docs: update usage

docs/index.rst

@@ -39,7 +39,6 @@ of the *Anemoi* packages.
 -  :doc:`graphs/node_attributes`
 -  :doc:`graphs/edges`
 -  :doc:`graphs/edge_attributes`
--  :doc:`graphs/masks`
 
 .. toctree::
    :maxdepth: 1
@@ -51,7 +50,6 @@ of the *Anemoi* packages.
    graphs/node_attributes
    graphs/edges
    graphs/edge_attributes
-   graphs/masks
 
 *********
  Modules
@@ -63,6 +61,7 @@ of the *Anemoi* packages.
 -  :doc:`modules/edge_attributes`
 -  :doc:`modules/graph_creator`
 -  :doc:`modules/graph_inspector`
+-  :doc:`modules/masks`
 
 .. toctree::
    :maxdepth: 1
@@ -75,14 +74,15 @@ of the *Anemoi* packages.
    modules/edge_attributes
    modules/graph_creator
    modules/graph_inspector
+   modules/masks
 
 *******************
  Command line tool
 *******************
 
 -  :doc:`cli/introduction`
 -  :doc:`cli/create`
--  :doc:`cli/inspect`
+-  :doc:`cli/describe`
 -  :doc:`cli/inspect`
 
 .. toctree::

docs/usage/limited_area.rst

@@ -7,20 +7,33 @@
 Anemoi Graphs brings another level of flexibility to the user by
 allowing the definition of limited area graphs.
 
+*****************************************
+ Define hidden nodes in area of interest
+*****************************************
+
+The user can use a regional dataset to define the `data` nodes over the
+region of interest. Then, it can define the hidden nodes only over the
+region of interest using any of the ``LimitedArea_____Nodes`` classes.
+
+.. literalinclude:: yaml/lam_nodes_wo_boundary.yaml
+   :language: yaml
+
 ************************************************
  Cut out regional dataset into a global dataset
 ************************************************
 
-In this case, the user can use 2 datasets to build the data nodes
-combining nodes from the LAM dataset and the global dataset (as boundary
-forcings). The class `CutOutZarrDatasetNodes` allows this functionality:
+In this case, the user may want to include boundary forcings to the
+region of interest. Anemoi Graphs allows the user to use 2 datasets to
+build the `data` nodes, combining nodes from the LAM dataset and the
+global dataset (as boundary forcings). The class
+``CutOutZarrDatasetNodes`` allows this functionality:
 
 .. literalinclude:: yaml/cutout_zarr.yaml
    :language: yaml
 
-The `CutOutZarrDatasetNodes` supports an optional `thinning` argument
-which can be used to sampling points from the regional dataset to reduce
-computation during development stage.
+The ``CutOutZarrDatasetNodes`` supports an optional ``thinning``
+argument which can be used to sampling points from the regional dataset
+to reduce computation during development stage.
 
 In addition, this node builder class will create an additional node
 attribute with a mask showing which node correspond to each of the 2
@@ -42,10 +55,9 @@ datasets.
  Define hidden nodes over region of interest
 *********************************************
 
-Once the ``data`` nodes are defined, the user can define the hidden
-nodes only over the region of interest. In this case, the area of
-interest is defined by the ``data`` nodes masked by the ``cutout``
-attribute.
+Once the `data` nodes are defined, the user can define the hidden nodes
+only over the region of interest. In this case, the area of interest is
+defined by the `data` nodes masked by the ``cutout`` attribute.
 
 .. literalinclude:: yaml/limited_area_nodes.yaml
    :language: yaml

docs/usage/yaml/lam_nodes_wo_boundary.yaml

@@ -0,0 +1,14 @@
+nodes:
+  data:
+    node_builder:
+      _target_: anemoi.graphs.nodes.CutOutZarrDatasetNodes
+      dataset: /path/to/regional-dataset.zarr
+    attributes: ...
+  hidden:
+    node_builder:
+      _target_: anemoi.graphs.nodes.LimitedAreaTriNodes
+      resolution: 5
+      reference_node_name: data
+    attributes: ...
+
+edges: ...