diff --git a/boa/__init__.py b/boa/__init__.py
index b3f6671..08a060e 100644
--- a/boa/__init__.py
+++ b/boa/__init__.py
@@ -10,6 +10,7 @@
     __version__ = "0.0.0"
 
 from boa.ax_instantiation_utils import *  # noqa
+from boa.controller import *  # noqa
 from boa.instantiation_base import *  # noqa
 from boa.metrics.modular_metric import *  # noqa
 from boa.runner import *  # noqa
diff --git a/boa/_doc_utils.py b/boa/_doc_utils.py
index 970d82a..8e4098f 100644
--- a/boa/_doc_utils.py
+++ b/boa/_doc_utils.py
@@ -1,26 +1,29 @@
-import inspect
-from pathlib import Path
+import importlib
+import pkgutil
 
-FILENAME = Path(__file__).name
+import boa
 
 
-def get_calling_file_path():
-    frames = inspect.stack()
-    frame = 1
-    while (file_path := Path(frames[frame].filename)).name == FILENAME:
-        frame += 1
-    return file_path
+def get_boa_submodules():
+    print(boa)
+    module_list = []
+    packages = []
+    for module_finder, modname, is_pkg in pkgutil.walk_packages(boa.__path__):
+        if is_pkg:
+            packages.append(modname)
+        if len(modname.split(".")) > 1:
+            module_list.append(modname)
+    return module_list
 
 
-def add_ref_to_rel_init():
-    file_path = get_calling_file_path()
+def import_boa_submod(submod_str):
+    return importlib.import_module(f"boa.{submod_str}")
 
-    parent = file_path.parent
-    pathing_ls = []
-    for part in reversed(parent.parts):
-        pathing_ls.append(part)
-        if part == "boa":
-            break
-    pathing = ".".join(module for module in reversed(pathing_ls))
 
-    return f"""**See More Information Here**: :mod:`{pathing}`"""
+def add_ref_to_all_submodules_inits():
+    module_list = get_boa_submodules()
+    for mod_str in module_list:
+        submod = import_boa_submod(mod_str)
+        info = f"""**Overview Information Here**: :mod:`{submod.__package__}`"""
+
+        submod.__doc__ = f"{submod.__doc__}\n\n{info}" if submod.__doc__ else info
diff --git a/boa/ax_instantiation_utils.py b/boa/ax_instantiation_utils.py
index 8e779aa..79ee642 100644
--- a/boa/ax_instantiation_utils.py
+++ b/boa/ax_instantiation_utils.py
@@ -1,3 +1,12 @@
+"""
+###################################
+Ax Instantiation Utility Functions
+###################################
+
+Utility functions to instantiate Ax objects
+
+"""
+
 from __future__ import annotations
 
 import copy
diff --git a/boa/controller.py b/boa/controller.py
index d0b4dc7..c44096f 100644
--- a/boa/controller.py
+++ b/boa/controller.py
@@ -1,3 +1,11 @@
+"""
+###################################
+Controller
+###################################
+
+"""
+
+
 import logging
 import os
 import time
@@ -5,11 +13,11 @@
 
 from ax.service.scheduler import Scheduler
 
-from boa import BaseWrapper
 from boa.ax_instantiation_utils import get_experiment, get_scheduler
 from boa.runner import WrappedJobRunner
 from boa.storage import scheduler_to_json_file
 from boa.utils import get_dictionary_from_callable
+from boa.wrappers.wrapper import BaseWrapper
 from boa.wrappers.wrapper_utils import get_dt_now_as_str
 
 
diff --git a/boa/metaclasses.py b/boa/metaclasses.py
index 1a1cb2f..df1eb0d 100644
--- a/boa/metaclasses.py
+++ b/boa/metaclasses.py
@@ -1,3 +1,14 @@
+"""
+########################
+Meta Classes
+########################
+
+Meta class modify class behaviors, such as having all subclasses of
+:class:`.BaseWrapper` will wrap functions in :func:`.cd_and_cd_back_dec`
+to make sure whatever directory changes users do inside a wrapper function,
+the directory is returned afterwards.
+
+"""
 import logging
 import traceback
 from abc import ABCMeta
diff --git a/boa/metrics/__init__.py b/boa/metrics/__init__.py
index c443a38..54230d6 100644
--- a/boa/metrics/__init__.py
+++ b/boa/metrics/__init__.py
@@ -1,8 +1,4 @@
-def foo():
-    return "hi"
-
-
-__doc__ = f"""
+"""
 ################################################
 Metrics Overview & Advanced Usage
 ################################################
@@ -17,8 +13,6 @@ def foo():
 
 See :doc:`/user_guide/configuration`
 
-
-{foo()}
 """
 
 from boa.metrics.metrics import *  # noqa
diff --git a/boa/metrics/metric_funcs.py b/boa/metrics/metric_funcs.py
index 62c29b4..600f4c2 100644
--- a/boa/metrics/metric_funcs.py
+++ b/boa/metrics/metric_funcs.py
@@ -1,10 +1,18 @@
+"""
+########################
+Metric Functions
+########################
+
+Functions used for Metrics
+
+"""
+
 import logging
 
 import numpy as np
 import scipy.stats as stats
 from sklearn.metrics import mean_squared_error
 
-from boa._doc_utils import add_ref_to_rel_init
 from boa.utils import get_dictionary_from_callable
 
 logger = logging.getLogger(__name__)
@@ -15,10 +23,12 @@ def normalized_root_mean_squared_error(y_true, y_pred, normalizer="iqr", **kwarg
 
     Parameters
     ----------
-    y_true : array-like of shape (n_samples,) or (n_samples, n_outputs)
+    y_true : array_like
+        With shape (n_samples,) or (n_samples, n_outputs)
         Ground truth (correct) target values.
 
-    y_pred : array-like of shape (n_samples,) or (n_samples, n_outputs)
+    y_pred : array_like
+        With shape (n_samples,) or (n_samples, n_outputs)
         Estimated target values.
 
     normalizer : str
@@ -30,7 +40,7 @@ def normalized_root_mean_squared_error(y_true, y_pred, normalizer="iqr", **kwarg
 
     Returns
     -------
-    nrmse : float or ndarray of floats
+    nrmse : float or numpy.ndarray[float]
         A normalized version of RMSE
     """
     rmse = mean_squared_error(y_true, y_pred, squared=False, **get_dictionary_from_callable(mean_squared_error, kwargs))
@@ -47,14 +57,3 @@ def normalized_root_mean_squared_error(y_true, y_pred, normalizer="iqr", **kwarg
 
     nrmse = rmse / norm
     return nrmse
-
-
-__doc__ = f"""
-########################
-Metric Functions
-########################
-
-Functions used for Metrics
-
-{add_ref_to_rel_init()}
-"""
diff --git a/boa/metrics/metrics.py b/boa/metrics/metrics.py
index c12072f..5c62123 100644
--- a/boa/metrics/metrics.py
+++ b/boa/metrics/metrics.py
@@ -1,6 +1,40 @@
+"""
+########################
+List of Metrics
+########################
+
+List of Metrics that are already defined in BOA
+
+Any of these Metrics can be used directly in your configuration file
+
+Examples
+========
+..  code-block:: YAML
+
+    # Single objective optimization config
+    optimization_options:
+        objective_options:
+            objectives:
+                # List all of your metrics here,
+                # only list 1 metric for a single objective optimization
+                - metric: RootMeanSquaredError
+
+..  code-block:: YAML
+
+    # MultiObjective Optimization config
+    optimization_options:
+        objective_options:
+            objectives:
+                # List all of your metrics here,
+                # only list multiple objectives for a multi objective optimization
+                - metric: RMSE
+                - metric: R2
+
+"""
+
+
 import numpy as np
 
-from boa._doc_utils import add_ref_to_rel_init
 from boa.metrics.metric_funcs import (
     normalized_root_mean_squared_error as normalized_root_mean_squared_error_,
 )
@@ -148,39 +182,3 @@ def __init__(self, metric_to_eval=normalized_root_mean_squared_error_, lower_is_
 
 NRMSE = NormalizedRootMeanSquaredError
 normalized_root_mean_squared_error = NormalizedRootMeanSquaredError
-
-
-__doc__ = f"""
-########################
-List of Metrics
-########################
-
-List of Metrics that are already defined in BOA
-
-Any of these Metrics can be used directly in your configuration file
-
-Examples
-========
-..  code-block:: YAML
-
-    # Single objective optimization config
-    optimization_options:
-        objective_options:
-            objectives:
-                # List all of your metrics here,
-                # only list 1 metric for a single objective optimization
-                - metric: RootMeanSquaredError
-
-..  code-block:: YAML
-
-    # MultiObjective Optimization config
-    optimization_options:
-        objective_options:
-            objectives:
-                # List all of your metrics here,
-                # only list multiple objectives for a multi objective optimization
-                - metric: RMSE
-                - metric: R2
-
-{add_ref_to_rel_init()}
-"""
diff --git a/boa/metrics/modular_metric.py b/boa/metrics/modular_metric.py
index 5a08a33..e8028f9 100644
--- a/boa/metrics/modular_metric.py
+++ b/boa/metrics/modular_metric.py
@@ -1,3 +1,10 @@
+"""
+########################
+Modular Metric
+########################
+
+"""
+
 from __future__ import annotations
 
 import logging
@@ -16,7 +23,6 @@
 from sklearn.metrics import __all__ as sklearn_all
 
 import boa.metrics.synthetic_funcs
-from boa._doc_utils import add_ref_to_rel_init
 from boa.metaclasses import MetricRegister
 from boa.utils import (
     extract_init_args,
@@ -155,8 +161,8 @@ class ModularMetric(NoisyFunctionMetric, metaclass=MetricRegister):
     ``metric_to_eval``.
 
     You can further customize the behavior of your metric by passing a
-    :class:`Wrapper<boa.wrapper.BaseWrapper>`, which has will run methods
-    such as  :meth:`~boa.wrapper.BaseWrapper.fetch_trial_data` before
+    :class:`Wrapper<.BaseWrapper>`, which has will run methods
+    such as  :meth:`~.BaseWrapper.fetch_trial_data` before
     calling the specified metric to evaluate, which can allow you
     to preprocess/prepare model output data for your metric calculation.
 
@@ -320,12 +326,3 @@ def __repr__(self) -> str:
 
         arg_str = " ".join(f"{k}={v}" for k, v in init_dict.items())
         return f"{self.__class__.__name__}({arg_str})"
-
-
-__doc__ = f"""
-########################
-Modular Metric
-########################
-
-{add_ref_to_rel_init()}
-"""
diff --git a/boa/metrics/synthetic_funcs.py b/boa/metrics/synthetic_funcs.py
index 4640055..436c182 100644
--- a/boa/metrics/synthetic_funcs.py
+++ b/boa/metrics/synthetic_funcs.py
@@ -1,9 +1,14 @@
+"""
+########################
+Synthetic Function
+########################
+
+"""
+
 from ax.utils.measurement.synthetic_functions import from_botorch
 from botorch.test_functions.synthetic import Hartmann
 from torch import Tensor
 
-from boa._doc_utils import add_ref_to_rel_init
-
 
 class Hartmann4(Hartmann):
     dim = 4
@@ -23,12 +28,3 @@ def optimizers(self) -> Tensor:
 
 
 hartmann4 = from_botorch(Hartmann4())
-
-
-__doc__ = f"""
-########################
-Synthetic Function
-########################
-
-{add_ref_to_rel_init()}
-"""
diff --git a/boa/runner.py b/boa/runner.py
index 6f0bc61..81ddc26 100644
--- a/boa/runner.py
+++ b/boa/runner.py
@@ -1,3 +1,12 @@
+"""
+###################################
+Wrapped Runner
+###################################
+
+Runner that calls your :mod:`.wrappers` to run your model and poll the trial status.
+
+"""
+
 from collections import defaultdict
 from typing import Any, Dict, Iterable, Set
 
diff --git a/boa/storage.py b/boa/storage.py
index b7d8561..af1a392 100644
--- a/boa/storage.py
+++ b/boa/storage.py
@@ -1,3 +1,13 @@
+"""
+########################
+Saving and Loading
+########################
+
+Functions for saving and loading your experiment to
+stop and restart.
+
+"""
+
 import json
 import logging
 import os
diff --git a/boa/utils.py b/boa/utils.py
index 7281455..7584d49 100644
--- a/boa/utils.py
+++ b/boa/utils.py
@@ -1,3 +1,13 @@
+"""
+###################################
+General Package Utility Functions
+###################################
+
+Utility functions useful for various package things like
+getting the signature matching
+
+"""
+
 from __future__ import annotations
 
 import inspect
diff --git a/boa/wrappers/wrapper.py b/boa/wrappers/wrapper.py
index 7be39bc..15359f2 100644
--- a/boa/wrappers/wrapper.py
+++ b/boa/wrappers/wrapper.py
@@ -1,3 +1,10 @@
+"""
+########################
+Base Wrapper
+########################
+
+"""
+
 from __future__ import annotations
 
 import logging
@@ -6,7 +13,6 @@
 
 from ax.core.base_trial import BaseTrial
 
-from boa._doc_utils import add_ref_to_rel_init
 from boa.metaclasses import WrapperRegister
 from boa.wrappers.wrapper_utils import (
     load_jsonlike,
@@ -187,12 +193,3 @@ def fetch_trial_data(self, trial: BaseTrial, metric_properties: dict, metric_nam
             A dictionary with the keys matching the keys of the metric function
                 used in the objective
         """
-
-
-__doc__ = f"""
-########################
-Base Wrapper
-########################
-
-{add_ref_to_rel_init()}
-"""
diff --git a/boa/wrappers/wrapper_utils.py b/boa/wrappers/wrapper_utils.py
index 9897da7..e1616cc 100644
--- a/boa/wrappers/wrapper_utils.py
+++ b/boa/wrappers/wrapper_utils.py
@@ -1,3 +1,12 @@
+"""
+########################
+Wrapper Utility Tools
+########################
+
+Utility tools for to ease model wrapping.
+
+"""
+
 from __future__ import annotations
 
 import datetime as dt
@@ -14,8 +23,6 @@
 from ax.core.parameter import ChoiceParameter, FixedParameter, RangeParameter
 from ax.utils.common.docutils import copy_doc
 
-from boa._doc_utils import add_ref_to_rel_init
-
 logger = logging.getLogger(__file__)
 
 
@@ -123,11 +130,11 @@ def load_json(file: os.PathLike | str, normalize: bool = True, *args, **kwargs)
     file : os.PathLike
         File path for the experiment configuration file
     normalize : bool
-        Whether to run boa.wrapper_utils.normalize_config after loading config
+        Whether to run :func:`.normalize_config` after loading config
         to run certain predictable configuration normalization. (default true)
     parameter_keys : str | list[Union[str, list[str], list[Union[str, int]]]]
         Alternative keys or paths to keys to parse  as parameters to optimize,
-        for more information, see :func:`~boa.wrapper_utils.wpr_params_to_boa`
+        for more information, see :func:`.wpr_params_to_boa`
 
     Examples
     --------
@@ -421,8 +428,8 @@ def get_dt_now_as_str(fmt: str = "%Y%m%dT%H%M%S"):
 
 
 def make_experiment_dir(
-    working_dir: os.PathLike = None,
-    experiment_dir: os.PathLike = None,
+    working_dir: os.PathLike | str = None,
+    experiment_dir: os.PathLike | str = None,
     experiment_name: str = "",
     append_timestamp: bool = True,
     exist_ok: bool = True,
@@ -433,10 +440,10 @@ def make_experiment_dir(
 
     Parameters
     ----------
-    working_dir : os.Pathlike
+    working_dir : os.PathLike | str
         Working directory, the parent directory where the experiment directory will be written.
         Specify either a working directory and an experiment name or an experiment_dir
-    experiment_dir : os.Pathlike
+    experiment_dir : os.PathLike | str
         The exact dir the experiment directory boa will use to write the runs to.
         Specify either a working directory and an experiment name or an experiment_dir
     experiment_name: str
@@ -450,7 +457,7 @@ def make_experiment_dir(
 
     Returns
     -------
-    Path
+    pathlib.Path
         Path to the directory for the experiment
     """
     if (working_dir and experiment_dir) or (not working_dir and not experiment_dir):
@@ -505,7 +512,7 @@ def get_trial_dir(experiment_dir: os.PathLike, trial_index: int, **kwargs):
 
     Returns
     -------
-    Path
+    pathlib.Path
         Directory for the trial
     """
     trial_dir = Path(experiment_dir) / zfilled_trial_index(trial_index, **kwargs)  # zero-padded trial index
@@ -529,21 +536,9 @@ def make_trial_dir(experiment_dir: os.PathLike, trial_index: int, **kwargs):
 
     Returns
     -------
-    Path
+    pathlib.Path
         Directory for the trial
     """
     trial_dir = get_trial_dir(experiment_dir, trial_index, **kwargs)
     trial_dir.mkdir()
     return trial_dir
-
-
-__doc__ = f"""
-########################
-Wrapper Utility Tools
-########################
-
-Utility tools for to ease model wrapping.
-
-{add_ref_to_rel_init()}
-
-"""
diff --git a/docs/code_reference.rst b/docs/code_reference.rst
index dc10910..239972c 100644
--- a/docs/code_reference.rst
+++ b/docs/code_reference.rst
@@ -3,8 +3,8 @@ Code reference
 ##############
 
 
-:mod:`boa.wrappers`: Wrapping tools
-===================================
+:mod:`Wrappers and Tools <boa.wrappers>`
+=============================================
 
 This is where you will find information about :doc:`BOA's </index>` Wrapper classes for optimization, as well as general wrapping utility functions that might be useful to wrap a model
 
@@ -18,8 +18,8 @@ This is where you will find information about :doc:`BOA's </index>` Wrapper clas
     boa.wrappers.wrapper_utils
 
 
-:mod:`boa.metrics`: Metrics
-============================
+:mod:`Metrics <boa.metrics>`:
+=================================
 
 This is where you will find information about :doc:`BOA's </index>` Metrics.
 
@@ -48,7 +48,9 @@ Advanced Usage/Direct Python Access
     :toctree: api
     :template: custom_module_template_short.rst
 
+    boa.controller
     boa.ax_instantiation_utils
     boa.runner
     boa.utils
     boa.metaclasses
+    boa.instantiation_base
diff --git a/docs/conf.py b/docs/conf.py
index 230b76c..f595a31 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -13,58 +13,62 @@
 import os
 import sys
 
-# sys.path.insert(0, os.path.abspath('.'))
-sys.path.insert(0, os.path.abspath('..'))
-# sys.path.insert(0, os.path.abspath("../boa/"))
-import importlib
+# sys.path.insert(0, os.path.abspath("."))
+sys.path.insert(0, os.path.abspath(".."))
+sys.path.insert(0, os.path.abspath("../boa/"))
 
-import jinja2
-import traitlets
-from docutils import nodes
-from docutils.parsers.rst import Directive
-from docutils.statemachine import ViewList
-from sphinx.ext.autodoc import ClassDocumenter
-from sphinx.util.nodes import nested_parse_with_titles
 
-from boa.metrics.synthetic_funcs import Hartmann4
+from boa._doc_utils import add_ref_to_all_submodules_inits
 
 # -- Project information -----------------------------------------------------
 
-project = 'boa'
-copyright = '2022, Madeline Scyphers, Justine Missik'
-author = 'Madeline Scyphers, Justine Missik'
+project = "boa"
+copyright = "2022, Madeline Scyphers, Justine Missik"
+author = "Madeline Scyphers, Justine Missik"
 
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# extensions coming with Sphinx (named "sphinx.ext.*") or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.todo',
-    'sphinx.ext.coverage',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.autosectionlabel',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.viewcode',
-    'sphinxext.remoteliteralinclude',
-    'myst_nb',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.autosectionlabel",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.viewcode",
+    "sphinxext.remoteliteralinclude",
+    "myst_nb",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 source_suffix = {
-    '.rst': 'restructuredtext',
-    '.ipynb': 'myst-nb',
-    '.md': 'myst-nb',
-    '.myst': 'myst-nb',
+    ".rst": "restructuredtext",
+    ".ipynb": "myst-nb",
+    ".md": "myst-nb",
+    ".myst": "myst-nb",
 }
 
+nitpicky = True
+nitpick_ignore = [
+    ('py:class', 'SearchSpace'),
+    ('py:class', 'Objective'),
+    ('py:class', 'BaseTrial'),
+    ('py:class', 'BaseTrial'),
+]
 
+nitpick_ignore_regex = [
+    (r'.*', r'.*ax.*'),
+    (r'.*', r'.*botorch.*'),
+    (r'.*', r'array.*like'),
+]
 
 # torch.nn has doc string reference sphinx has troubles resolving in its own code
 # Which get reference when we import from pytorch in general
@@ -79,31 +83,27 @@
 # 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 = ['_build', 'Thumbs.db', '.DS_Store', 'references']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "references"]
 
 # -- Autosummary -------------------------------------------------------------
 autosummary_generate = True  # Turn on sphinx.ext.autosummary
 autoclass_content = "both"  # Add __init__ doc (ie. params) to class summaries
 # autosummary_imported_members = True
-# html_show_sourcelink = False  # Remove 'view source code' from top of page (for html, not python)
+# html_show_sourcelink = False  # Remove "view source code" from top of page (for html, not python)
 autodoc_inherit_docstrings = True  # If no docstring, inherit from base class
-autodoc_member_order = 'bysource'
-
-autodoc_default_options = {
-    'ignore-module-all': False
-}
+autodoc_member_order = "bysource"
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'pydata_sphinx_theme'
+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".
-# html_static_path = ['_static']
+# html_static_path = ["_static"]
 
 html_theme_options = {
     "icon_links": [
@@ -125,86 +125,13 @@
 
 # external project mapping for intersphinx
 intersphinx_mapping = {
-    'fetch3': ('https://fetch3-nhl.readthedocs.io/en/latest', None),
-    'python': ('http://docs.python.org/3', None),
-    'numpy': ('http://docs.scipy.org/doc/numpy', None),
-    'scipy': ('http://docs.scipy.org/doc/scipy/reference', None),
-    'sklearn': ('http://scikit-learn.org/stable', None),
+    "fetch3": ("https://fetch3-nhl.readthedocs.io/en/latest", None),
+    "python": ("https://docs.python.org/3", None),
+    "numpy": ("https://numpy.org/doc/stable", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy", None),
+    "sklearn": ("https://scikit-learn.org/stable", None),
+    "torch": ("https://pytorch.org/docs/stable", None),
 }
-# intersphinx_mapping = {
-#     # "pytorch": ("https://pytorch.org/docs/stable/", None),
-#     "botorch": ("https://botorch.org/api/", None),
-#     "ax": ("https://ax.dev/versions/latest/api/", None)
-# }
-#
-#
-# class ExcludeClassDocumenter(ClassDocumenter):
-#
-#     directivetype = 'excluded-class'
-#     objtype = 'excludedclass'
-#     excluded_classes = [
-#         Hartmann4
-#     ]
-#
-#     @classmethod
-#     def can_document_member(cls, member, membername, isattr, parent):
-#         can_document = isinstance(member, type) and issubclass(member, Hartmann4)
-#         if can_document:
-#             print("\n\n\n\n\n", can_document)
-#             print(member)
-#         return can_document
-#
-#
-# EXCLUDE_INHERITED_CLASS = jinja2.Template(
-# u"""
-# .. autoclass:: {{ classname }}
-#    :members:
-#    :undoc-members:
-# """)
-#
-#
-# def _import_obj(args):
-#     """Utility to import the object given arguments to directive"""
-#     if len(args) == 1:
-#         mod, clsname = args[0].rsplit('.', 1)
-#     elif len(args) > 1 and args[-2] == ':module:':
-#         mod = args[-1]
-#         clsname = args[0].split('(')[0]
-#     else:
-#         raise ValueError("Args do not look as expected: {0}".format(args))
-#     mod = importlib.import_module(mod)
-#     return getattr(mod, clsname)
-#
-#
-# class ExcludeClassDirective(Directive):
-#     has_content = True
-#     required_arguments = 1
-#     optional_arguments = 20
-#
-#     def run(self):
-#
-#         print("\n\n\n\n\n\nrunning, class: ", self.arguments[0])
-#
-#         # generate the documentation string
-#         rst_text = EXCLUDE_INHERITED_CLASS.render(
-#             classname=self.arguments[0]
-#         )
-#
-#
-#
-#
-#         # parse and return documentation
-#         result = ViewList()
-#         for line in rst_text.split("\n"):
-#             result.append(line, "<excluded-class>")
-#         node = nodes.paragraph()
-#         node.document = self.state.document
-#         nested_parse_with_titles(self.state, result, node)
-#
-#
-#         return node.children
-#
-#
-# def setup(app):
-#     app.add_autodocumenter(ExcludeClassDocumenter)
-#     app.add_directive_to_domain('py', 'excluded-class', ExcludeClassDirective)
+
+# add a reference to the relative __init__.py of all files __doc__ in a submodules
+add_ref_to_all_submodules_inits()
diff --git a/docs/user_guide/package_overview.rst b/docs/user_guide/package_overview.rst
index e222b6e..8df60cb 100644
--- a/docs/user_guide/package_overview.rst
+++ b/docs/user_guide/package_overview.rst
@@ -26,7 +26,7 @@ See the :ref:`instructions for configurations files<configuration>` for details.
 Objective functions
 ====================
 
-When specifying your objective function to minimize or maximize, boa comes with a number of metrics you can use with your model output, such as MSE, :math:`R^2`, and others. For a list of current list of premade available of metrics, see See :class:`boa.metrics.metrics.METRICS`
+When specifying your objective function to minimize or maximize, boa comes with a number of metrics you can use with your model output, such as MSE, :math:`R^2`, and others. For a list of current list of premade available of metrics, see See :mod:`.metrics.metrics`
 
 
 
@@ -42,7 +42,7 @@ the model).
     A goal for the next stage of development is to allow for model wrapper functions to be written in other languages
     (e.g., R)
 
-See the :ref:`instructions for creating a model wrapper <wrapper-user-guide>` for details.
+See the :mod:`instructions for creating a model wrapper <boa.wrappers>` for details.
 
 ************************
 Creating a run script
@@ -58,6 +58,6 @@ See the :ref:`instructions for creating a run script <run_script>` for details.
 .. toctree::
     :maxdepth: 2
 
-    wrapper
+    ../api/boa.wrappers
     configuration
     run_script