Implement CAM4 aquaplanet (QPC4) configuration

.gitmodules

@@ -20,7 +20,7 @@
 [submodule "ncar-physics"]
         path          = src/physics/ncar_ccpp
 	url           = https://github.com/ESCOMP/atmospheric_physics
-	fxtag         = atmos_phys0_20_000
+	fxtag         = b47246dedfa7c377ac2bfb060e2d465beb931f2a
         fxrequired    = AlwaysRequired
         fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 [submodule "rrtmgp-data"]
@@ -32,33 +32,27 @@
 [submodule "ccs_config"]
         path          = ccs_config
         url           = https://github.com/ESMCI/ccs_config_cesm.git
-        fxtag         = ccs_config_cesm1.0.61
+        fxtag         = ccs_config_cesm1.0.65
         fxrequired    = ToplevelRequired
         fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 [submodule "cdeps"]
         path          = components/cdeps
         url           = https://github.com/ESCOMP/CDEPS.git
-        fxtag         = cdeps1.0.80
+        fxtag         = cdeps1.0.84
         fxrequired    = ToplevelRequired
         fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
 [submodule "cice"]
         path          = components/cice
         url           = https://github.com/ESCOMP/CESM_CICE
-        fxtag         = cesm3_cice6_6_0_13
+        fxtag         = cesm3_cice6_6_1_6
         fxrequired    = ToplevelRequired
         fxDONOTUSEurl = https://github.com/ESCOMP/CESM_CICE
 [submodule "cime"]
         path          = cime
         url           = https://github.com/ESMCI/cime
-        fxtag         = cime6.1.126
+        fxtag         = cime6.1.145
         fxrequired    = ToplevelRequired
 	fxDONOTUSEurl = https://github.com/ESMCI/cime
-[submodule "cism"]
-        path          = components/cism
-        url           = https://github.com/ESCOMP/CISM-wrapper
-        fxtag         = cismwrap_2_2_010
-        fxrequired    = ToplevelRequired
-        fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
 [submodule "clm"]
         path          = components/clm
         url           = https://github.com/ESCOMP/CTSM
@@ -68,7 +62,7 @@
 [submodule "cmeps"]
         path          = components/cmeps
         url           = https://github.com/ESCOMP/CMEPS.git
-        fxtag         = cmeps1.1.16
+        fxtag         = cmeps1.1.24
         fxrequired    = ToplevelRequired
 	fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 [submodule "fms"]
@@ -80,7 +74,7 @@
 [submodule "mizuRoute"]
         path          = components/mizuRoute
         url           = https://github.com/ESCOMP/mizuRoute
-        fxtag         = v3.0.0
+        fxtag         = v3.0.1
         fxrequired    = ToplevelRequired
         fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
 [submodule "mosart"]
@@ -104,12 +98,12 @@
 [submodule "share"]
         path          = share
         url           = https://github.com/ESCOMP/CESM_share
-        fxtag         = share1.1.9
+        fxtag         = share1.1.16
         fxrequired    = ToplevelRequired
 	fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
 [submodule "tools/CUPiD"]
 	path = tools/CUPiD
 	url = https://github.com/NCAR/CUPiD.git
-	fxtag         = v0.3.1
+	fxtag         = v0.4.0
 	fxrequired    = ToplevelRequired
 	fxDONOTUSEurl = https://github.com/NCAR/CUPiD.git

.lib/git-fleximod/.github/workflows/pytest.yaml

@@ -18,7 +18,7 @@ jobs:
       # reference the matrixe python version here.
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.9'
+          python-version: '3.12'
 
       # Cache the installation of Poetry itself, e.g. the next step. This prevents the workflow
       # from installing Poetry every time, which can be slow. Note the use of the Poetry version
@@ -29,7 +29,7 @@ jobs:
         uses: actions/cache@v4
         with:
           path: ~/.local
-          key: poetry-1.7.1
+          key: poetry-1.8.2
 
       # Install Poetry. You could do this manually, or there are several actions that do this.
       # `snok/install-poetry` seems to be minimal yet complete, and really just calls out to
@@ -42,7 +42,7 @@ jobs:
       # cache it.
       - uses: snok/install-poetry@v1
         with:
-          version: 1.7.1
+          version: 1.8.2
           virtualenvs-create: true
           virtualenvs-in-project: true
 
@@ -73,5 +73,7 @@ jobs:
       - run: |
           git config --global user.name "${GITHUB_ACTOR}"
           git config --global user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com"
-          poetry run pytest
-
+          poetry run pytest --doctest-modules
+#      - name: Setup tmate session
+#        if: ${{ failure() }}
+#        uses: mxschmitt/action-tmate@v3

.lib/git-fleximod/.pre-commit-config.yaml

@@ -2,7 +2,7 @@ exclude: ^utils/.*$
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v6.0.0
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace

.lib/git-fleximod/CODE_OF_CONDUCT.md

@@ -17,7 +17,7 @@ Examples of behaviors that contribute to a positive environment include:
 * Communicate openly with respect for others, critiquing ideas rather than individuals and gracefully accepting criticism
 * Acknowledging the contributions of others
 * Avoid personal attacks directed toward other participants
-* Be mindful of your surroundings and of your fellow participants 
+* Be mindful of your surroundings and of your fellow participants
 * Alert UCAR staff and suppliers/vendors if you notice a dangerous situation or someone in distress
 * Respect the rules and policies of the project and venue
 
@@ -29,7 +29,7 @@ Examples of unacceptable behavior include, but are not limited to:
 * Personal attacks directed at other guests, members, participants, etc.
 * Publishing others' private information, such as a physical or electronic address, without explicit permission
 * Alarming, intimidating, threatening, or hostile comments or conduct
-* Inappropriate use of nudity and/or sexual images 
+* Inappropriate use of nudity and/or sexual images
 * Threatening or stalking anyone, including a participant
 * Other conduct which could reasonably be considered inappropriate in a professional setting
 
@@ -60,7 +60,7 @@ the [Attribution](#attribution) section.
 ## Reporting
 Instances of unacceptable behavior can be brought to the attention of the project administrator(s) who may take any action as
 outlined in the [Consequences](#consequences) section below.
-However, making a report to a project administrator is not considered an 'official report' to UCAR. 
+However, making a report to a project administrator is not considered an 'official report' to UCAR.
 
 Instances of unacceptable behavior may also be reported directly to UCAR pursuant to [UCAR's Harassment Reporting and Complaint
 Procedure](https://www2.fin.ucar.edu/procedures/hr/harassment-reporting-and-complaint-procedure), or anonymously through [UCAR's

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

@@ -1,8 +1,8 @@
 from pathlib import Path
 import argparse, os, sys
-from git_fleximod import utils
 
-__version__ = "1.0.3"
+__version__ = "1.1.1"
+
 
 class CustomArgumentParser(argparse.ArgumentParser):
     def print_help(self, file=None):
@@ -17,13 +17,28 @@ def print_help(self, file=None):
         for path in candidate_paths:
             if os.path.exists(path):
                 with open(path) as f:
-                    print( f.read(), file=file)
+                    print(f.read(), file=file)
                     return
-        print( "README.md not found.", file=file)
+        print("README.md not found.", file=file)
+
 
 def find_root_dir(filename=".gitmodules"):
-    """ finds the highest directory in tree
-    which contains a file called filename """
+    """
+    Finds the highest directory in tree which contains a file called filename.
+
+    >>> import tempfile, os
+    >>> cwd = os.getcwd()
+    >>> with tempfile.TemporaryDirectory() as tmp:
+    ...     subdir = Path(tmp) / 'subdir'
+    ...     subdir.mkdir()
+    ...     f = Path(tmp) / '.gitmodules'
+    ...     _ = f.write_text('')
+    ...     os.chdir(subdir)
+    ...     result = find_root_dir('.gitmodules') == str(tmp)
+    ...     os.chdir(cwd)
+    ...     result
+    True
+    """
     d = Path.cwd()
     root = Path(d.root)
     dirlist = []
@@ -40,6 +55,7 @@ def find_root_dir(filename=".gitmodules"):
             return str(dl)
     return None
 
+
 def get_parser():
     description = """
     %(prog)s manages checking out groups of gitsubmodules with additional support for Earth System Models
@@ -116,6 +132,13 @@ def get_parser():
         "verbosity level each time.",
     )
 
+    parser.add_argument(
+        "--no-mods-details",
+        action="store_true",
+        default=False,
+        help="Suppress details on local mods in status output.",
+    )
+
     parser.add_argument(
         "-V",
         "--version",