Base namelist dimension names on corresponding variable name (#437)

Tag name (required for release branches):
Originator(s): @nusbaume 

Description (include the issue title, and the keyword ['closes',
'fixes', 'resolves'] followed by the issue number):

This PR changes how the standard name for a namelist variable dimension
is generated, with the standard name now based off the corresponding
namelist variable name, plus an additional numerical suffix included for
any additional dimensions needed for that particular namelist variable.

This PR also makes all namelist variable dimensions public, and thus
directly accessible by CCPP-ized physics schemes.

Fixes #436 

Describe any changes made to build system:

M       cime_config/create_readnl_files.py
- Change namelist variable dimension naming convention, and make all
dimensions public. Also update doctests.

Describe any changes made to the namelist: N/A

List any changes to the defaults for the input datasets (e.g. boundary
datasets): N/A

List all files eliminated and why: N/A

List all files added and what they do: N/A

List all existing files that have been modified, and describe the
changes:
(Helpful git command: `git diff --name-status
development...<your_branch_name>`)

M test/unit/python/sample_files/namelist_files/kumquat_namelist.F90
M test/unit/python/sample_files/namelist_files/kumquat_namelist.meta
- Update unit test files to expect new namelist variable dimension
standard names and Fortran declarations.

M       .lib/git-fleximod/README.md
M       .lib/git-fleximod/git_fleximod/cli.py
M       .lib/git-fleximod/git_fleximod/submodule.py
M       .lib/git-fleximod/pyproject.toml
M       .lib/git-fleximod/tbump.toml
  - Update git-fleximod to version 1.0.3

M       .github/workflows/branch_push_workflow.yml
M       .github/workflows/fleximod_test.yaml
M       .github/workflows/python_unit_tests.yml
M       .github/workflows/source_code_lint.yml
  - Update checkout and setup-python to versions 5 and 6, respectively.

If there are new failures (compared to the
`test/existing-test-failures.txt` file),
have them OK'd by the gatekeeper, note them here, and add them to the
file.
If there are baseline differences, include the test and the reason for
the
diff. What is the nature of the change? Roundoff?

derecho/intel/aux_sima: No new test failures (only expected multitape
failure)

derecho/gnu/aux_sima:  ALL PASS

If this changes climate describe any run(s) done to evaluate the new
climate in enough detail that it(they) could be reproduced:

CAM-SIMA date used for the baseline comparison tests if different than
latest:

Author: nusbaume

.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