noresm2_5_alpha08: Update CAM, CTSM and add git-fleximod

.gitignore

@@ -1,11 +1,3 @@
-# managed directories that are checked out by the externals tool
-cime/
-components/
-libraries/
-share/
-ccs_config/
-tools/statistical_ensemble_test/
-
 # generated local files
 *.log
 

.gitmodules

@@ -0,0 +1,151 @@
+# 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.
+#
+
+#-----------------------------
+# Libraries
+#-----------------------------
+
+[submodule "parallelio"]
+path = libraries/parallelio
+url = https://github.com/NCAR/ParallelIO
+fxtag = pio2_6_2
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/NCAR/ParallelIO
+
+[submodule "mct"]
+path = libraries/mct
+url = https://github.com/MCSclimate/MCT
+fxtag = MCT_2.11.0
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/MCSclimate/MCT
+
+#-----------------------------
+# Configuration/CCS
+#-----------------------------
+
+[submodule "ccs_config"]
+path = ccs_config
+url = https://github.com/NorESMhub/ccs_config_noresm.git
+fxtag = ccs_config_noresm0.0.38
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/NorESMhub/ccs_config_noresm.git
+
+[submodule "cime"]
+path = cime
+url = https://github.com/NorESMhub/cime.git
+fxtag = cime6.1.28_noresm_v0
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/NorESMhub/cime.git
+
+#-----------------------------
+# Share
+#-----------------------------
+
+[submodule "share"]
+path = share
+url = https://github.com/NorESMHub/NorESM_share
+fxtag = share1.1.2_noresm_v0
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/NorESMHub/NorESM_share
+
+#-----------------------------
+# Components
+#-----------------------------
+
+[submodule "blom"]
+path = components/blom
+url = https://github.com/NorESMhub/BLOM.git
+fxtag = dev1.6.1.8
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/NorESMhub/BLOM.git
+
+[submodule "cam"]
+path = components/cam
+url = https://github.com/NorESMhub/CAM.git
+fxtag = noresm2_5_016_cam6_4_041
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/NorESMhub/CAM.git
+
+[submodule "cdeps"]
+path = components/cdeps
+url = https://github.com/ESCOMP/CDEPS.git
+fxtag = cdeps1.0.53
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
+
+[submodule "cice6"]
+path = components/cice
+url = https://github.com/NorESMhub/NorESM_CICE
+fxtag = cesm_cice6_5_0_20240702_noresm_v2
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/NorESMhub/NorESM_CICE
+
+[submodule "cism"]
+path = components/cism
+url = https://github.com/ESCOMP/CISM-wrapper
+fxtag = cismwrap_2_2_002_noresm_v1
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
+
+[submodule "clm"]
+path = components/clm
+url = https://github.com/NorESMhub/CTSM
+fxtag = ctsm5.3.11-noresm_v1
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/NorESMhub/CTSM
+
+[submodule "cmeps"]
+path = components/cmeps
+url = https://github.com/NorESMhub/CMEPS.git
+fxtag = cmeps1.0.20_noresm_v0
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/NorESMhub/CMEPS.git
+
+[submodule "mosart"]
+path = components/mosart
+url = https://github.com/ESCOMP/MOSART
+fxtag = mosart1.1.02
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
+
+[submodule "ww3"]
+path = components/ww3
+url = https://github.com/NorESMhub/WW3_interface.git
+fxtag = ww3_interface_noresm0.0.15
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/NorESMhub/WW3_interface.git
+
+#-----------------------------
+# Tools
+#-----------------------------
+
+[submodule "pycect"]
+path = tools/statistical_ensemble_test/pyCECT
+url = https://github.com/NCAR/PyCECT.git
+fxtag = 3.2.2
+fxrequired = ToplevelOptional

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

@@ -0,0 +1,129 @@
+from pathlib import Path
+import argparse
+from git_fleximod import utils
+
+__version__ = "0.9.2"
+
+def find_root_dir(filename=".gitmodules"):
+    """ finds the highest directory in tree
+    which contains a file called filename """
+    d = Path.cwd()
+    root = Path(d.root)
+    dirlist = []
+    dl = d
+    while dl != root:
+        dirlist.append(dl)
+        dl = dl.parent
+    dirlist.append(root)
+    dirlist.reverse()
+
+    for dl in dirlist:
+        attempt = dl / filename
+        if attempt.is_file():
+            return str(dl)
+    return None
+
+
+def get_parser():
+    description = """
+    %(prog)s manages checking out groups of gitsubmodules with additional support for Earth System Models
+    """
+    parser = argparse.ArgumentParser(
+        description=description, formatter_class=argparse.RawDescriptionHelpFormatter
+    )
+
+    #
+    # user options
+    #
+    choices = ["update", "status", "test"]
+    parser.add_argument(
+        "action",
+        choices=choices,
+        default="update",
+        help=f"Subcommand of git-fleximod, choices are {choices[:-1]}",
+    )
+
+    parser.add_argument(
+        "components",
+        nargs="*",
+        help="Specific component(s) to checkout. By default, "
+        "all required submodules are checked out.",
+    )
+
+    parser.add_argument(
+        "-C",
+        "--path",
+        default=find_root_dir(),
+        help="Toplevel repository directory.  Defaults to top git directory relative to current.",
+    )
+
+    parser.add_argument(
+        "-g",
+        "--gitmodules",
+        nargs="?",
+        default=".gitmodules",
+        help="The submodule description filename. " "Default: %(default)s.",
+    )
+
+    parser.add_argument(
+        "-x",
+        "--exclude",
+        nargs="*",
+        help="Component(s) listed in the gitmodules file which should be ignored.",
+    )
+    parser.add_argument(
+        "-f",
+        "--force",
+        action="store_true",
+        default=False,
+        help="Override cautions and update or checkout over locally modified repository.",
+    )
+
+    parser.add_argument(
+        "-o",
+        "--optional",
+        action="store_true",
+        default=False,
+        help="By default only the required submodules "
+        "are checked out. This flag will also checkout the "
+        "optional submodules relative to the toplevel directory.",
+    )
+
+    parser.add_argument(
+        "-v",
+        "--verbose",
+        action="count",
+        default=0,
+        help="Output additional information to "
+        "the screen and log file. This flag can be "
+        "used up to two times, increasing the "
+        "verbosity level each time.",
+    )
+
+    parser.add_argument(
+        "-V",
+        "--version",
+        action="version",
+        version=f"%(prog)s {__version__}",
+        help="Print version and exit.",
+    )
+
+    #
+    # developer options
+    #
+    parser.add_argument(
+        "--backtrace",
+        action="store_true",
+        help="DEVELOPER: show exception backtraces as extra " "debugging output",
+    )
+
+    parser.add_argument(
+        "-d",
+        "--debug",
+        action="store_true",
+        default=False,
+        help="DEVELOPER: output additional debugging "
+        "information to the screen and log file.",
+    )
+
+    return parser