     "get_build_info",
     "set_debug_callback",
     "set_error_callback",