Merge branch 'development' into hplin/registry_cnst_ic

Author: jimmielin

.github/workflows/branch_push_workflow.yml

@@ -20,10 +20,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     # Acquire github action routines
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     # Acquire specific version of python
     - name: Set up Python 3.11
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.11' # Semantic version range syntax or exact version of a Python version
     # Install required python packages

.github/workflows/fleximod_test.yaml

@@ -10,7 +10,7 @@ jobs:
         python-version: ["3.8", "3.x"]
     steps:
       - id: checkout-CESM
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - id: run-fleximod
         run: |
           $GITHUB_WORKSPACE/bin/git-fleximod update -o

.github/workflows/python_unit_tests.yml

@@ -26,10 +26,10 @@ jobs:
       fail-fast: false
     steps:
     # Acquire github action routines:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v5
     # Acquire specific version of python:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     # Install xmllint so tests pass:

.github/workflows/source_code_lint.yml

@@ -14,10 +14,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     # acquire github action routines
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v5
     # acquire specific version of python
     - name: Set up Python 3.10
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v6
       with:
         python-version: "3.10" # Use python 3.10
     # install required python packages

.lib/git-fleximod/README.md

@@ -25,7 +25,7 @@ Git-fleximod is a Python-based tool that extends Git's submodule and sparse chec
 
 ## Supported .gitmodules Variables
 
-    fxtag: Specify a specific tag or branch to checkout for a submodule.
+    fxtag: Specify a specific tag or hash to checkout for a submodule.  Branches are not acceptable.
     fxrequired: Mark a submodule's checkout behavior, with allowed values:
       - ToplevelRequired: Top-level and required (checked out only when this is the Toplevel module).
       - ToplevelOptional: Top-level and optional (checked out with --optional flag if this is the Toplevel module).

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

@@ -2,7 +2,7 @@
 import argparse, os, sys
 from git_fleximod import utils
 
-__version__ = "1.0.2"
+__version__ = "1.0.3"
 
 class CustomArgumentParser(argparse.ArgumentParser):
     def print_help(self, file=None):

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

@@ -400,6 +400,9 @@ async def update(self):
                     # This is a tag
                     tag = f"refs/tags/{self.fxtag}:refs/tags/{self.fxtag}"
                     status,_ = smgit.git_operation("fetch", newremote, tag)
+                else:
+                    # This is likely a hash, so fetch full history just in case
+                    status,_ = smgit.git_operation("fetch", newremote)
                 if status == 0:
                     status,_ = smgit.git_operation("checkout", self.fxtag)
                 if status:

.lib/git-fleximod/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "1.0.2"
+version = "1.0.3"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <[email protected]>"]
 maintainers = ["Jim Edwards <[email protected]>"]

.lib/git-fleximod/tbump.toml

@@ -2,7 +2,7 @@
 github_url = "https://github.com/jedwards4b/git-fleximod/"
 
 [version]
-current = "1.0.2"
+current = "1.0.3"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before

cime_config/create_readnl_files.py

@@ -160,7 +160,7 @@ class NLVar:
     """Class to hold information about a namelist variable entry"""
 
     # For unique dimension names
-    __new_dim_suffix = 0
+    __new_dim_suffix = {}
 
     # For validity error messages
     __kind_errstr = "Conflicting kind arguments, '{}' and '{}' for '{}'"
@@ -327,9 +327,9 @@ def _parse_array_desc(cls, alen, name):
            should have been sanitized by _parse_xml_type.
 
         >>> NLVar._parse_array_desc("10", "foo")
-        ((10,), ('cam_nl_autogen1_dimension',))
+        ((10,), ('foo_dimension',))
         >>> NLVar._parse_array_desc("15,3", "bar")
-        ((15, 3), ('cam_nl_autogen2_dimension', 'cam_nl_autogen3_dimension'))
+        ((15, 3), ('bar_dimension', 'bar_dimension_2'))
         >>> NLVar._parse_array_desc("15,,3", "foobar")
         Traceback (most recent call last):
         ...
@@ -338,7 +338,7 @@ def _parse_array_desc(cls, alen, name):
         if alen:
             try:
                 alens = tuple([int(x.strip()) for x in alen.split(',')])
-                anames = tuple([cls._new_nl_dimname() for x in alens])
+                anames = tuple([cls._new_nl_dimname(name) for x in alens])
             except:
                 emsg = f"Invalid array argument, '{alen}', for {name}"
                 raise ParseInternalError(emsg)
@@ -462,10 +462,23 @@ def write_decl(self, file, indent, intent=None):
         file.write(decl, indent)
 
     @classmethod
-    def _new_nl_dimname(cls):
+    def _new_nl_dimname(cls, var_name):
         """Return a new dimension name for use with a namelist array variable"""
-        cls.__new_dim_suffix += 1
-        return f"cam_nl_autogen{cls.__new_dim_suffix}_dimension"
+
+        # Update number of dimensions for the
+        # specified namelist variable:
+        if var_name in cls.__new_dim_suffix:
+            cls.__new_dim_suffix[var_name] += 1
+        else:
+            cls.__new_dim_suffix[var_name] = 1
+
+        # Create new dimension name based
+        # on the variable name and number of
+        # variable dimensions:
+        if cls.__new_dim_suffix[var_name] > 1:
+            return f"{var_name}_dimension_{cls.__new_dim_suffix[var_name]}"
+        else:
+            return f"{var_name}_dimension"
 
     def var_mpi_type(self):
         """Return the MPI variable type constant of this NLVar object.
@@ -483,7 +496,7 @@ def write_dimension_decls(self, ofile, indent):
         """
         for index, alen in enumerate(self.array_len):
             aname = self.__array_names[index]
-            ofile.write(f"integer, parameter   :: {aname} = {alen}", indent)
+            ofile.write(f"integer, public, parameter :: {aname} = {alen}", indent)
         # end for
 
     @property