Merge branch 'develop' into feature/proftrace

.gitignore

@@ -131,5 +131,17 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
-.swp*
+# Ignore the following
+*.[aox]
+*.mod
+*.la
+*.lo
+
+# Ignore editor caches
+.*.sw[a-p]
+*DS_Store*
 *~
+
+# Ignore the following directories anywhere in the tree
+bin/
+

README.md

@@ -1,50 +1,32 @@
-__Kevin Dougherty__
 __September 2020__
 
+__Kevin Dougherty__
 
 # PyGSI
-Scripts used to validate GSI diagnostic files for JEDI
-
-
-# Anaconda Environment
-> Please read the documents for managing environments.  
-> Reference: https://github.com/Unidata/unidata-users-workshop  
-> Reference: https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html
-> Reference: https://www.youtube.com/watch?v=15DNH25UCi0
-
-I installed the Anaconda python distribution and created a new environment using the 'environment.yml' file provided in this directory. The name of the environment is DA_Diags. You can copy the the .yml file and run the following command in your terminal
-
-    conda env create -f ./environment.yml
-
-On a windows computer, to activate the `DA_Diags` environment, do this in the Windows Command Prompt:
-
-    activate DA_Diags
-
-Or, if you are in the PowerShell
-
-    cmd
-    activate DA_Diags
-
-If you are using a `bash` shell in Linux:
-
-    conda init bash  # Only need to do this once to initialize the correct shell
-    conda activate DA_Diags
-
-If you are using a `tcsh` shell in Linux:
-
-    conda init tsch  # Only need to do this once to initialize the correct shell
-    conda activate DA_Diags
-
-
-## Update environment
-Deactivate the environment
-
-    conda deactivate DA_Diags
-
-Update the environment.yml file, and update the conda environment
-
-    conda env update -f environment.yml
-
-List all the available environments
-
-    conda info --envs
+PyGSI is a collection of tools that read, filter, and plot diagnostic GSI netCDF4 files. 
+
+# Environment
+
+## On Supported Platforms
+To load the proper environment when working on Hera, use the following commands:
+```
+cd PyGSI
+module use modulefiles
+module load PyGSI/hera
+```
+
+To load the environment on Orion, use the following commands:
+```
+cd PyGSI
+module use modulefiles
+module load PyGSI/orion
+```
+
+## On Local Machine
+If working on a local machine, users can install PyGSI using pip.
+```
+cd PyGSI
+pip install .
+```
+
+For further instructions on how to use the tools within PyGSI, users can navigate to the documentation page here: [https://noaa-emc.github.io/PyGSI/#/](https://noaa-emc.github.io/PyGSI/#/).

fix/cloudy_radiance_info.txt

@@ -0,0 +1,62 @@
+radiance_mod_instr_input::
+!obsname    obsloc    ex_obserr  ex_biascor  cld_effect
+ gmi        sea       ex_obserr3   .true.      .false.
+ amsua      sea       ex_obserr1   .true.      .true.
+ atms       sea       ex_obserr1   .true.      .true.
+::
+
+obs_amsua::
+!  Parameters for the observation error model
+!  cclr [kg/m2] & ccld [kg/m2]: range of cloud amounts 
+!  over which the main increase in error take place
+!  ch   cclr   ccld
+    1   0.050  0.600
+    2   0.030  0.450
+    3   0.030  0.400
+    4   0.020  0.450
+    5   0.000  1.000
+    6   0.100  1.500
+   15   0.030  0.200
+::        
+
+obs_atms::
+!  Parameters for the observation error model
+!  cclr [kg/m2] & ccld [kg/m2]: range of cloud amounts
+!  over which the main increase in error take place
+!  ch   cclr   ccld
+    1   0.030  0.350
+    2   0.030  0.380
+    3   0.030  0.400
+    4   0.020  0.450
+    5   0.030  0.500
+    6   0.080  1.000
+    7   0.150  1.000
+   16   0.020  0.350
+   17   0.030  0.500
+   18   0.030  0.500
+   19   0.030  0.500
+   20   0.030  0.500
+   21   0.050  0.500
+   22   0.100  0.500
+::
+
+obs_gmi::
+!  Parameters for the observation error model
+!  cclr [kg/m2] & ccld [kg/m2]: range of cloud amounts
+!  over which the main increase in error take place
+!  ch   cclr   ccld  
+    1   0.050  0.200 
+    2   0.050  0.200 
+    3   0.050  0.200 
+    4   0.050  0.200 
+    5   0.050  0.200 
+    6   0.050  0.200 
+    7   0.050  0.200 
+    8   0.050  0.200 
+    9   0.050  0.200 
+   10   0.050  0.300 
+   11   0.050  0.200 
+   12   0.050  0.300 
+   13   0.050  0.300 
+::
+

modulefiles/PyGSI/hera.lua

@@ -0,0 +1,20 @@
+help([[
+Load environment for running PyGSI.
+]])
+
+local pkgName    = myModuleName()
+local pkgVersion = myModuleVersion()
+local pkgNameVer = myModuleFullName()
+
+conflict(pkgName)
+
+prepend_path("MODULEPATH", '/scratch1/NCEPDEV/da/python/opt/modulefiles/stack')
+
+load("hpc/1.2.0")
+load("miniconda3/4.6.14")
+load("eva/1.0.0")
+
+whatis("Name: ".. pkgName)
+whatis("Version: ".. pkgVersion)
+whatis("Category: PyGSI")
+whatis("Description: Load all libraries needed for PyGSI")

modulefiles/PyGSI/orion.lua

@@ -0,0 +1,19 @@
+-- NOAA HPC Orion Modulefile for PyGSI
+help([[
+]])
+
+local pkgName    = myModuleName()
+local pkgVersion = myModuleVersion()
+local pkgNameVer = myModuleFullName()
+
+prepend_path("MODULEPATH", '/work2/noaa/da/python/opt/modulefiles/stack')
+
+load("hpc/1.2.0")
+load("miniconda3/4.6.14")
+load("eva/1.0.0")
+
+whatis("Name: ".. pkgName)
+whatis("Version: " .. pkgVersion)
+whatis("Category: PyGSI")
+whatis("Description: Load all libraries needed for PyGSI")
+