Clean up input-data directories; Fix MERRA2 input; Add tests on Jet; Update CICE cap & fix time manager (was PR#664)

.gitmodules

@@ -4,8 +4,10 @@
   branch = develop
 [submodule "NEMS"]
   path = NEMS
-  url = https://github.com/NOAA-EMC/NEMS
-  branch = develop
+  #url = https://github.com/NOAA-EMC/NEMS
+  #branch = develop
+  url = https://github.com/hafs-community/NEMS.git
+  branch = hafs_couplehycom_cdeps
 [submodule "WW3"]
   path = WW3
   url = https://github.com/NOAA-EMC/WW3
@@ -28,8 +30,10 @@
   branch = dev/emc
 [submodule "CICE"]
   path = CICE-interface/CICE
-  url = https://github.com/NOAA-EMC/CICE
-  branch = emc/develop
+  #url = https://github.com/NOAA-EMC/CICE
+  #branch = emc/develop
+  url = https://github.com/DeniseWorthen/CICE
+  branch = feature/updcice
 [submodule "DATM"]
   path = DATM
   url = https://github.com/NOAA-EMC/NEMSdatm

.readthedocs.yaml

@@ -0,0 +1,23 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: doc/UsersGuide/source/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - requirements: doc/UsersGuide/requirements.txt

CICE-interface/cice_files.cmake

@@ -154,6 +154,7 @@ list(APPEND cice_nuopc_cmeps_driver_files
   CICE/cicecore/drivers/nuopc/cmeps/ice_prescribed_mod.F90
   CICE/cicecore/drivers/nuopc/cmeps/ice_scam.F90
   CICE/cicecore/drivers/nuopc/cmeps/ice_shr_methods.F90
+  CICE/cicecore/drivers/nuopc/cmeps/ice_mesh_mod.F90
 )
 
 #-- Using NUOPC DMI driver

doc/UsersGuide/source/_static/custom.css

@@ -0,0 +1,19 @@
+@import "default.css";
+
+div.admonition-todo {
+border-top: 2px solid red;
+border-bottom: 2px solid red;
+border-left: 2px solid red;
+border-right: 2px solid red;
+background-color: #ff6347
+}
+
+p.admonition-title {
+    display: offline;
+}
+
+/*p.first.admonition-title {
+background-color: #aa6347;
+width: 100%;
+}
+*/

doc/UsersGuide/source/conf.py

@@ -104,7 +104,7 @@
 html_static_path = ['_static']
 
 def setup(app):
-    app.add_stylesheet('custom.css')  # may also be an URL
+    app.add_css_file('custom.css')  # may also be an URL
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.