.travis.yml

@@ -10,6 +10,7 @@ before_install:
 
 install:
     - conda install --yes sphinx
+    - pip install sphinx_rtd_theme
 
 # Blacklist
 branches:

Doxyfile

@@ -1,5 +1,5 @@
 PROJECT_NAME           = "stochastic physics"
-PROJECT_NUMBER         = v0.0.1
+PROJECT_NUMBER         = v1
 STRIP_FROM_PATH        = 
 INPUT                  = 
 FILE_PATTERNS          = *.md  \

LICENSE.md

@@ -0,0 +1,21 @@
+Copyright 2020 The Regents of the University of Colorado
+
+The stochastic_physics code incorporated in the Unified Forecast System (UFS) 
+was jointly developed by the National Oceanic and Atmospheric Administration and the 
+University of Colorado, Boulder. The gold standard copy of the Code 
+will be maintained by NOAA at https://github.com/noaa-psd/stochastic_physics.
+
+In cooperation with the Copyright Holder, the National Oceanic and 
+Atmospheric Administration is releasing this code under the 
+GNU Lesser General PUblic License v3.0 (the "License"); you may not use this 
+file except in compliance with the License. 
+
+You may obtain a copy of the License at
+
+    https://www.gnu.org/licenses/lgpl-3.0.en.html
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License

docs/source/conf.py

@@ -19,7 +19,7 @@
 # -- Project information -----------------------------------------------------
 
 project = 'UFS stochastic physics'
-copyright = '2019, Philip Pegion'
+copyright = '2020,  The Regents of the University of Colorado'
 author = 'Philip Pegion'
 
 # The full version, including alpha/beta/rc tags
@@ -61,7 +61,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = 'sphinx_rtd_theme'
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

docs/source/developers_guide.rst

@@ -3,7 +3,7 @@ Developer's guide
 
 Code is housed on github at https://github.com/noaa-psd/stochastic_physics.  Please read more about the Development process at https://github.com/ufs-community/ufs/wiki/Development-Processes#Developing-with-Gitflow.
 
-Please make a fork and checkout the entire ufs-community weather model at https://github.com/ufs-community/ufs/wiki/Development-Processes#Developing-with-Gitflow and point to your fork of the stochastic_physics submodule.
+Please make a fork and checkout the entire ufs-community weather model at https://github.com/ufs-community/ufs-weather-model and point to your fork of the stochastic_physics submodule.
 
 Standalone testing
 """"""""""""""""""

docs/source/getting_started.rst

@@ -6,3 +6,5 @@ You should get the full system at https://github.com/ufs-community/ufs-weather-m
 
 In order to enable stochastic physics in a model run, you will need to turn it on via `namelist options <namelist_options.html>`_
 
+If using the CIME workflow decribed at https://ufs-mrweather-app.readthedocs.io/en/latest/, please add do_sppt=T, etc. to user_nl_ufsatm in the case directory.
+

main.doc

@@ -16,11 +16,11 @@
  *SHUM multiply the low-level specific humidity by a small random number each time-step. It attempts to address missing physics (cold pools, gust fronts), most active in convective regions
  *Land surface perturbations allow for land surface parameters such as Albedo, Soil Hydraulic Conductivity, LAI, and roughness lengths to vary in space. Addresses error in the land model and land-atmosphere interactions
  *
- *Due to the model’s numerics, any stochastic perturbation needs to be correlated in space and time in order to have the desired effect of upscale growth of the perturbations. This is achieved by creating a random pattern that has a specified decorrelation length-scale and is a first order auto-regressive process AR(1) in time with a specified decorrelation time-scale.  (The CA random pattern generator also satisfies this condition)~
+ *Due to the model’s numerics, any stochastic perturbation needs to be correlated in space and time in order to have the desired effect of upscale growth of the perturbations. This is achieved by creating a random pattern that has a specified decorrelation length-scale and is a first order auto-regressive process AR(1) in time with a specified decorrelation time-scale.  (The CA random pattern generator also satisfies this condition).
  *
  * \section install_sec Installation
  *
- * \subsection step1 1: clone the enitre github repo: 
+ * \subsection step1 1: clone the entire github repo: 
  * >git clone https://github.com/ufs-community/ufs-weather-model  
  *
  * >cd ufs-weather-model