cshenry · freiburgermsu · Aug 26, 2026
diff --git a/README.rst b/README.rst
diff --git a/docs/index.rst b/docs/index.rst
@@ -1,21 +1,21 @@
-.. sample documentation master file, created by
-   sphinx-quickstart on Mon Apr 16 21:22:43 2012.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-Welcome to sample's documentation!
-==================================
-
-Contents:
-
-.. toctree::
-   :maxdepth: 2
-
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+.. sample documentation master file, created by
+   sphinx-quickstart on Mon Apr 16 21:22:43 2012.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to sample's documentation!
+==================================
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/source/api.rst b/docs/source/api.rst
@@ -1,12 +1,90 @@
-ModelSEEDpy API
-________________________________________________________________________
-
-The detailed documentation of all user-operable classes and functions in the ModelSEEDpy library are provided.
-
-.. toctree::
-
-   contents
-   core/core_index
-   community/community_index
-   fbapkg/fbapkg_index
-   ml/ml_index
+ModelSEEDpy API
+________________________________________________________________________
+
+The detailed documentation of all user-operable classes and functions in the ModelSEEDpy library are provided.
+
+
+core
+---------
+
+The ``core`` sub-library permits parsing and manipulating metabolic models::
+
+ from modelseedpy.core import *   
+
+
+.. toctree::
+   :includehidden:
+
+   core/biology_api
+   core/fbahelper_api
+   core/gapfillinghelper_api
+   core/msatpcorrection_api
+   core/msbuilder_api
+   core/mseditorapi_api
+   core/msgenome_api
+   core/msgapfill_api
+   core/msgenomeclassifier_api
+   core/msgrowthphenotypes_api
+   core/msmedia_api
+   core/msmodel_api
+   core/msmodelutils_api
+   core/mstemplate_api
+   core/rpcclient_api
+   core/template_api
+
+
+community
+------------
+
+The ``community`` sub-library compatibilizes transport reactions of individual models for a community model and simulates interactions amongst community members::
+
+ from modelseedpy.community import *   
+
+
+.. toctree::
+   :includehidden:
+
+   community/commkineticpkg_api
+   community/dfbapkg_api
+   community/mssmetana_api
+   community/mscommphitting_api
+   community/mscommunity_api
+   community/mscompatibility_api
+
+
+fbapkg
+------------
+
+The ``fbapkg`` sub-library constrains and investigates metabolic models through Flux Balance Analysis methods::
+
+ from modelseedpy.fbapkg import *   
+
+.. toctree::
+   :includehidden:
+
+   fbapkg/bilevel_api
+   fbapkg/changeoptpkg_api
+   fbapkg/drainfluxes_api
+   fbapkg/elementuptakepkg_api
+   fbapkg/flexiblebiomass_api
+   fbapkg/fluxfitting_api
+   fbapkg/gapfillingpkg_api
+   fbapkg/kbasemedia_api
+   fbapkg/metabofba_api
+   fbapkg/proteomefitting_api
+   fbapkg/reactionuse_api
+   fbapkg/tfa_api
+
+
+ml
+------------
+
+The ``ml`` sub-library supports parsing features from genomes, with accessibility to KBase::
+
+ from modelseedpy.ml import *   
+
+
+.. toctree::
+   :includehidden:
+
+   ml/predict_phenotypes_api
diff --git a/docs/source/build.rst b/docs/source/build.rst
@@ -1,6 +1,6 @@
-Building a Model
-________________________________________________________________________
-
-Models are constructed through the following sequence.
-
-1)
+Building a Model
+________________________________________________________________________
+
+Models are constructed through the following sequence.
+
+1)
diff --git a/docs/source/community/community_index.rst b/docs/source/community/community_index.rst