Merge pull request #271 from xylar/fix-multisphinx

Don't include v0.1.0 in the docs

docs/conf.py

@@ -107,6 +107,7 @@
     ],
 }
 
-smv_tag_whitelist = r"^\d+\.\d+.\d+$"  # Include tags like "tags/2.5.0"
+# Include tags like "tags/1.0.0" -- 0.1.0-0.4.0 don't build
+smv_tag_whitelist = r'^(?!(0.1.0|0.2.0|0.3.0|0.4.0))\d+\.\d+.\d+$'
 smv_branch_whitelist = "main"
 smv_remote_whitelist = "origin"

docs/developers_guide/ocean/framework.md

@@ -226,7 +226,7 @@ convergence is being tested in space (or space and time together). The
 `base_resolution` is applied to all steps when convergence in time is tested.
 `base_resolution` times `dt_per_km` determines the base timestep in that case
 and is then multiplied by the `refinement_factors` to determine which time steps
-to test. When spherical meshes are being tested, the values in the 
+to test. When spherical meshes are being tested, the values in the
 `convergence` section are overridden by their values in the
 `spherical_convergence` section with a prefix indicating the mesh type.
 
@@ -441,7 +441,7 @@ mpas-ocean:
 on the associated config options (first at setup and again at runtime in case
 the config options have changed).
 
-In addition, the {py:class}`polaris.ocean.convergence.ConvergenceAnalysis`
+In addition, the {py:class}`polaris.ocean.convergence.analysis.ConvergenceAnalysis`
 step can serve as a parent class for analysis steps in convergence tests.  This
 parent class computes the error norm for the output from each resolution's
 forward step. It also produces the convergence plot.
@@ -486,12 +486,12 @@ class Analysis(ConvergenceAnalysis):
 ```
 
 Many tasks will also need to override the
-{py:meth}`polaris.ocean.convergence.ConvergenceAnalysis.exact_solution()`
+{py:meth}`polaris.ocean.convergence.analysis.ConvergenceAnalysis.exact_solution()`
 method. If not overridden, the analysis step will compute the difference of the
 output from the initial state.
 
 In some cases, the child class will also need to override the
-{py:meth}`polaris.ocean.convergence.ConvergenceAnalysis.get_output_field()`
+{py:meth}`polaris.ocean.convergence.analysis.ConvergenceAnalysis.get_output_field()`
 method if the requested field is not available directly from the output put
 rather needs to be computed.  The default behavior is to read the requested
 variable (the value associate the `'name'` key) at the time index closest to

docs/developers_guide/ocean/tasks/correlated_tracers_2d.md

@@ -12,7 +12,7 @@ of convergence.
 
 ## framework
 
-The config options for the `correlated_tracers_2d` test is described in 
+The config options for the `correlated_tracers_2d` test is described in
 {ref}`ocean-correlated-tracers-2d` in the User's Guide.
 
 Additionally, the test uses a `forward.yaml` file with a few common
@@ -41,14 +41,14 @@ descends from {py:class}`polaris.ocean.convergence.spherical.SphericalConvergenc
 and defines a step for running MPAS-Ocean from an initial condition produced in
 an `init` step. See {ref}`dev-ocean-convergence` for some relevant
 discussion of the parent class. The time step is determined from the resolution
-based on the `dt_per_km` config option in the `[convergence_forward]` 
+based on the `dt_per_km` config option in the `[convergence_forward]`
 section.  Other model config options are taken from `forward.yaml`.
 
 ### analysis
 
 The class {py:class}`polaris.ocean.tasks.sphere_transport.analysis.Analysis`
 descends from
-{py:class}`polaris.ocean.convergence.ConvergenceAnalysis`,
+{py:class}`polaris.ocean.convergence.analysis.ConvergenceAnalysis`,
 and defines a step for computing the error norm (L2) for the results
 at each resolution for tracers and layer thickness, saving them in
 `convergence_*.csv` and plotting them in `convergence_*.png`.

docs/developers_guide/ocean/tasks/divergent_2d.md

@@ -12,7 +12,7 @@ of convergence.
 
 ## framework
 
-The config options for the `divergent_2d` test is described in 
+The config options for the `divergent_2d` test is described in
 {ref}`ocean-divergent-2d` in the User's Guide.
 
 Additionally, the test uses a `forward.yaml` file with a few common
@@ -41,14 +41,14 @@ descends from {py:class}`polaris.ocean.convergence.spherical.SphericalConvergenc
 and defines a step for running MPAS-Ocean from an initial condition produced in
 an `init` step. See {ref}`dev-ocean-convergence` for some relevant
 discussion of the parent class. The time step is determined from the resolution
-based on the `dt_per_km` config option in the `[convergence_forward]` 
+based on the `dt_per_km` config option in the `[convergence_forward]`
 section.  Other model config options are taken from `forward.yaml`.
 
 ### analysis
 
 The class {py:class}`polaris.ocean.tasks.sphere_transport.analysis.Analysis`
 descends from
-{py:class}`polaris.ocean.convergence.ConvergenceAnalysis`,
+{py:class}`polaris.ocean.convergence.analysis.ConvergenceAnalysis`,
 and defines a step for computing the error norm (L2) for the results
 at each resolution for tracers and layer thickness, saving them in
 `convergence_*.csv` and plotting them in `convergence_*.png`.

docs/developers_guide/ocean/tasks/geostrophic.md

@@ -10,7 +10,7 @@ used to produce the initial condition to determine the rate of convergence.
 
 ## framework
 
-The config options for the `geostrophic` tests are described in 
+The config options for the `geostrophic` tests are described in
 {ref}`ocean-geostrophic` in the User's Guide.
 
 Additionally, the test uses a `forward.yaml` file with a few common
@@ -37,14 +37,14 @@ descends from {py:class}`polaris.ocean.convergence.spherical.SphericalConvergenc
 and defines a step for running MPAS-Ocean from an initial condition produced in
 an `init` step. See {ref}`dev-ocean-convergence` for some relevant
 discussion of the parent class. The time step is determined from the resolution
-based on the `dt_per_km` config option in the `[spherical_convergences]` 
+based on the `dt_per_km` config option in the `[spherical_convergences]`
 section.  Other model config options are taken from `forward.yaml`.
 
 ### analysis
 
 The class {py:class}`polaris.ocean.tasks.geostrophic.analysis.Analysis`
 descends from
-{py:class}`polaris.ocean.convergence.ConvergenceAnalysis`,
+{py:class}`polaris.ocean.convergence.analysis.ConvergenceAnalysis`,
 and defines a step for computing the error norm (L2) for the water-column
 thickness and normal velocity at each resolution, saving them in
 `convergence_h.csv` and `convergence_normalVelocity.csv`, and plotting them

docs/developers_guide/ocean/tasks/inertial_gravity_wave.md

@@ -1,4 +1,4 @@
-(dev-ocean-inertial-gravity-wave)= 
+(dev-ocean-inertial-gravity-wave)=
 
 # inertial_gravity_wave
 
@@ -8,11 +8,11 @@ is a linear shallow water test case at 4 resolutions (200, 100, 50, and
 
 The {py:class}`polaris.ocean.tasks.inertial_gravity_wave.InertialGravityWave`
 test performs a 10-hour run with a series of resolutions.  The convergence rate
-is calculated and visualizations are generated.  
+is calculated and visualizations are generated.
 
 ## framework
 
-The config options for the `inertial_gravity_wave` test are described in 
+The config options for the `inertial_gravity_wave` test are described in
 {ref}`ocean-inertial-gravity-wave` in the User's Guide.
 
 Additionally, the test uses a `forward.yaml` file with a few common
@@ -55,19 +55,19 @@ Namelist and streams files are updated by the parent class with time steps
 determined algorithmically based on config options. The number
 of cells is approximated from config options in
 {py:meth}`polaris.ocean.tasks.inertial_gravity_wave.forward.Forward.compute_cell_count()`
-so that this can be used to constrain the number of MPI tasks that Polaris 
-tasks have as  their target and minimum (if the resources are not explicitly 
-prescribed).  For MPAS-Ocean, PIO namelist options are modified and a graph 
-partition is generated as part of `runtime_setup()`.  Then, the ocean model 
-is run. Finally, validation of `layerThickness` and `normalVelocity` are 
-performed against a baseline if one is provided when calling 
+so that this can be used to constrain the number of MPI tasks that Polaris
+tasks have as  their target and minimum (if the resources are not explicitly
+prescribed).  For MPAS-Ocean, PIO namelist options are modified and a graph
+partition is generated as part of `runtime_setup()`.  Then, the ocean model
+is run. Finally, validation of `layerThickness` and `normalVelocity` are
+performed against a baseline if one is provided when calling
 {ref}`dev-polaris-setup`.
 
 ### analysis
 
 The class
 {py:class}`polaris.ocean.tasks.inertial_gravity_wave.analysis.Analysis`
-descends from {py:class}`polaris.ocean.convergence.ConvergenceAnalysis`
+descends from {py:class}`polaris.ocean.convergence.analysis.ConvergenceAnalysis`
 a step for computing the error from the final simulated field
 and the exact solution. It uses the config options to determine whether the
 convergence rate falls within acceptable bounds.

docs/developers_guide/ocean/tasks/manufactured_solution.md

@@ -3,20 +3,20 @@
 # manufactured_solution
 
 The manufactured solution test in `polaris.ocean.tasks.manufactured_solution`
-uses the Method of Manufactured Solutions (see 
+uses the Method of Manufactured Solutions (see
 {ref}`ocean-manufactured-solution`) at 4 resolutions (200, 100, 50, and 25 km).
 
 The {py:class}`polaris.ocean.tasks.manufactured_solution.ManufacturedSolution`
-test performs a 10-hour run. 
+test performs a 10-hour run.
 
 ## framework
 
-The config options for the `manufactured_solution` test are described in 
+The config options for the `manufactured_solution` test are described in
 {ref}`ocean-manufactured-solution` in the User's Guide.
 
 Additionally, the test uses a `forward.yaml` file with
-a few common model config options related to run duration and default 
-horizontal  and vertical momentum and tracer diffusion, as well as defining 
+a few common model config options related to run duration and default
+horizontal  and vertical momentum and tracer diffusion, as well as defining
 `mesh`, `input`, `restart`, and `output` streams.
 
 ### exact_solution
@@ -52,18 +52,18 @@ Namelist and streams files are updated by the parent class with time steps
 determined algorithmically based on config options. The number
 of cells is approximated from config options in
 {py:meth}`polaris.ocean.tasks.inertial_gravity_wave.forward.Forward.compute_cell_count()`
-so that this can be used to constrain the number of MPI tasks that Polaris 
-tasks have as  their target and minimum (if the resources are not explicitly 
-prescribed).  For MPAS-Ocean, PIO namelist options are modified and a graph 
-partition is generated as part of `runtime_setup()`.  Then, the ocean model 
-is run.  Finally, validation of `temperature`, `layerThickness` and 
-`normalVelocity` are performed against a baseline if one is provided when 
+so that this can be used to constrain the number of MPI tasks that Polaris
+tasks have as  their target and minimum (if the resources are not explicitly
+prescribed).  For MPAS-Ocean, PIO namelist options are modified and a graph
+partition is generated as part of `runtime_setup()`.  Then, the ocean model
+is run.  Finally, validation of `temperature`, `layerThickness` and
+`normalVelocity` are performed against a baseline if one is provided when
 calling {ref}`dev-polaris-setup`.
 
 ### analysis
 
 The class {py:class}`polaris.ocean.tasks.manufactured_solution.analysis.Analysis`
-descends from {py:class}`polaris.ocean.convergence.ConvergenceAnalysis`
+descends from {py:class}`polaris.ocean.convergence.analysis.ConvergenceAnalysis`
 a step for computing the error from the final simulated field
 and the exact solution. It uses the config options to determine whether the
 convergence rate falls within acceptable bounds.

docs/developers_guide/ocean/tasks/nondivergent_2d.md

@@ -12,7 +12,7 @@ of convergence.
 
 ## framework
 
-The config options for the `nondivergent_2d` test is described in 
+The config options for the `nondivergent_2d` test is described in
 {ref}`ocean-nondivergent-2d` in the User's Guide.
 
 Additionally, the test uses a `forward.yaml` file with a few common
@@ -41,14 +41,14 @@ descends from {py:class}`polaris.ocean.convergence.spherical.SphericalConvergenc
 and defines a step for running MPAS-Ocean from an initial condition produced in
 an `init` step. See {ref}`dev-ocean-convergence` for some relevant
 discussion of the parent class. The time step is determined from the resolution
-based on the `dt_per_km` config option in the `[convergence_forward]` 
+based on the `dt_per_km` config option in the `[convergence_forward]`
 section.  Other model config options are taken from `forward.yaml`.
 
 ### analysis
 
 The class {py:class}`polaris.ocean.tasks.sphere_transport.analysis.Analysis`
 descends from
-{py:class}`polaris.ocean.convergence.ConvergenceAnalysis`,
+{py:class}`polaris.ocean.convergence.analysis.ConvergenceAnalysis`,
 and defines a step for computing the error norm (L2) for the results
 at each resolution for tracers and layer thickness, saving them in
 `convergence_*.csv` and plotting them in `convergence_*.png`.

docs/developers_guide/ocean/tasks/rotation_2d.md

@@ -12,7 +12,7 @@ of convergence.
 
 ## framework
 
-The config options for the `rotation_2d` test is described in 
+The config options for the `rotation_2d` test is described in
 {ref}`ocean-rotation-2d` in the User's Guide.
 
 Additionally, the test uses a `forward.yaml` file with a few common
@@ -41,14 +41,14 @@ descends from {py:class}`polaris.ocean.convergence.spherical.SphericalConvergenc
 and defines a step for running MPAS-Ocean from an initial condition produced in
 an `init` step. See {ref}`dev-ocean-convergence` for some relevant
 discussion of the parent class. The time step is determined from the resolution
-based on the `dt_per_km` config option in the `[convergence_forward]` 
+based on the `dt_per_km` config option in the `[convergence_forward]`
 section.  Other model config options are taken from `forward.yaml`.
 
 ### analysis
 
 The class {py:class}`polaris.ocean.tasks.sphere_transport.analysis.Analysis`
 descends from
-{py:class}`polaris.ocean.convergence.ConvergenceAnalysis`,
+{py:class}`polaris.ocean.convergence.analysis.ConvergenceAnalysis`,
 and defines a step for computing the error norm (L2) for the results
 at each resolution for tracers and layer thickness, saving them in
 `convergence_*.csv` and plotting them in `convergence_*.png`.