docs(api): regenerate autodoc stubs after trajectory refactor

harryswift01 · harryswift01 · commit 81b0defaf38d · 2026-05-22T09:32:31.000+01:00
diff --git a/docs/api/CodeEntropy.entropy.nodes.orientational.rst b/docs/api/CodeEntropy.entropy.nodes.orientational.rst
@@ -0,0 +1,7 @@
+CodeEntropy.entropy.nodes.orientational module
+==============================================
+
+.. automodule:: CodeEntropy.entropy.nodes.orientational
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.entropy.nodes.rst b/docs/api/CodeEntropy.entropy.nodes.rst
@@ -14,4 +14,5 @@ Submodules
 
    CodeEntropy.entropy.nodes.aggregate
    CodeEntropy.entropy.nodes.configurational
+   CodeEntropy.entropy.nodes.orientational
    CodeEntropy.entropy.nodes.vibrational
diff --git a/docs/api/CodeEntropy.levels.mda.rst b/docs/api/CodeEntropy.levels.mda.rst
diff --git a/docs/api/CodeEntropy.levels.neighbors.rst b/docs/api/CodeEntropy.levels.neighbors.rst
@@ -0,0 +1,7 @@
+CodeEntropy.levels.neighbors module
+===================================
+
+.. automodule:: CodeEntropy.levels.neighbors
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.levels.nodes.find_neighbors.rst b/docs/api/CodeEntropy.levels.nodes.find_neighbors.rst
@@ -0,0 +1,7 @@
+CodeEntropy.levels.nodes.find\_neighbors module
+===============================================
+
+.. automodule:: CodeEntropy.levels.nodes.find_neighbors
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.levels.nodes.rst b/docs/api/CodeEntropy.levels.nodes.rst
@@ -18,3 +18,4 @@ Submodules
    CodeEntropy.levels.nodes.covariance
    CodeEntropy.levels.nodes.detect_levels
    CodeEntropy.levels.nodes.detect_molecules
+   CodeEntropy.levels.nodes.find_neighbors
diff --git a/docs/api/CodeEntropy.levels.rst b/docs/api/CodeEntropy.levels.rst
@@ -27,4 +27,5 @@ Submodules
    CodeEntropy.levels.hierarchy
    CodeEntropy.levels.level_dag
    CodeEntropy.levels.linalg
-   CodeEntropy.levels.mda
+   CodeEntropy.levels.neighbors
+   CodeEntropy.levels.search
diff --git a/docs/api/CodeEntropy.levels.search.rst b/docs/api/CodeEntropy.levels.search.rst
@@ -0,0 +1,7 @@
+CodeEntropy.levels.search module
+================================
+
+.. automodule:: CodeEntropy.levels.search
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.rst b/docs/api/CodeEntropy.rst
@@ -18,6 +18,7 @@ Subpackages
    CodeEntropy.levels
    CodeEntropy.molecules
    CodeEntropy.results
+   CodeEntropy.trajectory
 
 Submodules
 ----------
diff --git a/docs/api/CodeEntropy.trajectory.frames.rst b/docs/api/CodeEntropy.trajectory.frames.rst
@@ -0,0 +1,7 @@
+CodeEntropy.trajectory.frames module
+====================================
+
+.. automodule:: CodeEntropy.trajectory.frames
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.trajectory.mda.rst b/docs/api/CodeEntropy.trajectory.mda.rst
@@ -0,0 +1,7 @@
+CodeEntropy.trajectory.mda module
+=================================
+
+.. automodule:: CodeEntropy.trajectory.mda
+   :members:
+   :show-inheritance:
+   :undoc-members:
diff --git a/docs/api/CodeEntropy.trajectory.rst b/docs/api/CodeEntropy.trajectory.rst
@@ -0,0 +1,17 @@
+CodeEntropy.trajectory package
+==============================
+
+.. automodule:: CodeEntropy.trajectory
+   :members:
+   :show-inheritance:
+   :undoc-members:
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   CodeEntropy.trajectory.frames
+   CodeEntropy.trajectory.mda
+   CodeEntropy.trajectory.source
diff --git a/docs/api/CodeEntropy.trajectory.source.rst b/docs/api/CodeEntropy.trajectory.source.rst
@@ -0,0 +1,7 @@
+CodeEntropy.trajectory.source module
+====================================
+
+.. automodule:: CodeEntropy.trajectory.source
+   :members:
+   :show-inheritance:
+   :undoc-members:
