OpenFreeEnergy · Yoshanuikabundi · Oct 4, 2023 · Oct 4, 2023 · Oct 4, 2023 · Oct 4, 2023
diff --git a/docs/_templates/autosummary/base.rst b/docs/_templates/autosummary/base.rst
diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst
diff --git a/docs/_templates/autosummary/top-level-module.rst b/docs/_templates/autosummary/top-level-module.rst
@@ -0,0 +1,6 @@
+{% extends "autosummary/module.rst" %}
+{% block title -%}
+
+{{ ("``" ~ fullname ~ "``") | underline('=')}}
+
+{%- endblock %}
diff --git a/docs/conf.py b/docs/conf.py
@@ -21,7 +21,7 @@
 import nbsphinx
 import nbformat
 
-sys.path.insert(0, os.path.abspath('../'))
+sys.path.insert(0, os.path.abspath("../"))
 
 
 os.environ["SPHINX"] = "True"
@@ -79,9 +79,10 @@
 autodoc_default_options = {
     "members": True,
     "member-order": "bysource",
-    "inherited-members": "GufeTokenizable,BaseModel",
+    "inherited-members": "GufeTokenizable,BaseModel,SettingsBaseModel",
     "undoc-members": True,
     "special-members": "__call__",
+    "exclude-members": "get_defaults",
 }
 toc_object_entries_show_parents = "hide"
 
@@ -107,8 +108,45 @@
     "openmmtools",
     "mdtraj",
     "openmmforcefields",
+    "netCDF4",
+    "py3Dmol",
 ]
 
+# API docs settings
+autosummary_generate = True
+# Document imported items iff they're in __all__
+autosummary_imported_members = False
+autosummary_ignore_module_all = False
+# Autosummary template configuration
+autosummary_context = {
+    # Modules to exclude from API docs
+    "exclude_modules": [
+        "openfe.tests",
+    ],
+    "show_inheritance": True,
+    "show_inherited_members": False,
+    "show_undoc_members": True,
+}
+
+autodoc_preserve_defaults = True
+autodoc_inherit_docstrings = True
+autodoc_typehints_format = "short"
+# Fold the __init__ or __new__ methods' signature into class documentation
+autoclass_content = "both"
+autodoc_class_signature = "mixed"
+# Workaround for autodoc_typehints_format not working for attributes
+# see https://github.com/sphinx-doc/sphinx/issues/10290#issuecomment-1079740009
+python_use_unqualified_type_names = True
+
+
+autodoc_pydantic_model_show_json = False
+autodoc_pydantic_model_show_field_summary = False
+autodoc_pydantic_model_show_config_member = False
+autodoc_pydantic_model_show_config_summary = False
+autodoc_pydantic_model_show_validator_members = False
+autodoc_pydantic_model_show_validator_summary = False
+autodoc_pydantic_field_list_validators = False
+
 # Extensions for the myst parser
 myst_enable_extensions = [
     "dollarmath",
@@ -137,6 +175,7 @@
         }
     ],
     "accent_color": "DarkGoldenYellow",
+    "navigation_depth": 8,
 }
 html_logo = "_static/Squaredcircle.svg"
 

diff --git a/docs/cookbook/index.rst b/docs/cookbook/index.rst
@@ -21,6 +21,7 @@ The typical way to use the Python API is to load a number of molecules you want
         - .. container:: flowchart-sidebyside
 
             -   -
+
                     .. rst-class:: flowchart-spacer
                 -
 

diff --git a/docs/cookbook/under_the_hood.rst b/docs/cookbook/under_the_hood.rst
@@ -104,7 +104,7 @@ If you want to implement your own atom mapper or free energy procedure, or you w
             -
                 -
                     .. rst-class:: arrow-down
-                - :any:`executors`
+                - :any:`openfe.orchestration`
 
         - :class:`ProtocolDAGResult`
             A completed transformation.

diff --git a/docs/environment.yaml b/docs/environment.yaml
@@ -16,6 +16,7 @@ dependencies:
 - gitpython
 - tqdm
 - libsass
+- cinnabar
 - nbsphinx
 - nbsphinx-link
 - myst-parser

diff --git a/docs/index.rst b/docs/index.rst
@@ -76,7 +76,7 @@ The **OpenFE** toolkit provides open-source frameworks for calculating alchemica
     .. grid-item-card:: Relative Free Energy Protocol
         :img-top: _static/Rocket.svg
         :text-align: center
-        :link: reference/api/openmm_rfe
+        :link: reference/api/generated/openfe.protocols.openmm_rfe
         :link-type: doc
 
         Documentation for OpenFE's OpenMM-based Hybrid Topology Relative Free

diff --git a/docs/reference/api/alchemical_network_planning.rst b/docs/reference/api/alchemical_network_planning.rst
diff --git a/docs/reference/api/data.rst b/docs/reference/api/data.rst
diff --git a/docs/reference/api/defining_and_executing_simulations.rst b/docs/reference/api/defining_and_executing_simulations.rst
diff --git a/docs/reference/api/index.rst b/docs/reference/api/index.rst
@@ -3,12 +3,24 @@
 OpenFE API Reference
 ====================
 
-.. toctree::
-    :maxdepth: 2
-
-    data
-    systems_and_components
-    ligand_network
-    alchemical_network_planning
-    defining_and_executing_simulations
-    openmm_rfe
+``openfe``
+----------
+
+.. automodule:: openfe
+    :no-members:
+    :noindex:
+
+    .. rubric:: Modules
+
+    .. autosummary::
+        :nosignatures:
+        :toctree: generated/
+        :recursive:
+        :template: autosummary/top-level-module.rst
+
+        setup
+        orchestration
+        analysis
+        protocols
+        storage
+        utils
diff --git a/docs/reference/api/ligand_network.rst b/docs/reference/api/ligand_network.rst