Fix nonhydro documentation

docs/developers_guide/ocean/api.rst

@@ -485,34 +485,33 @@ nonhydro
 .. currentmodule:: compass.ocean.tests.nonhydro
 
 .. autosummary::
-      :toctree: generated/
+   :toctree: generated/
 
    Nonhydro
-   configure
 
    stratified_seiche.StratifiedSeiche
-   stratified_seiche.StratifiedSeiche.setup
-   stratified_seiche.InitialState
-   stratified_seiche.InitialState.setup
-   stratified_seiche.InitialState.run
-   stratified_seiche.Forward
-   stratified_seiche.Forward.setup
-   stratified_seiche.Forward.run
-   stratified_seiche.Visualize
-   stratified_seiche.Visualize.setup 
-   stratified_seiche.Visualize.run
+   stratified_seiche.StratifiedSeiche.configure
+   stratified_seiche.initial_state.InitialState
+   stratified_seiche.initial_state.InitialState.setup
+   stratified_seiche.initial_state.InitialState.run
+   stratified_seiche.forward.Forward
+   stratified_seiche.forward.Forward.setup
+   stratified_seiche.forward.Forward.run
+   stratified_seiche.visualize.Visualize
+   stratified_seiche.visualize.Visualize.setup
+   stratified_seiche.visualize.Visualize.run
 
    solitary_wave.SolitaryWave
-   solitary_wave.SolitaryWave.setup
-   solitary_wave.InitialState
-   solitary_wave.InitialState.setup
-   solitary_wave.InitialState.run
-   solitary_wave.Forward
-   solitary_wave.Forward.setup
-   solitary_wave.Forward.run
-   solitary_wave.Visualize
-   solitary_wave.Visualize.setup
-   solitary_wave.Visualize.run
+   solitary_wave.SolitaryWave.configure
+   solitary_wave.initial_state.InitialState
+   solitary_wave.initial_state.InitialState.setup
+   solitary_wave.initial_state.InitialState.run
+   solitary_wave.forward.Forward
+   solitary_wave.forward.Forward.setup
+   solitary_wave.forward.Forward.run
+   solitary_wave.visualize.Visualize
+   solitary_wave.visualize.Visualize.setup
+   solitary_wave.visualize.Visualize.run
 
 planar_convergence
 ~~~~~~~~~~~~~~~~~~
@@ -828,4 +827,4 @@ ocean framework
    vertical.zlevel.compute_min_max_level_cell
    vertical.zlevel.compute_z_level_layer_thickness
    vertical.zlevel.compute_z_level_resting_thickness
-   vertical.zstar.init_z_star_vertical_coord
+   vertical.zstar.init_z_star_vertical_coord

docs/developers_guide/ocean/test_groups/index.rst

@@ -18,9 +18,10 @@ Test groups
    internal_wave
    isomip_plus
    merry_go_round
+   nonhydro
    planar_convergence
    soma
    sphere_transport
    spherical_harmonic_transform
    tides
-   ziso
+   ziso

docs/developers_guide/ocean/test_groups/nonhydro.rst

@@ -1,7 +1,7 @@
 .. _dev_ocean_nonhydro:
 
 nonhydro
-==================
+========
 
 The ``nonhydro`` test group
 (:py:class:`compass.ocean.tests.nonhydro.Nonhydro`)
@@ -28,7 +28,7 @@ elliptic problem.
 initial_state
 ~~~~~~~~~~~~~
 
-The class :py:class:`compass.ocean.tests.nonhydro_stratified_seiche.initial_state.InitialState`
+The class :py:class:`compass.ocean.tests.nonhydro.stratified_seiche.initial_state.InitialState`
 sets up the initial state for the stratified seiche test case.
 
 First, a planar mesh is generated using :py:func:`mpas_tools.planar_hex.make_planar_hex_mesh()`.  
@@ -40,7 +40,7 @@ velocity.
 forward
 ~~~~~~~
 
-The class :py:class:`compass.ocean.tests.stratified_seiche.forward.Forward`
+The class :py:class:`compass.ocean.tests.nonhydro.stratified_seiche.forward.Forward`
 defines a step for running MPAS-Ocean from the initial condition produced in
 the ``initial_state`` step.  The ``nonhydro_mode`` argument is a boolean that
 determines if the hydrostatic or the nonhydrostatic model is run. 
@@ -79,7 +79,7 @@ nonhydrostatic run share the same ``streams.forward`` file that defines
 initial_state
 ~~~~~~~~~~~~~
 
-The class :py:class:`compass.ocean.tests.nonhydro_solitary_wave.initial_state.InitialState`
+The class :py:class:`compass.ocean.tests.nonhydro.solitary_wave.initial_state.InitialState`
 sets up the initial state for the solitary test case.
 
 First, a planar mesh is generated using :py:func:`mpas_tools.planar_hex.make_planar_hex_mesh()`.
@@ -91,7 +91,7 @@ velocity.
 forward
 ~~~~~~~
 
-The class :py:class:`compass.ocean.tests.solitary_wave.forward.Forward`
+The class :py:class:`compass.ocean.tests.nonhydro.solitary_wave.forward.Forward`
 defines a step for running MPAS-Ocean from the initial condition produced in
 the ``initial_state`` step.  The ``nonhydro_mode`` argument is a boolean that
 determines if the hydrostatic or the nonhydrostatic model is run.
@@ -109,4 +109,4 @@ The ``visualize`` step defined by
 makes plots of the temperature profile at 40h for the hydrostatic
 and nonhydrostatic case. The plot shows that the nonhydrostatic result 
 leads to a train of rank-ordered solitary-like internal gravity waves, 
-whereas the hydrostatic model fails to capture correct physics. 
+whereas the hydrostatic model fails to capture correct physics. 

docs/users_guide/machines/chicoma.rst

@@ -66,7 +66,9 @@ Archiving
 LANL uses slurm. To obtain an interactive node:
 
 .. code-block:: bash
+
     salloc -N 1 -t 2:0:0 --qos=interactive
+
 Use ``--account=ACCOUNT_NAME`` to change to a particular account.
 
 Chicoma-CPU
@@ -189,4 +191,4 @@ To build the MPAS model with
 
 .. code-block:: bash
 
-    make [DEBUG=true] [OPENMP=true] [ALBANY=true] gnu-cray
+    make [DEBUG=true] [OPENMP=true] [ALBANY=true] gnu-cray

docs/users_guide/ocean/test_groups/index.rst

@@ -22,9 +22,10 @@ coming months.
    internal_wave
    isomip_plus
    merry_go_round
+   nonhydro
    planar_convergence
    soma
    sphere_transport
    spherical_harmonic_transform
    tides
-   ziso
+   ziso