docs(auto): update the auto-documentation with changes made with dihedral optimistaions

harryswift01 · harryswift01 · commit 5e56482fbd86 · 2026-06-24T12:28:09.000+01:00
diff --git a/docs/api/CodeEntropy.config.rst b/docs/api/CodeEntropy.config.rst
@@ -1,11 +1,6 @@
 CodeEntropy.config package
 ==========================
 
-.. automodule:: CodeEntropy.config
-   :members:
-   :show-inheritance:
-   :undoc-members:
-
 Submodules
 ----------
 
@@ -14,3 +9,11 @@ Submodules
 
    CodeEntropy.config.argparse
    CodeEntropy.config.runtime
+
+Module contents
+---------------
+
+.. automodule:: CodeEntropy.config
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.core.rst b/docs/api/CodeEntropy.core.rst
@@ -1,11 +1,6 @@
 CodeEntropy.core package
 ========================
 
-.. automodule:: CodeEntropy.core
-   :members:
-   :show-inheritance:
-   :undoc-members:
-
 Submodules
 ----------
 
@@ -14,3 +9,11 @@ Submodules
 
    CodeEntropy.core.dask_clusters
    CodeEntropy.core.logging
+
+Module contents
+---------------
+
+.. automodule:: CodeEntropy.core
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.entropy.nodes.rst b/docs/api/CodeEntropy.entropy.nodes.rst
@@ -1,11 +1,6 @@
 CodeEntropy.entropy.nodes package
 =================================
 
-.. automodule:: CodeEntropy.entropy.nodes
-   :members:
-   :show-inheritance:
-   :undoc-members:
-
 Submodules
 ----------
 
@@ -16,3 +11,11 @@ Submodules
    CodeEntropy.entropy.nodes.configurational
    CodeEntropy.entropy.nodes.orientational
    CodeEntropy.entropy.nodes.vibrational
+
+Module contents
+---------------
+
+.. automodule:: CodeEntropy.entropy.nodes
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.entropy.rst b/docs/api/CodeEntropy.entropy.rst
@@ -1,11 +1,6 @@
 CodeEntropy.entropy package
 ===========================
 
-.. automodule:: CodeEntropy.entropy
-   :members:
-   :show-inheritance:
-   :undoc-members:
-
 Subpackages
 -----------
 
@@ -26,3 +21,11 @@ Submodules
    CodeEntropy.entropy.vibrational
    CodeEntropy.entropy.water
    CodeEntropy.entropy.workflow
+
+Module contents
+---------------
+
+.. automodule:: CodeEntropy.entropy
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.levels.dihedrals.angle_observations.rst b/docs/api/CodeEntropy.levels.dihedrals.angle_observations.rst
@@ -0,0 +1,7 @@
+CodeEntropy.levels.dihedrals.angle\_observations module
+=======================================================
+
+.. automodule:: CodeEntropy.levels.dihedrals.angle_observations
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.levels.dihedrals.conformational_state_builder.rst b/docs/api/CodeEntropy.levels.dihedrals.conformational_state_builder.rst
@@ -0,0 +1,7 @@
+CodeEntropy.levels.dihedrals.conformational\_state\_builder module
+==================================================================
+
+.. automodule:: CodeEntropy.levels.dihedrals.conformational_state_builder
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.levels.dihedrals.kernels.rst b/docs/api/CodeEntropy.levels.dihedrals.kernels.rst
@@ -1,7 +1,7 @@
-CodeEntropy.levels.conformation\_dag module
+CodeEntropy.levels.dihedrals.kernels module
 ===========================================
 
-.. automodule:: CodeEntropy.levels.conformation_dag
+.. automodule:: CodeEntropy.levels.dihedrals.kernels
    :members:
    :show-inheritance:
    :undoc-members:
diff --git a/docs/api/CodeEntropy.levels.dihedrals.peak_detection.rst b/docs/api/CodeEntropy.levels.dihedrals.peak_detection.rst
@@ -0,0 +1,7 @@
+CodeEntropy.levels.dihedrals.peak\_detection module
+===================================================
+
+.. automodule:: CodeEntropy.levels.dihedrals.peak_detection
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.levels.dihedrals.rst b/docs/api/CodeEntropy.levels.dihedrals.rst
@@ -1,5 +1,21 @@
-CodeEntropy.levels.dihedrals module
-===================================
+CodeEntropy.levels.dihedrals package
+====================================
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   CodeEntropy.levels.dihedrals.angle_observations
+   CodeEntropy.levels.dihedrals.conformational_state_builder
+   CodeEntropy.levels.dihedrals.kernels
+   CodeEntropy.levels.dihedrals.peak_detection
+   CodeEntropy.levels.dihedrals.state_assignment
+   CodeEntropy.levels.dihedrals.topology
+
+Module contents
+---------------
 
 .. automodule:: CodeEntropy.levels.dihedrals
    :members:
diff --git a/docs/api/CodeEntropy.levels.dihedrals.state_assignment.rst b/docs/api/CodeEntropy.levels.dihedrals.state_assignment.rst
@@ -0,0 +1,7 @@
+CodeEntropy.levels.dihedrals.state\_assignment module
+=====================================================
+
+.. automodule:: CodeEntropy.levels.dihedrals.state_assignment
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.levels.dihedrals.topology.rst b/docs/api/CodeEntropy.levels.dihedrals.topology.rst
@@ -0,0 +1,7 @@
+CodeEntropy.levels.dihedrals.topology module
+============================================
+
+.. automodule:: CodeEntropy.levels.dihedrals.topology
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.levels.execution.chunks.rst b/docs/api/CodeEntropy.levels.execution.chunks.rst
@@ -0,0 +1,7 @@
+CodeEntropy.levels.execution.chunks module
+==========================================
+
+.. automodule:: CodeEntropy.levels.execution.chunks
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.levels.execution.policy.rst b/docs/api/CodeEntropy.levels.execution.policy.rst
@@ -0,0 +1,7 @@
+CodeEntropy.levels.execution.policy module
+==========================================
+
+.. automodule:: CodeEntropy.levels.execution.policy
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.levels.execution.reducers.rst b/docs/api/CodeEntropy.levels.execution.reducers.rst
@@ -0,0 +1,7 @@
+CodeEntropy.levels.execution.reducers module
+============================================
+
+.. automodule:: CodeEntropy.levels.execution.reducers
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.levels.execution.rst b/docs/api/CodeEntropy.levels.execution.rst
@@ -0,0 +1,22 @@
+CodeEntropy.levels.execution package
+====================================
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   CodeEntropy.levels.execution.chunks
+   CodeEntropy.levels.execution.policy
+   CodeEntropy.levels.execution.reducers
+   CodeEntropy.levels.execution.scheduler
+   CodeEntropy.levels.execution.tasks
+
+Module contents
+---------------
+
+.. automodule:: CodeEntropy.levels.execution
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.levels.execution.scheduler.rst b/docs/api/CodeEntropy.levels.execution.scheduler.rst
@@ -0,0 +1,7 @@
+CodeEntropy.levels.execution.scheduler module
+=============================================
+
+.. automodule:: CodeEntropy.levels.execution.scheduler
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.levels.execution.tasks.rst b/docs/api/CodeEntropy.levels.execution.tasks.rst
@@ -0,0 +1,7 @@
+CodeEntropy.levels.execution.tasks module
+=========================================
+
+.. automodule:: CodeEntropy.levels.execution.tasks
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.levels.frame_dag.rst b/docs/api/CodeEntropy.levels.frame_dag.rst
diff --git a/docs/api/CodeEntropy.levels.graph.conformation_dag.rst b/docs/api/CodeEntropy.levels.graph.conformation_dag.rst
@@ -0,0 +1,7 @@
+CodeEntropy.levels.graph.conformation\_dag module
+=================================================
+
+.. automodule:: CodeEntropy.levels.graph.conformation_dag
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.levels.graph.frame_dag.rst b/docs/api/CodeEntropy.levels.graph.frame_dag.rst
@@ -0,0 +1,7 @@
+CodeEntropy.levels.graph.frame\_dag module
+==========================================
+
+.. automodule:: CodeEntropy.levels.graph.frame_dag
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.levels.graph.level_dag.rst b/docs/api/CodeEntropy.levels.graph.level_dag.rst
@@ -0,0 +1,7 @@
+CodeEntropy.levels.graph.level\_dag module
+==========================================
+
+.. automodule:: CodeEntropy.levels.graph.level_dag
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.levels.graph.rst b/docs/api/CodeEntropy.levels.graph.rst
@@ -0,0 +1,20 @@
+CodeEntropy.levels.graph package
+================================
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   CodeEntropy.levels.graph.conformation_dag
+   CodeEntropy.levels.graph.frame_dag
+   CodeEntropy.levels.graph.level_dag
+
+Module contents
+---------------
+
+.. automodule:: CodeEntropy.levels.graph
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.levels.level_dag.rst b/docs/api/CodeEntropy.levels.level_dag.rst
diff --git a/docs/api/CodeEntropy.levels.nodes.axes_topology.rst b/docs/api/CodeEntropy.levels.nodes.axes_topology.rst
@@ -0,0 +1,7 @@
+CodeEntropy.levels.nodes.axes\_topology module
+==============================================
+
+.. automodule:: CodeEntropy.levels.nodes.axes_topology
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.levels.nodes.rst b/docs/api/CodeEntropy.levels.nodes.rst
@@ -1,19 +1,23 @@
 CodeEntropy.levels.nodes package
 ================================
 
-.. automodule:: CodeEntropy.levels.nodes
-   :members:
-   :show-inheritance:
-   :undoc-members:
-
 Submodules
 ----------
 
 .. toctree::
    :maxdepth: 4
 
    CodeEntropy.levels.nodes.accumulators
+   CodeEntropy.levels.nodes.axes_topology
    CodeEntropy.levels.nodes.beads
    CodeEntropy.levels.nodes.covariance
    CodeEntropy.levels.nodes.detect_levels
    CodeEntropy.levels.nodes.detect_molecules
+
+Module contents
+---------------
+
+.. automodule:: CodeEntropy.levels.nodes
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.levels.rst b/docs/api/CodeEntropy.levels.rst
@@ -1,17 +1,15 @@
 CodeEntropy.levels package
 ==========================
 
-.. automodule:: CodeEntropy.levels
-   :members:
-   :show-inheritance:
-   :undoc-members:
-
 Subpackages
 -----------
 
 .. toctree::
    :maxdepth: 4
 
+   CodeEntropy.levels.dihedrals
+   CodeEntropy.levels.execution
+   CodeEntropy.levels.graph
    CodeEntropy.levels.nodes
 
 Submodules
@@ -21,12 +19,16 @@ Submodules
    :maxdepth: 4
 
    CodeEntropy.levels.axes
-   CodeEntropy.levels.conformation_dag
-   CodeEntropy.levels.dihedrals
    CodeEntropy.levels.forces
-   CodeEntropy.levels.frame_dag
    CodeEntropy.levels.hierarchy
-   CodeEntropy.levels.level_dag
    CodeEntropy.levels.linalg
    CodeEntropy.levels.neighbors
    CodeEntropy.levels.search
+
+Module contents
+---------------
+
+.. automodule:: CodeEntropy.levels
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.molecules.rst b/docs/api/CodeEntropy.molecules.rst
@@ -1,15 +1,18 @@
 CodeEntropy.molecules package
 =============================
 
-.. automodule:: CodeEntropy.molecules
-   :members:
-   :show-inheritance:
-   :undoc-members:
-
 Submodules
 ----------
 
 .. toctree::
    :maxdepth: 4
 
    CodeEntropy.molecules.grouping
+
+Module contents
+---------------
+
+.. automodule:: CodeEntropy.molecules
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.results.rst b/docs/api/CodeEntropy.results.rst
diff --git a/docs/api/CodeEntropy.rst b/docs/api/CodeEntropy.rst
diff --git a/docs/api/CodeEntropy.trajectory.rst b/docs/api/CodeEntropy.trajectory.rst
