noresm3_0_001_cam6_4_070: Update noresm branch from ESCOMP

.github/workflows/fleximod_test.yaml

@@ -0,0 +1,29 @@
+on: pull_request
+
+jobs:
+  fleximod-test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        # oldest supported and latest supported
+        python-version: ["3.7", "3.x"]
+    steps:
+      - id: checkout-CESM
+        uses: actions/checkout@v4
+      - id: run-fleximod
+        run: |
+          $GITHUB_WORKSPACE/bin/git-fleximod --optional update
+          echo
+          echo "Update complete, checking status"
+          echo
+          $GITHUB_WORKSPACE/bin/git-fleximod test
+      - id: check-cleanliness
+        run: |
+          echo
+          echo "Checking if git fleximod matches expected externals"
+          echo
+          git diff --exit-code
+#      - name: Setup tmate session
+#        if: ${{ failure() }}
+#        uses: mxschmitt/action-tmate@v3

.gitmodules

@@ -33,21 +33,14 @@
 [submodule "atmos_phys"]
 	path = src/atmos_phys
 	url = https://github.com/ESCOMP/atmospheric_physics
-	fxtag = atmos_phys0_05_001
+	fxtag = atmos_phys0_08_000
 	fxrequired = AlwaysRequired
 	fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 
-[submodule "camnor_phys"]
-	path = src/physics/camnor_phys
-	url = https://github.com/NorESMhub/CAM-Nor-physics
-	fxtag = camnor_noresm_v0.0.6
-  fxrequired = AlwaysRequired
-  fxDONOTUSEurl = https://github.com/NorESMhub/CAM-Nor-physics
-
 [submodule "carma"]
 	path = src/physics/carma/base
 	url = https://github.com/ESCOMP/CARMA_base.git
-	fxtag = carma4_01
+	fxtag = carma4_09
 	fxrequired = AlwaysRequired
 	fxDONOTUSEurl = https://github.com/ESCOMP/CARMA_base.git
 
@@ -84,7 +77,7 @@
 [submodule "oslo_aero"]
 	path = src/chemistry/oslo_aero
 	url = https://github.com/NorESMhub/OSLO_AERO
-	fxtag = oslo_aero_2_5a08d
+	fxtag = oslo_aero_3_0a001
 	fxrequired = AlwaysRequired
 	fxDONOTUSEurl = https://github.com/NorESMhub/OSLO_AERO.git
 
@@ -156,6 +149,24 @@
 	fxrequired = AlwaysOptional
 	fxDONOTUSEurl = https://github.com/MPAS-Dev/MPAS-Model.git
 
+#-----------------------------
+# Tools
+#-----------------------------
+
+[submodule "AeroTab"]
+path = tools/AeroTab
+url = https://github.com/NorESMhub/AeroTab
+fxtag = aerotab1_00_000
+fxrequired = AlwaysOptional
+fxDONOTUSEurl = https://github.com/NorESMhub/AeroTab
+
+[submodule "CUPiD"]
+path = tools/CUPiD
+url = https://github.com/NCAR/CUPiD.git
+fxtag = v0.1.4
+fxrequired = AlwaysOptional
+fxDONOTUSEurl = https://github.com/NCAR/CUPiD.git
+
 #-----------------------------
 # CESM libraries
 #-----------------------------
@@ -167,28 +178,17 @@ 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
+fxtag = ccs_config_noresm0.0.44
 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
+fxtag = cime6.1.73_noresm_v0
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/NorESMhub/cime.git
 
@@ -199,7 +199,7 @@ fxDONOTUSEurl = https://github.com/NorESMhub/cime.git
 [submodule "share"]
 path = share
 url = https://github.com/NorESMHub/NorESM_share
-fxtag = share1.1.2_noresm_v0
+fxtag = share1.1.9_noresm_v0
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/NorESMHub/NorESM_share
 
@@ -209,42 +209,42 @@ fxDONOTUSEurl = https://github.com/NorESMHub/NorESM_share
 
 [submodule "cdeps"]
 path = components/cdeps
-url = https://github.com/ESCOMP/CDEPS.git
-fxtag = cdeps1.0.51
+url = https://github.com/NorESMHub/CDEPS.git
+fxtag = cdeps1.0.70_noresm_v0
 fxrequired = ToplevelRequired
-fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
+fxDONOTUSEurl = https://github.com/NorESMHub/CDEPS.git
 
 [submodule "cice6"]
 path = components/cice
 url = https://github.com/NorESMhub/NorESM_CICE
-fxtag = cesm_cice6_5_0_20240702_noresm_v2
+fxtag = cesm_cice6_5_0_20240702_noresm_v3
 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_001
+url = https://github.com/NorESMhub/CISM-wrapper
+fxtag = cismwrap_2_2_006_noresm_v0
 fxrequired = ToplevelRequired
-fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
+fxDONOTUSEurl = https://github.com/NorESMhub/CISM-wrapper
 
 [submodule "clm"]
 path = components/clm
 url = https://github.com/NorESMhub/CTSM
-fxtag = ctsm5.3.0-noresm_v0
+fxtag = ctsm5.3.030-noresm_v0
 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
+fxtag = cmeps1.0.39_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
+fxtag = mosart1.1.08
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/MOSART

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

@@ -2,27 +2,31 @@
 import argparse
 from git_fleximod import utils
 
-__version__ = "0.8.4"
+__version__ = "0.9.4"
 
 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
-
+    try:
+        root = utils.execute_subprocess(["git","rev-parse", "--show-toplevel"],
+                                        output_to_caller=True ).rstrip()
+    except:
+        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
+    return Path(root)
 
 def get_parser():
     description = """

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

@@ -124,8 +124,8 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
     # set the repository remote
 
     logger.info("Setting remote origin in {}/{}".format(root_dir, path))
-    status = sprepo_git.git_operation("remote", "-v")
-    if url not in status:
+    _, remotelist = sprepo_git.git_operation("remote", "-v")
+    if url not in remotelist:
         sprepo_git.git_operation("remote", "add", "origin", url)
 
     topgit = os.path.join(gitroot, ".git")
@@ -181,6 +181,8 @@ def init_submodule_from_gitmodules(gitmodules, name, root_dir, logger):
     url = gitmodules.get(name, "url")
     assert path and url, f"Malformed .gitmodules file {path} {url}"
     tag = gitmodules.get(name, "fxtag")
+    if not tag:
+        tag = gitmodules.get(name, "hash")
     fxurl = gitmodules.get(name, "fxDONOTUSEurl")
     fxsparse = gitmodules.get(name, "fxsparse")
     fxrequired = gitmodules.get(name, "fxrequired")
@@ -213,7 +215,7 @@ def submodules_status(gitmodules, root_dir, toplevel=False, depth=0):
 
 def git_toplevelroot(root_dir, logger):
     rgit = GitInterface(root_dir, logger)
-    superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
+    _, superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
     return superroot
 
 def submodules_update(gitmodules, root_dir, requiredlist, force):
@@ -250,7 +252,6 @@ def submodules_update(gitmodules, root_dir, requiredlist, force):
                 newrequiredlist = ["AlwaysRequired"]
                 if optional:
                     newrequiredlist.append("AlwaysOptional")
-
                 submodules_update(gitsubmodules, repodir, newrequiredlist, force=force)
 
 def local_mods_output():
@@ -342,7 +343,7 @@ def main():
         excludelist=excludelist,
     )
     if not gitmodules.sections():
-        sys.exit("No submodule components found")
+        sys.exit(f"No submodule components found, root_dir={root_dir}")
     retval = 0
     if action == "update":
         submodules_update(gitmodules, root_dir, fxrequired, force)

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

@@ -59,11 +59,12 @@ def git_operation(self, operation, *args, **kwargs):
         command = self._git_command(operation, *newargs)
         if isinstance(command, list):
             try:
-                return utils.execute_subprocess(command, output_to_caller=True)
+                status, output = utils.execute_subprocess(command, status_to_caller=True, output_to_caller=True)
+                return status, output.rstrip()
             except Exception as e:
                 sys.exit(e)
         else:
-            return command
+            return 0, command
 
     def config_get_value(self, section, name):
         if self._use_module:
@@ -81,6 +82,8 @@ def config_get_value(self, section, name):
     def config_set_value(self, section, name, value):
         if self._use_module:
             with self.repo.config_writer() as writer:
+                if "." in section:  
+                    section = section.replace("."," \"")+'"'           
                 writer.set_value(section, name, value)
             writer.release()  # Ensure changes are saved
         else: