Merge remote-tracking branch 'upstream/cam_development' into clubb_intr_gpuization

Author: nusbaume

.gitmodules

@@ -36,7 +36,7 @@
 [submodule "atmos_phys"]
 	path = src/atmos_phys
 	url = https://github.com/ESCOMP/atmospheric_physics
-        fxtag = atmos_phys0_05_000
+        fxtag = atmos_phys0_07_001
         fxrequired = AlwaysRequired
 	fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 
@@ -144,42 +144,42 @@ fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
 [submodule "ccs_config"]
 path = ccs_config
 url = https://github.com/ESMCI/ccs_config_cesm.git
-fxtag = ccs_config_cesm1.0.0
+fxtag = ccs_config_cesm1.0.8
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 
 [submodule "cime"]
 path = cime
 url = https://github.com/ESMCI/cime
-fxtag = cime6.1.0
+fxtag = cime6.1.56
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESMCI/cime
 
 [submodule "cmeps"]
 path = components/cmeps
 url = https://github.com/ESCOMP/CMEPS.git
-fxtag = cmeps1.0.2
+fxtag = cmeps1.0.32
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 
 [submodule "cdeps"]
 path = components/cdeps
 url = https://github.com/ESCOMP/CDEPS.git
-fxtag = cdeps1.0.48
+fxtag = cdeps1.0.61
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
 
 [submodule "share"]
 path = share
 url = https://github.com/ESCOMP/CESM_share
-fxtag = share1.1.2
+fxtag = share1.1.6
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
 
 [submodule "parallelio"]
 path = libraries/parallelio
 url = https://github.com/NCAR/ParallelIO
-fxtag = pio2_6_2
+fxtag = pio2_6_3
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/NCAR/ParallelIO
 
@@ -193,13 +193,13 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CESM_CICE
 [submodule "clm"]
 path = components/clm
 url = https://github.com/ESCOMP/CTSM
-fxtag = ctsm5.2.027
+fxtag = ctsm5.3.016
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CTSM
 
 [submodule "fms"]
 path = libraries/FMS
 url = https://github.com/ESCOMP/FMS_interface
-fxtag = fi_240516
+fxtag = fi_240828
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/FMS_interface

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

@@ -2,27 +2,31 @@
 import argparse
 from git_fleximod import utils
 
-__version__ = "0.8.4"
+__version__ = "0.9.3"
 
 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")
@@ -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):
@@ -342,7 +342,7 @@ 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: