Merge branch 'b4b-dev' into gitfleximodupdatev0.8.2

Make sure git-fleximod is pointing to 0.8.2
 Conflicts:
	.lib/git-fleximod/git_fleximod/cli.py
	.lib/git-fleximod/git_fleximod/git_fleximod.py
	.lib/git-fleximod/pyproject.toml
	.lib/git-fleximod/tbump.toml

.gitignore

@@ -1,7 +1,3 @@
-# ignore svn directories
-**/.svn/**
-.svn/
-
 # netcdf files
 *.nc
 # but don't ignore netcdf files here:

.gitmodules

@@ -1,90 +1,130 @@
+# This is a git submodule file with additional support for
+# git-fleximod (https://github.com/ESMCI/git-fleximod)
+#
+# The additional flags supported by git-fleximod are
+# fxtag - the tag associated with the submodule, this tag can be tested for
+#         consistancy with the submodule hash using git-fleximod status
+#         the hash can be updated to the tag using git-fleximod update
+#
+# fxrequired - indicates if a given submodule should be checked out on install
+#              submoudules can be toplevel or internal and required or optional
+#              toplevel means that the submodule should only be checked out if the
+#              module is the toplevel of the git repo (is not a submodule itself)
+#              internal means that the submodule is needed by the component whether
+#              the component is toplevel or the submodule of another repo
+#              required means that the submodule should always be checked out
+#              optional means that the submodule should only be checked out if the
+#              optional flag is provided to git-fleximod or the submodule name is
+#              explicitly listed on the git-fleximod command line.
+#
+# fxsparse -   this is a path to a git sparse checkout file indicating that the
+#              submodule should be checked out in sparse mode
+#
+# fxDONOTUSEurl    -   this field is used by git-fleximod test to insure that the url is pointing
+#              to the official url of the repo and not to an unofficial fork.
+#              It is intended for use of github workflows to test commits to protected
+#              repository branches.
+#
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
 fxtag = sci.1.73.0_api.35.0.0
 fxrequired = AlwaysRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/fates-release
 
 [submodule "cism"]
 path = components/cism
 url = https://github.com/ESCOMP/CISM-wrapper
 fxtag = cismwrap_2_2_001
 fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
 
 [submodule "rtm"]
 path = components/rtm
 url = https://github.com/ESCOMP/RTM
 fxtag = rtm1_0_79
 fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/RTM
 
 [submodule "mosart"]
 path = components/mosart
 url = https://github.com/ESCOMP/MOSART
 fxtag = mosart1_0_49
 fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
 
 [submodule "mizuRoute"]
 path = components/mizuRoute
 url = https://github.com/ESCOMP/mizuRoute
 fxtag = cesm-coupling.n02_v2.1.2
 fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
 
 [submodule "ccs_config"]
 path = ccs_config
 url = https://github.com/ESMCI/ccs_config_cesm.git
 fxtag = ccs_config_cesm0.0.106
 fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 
 [submodule "cime"]
 path = cime
 url = https://github.com/ESMCI/cime
 fxtag = cime6.0.246
 fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/cime
 
 [submodule "cmeps"]
 path = components/cmeps
 url = https://github.com/ESCOMP/CMEPS.git
 fxtag = cmeps0.14.63
 fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 
 [submodule "cdeps"]
 path = components/cdeps
 url = https://github.com/ESCOMP/CDEPS.git
 fxtag = cdeps1.0.34
 fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
 
 [submodule "share"]
 path = share
 url = https://github.com/ESCOMP/CESM_share
 fxtag = share1.0.19
 fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
 
 [submodule "mct"]
 path = libraries/mct
 url = https://github.com/MCSclimate/MCT
 fxtag = MCT_2.11.0
 fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/MCSclimate/MCT
 
 [submodule "parallelio"]
 path = libraries/parallelio
 url = https://github.com/NCAR/ParallelIO
 fxtag = pio2_6_2
 fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/ParallelIO
 
 [submodule "doc-builder"]
 path = doc/doc-builder
 url = https://github.com/ESMCI/doc-builder
 fxtag = v1.0.8
 fxrequired = ToplevelOptional
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/doc-builder

.lib/git-fleximod/git_fleximod/git_fleximod.py

@@ -252,6 +252,8 @@ def submodules_update(gitmodules, root_dir, requiredlist, force):
 
                 submodules_update(gitsubmodules, repodir, newrequiredlist, force=force)
 
+
+
 def local_mods_output():
     text = """\
     The submodules labeled with 'M' above are not in a clean state.

README

@@ -49,7 +49,7 @@ src --------------- CTSM Source code.
 lilac ------------- Lightweight Infrastructure for Land-Atmosphere Coupling (for coupling to a host atmosphere model)
 tools ------------- CTSM Offline tools to prepare input datasets and process output.
 cime_config ------- Configuration files of cime for compsets and CTSM settings
-bin/git-fleximod -- Script to manage the external source directories
+bin/git-fleximod -- Script to manage the needed sub-component source directories (handled with git submodule)
 py_env_create ----- Script to setup the python environment for CTSM python tools using conda
 python ------------ Python modules used in tools and testing and automated checking of ALL CTSM python scirpts
 

README_GITFLEXIMOD.rst

@@ -9,7 +9,7 @@ To obtain the CTSM code you need to do the following:
 
 #. Clone the repository. ::
 
-      git clone https://github.com/escomp/ctsm.git my_ctsm_sandbox
+      git clone https://github.com/ESCOMP/CTSM.git my_ctsm_sandbox
 
    This will create a directory ``my_ctsm_sandbox/`` in your current working directory.
 
@@ -25,6 +25,10 @@ To obtain the CTSM code you need to do the following:
    Additional documentation for git-fleximod appears here:
    https://github.com/ESMCI/git-fleximod?tab=readme-ov-file#git-fleximod
 
+"components" here refers to seperate git repositories for seperable parts of 
+the code (such as the MOSART or mizuRoute river models). Because they are
+managed with "submodule" in git hereafter we will refer to them as "submodule(s)".
+
 At this point you have a working version of CTSM.
 
 To see full details of how to set up a case, compile and run, see the CIME documentation at http://esmci.github.io/cime/ .
@@ -33,19 +37,19 @@ More details on git-fleximod
 ----------------------------
 
 The file **.gitmodules** in your top-level CTSM directory tells
-**git-fleximod** which tag/branch of each component should be
-brought in to generate your sandbox.
+**git-fleximod** which tag/branch of each submodule
+should be brought in to generate your sandbox.
 
-NOTE: If you manually modify an external without updating .gitmodules,
+NOTE: If you manually modify a submodule without updating .gitmodules,
 e.g. switch to a different tag, then rerunning git-fleximod will warn you of
 local changes you need to resolve.
-git-fleximod will not change a modified external back to what is specified in
+git-fleximod will not change a modified submodule back to what is specified in
 .gitmodules without the --force option.
 See below documentation `Customizing your CTSM sandbox`_ for more details.
 
 **You need to rerun git-fleximod whenever .gitmodules has
 changed** (unless you have already manually updated the relevant
-external(s) to have the correct branch/tag checked out). Common times
+submodule(s) to have the correct branch/tag checked out). Common times
 when this is needed are:
 
 * After checking out a new CTSM branch/tag
@@ -74,7 +78,7 @@ changes, or if you have any ongoing CTSM cases that were created from
 this sandbox. In these cases, it is often easiest to do a second **git
 clone**.
 
-Pointing to a different version of a component
+Pointing to a different version of a submodule
 ----------------------------------------------
 
 Each entry in **.gitmodules** has the following form (we use CIME as an
@@ -92,11 +96,11 @@ Each entry specifies either a tag or a hash. To point to a new tag or hash:
 #. Modify the relevant entry/entries in **.gitmodules** (e.g., changing
    ``cime6.0.246`` to ``cime6.0.247`` above)
 
-#. Checkout the new component(s)::
+#. Checkout the new submodule(s)::
 
-     ./bin/git-fleximod update <component>
+     ./bin/git-fleximod update <submodule>
 
-Keep in mind that changing individual components from a tag may result
+Keep in mind that changing individual submodule from a tag may result
 in an invalid model (won't compile, won't run, not scientifically
 meaningful) and is unsupported.
 
@@ -105,11 +109,10 @@ Committing your change to .gitmodules
 
 After making this change, it's a good idea to commit the change in your
 local CTSM git repository. First create a branch in your local
-repository, then commit it. (Unlike with subversion, branches are stored
-locally unless you explicitly push them up to GitHub. Feel free to
-create whatever local branches you'd like.) For example::
+repository, then commit it.  Feel free to create whatever local branches
+you'd like in git. For example::
 
   git checkout -b my_ctsm_branch
   git add .gitmodules
-  git commit -m "Update CIME to cime5.4.0-alpha.20"
+  git commit -m "Update CIME to cime6.0.247"
 

bld/CLMBuildNamelist.pm

@@ -2248,6 +2248,7 @@ sub setup_logic_urban {
 
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'building_temp_method');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_hac');
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_explicit_ac');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_traffic');
 }
 
@@ -3524,6 +3525,7 @@ sub setup_logic_hillslope {
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hillslope_pft_distribution_method' );
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hillslope_soil_profile_method' );
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_hillslope_routing', 'use_hillslope'=>$nl_flags->{'use_hillslope'} );
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hillslope_fsat_equals_zero', 'use_hillslope'=>$nl_flags->{'use_hillslope'} );
   my $use_hillslope = $nl->get_value('use_hillslope');
   my $use_hillslope_routing = $nl->get_value('use_hillslope_routing');
   if ( (! &value_is_true($use_hillslope)) && &value_is_true($use_hillslope_routing) ) {
@@ -3868,7 +3870,7 @@ sub setup_logic_urbantv_streams {
                  'sim_year_range'=>$nl_flags->{'sim_year_range'});
   }
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_urbantv', 'phys'=>$nl_flags->{'phys'},
-              'hgrid'=>"0.9x1.25" );
+              'hgrid'=>"0.9x1.25", 'urban_explicit_ac'=>$nl->get_value('urban_explicit_ac') );
   if ($opts->{'driver'} eq "nuopc" ) {
       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_urbantv', 'phys'=>$nl_flags->{'phys'},
                   'hgrid'=>"0.9x1.25" );
@@ -3981,7 +3983,7 @@ sub setup_logic_dust_emis {
         foreach my $option ( @zender_files_in_lnd_opts ) {
            add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $option,
                        'dust_emis_method'=>$dust_emis_method, 'zender_soil_erod_source'=>$zender_source,
-                       'hgrid'=>$nl_flags->{'res'}, 'lnd_tuning_mod'=>$nl_flags->{'lnd_tuning_mode'} );
+                       'hgrid'=>$nl_flags->{'res'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} );
         }
      } else {
         foreach my $option ( @zender_files_in_lnd_opts ) {