Update externals based on ESCOMP/CESM tag 'cesm3_0_beta03'

.gitmodules

@@ -30,14 +30,14 @@
         path = ccs_config
         url = https://github.com/EarthWorksOrg/ccs_config_cesm.git
         fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
-        fxtag = ccs_config-ew2.3.004
+        fxtag = ccs_config-ew2.3.005
         fxrequired = ToplevelRequired
 
 [submodule "cime"]
         path = cime
         url = https://github.com/EarthWorksOrg/cime
         fxDONOTUSEurl = https://github.com/ESMCI/cime
-        fxtag = cime-ew2.3.003
+        fxtag = cime-ew2.3.004
         fxrequired = ToplevelRequired
 
 # EarthWorks is not using fms
@@ -46,7 +46,7 @@
 #         url = https://github.com/ESCOMP/FMS_interface
 #         fxDONOTUSEurl = https://github.com/ESCOMP/FMS_interface
 #         fxrequired = ToplevelRequired
-#         fxtag = fi_240516
+#         fxtag = fi_240828
 
 [submodule "share"]
         path = share
@@ -59,15 +59,15 @@
         path = components/cam
         url = https://www.github.com/EarthWorksOrg/CAM
         fxDONOTUSEurl = https://www.github.com/ESCOMP/CAM
-        fxtag = cam-ew2.3.006
+        fxtag = cam-ew2.3.007
         fxrequired = ToplevelRequired
 
 [submodule "clm"]
         path = components/clm
-        url = https://github.com/EarthWorksOrg/CTSM
+        url = https://github.com/ESCOMP/CTSM
         fxDONOTUSEurl = https://github.com/ESCOMP/CTSM
         fxrequired = ToplevelRequired
-        fxtag = ctsm-ew2.3.004
+        fxtag = ctsm5.3.002
 
 [submodule "cice"]
         path = components/cice
@@ -82,7 +82,7 @@
 #         url = https://github.com/ESCOMP/MOM_interface
 #         fxDONOTUSEurl = https://github.com/ESCOMP/MOM_interface
 #         fxrequired = ToplevelRequired
-#         fxtag = mi_240705
+#         fxtag = mi_240923
 
 # EarthWorks is not using cism
 # [submodule "cism"]
@@ -97,14 +97,14 @@
         url = https://github.com/ESCOMP/CDEPS
         fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS
         fxrequired = ToplevelRequired
-        fxtag = cdeps1.0.45
+        fxtag = cdeps1.0.53
 
 [submodule "cmeps"]
         path = components/cmeps
         url = https://github.com/EarthWorksOrg/CMEPS.git
         fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
         fxrequired = ToplevelRequired
-        fxtag = cmeps-ew2.3.004
+        fxtag = cmeps-ew2.3.005
 
 # EarthWorks is not using rtm
 # [submodule "rtm"]
@@ -119,7 +119,7 @@
 #         path = components/ww3
 #         url = https://github.com/ESCOMP/WW3_interface
 #         fxDONOTUSEurl = https://github.com/ESCOMP/WW3_interface
-#         fxtag = ww3i_0.0.2
+#         fxtag = main_0.0.14
 #         fxrequired = ToplevelRequired
 
 # EarthWorks is not using mizuroute
@@ -142,7 +142,7 @@
         url = https://github.com/NCAR/ParallelIO
         fxDONOTUSEurl = https://github.com/NCAR/ParallelIO
         fxrequired = ToplevelRequired
-        fxtag = pio2_6_2
+        fxtag = pio2_6_3
 
 [submodule "mpi-serial"]
         path = libraries/mpi-serial

.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
 
@@ -74,4 +74,7 @@ jobs:
           git config --global user.name "${GITHUB_ACTOR}"
           git config --global user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com"
           poetry run pytest
+      - name: Setup tmate session
+        if: ${{ failure() }}
+        uses: mxschmitt/action-tmate@v3
 

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

@@ -2,7 +2,7 @@
 import argparse
 from git_fleximod import utils
 
-__version__ = "0.8.4"
+__version__ = "0.9.2"
 
 def find_root_dir(filename=".gitmodules"):
     """ finds the highest directory in tree

.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")
@@ -213,7 +213,7 @@ 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):

.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: