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Merge pull request #2395 from Parcels-code/reference-api-v4
v4 Reference API using autoapi
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‎docs/_autoapi_templates/python/class.rst‎

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{# Adapted from sphinx-autoapi https://github.com/readthedocs/sphinx-autoapi #}
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{% if obj.display %}
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{% if is_own_page %}
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{{ obj.id }}
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{{ "=" * obj.id | length }}
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{% endif %}
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{% set visible_children = obj.children|selectattr("display")|list %}
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{% set own_page_children = visible_children|selectattr("type", "in", own_page_types)|list %}
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{% if is_own_page and own_page_children %}
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.. toctree::
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:hidden:
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{% for child in own_page_children %}
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{{ child.include_path }}
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{% endfor %}
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{% endif %}
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.. py:{{ obj.type }}:: {% if is_own_page %}{{ obj.id }}{% else %}{{ obj.short_name }}{% endif %}{% if obj.args %}({{ obj.args }}){% endif %}
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{% for (args, return_annotation) in obj.overloads %}
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{{ " " * (obj.type | length) }} {{ obj.short_name }}{% if args %}({{ args }}){% endif %}
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{% endfor %}
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{% if obj.bases %}
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{% if "show-inheritance" in autoapi_options %}
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Bases: {% for base in obj.bases %}{{ base|link_objs }}{% if not loop.last %}, {% endif %}{% endfor %}
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{% endif %}
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{% if "show-inheritance-diagram" in autoapi_options and obj.bases != ["object"] %}
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.. autoapi-inheritance-diagram:: {{ obj.obj["full_name"] }}
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:parts: 1
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{% if "private-members" in autoapi_options %}
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:private-bases:
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{% endif %}
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{% endif %}
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{% endif %}
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{% if obj.docstring %}
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{{ obj.docstring|indent(3) }}
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{% endif %}
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{% for obj_item in visible_children %}
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{% if obj_item.type not in own_page_types %}
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{{ obj_item.render()|indent(3) }}
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{% endif %}
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{% endfor %}
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{% if is_own_page and own_page_children %}
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{% set visible_methods = visible_children|selectattr("type", "equalto", "method")|list %}
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{% if visible_methods %}
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Methods
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-------
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.. autoapisummary::
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{% for method in visible_methods %}
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{{ method.id }}
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{% endfor %}
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{% endif %}
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{% set visible_attributes = visible_children|selectattr("type", "equalto", "attribute")|list %}
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{% if visible_attributes %}
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Attributes
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----------
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.. autoapisummary::
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{% for attribute in visible_attributes %}
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{{ attribute.id }}
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{% endfor %}
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{% endif %}
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{% set visible_exceptions = own_page_children|selectattr("type", "equalto", "exception")|list %}
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{% if visible_exceptions %}
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Exceptions
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----------
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.. autoapisummary::
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{% for exception in visible_exceptions %}
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{{ exception.id }}
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{% endfor %}
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{% endif %}
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{% set visible_classes = own_page_children|selectattr("type", "equalto", "class")|list %}
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{% if visible_classes %}
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Classes
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-------
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.. autoapisummary::
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{% for klass in visible_classes %}
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{{ klass.id }}
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{% endfor %}
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{% endif %}
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{% endif %}
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{% endif %}

‎docs/_autoapi_templates/python/module.rst‎

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{# Adapted from sphinx-autoapi https://github.com/readthedocs/sphinx-autoapi #}
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{% if obj.display %}
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{% if is_own_page %}
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{{ obj.id }}
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{{ "=" * obj.id|length }}
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.. py:module:: {{ obj.name }}
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{% if obj.docstring %}
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.. autoapi-nested-parse::
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{{ obj.docstring|indent(3) }}
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{% endif %}
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{% block content %}
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{% set visible_children = obj.children|selectattr("display")|list %}
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{% if visible_children %}
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{% set visible_classes = visible_children|selectattr("type", "equalto", "class")|list %}
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{% if visible_classes %}
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{% if "class" in own_page_types or "show-module-summary" in autoapi_options %}
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Classes
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-------
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{% if "class" in own_page_types %}
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.. toctree::
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:hidden:
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:caption: Classes
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{% for klass in visible_classes %}
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{{ klass.include_path }}
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{% endfor %}
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{% endif %}
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.. autoapisummary::
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{% for klass in visible_classes %}
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{{ klass.id }}
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{% endfor %}
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{% endif %}
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{% endif %}
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{% set visible_exceptions = visible_children|selectattr("type", "equalto", "exception")|list %}
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{% if visible_exceptions %}
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{% if "exception" in own_page_types or "show-module-summary" in autoapi_options %}
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Exceptions
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----------
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{% if "exception" in own_page_types %}
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.. toctree::
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:hidden:
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{% for exception in visible_exceptions %}
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{{ exception.include_path }}
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{% endfor %}
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{% endif %}
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.. autoapisummary::
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{% for exception in visible_exceptions %}
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{{ exception.id }}
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{% endfor %}
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{% endif %}
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{% endif %}
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{% set visible_attributes = visible_children|selectattr("type", "equalto", "data")|list %}
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{% if visible_attributes %}
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{% if "attribute" in own_page_types or "show-module-summary" in autoapi_options %}
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Attributes
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----------
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{% if "attribute" in own_page_types %}
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.. toctree::
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:hidden:
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{% for attribute in visible_attributes %}
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{{ attribute.include_path }}
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{% endfor %}
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{% endif %}
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.. autoapisummary::
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{% for attribute in visible_attributes %}
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{{ attribute.id }}
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{% endfor %}
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{% endif %}
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{% endif %}
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{% set visible_functions = visible_children|selectattr("type", "equalto", "function")|list %}
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{% if visible_functions %}
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{% if "function" in own_page_types or "show-module-summary" in autoapi_options %}
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Functions
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---------
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{% if "function" in own_page_types %}
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.. toctree::
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:hidden:
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{% for function in visible_functions %}
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{{ function.include_path }}
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{% endfor %}
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{% endif %}
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.. autoapisummary::
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{% for function in visible_functions %}
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{{ function.id }}
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{% endfor %}
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{% endif %}
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{% endif %}
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{% set visible_subpackages = obj.subpackages|selectattr("display")|list %}
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{% set visible_submodules = obj.submodules|selectattr("display")|list %}
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{% set visible_submodules = (visible_subpackages + visible_submodules)|sort %}
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{% if visible_submodules %}
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.. toctree::
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:caption: Submodules
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:maxdepth: 1
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{% for submodule in visible_submodules %}
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{{ submodule.include_path }}
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{% endfor %}
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{% endif %}
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{% set this_page_children = visible_children|rejectattr("type", "in", own_page_types)|list %}
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{% if this_page_children %}
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{{ obj.type|title }} Contents
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{{ "-" * obj.type|length }}---------
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{% for obj_item in this_page_children %}
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{{ obj_item.render()|indent(0) }}
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{% endfor %}
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{% endif %}
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{% endif %}
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{% endblock %}
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{% else %}
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.. py:module:: {{ obj.name }}
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{% if obj.docstring %}
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.. autoapi-nested-parse::
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{{ obj.docstring|indent(6) }}
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{% endif %}
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{% for obj_item in visible_children %}
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{{ obj_item.render()|indent(3) }}
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{% endfor %}
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{% endif %}
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{% endif %}

‎docs/conf.py‎

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"""Sphinx configuration file for Parcels documentation."""
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"""autoSphinx configuration file for Parcels documentation."""
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# parcels documentation build configuration file, created by
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# sphinx-quickstart on Tue Oct 20 09:58:20 2015.
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#
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"numpydoc",
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"sphinxcontrib.mermaid",
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"sphinx_design",
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"autoapi.extension",
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]
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# Add any paths that contain templates here, relative to this directory.
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# directories to ignore when looking for source files.
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exclude_patterns = [
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"_build",
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"_autoapi_templates",
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"jupyter_execute",
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"**.ipynb_checkpoints",
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"user_guide/examples_v3",
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nb_execution_excludepatterns = ["jupyter_execute", ".jupyter_cache"]
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nb_execution_raise_on_error = True
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nb_execution_timeout = 75
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# -- Options for autoapi --------------------------------------------------
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autoapi_dirs = ["../src/parcels"]
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# autoapi_add_toctree_entry = False
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autoapi_root = "reference"
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autoapi_options = [
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"members",
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# "show-inheritance",
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"undoc-members",
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"show-module-summary",
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"imported-members",
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]
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autoapi_member_order = "bysource"
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autodoc_typehints = "none"
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autoapi_template_dir = "_autoapi_templates"
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autoapi_own_page_level = "class"

‎docs/index.md‎

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You can browse the documentation for older versions by using the version switcher in the bottom right.
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```
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**Useful links**: [Installation instructions](getting_started/installation.md) | [Discussions on GitHub](https://github.com/Parcels-code/parcels/discussions) | [Issue on GitHub](https://github.com/Parcels-code/parcels/issues) | [Parcels website](https://parcels-code.org/) | [CLAM community website](https://clam-community.github.io/) | [API reference](reference.md)
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**Useful links**: [Installation instructions](getting_started/installation.md) | [Discussions on GitHub](https://github.com/Parcels-code/parcels/discussions) | [Issue on GitHub](https://github.com/Parcels-code/parcels/issues) | [Parcels website](https://parcels-code.org/) | [CLAM community website](https://clam-community.github.io/) | [API reference](reference/parcels/index)
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`````{grid} 1 2 2 2
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:gutter: 4
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User guide <user_guide/index>
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Community <community/index>
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Development <development/index>
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API reference <reference>
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API reference <reference/parcels/index>
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v4 <v4/index>
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Parcels website <https://parcels-code.org/>
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```

‎docs/reference.md‎

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‎pixi.toml‎

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gsw = "*"
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[feature.docs.dependencies]
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parcels = { path = "." }
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numpydoc = "!=1.9.0"
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myst-nb = "*"
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ipython = "*"
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sphinx-autobuild = "*"
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sphinxcontrib-mermaid = "*"
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sphinx-design = "*"
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sphinx-autoapi = "*"
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[feature.docs.tasks]
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docs = "sphinx-build docs docs/_build"

‎pyproject.toml‎

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# TODO: ignore for now (requires more work). Remove ignore once fixed
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# Missing docstring in public module
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"D100",
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# Missing docstring in public class
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"D101",
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# Missing docstring in public method
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"D102",
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# Missing docstring in public function
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"D103",
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# Missing docstring in public package
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"D104",
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# Missing docstring in magic method
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"F811",
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]
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[tool.ruff.lint.per-file-ignores]
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# Ignore docstring rules everywhere except for the stable files (particleset.py, interpolators.py).
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"!src/parcels/{_core/basegrid,_core/field,_core/fieldset,_core/kernel,_core/particle,_core/particlefile,_core/particleset,_core/uxgrid,_core/xgrid,kernels/advection,kernels/advectiondiffusion,interpolators}.py" = [
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# Missing docstring in public class
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"D101",
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# Missing docstring in public method
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"D102",
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# Missing docstring in public function
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"D103",
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]
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[tool.ruff.lint.pydocstyle]
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convention = "numpy"
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