OpenFreeEnergy · atravitz · Jan 9, 2026 · Dec 4, 2025 · Dec 4, 2025 · Dec 9, 2025
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -12,6 +12,7 @@ repos:
     - id: trailing-whitespace
       exclude: '\.(pdb|gro|top|sdf|xml|cif|graphml)$'
     - id: check-added-large-files
+      args: ["--maxkb=4000"]
     - id: check-case-conflict
     - id: check-symlinks
     - id: check-toml

diff --git a/dev/advanced_topics.ipynb b/dev/advanced_topics.ipynb
diff --git a/docs/_static/img/cyclic_graph_ipy_widget.png b/docs/_static/img/cyclic_graph_ipy_widget.png
diff --git a/docs/_static/img/cyclic_graph_pyplot_fig.png b/docs/_static/img/cyclic_graph_pyplot_fig.png
diff --git a/docs/guide/application_network_planning_fe_calculations.rst b/docs/guide/application_network_planning_fe_calculations.rst
@@ -45,6 +45,3 @@ Network, N-Node Edges Network, and Cyclic Network. Notably, the Twin Star
 Network and the Cyclic Network focus on constructing a set of cycles.
 
 So in applied cases we suggest the slightly more redundant networks in order to build up a robust network for the calculations.
-
-tutorial: :doc:`/tutorials/building_networks`.
-NetworkPlanner: :doc:`/guide/network_planner`.
diff --git a/docs/tutorials/basic_network_generation.ipynb b/docs/tutorials/basic_network_generation.ipynb
diff --git a/docs/tutorials/building_networks.rst b/docs/tutorials/building_networks.rst
diff --git a/docs/tutorials/index.rst b/docs/tutorials/index.rst
@@ -14,26 +14,28 @@ A simple first-use tutorial for building a ``LigandNetwork`` with **konnektor**.
 .. toctree::
    :maxdepth: 2
 
-   building_networks
+   basic_network_generation
 
 
-Using **konnektor**
--------------------
+Exploring the different **konnektor** network types
+---------------------------------------------------
 
-A longer tutorial which demonstrates how to use some of the different **konnektor** features on toy and real example cases.
+A tutorial that demonstrates a variety of different network types that can be built with **konnektor**.
 
 .. toctree::
    :maxdepth: 2
 
-   konnektor_example
+   network_generation_algorithms
 
 
-Exploring the different **konnektor** network types
----------------------------------------------------
+.. TODO: add this back once https://github.com/OpenFreeEnergy/konnektor/issues/202 is resolved
 
-A tutorial that demonstrates a variety of different network types that can be built with **konnektor**.
+.. Advanced Topics
+.. ---------------
 
-.. toctree::
-   :maxdepth: 2
+.. A longer tutorial which demonstrates how to use some of the different **konnektor** features.
+
+.. .. toctree::
+..    :maxdepth: 2
 
-   konnektor_networks
+..    advanced_topics
diff --git a/docs/tutorials/konnektor_example.ipynb b/docs/tutorials/konnektor_example.ipynb
diff --git a/docs/tutorials/konnektor_networks.ipynb b/docs/tutorials/konnektor_networks.ipynb
diff --git a/docs/tutorials/network_generation_algorithms.ipynb b/docs/tutorials/network_generation_algorithms.ipynb