From 3fb677a8326371579c980f61db38b9454742c7b8 Mon Sep 17 00:00:00 2001
From: Cheryl Craig <cacraig@ucar.edu>
Date: Wed, 3 Dec 2025 14:29:54 -0700
Subject: [PATCH 1/3] Squashed '.lib/git-fleximod/' changes from
 d4ebd399..5796799a

5796799a Bump to 1.1.1
8b1259b8 Merge pull request #90 from ESMCI/add_doctests
bf8ab483 remove CI pylint test
5a3bc529 update wrapt
53d434cf update wrapt
edc3d24f update wrapt
2743863d update wrapt
912e3098 update wrapt
34432fd1 update wrapt
df8ec2b6 more updates
4093354e update pre-commit-hooks
95aee9eb update pre-commit-hooks
a38f5c74 update pre-commit-hooks
5e4a1234 update pre-commit-hooks
074c63a7 update pre-commit-hooks
ce6957e0 update pre-commit-hooks
19e07700 update pre-commit-hooks
2b16d9d3 update pre-commit-hooks
c8ee10dd update pre-commit-hooks
7fc5fad9 fix doctest in cli.py
6ca52ff4 add more doctests
5a6fd5a4 add more doctests
30116877 add doctests to workflow
c68eec46 add pre-commit test to workflow
309d9864 pre-commit cleanup
6d121624 add some doctests
493940fc Merge pull request #89 from ESMCI/fix/overwrite_local_mod
cb8c95bb fix the 3rd test
86590829 add a test of 3rd scenario
351a2399 add a test of 2nd scenario
b901ff53 add a test
1c8b8058 remove commented code
eab580b5 fix issue with overwritting local mods
9d0d74a0 Bump to 1.1.0
bce9bf76 Merge pull request #87 from billsacks/fix_modified_output
a8d24c0d Fix imports to hopefully work in automated testing
9d63e762 Normalize whitespace in tests
7f4b9a47 Fix alignment of tree indicators
74ef626d Allow suppressing details of local mods in status output
7642150c Indent child submodules with a nice tree-like output
f4053683 Fix status output when there are local modifications

git-subtree-dir: .lib/git-fleximod
git-subtree-split: 5796799a6c414bed35bb473fab0e5b6c2257a950
---
 .github/workflows/pytest.yaml  |    9 +-
 .pre-commit-config.yaml        |    2 +-
 CODE_OF_CONDUCT.md             |    6 +-
 git_fleximod/cli.py            |   35 +-
 git_fleximod/git_fleximod.py   |  104 ++--
 git_fleximod/gitinterface.py   |   77 ++-
 git_fleximod/gitmodules.py     |    9 +-
 git_fleximod/metoflexi.py      |   65 +-
 git_fleximod/submodule.py      |  259 +++++---
 git_fleximod/utils.py          |   44 +-
 poetry.lock                    | 1058 +++++++++++++++++++++++---------
 pyproject.toml                 |    7 +-
 tbump.toml                     |    2 +-
 tests/conftest.py              |  153 +++--
 tests/test_a_import.py         |    1 +
 tests/test_b_update.py         |  105 +++-
 tests/test_c_required.py       |   26 +-
 tests/test_d_complex.py        |  120 ++--
 tests/test_e_complex_update.py |  126 ++--
 tests/utils_for_tests.py       |   13 +
 20 files changed, 1561 insertions(+), 660 deletions(-)
 create mode 100644 tests/utils_for_tests.py

diff --git a/.github/workflows/pytest.yaml b/.github/workflows/pytest.yaml
index 6cb8102b94..1d8d10f544 100644
--- a/.github/workflows/pytest.yaml
+++ b/.github/workflows/pytest.yaml
@@ -73,8 +73,7 @@ jobs:
       - run: |
           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
-
+          poetry run pytest --doctest-modules
+#      - name: Setup tmate session
+#        if: ${{ failure() }}
+#        uses: mxschmitt/action-tmate@v3
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 2f6089da72..fc6ec61b6f 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@ exclude: ^utils/.*$
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v6.0.0
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
index 84f2925bba..f2c52d5b77 100644
--- a/CODE_OF_CONDUCT.md
+++ b/CODE_OF_CONDUCT.md
@@ -17,7 +17,7 @@ Examples of behaviors that contribute to a positive environment include:
 * Communicate openly with respect for others, critiquing ideas rather than individuals and gracefully accepting criticism
 * Acknowledging the contributions of others
 * Avoid personal attacks directed toward other participants
-* Be mindful of your surroundings and of your fellow participants 
+* Be mindful of your surroundings and of your fellow participants
 * Alert UCAR staff and suppliers/vendors if you notice a dangerous situation or someone in distress
 * Respect the rules and policies of the project and venue
 
@@ -29,7 +29,7 @@ Examples of unacceptable behavior include, but are not limited to:
 * Personal attacks directed at other guests, members, participants, etc.
 * Publishing others' private information, such as a physical or electronic address, without explicit permission
 * Alarming, intimidating, threatening, or hostile comments or conduct
-* Inappropriate use of nudity and/or sexual images 
+* Inappropriate use of nudity and/or sexual images
 * Threatening or stalking anyone, including a participant
 * Other conduct which could reasonably be considered inappropriate in a professional setting
 
@@ -60,7 +60,7 @@ the [Attribution](#attribution) section.
 ## Reporting
 Instances of unacceptable behavior can be brought to the attention of the project administrator(s) who may take any action as
 outlined in the [Consequences](#consequences) section below.
-However, making a report to a project administrator is not considered an 'official report' to UCAR. 
+However, making a report to a project administrator is not considered an 'official report' to UCAR.
 
 Instances of unacceptable behavior may also be reported directly to UCAR pursuant to [UCAR's Harassment Reporting and Complaint
 Procedure](https://www2.fin.ucar.edu/procedures/hr/harassment-reporting-and-complaint-procedure), or anonymously through [UCAR's
diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py
index e4acc55582..9551bc96b8 100644
--- a/git_fleximod/cli.py
+++ b/git_fleximod/cli.py
@@ -1,8 +1,8 @@
 from pathlib import Path
 import argparse, os, sys
-from git_fleximod import utils
 
-__version__ = "1.0.3"
+__version__ = "1.1.1"
+
 
 class CustomArgumentParser(argparse.ArgumentParser):
     def print_help(self, file=None):
@@ -17,13 +17,28 @@ def print_help(self, file=None):
         for path in candidate_paths:
             if os.path.exists(path):
                 with open(path) as f:
-                    print( f.read(), file=file)
+                    print(f.read(), file=file)
                     return
-        print( "README.md not found.", file=file)
+        print("README.md not found.", file=file)
+
 
 def find_root_dir(filename=".gitmodules"):
-    """ finds the highest directory in tree
-    which contains a file called filename """
+    """
+    Finds the highest directory in tree which contains a file called filename.
+
+    >>> import tempfile, os
+    >>> cwd = os.getcwd()
+    >>> with tempfile.TemporaryDirectory() as tmp:
+    ...     subdir = Path(tmp) / 'subdir'
+    ...     subdir.mkdir()
+    ...     f = Path(tmp) / '.gitmodules'
+    ...     _ = f.write_text('')
+    ...     os.chdir(subdir)
+    ...     result = find_root_dir('.gitmodules') == str(tmp)
+    ...     os.chdir(cwd)
+    ...     result
+    True
+    """
     d = Path.cwd()
     root = Path(d.root)
     dirlist = []
@@ -40,6 +55,7 @@ def find_root_dir(filename=".gitmodules"):
             return str(dl)
     return None
 
+
 def get_parser():
     description = """
     %(prog)s manages checking out groups of gitsubmodules with additional support for Earth System Models
@@ -116,6 +132,13 @@ def get_parser():
         "verbosity level each time.",
     )
 
+    parser.add_argument(
+        "--no-mods-details",
+        action="store_true",
+        default=False,
+        help="Suppress details on local mods in status output.",
+    )
+
     parser.add_argument(
         "-V",
         "--version",
diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py
index b3c4fece4e..ce63b8bd10 100755
--- a/git_fleximod/git_fleximod.py
+++ b/git_fleximod/git_fleximod.py
@@ -7,21 +7,27 @@
 
 import os
 import shutil
-import logging
-import textwrap
 import asyncio
+import logging
+from configparser import NoOptionError
 from git_fleximod import utils
 from git_fleximod import cli
 from git_fleximod.gitinterface import GitInterface
 from git_fleximod.gitmodules import GitModules
 from git_fleximod.submodule import Submodule
 
-# logger variable is global
-logger = None
+logger = logging.getLogger(__name__)
 
 
 def fxrequired_allowed_values():
-    return ["ToplevelRequired", "ToplevelOptional", "AlwaysRequired", "AlwaysOptional", "TopLevelRequired", "TopLevelOptional"]
+    return [
+        "ToplevelRequired",
+        "ToplevelOptional",
+        "AlwaysRequired",
+        "AlwaysOptional",
+        "TopLevelRequired",
+        "TopLevelOptional",
+    ]
 
 
 def commandline_arguments(args=None):
@@ -69,6 +75,7 @@ def commandline_arguments(args=None):
         options.components,
         options.exclude,
         options.force,
+        options.no_mods_details,
         action,
     )
 
@@ -151,8 +158,8 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
 
     if os.path.isdir(os.path.join(root_dir, path, ".git")):
         with utils.pushd(sprep_repo):
-            if os.path.isdir(os.path.join(topgit,".git")):
-                shutil.rmtree(os.path.join(topgit,".git"))
+            if os.path.isdir(os.path.join(topgit, ".git")):
+                shutil.rmtree(os.path.join(topgit, ".git"))
             shutil.move(".git", topgit)
             with open(".git", "w") as f:
                 f.write("gitdir: " + os.path.relpath(topgit))
@@ -167,7 +174,6 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
         with utils.pushd(sprep_repo):
             if os.path.isfile(sparsefile):
                 shutil.copy(sparsefile, gitsparse)
-                
 
     # Finally checkout the repo
     sprepo_git.git_operation("fetch", "origin", "--tags")
@@ -177,7 +183,8 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
     rgit.config_set_value(f'submodule "{name}"', "active", "true")
     rgit.config_set_value(f'submodule "{name}"', "url", url)
 
-def init_submodule_from_gitmodules(gitmodules, name, root_dir, logger):
+
+def init_submodule_from_gitmodules(gitmodules, name, root_dir, llogger):
     path = gitmodules.get(name, "path")
     url = gitmodules.get(name, "url")
     assert path and url, f"Malformed .gitmodules file {path} {url}"
@@ -187,60 +194,73 @@ def init_submodule_from_gitmodules(gitmodules, name, root_dir, logger):
     fxurl = gitmodules.get(name, "fxDONOTUSEurl")
     fxsparse = gitmodules.get(name, "fxsparse")
     fxrequired = gitmodules.get(name, "fxrequired")
-    return Submodule(root_dir, name, path, url, fxtag=tag, fxurl=fxurl, fxsparse=fxsparse, fxrequired=fxrequired, logger=logger)
+    return Submodule(
+        root_dir,
+        name,
+        path,
+        url,
+        fxtag=tag,
+        fxurl=fxurl,
+        fxsparse=fxsparse,
+        fxrequired=fxrequired,
+        logger=llogger,
+    )
 
-def submodules_status(gitmodules, root_dir, toplevel=False, depth=0):
+
+def submodules_status(
+    gitmodules, root_dir, toplevel=False, depth=0, no_mods_details=False
+):
     testfails = 0
     localmods = 0
     needsupdate = 0
-    wrapper = textwrap.TextWrapper(initial_indent=' '*(depth*10), width=120,subsequent_indent=' '*(depth*20))
     for name in gitmodules.sections():
         submod = init_submodule_from_gitmodules(gitmodules, name, root_dir, logger)
-            
-        result,n,l,t = submod.status()
+
+        result, n, l, t = submod.status(depth=depth, no_mods_details=no_mods_details)
         if toplevel or not submod.toplevel():
-            print(wrapper.fill(result))
+            print(result)
             testfails += t
             localmods += l
             needsupdate += n
         subdir = os.path.join(root_dir, submod.path)
         if os.path.exists(os.path.join(subdir, ".gitmodules")):
             gsubmod = GitModules(logger, confpath=subdir)
-            t,l,n = submodules_status(gsubmod, subdir, depth=depth+1)
+            t, l, n = submodules_status(
+                gsubmod, subdir, depth=depth + 1, no_mods_details=no_mods_details
+            )
             if toplevel or not submod.toplevel():
                 testfails += t
                 localmods += l
                 needsupdate += n
-            
+
     return testfails, localmods, needsupdate
 
-def git_toplevelroot(root_dir, logger):
-    rgit = GitInterface(root_dir, logger)
+
+def git_toplevelroot(root_dir, llogger):
+    rgit = GitInterface(root_dir, llogger)
     _, superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
     return superroot
 
+
 async def submodules_update(gitmodules, root_dir, requiredlist, force):
     async def update_submodule(name, requiredlist, force):
         submod = init_submodule_from_gitmodules(gitmodules, name, root_dir, logger)
 
-        _, needsupdate, localmods, testfails = submod.status()
         if not submod.fxrequired:
             submod.fxrequired = "AlwaysRequired"
-        fxrequired = submod.fxrequired    
+        fxrequired = submod.fxrequired
         allowedvalues = fxrequired_allowed_values()
         assert fxrequired in allowedvalues
 
         superroot = git_toplevelroot(root_dir, logger)
-                                     
-        if (
-            fxrequired
-            and ((superroot and "Toplevel" in fxrequired)
-            or fxrequired not in requiredlist)
+
+        if fxrequired and (
+            (superroot and "Toplevel" in fxrequired) or fxrequired not in requiredlist
         ):
             if "Optional" in fxrequired and "Optional" not in requiredlist:
                 if fxrequired.startswith("Always"):
                     print(f"Skipping optional component {name:>20}")
-                return # continue to next submodule
+                return  # continue to next submodule
         optional = "AlwaysOptional" in requiredlist
 
         if fxrequired in requiredlist:
@@ -253,11 +273,16 @@ async def update_submodule(name, requiredlist, force):
                 newrequiredlist = ["AlwaysRequired"]
                 if optional:
                     newrequiredlist.append("AlwaysOptional")
-                await submodules_update(gitsubmodules, repodir, newrequiredlist, force=force)
+                await submodules_update(
+                    gitsubmodules, repodir, newrequiredlist, force=force
+                )
 
-    tasks = [update_submodule(name, requiredlist, force) for name in gitmodules.sections()]
+    tasks = [
+        update_submodule(name, requiredlist, force) for name in gitmodules.sections()
+    ]
     await asyncio.gather(*tasks)
 
+
 def local_mods_output():
     text = """\
     The submodules labeled with 'M' above are not in a clean state.
@@ -271,7 +296,8 @@ def local_mods_output():
 """
     print(text)
 
-def submodules_test(gitmodules, root_dir):
+
+def submodules_test(gitmodules, root_dir, no_mods_details=False):
     """
     This function tests the git submodules based on the provided parameters.
 
@@ -282,12 +308,15 @@ def submodules_test(gitmodules, root_dir):
     Parameters:
     gitmodules (ConfigParser): The gitmodules configuration.
     root_dir (str): The root directory for the git operation.
+    no_mods_details (bool, optional): If True, suppress details on local mods in status output
 
     Returns:
     int: The number of test failures.
     """
     # First check that fxtags are present and in sync with submodule hashes
-    testfails, localmods, needsupdate = submodules_status(gitmodules, root_dir)
+    testfails, localmods, needsupdate = submodules_status(
+        gitmodules, root_dir, no_mods_details=no_mods_details
+    )
     print("")
     # Then make sure that urls are consistant with fxurls (not forks and not ssh)
     # and that sparse checkout files exist
@@ -315,14 +344,17 @@ def main():
         includelist,
         excludelist,
         force,
+        no_mods_details,
         action,
     ) = commandline_arguments()
     # Get a logger for the package
     global logger
     logger = logging.getLogger(__name__)
 
-    logger.info("action is {} root_dir={} file_name={}".format(action, root_dir, file_name))
-    
+    logger.info(
+        "action is {} root_dir={} file_name={}".format(action, root_dir, file_name)
+    )
+
     if not root_dir or not os.path.isfile(os.path.join(root_dir, file_name)):
         if root_dir:
             file_path = utils.find_upwards(root_dir, file_name)
@@ -352,7 +384,9 @@ def main():
     if action == "update":
         asyncio.run(submodules_update(gitmodules, root_dir, fxrequired, force))
     elif action == "status":
-        tfails, lmods, updates = submodules_status(gitmodules, root_dir, toplevel=True)
+        tfails, lmods, updates = submodules_status(
+            gitmodules, root_dir, toplevel=True, no_mods_details=no_mods_details
+        )
         if tfails + lmods + updates > 0:
             print(
                 f"    testfails = {tfails}, local mods = {lmods}, needs updates {updates}\n"
@@ -360,7 +394,7 @@ def main():
             if lmods > 0:
                 local_mods_output()
     elif action == "test":
-        retval = submodules_test(gitmodules, root_dir)
+        retval = submodules_test(gitmodules, root_dir, no_mods_details=no_mods_details)
     else:
         utils.fatal_error(f"unrecognized action request {action}")
     return retval
diff --git a/git_fleximod/gitinterface.py b/git_fleximod/gitinterface.py
index 022426d28c..cdd99748b5 100644
--- a/git_fleximod/gitinterface.py
+++ b/git_fleximod/gitinterface.py
@@ -1,19 +1,33 @@
-import os
+# git_fleximod/gitinterface.py
 import sys
 from . import utils
 from pathlib import Path
 import asyncio
 
+
 class GitInterface:
     def __init__(self, repo_path, logger):
-        logger.debug("Initialize GitInterface for {}".format(repo_path))
         if isinstance(repo_path, str):
             self.repo_path = Path(repo_path).resolve()
         elif isinstance(repo_path, Path):
             self.repo_path = repo_path.resolve()
         else:
             raise TypeError("repo_path must be a str or Path object")
-        self.logger = logger
+        if logger is not None:
+            self.logger = logger
+        else:
+            import logging
+
+            self.logger = logging.getLogger(__name__)
+            if not self.logger.hasHandlers():
+                handler = logging.StreamHandler()
+                formatter = logging.Formatter(
+                    "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
+                )
+                handler.setFormatter(formatter)
+                self.logger.addHandler(handler)
+                self.logger.setLevel(logging.DEBUG)
+        self.logger.debug("Initialize GitInterface for {}".format(repo_path))
         try:
             import git
 
@@ -32,6 +46,12 @@ def __init__(self, repo_path, logger):
         self.logger.info(msg)
 
     def _git_command(self, operation, *args):
+        """
+        Internal: Build git command or call GitPython.
+        >>> gi = GitInterface('.', None)
+        >>> isinstance(gi._git_command('status'), list) or isinstance(gi._git_command('status'), str)
+        True
+        """
         self.logger.info(operation)
         if self._use_module and operation != "submodule":
             try:
@@ -60,6 +80,15 @@ def _git_operation_command(self, operation, args):
 
     # pylint: disable=unused-argument
     def git_operation(self, operation, *args, **kwargs):
+        """
+        Run a git operation and return status and output.
+        >>> gi = GitInterface('.', None)
+        >>> status, output = gi.git_operation('status')
+        >>> isinstance(status, int)
+        True
+        >>> isinstance(output, str)
+        True
+        """
         newargs = []
         for a in args:
             # Do not use ssh interface
@@ -70,7 +99,9 @@ def git_operation(self, operation, *args, **kwargs):
         command = self._git_command(operation, *newargs)
         if isinstance(command, list):
             try:
-                status, output = utils.execute_subprocess(command, status_to_caller=True, 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)
@@ -79,13 +110,17 @@ def git_operation(self, operation, *args, **kwargs):
 
     # pylint: disable=unused-argument
     async def git_operation_async(self, operation, *args, **kwargs):
+        """
+        Asynchronously run a git operation.
+        (Doc test not run: async context)
+        """
         command = self._git_operation_command(operation, args)
         if isinstance(command, list):
             try:
                 process = await asyncio.create_subprocess_exec(
                     *command,
                     stdout=asyncio.subprocess.PIPE,
-                    stderr=asyncio.subprocess.PIPE
+                    stderr=asyncio.subprocess.PIPE,
                 )
                 stdout, stderr = await process.communicate()
                 status = process.returncode
@@ -97,6 +132,12 @@ async def git_operation_async(self, operation, *args, **kwargs):
             return 0, command
 
     def config_get_value(self, section, name):
+        """
+        Get a git config value.
+        >>> gi = GitInterface('.', None)
+        >>> gi.config_get_value('user', 'name') is None or isinstance(gi.config_get_value('user', 'name'), str)
+        True
+        """
         if self._use_module:
             config = self.repo.config_reader()
             try:
@@ -105,18 +146,36 @@ def config_get_value(self, section, name):
                 val = None
             return val
         else:
-            cmd = ("git", "-C", str(self.repo_path), "config", "--get", f"{section}.{name}")
+            cmd = (
+                "git",
+                "-C",
+                str(self.repo_path),
+                "config",
+                "--get",
+                f"{section}.{name}",
+            )
             output = utils.execute_subprocess(cmd, output_to_caller=True)
             return output.strip()
 
     def config_set_value(self, section, name, value):
+        """
+        Set a git config value.
+        (Doc test not run: modifies config)
+        """
         if self._use_module:
             with self.repo.config_writer() as writer:
-                if "." in section:  
-                    section = section.replace("."," \"")+'"'           
+                if "." in section:
+                    section = section.replace(".", ' "') + '"'
                 writer.set_value(section, name, value)
             writer.release()  # Ensure changes are saved
         else:
-            cmd = ("git", "-C", str(self.repo_path), "config", f"{section}.{name}", value)
+            cmd = (
+                "git",
+                "-C",
+                str(self.repo_path),
+                "config",
+                f"{section}.{name}",
+                value,
+            )
             self.logger.info(cmd)
             utils.execute_subprocess(cmd, output_to_caller=True)
diff --git a/git_fleximod/gitmodules.py b/git_fleximod/gitmodules.py
index cf8b350dd6..7e02848970 100644
--- a/git_fleximod/gitmodules.py
+++ b/git_fleximod/gitmodules.py
@@ -1,4 +1,4 @@
-import shutil, os
+# git_fleximod/gitmodules.py
 from pathlib import Path
 from configparser import RawConfigParser, ConfigParser
 from .lstripreader import LstripReader
@@ -26,19 +26,18 @@ def __init__(
             )
         )
         super().__init__()
-        self.conf_file = (Path(confpath) / Path(conffile))
+        self.conf_file = Path(confpath) / Path(conffile)
         if self.conf_file.exists():
             self.read_file(LstripReader(str(self.conf_file)), source=conffile)
         self.includelist = includelist
         self.excludelist = excludelist
         self.isdirty = False
-        
+
     def reload(self):
         self.clear()
         if self.conf_file.exists():
             self.read_file(LstripReader(str(self.conf_file)), source=self.conf_file)
 
-        
     def set(self, name, option, value):
         """
         Sets a configuration value for a specific submodule:
@@ -74,7 +73,7 @@ def save(self):
             with open(self.conf_file, "w") as fd:
                 self.write(fd)
         self.isdirty = False
-        
+
     def __del__(self):
         self.save()
 
diff --git a/git_fleximod/metoflexi.py b/git_fleximod/metoflexi.py
index cc347db2dd..d605b347f6 100755
--- a/git_fleximod/metoflexi.py
+++ b/git_fleximod/metoflexi.py
@@ -11,6 +11,7 @@
 
 logger = None
 
+
 def find_root_dir(filename=".git"):
     d = Path.cwd()
     root = Path(d.root)
@@ -30,10 +31,13 @@ def get_parser():
         description=description, formatter_class=argparse.RawDescriptionHelpFormatter
     )
 
-    parser.add_argument('-e', '--externals', nargs='?',
-                        default='Externals.cfg',
-                        help='The externals description filename. '
-                        'Default: %(default)s.')
+    parser.add_argument(
+        "-e",
+        "--externals",
+        nargs="?",
+        default="Externals.cfg",
+        help="The externals description filename. " "Default: %(default)s.",
+    )
 
     parser.add_argument(
         "-C",
@@ -70,6 +74,7 @@ def get_parser():
 
     return parser
 
+
 def commandline_arguments(args=None):
     parser = get_parser()
 
@@ -92,11 +97,8 @@ def commandline_arguments(args=None):
         level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers
     )
 
-    return(
-        options.path,
-        options.gitmodules,
-        options.externals
-        )
+    return (options.path, options.gitmodules, options.externals)
+
 
 class ExternalRepoTranslator:
     """
@@ -110,12 +112,13 @@ def __init__(self, rootpath, gitmodules, externals):
         self.externals = (rootpath / Path(externals)).resolve()
         print(f"Translating {self.externals}")
         self.git = GitInterface(rootpath, logger)
-        
-#    def __del__(self):
-#        if (self.rootpath / "save.gitignore"):
-            
 
-    def translate_single_repo(self, section, tag, url, path, efile, hash_, sparse, protocol):
+    #    def __del__(self):
+    #        if (self.rootpath / "save.gitignore"):
+
+    def translate_single_repo(
+        self, section, tag, url, path, efile, hash_, sparse, protocol
+    ):
         """
         Translates a single repository based on configuration details.
 
@@ -145,13 +148,13 @@ def translate_single_repo(self, section, tag, url, path, efile, hash_, sparse, p
                 self.gitmodules.set(section, "fxtag", tag)
             if hash_:
                 self.gitmodules.set(section, "fxtag", hash_)
-            
+
             self.gitmodules.set(section, "fxDONOTUSEurl", url)
             if sparse:
                 self.gitmodules.set(section, "fxsparse", sparse)
             self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
         else:
-            newpath = (self.rootpath / Path(path))
+            newpath = self.rootpath / Path(path)
             if newpath.exists():
                 shutil.rmtree(newpath)
                 logger.info("Creating directory {}".format(newpath))
@@ -159,7 +162,9 @@ def translate_single_repo(self, section, tag, url, path, efile, hash_, sparse, p
             if tag:
                 logger.info("cloning {}".format(section))
                 try:
-                    self.git.git_operation("clone", "-b", tag, "--depth", "1", url, path)
+                    self.git.git_operation(
+                        "clone", "-b", tag, "--depth", "1", url, path
+                    )
                 except:
                     self.git.git_operation("clone", url, path)
                     with utils.pushd(newpath):
@@ -172,27 +177,28 @@ def translate_single_repo(self, section, tag, url, path, efile, hash_, sparse, p
                 git.git_operation("checkout", hash_)
             if sparse:
                 print("setting as sparse submodule {}".format(section))
-                sparsefile = (newpath / Path(sparse))
-                newfile = (newpath / ".git" / "info" / "sparse-checkout")
+                sparsefile = newpath / Path(sparse)
+                newfile = newpath / ".git" / "info" / "sparse-checkout"
                 print(f"sparsefile {sparsefile} newfile {newfile}")
                 shutil.copy(sparsefile, newfile)
-        
-            logger.info("adding submodule {}".format(section))        
+
+            logger.info("adding submodule {}".format(section))
             self.gitmodules.save()
-            self.git.git_operation("submodule", "add", "-f", "--name", section, url, path)
-            self.git.git_operation("submodule","absorbgitdirs")
+            self.git.git_operation(
+                "submodule", "add", "-f", "--name", section, url, path
+            )
+            self.git.git_operation("submodule", "absorbgitdirs")
             self.gitmodules.reload()
             if tag:
                 self.gitmodules.set(section, "fxtag", tag)
             if hash_:
                 self.gitmodules.set(section, "fxtag", hash_)
-            
+
             self.gitmodules.set(section, "fxDONOTUSEurl", url)
             if sparse:
                 self.gitmodules.set(section, "fxsparse", sparse)
             self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
-    
-        
+
     def translate_repo(self):
         """
         Translates external repositories defined within an external file.
@@ -218,8 +224,9 @@ def translate_repo(self):
             sparse = econfig.get(section, "sparse", raw=False, fallback=None)
             protocol = econfig.get(section, "protocol", raw=False, fallback=None)
 
-            self.translate_single_repo(section, tag, url, path, efile, hash_, sparse, protocol)
-
+            self.translate_single_repo(
+                section, tag, url, path, efile, hash_, sparse, protocol
+            )
 
 
 def _main():
@@ -231,6 +238,6 @@ def _main():
         logger.info("Translating {}".format(rootpath))
         t.translate_repo()
 
-        
+
 if __name__ == "__main__":
     sys.exit(_main())
diff --git a/git_fleximod/submodule.py b/git_fleximod/submodule.py
index 5a8c3f935e..b786ae9400 100644
--- a/git_fleximod/submodule.py
+++ b/git_fleximod/submodule.py
@@ -6,7 +6,8 @@
 from git_fleximod import utils
 from git_fleximod.gitinterface import GitInterface
 
-class Submodule():
+
+class Submodule:
     """
     Represents a Git submodule with enhanced features for flexible management.
 
@@ -21,9 +22,29 @@ class Submodule():
         fxrequired (str): Indicates if the submodule is optional or required (optional).
         logger (logging.Logger): Logger instance for logging (optional).
     """
-    def __init__(self, root_dir, name, path, url, fxtag=None, fxurl=None, fxsparse=None, fxrequired=None, logger=None):
+
+    def __init__(
+        self,
+        root_dir,
+        name,
+        path,
+        url,
+        fxtag=None,
+        fxurl=None,
+        fxsparse=None,
+        fxrequired=None,
+        logger=None,
+    ):
         """
         Initializes a new Submodule instance with the provided attributes.
+
+        >>> sm = Submodule('.', 'foo', 'bar', 'https://example.com')
+        >>> sm.name
+        'foo'
+        >>> sm.path
+        'bar'
+        >>> sm.url
+        'https://example.com'
         """
         self.name = name
         self.root_dir = root_dir
@@ -38,13 +59,19 @@ def __init__(self, root_dir, name, path, url, fxtag=None, fxurl=None, fxsparse=N
             self.fxrequired = "AlwaysRequired"
         self.logger = logger
 
-    def status(self):
+    def status(self, depth=0, no_mods_details=False):
         """
         Checks the status of the submodule and returns 4 parameters:
         - result (str): The status of the submodule.
         - needsupdate (bool): An indicator if the submodule needs to be updated.
         - localmods (bool): An indicator if the submodule has local modifications.
         - testfails (bool): An indicator if the submodule has failed a test, this is used for testing purposes.
+
+        Args:
+            depth (int, optional): depth of this submodule relative to root, used to
+                                   indent output for nested submodules
+            no_mods_details (bool, optional): if True, suppress details on local mods in
+                                              status output
         """
 
         smpath = os.path.join(self.root_dir, self.path)
@@ -52,16 +79,27 @@ def status(self):
         localmods = False
         needsupdate = False
         ahash = None
+
+        # The following prefix gives a tree-like output:
+        tree_prefix_spaces = 3
+        if depth == 0:
+            tree_prefix = ""
+        else:
+            tree_prefix = " " * tree_prefix_spaces * (depth - 1) + "└─ "
+
+        full_name = tree_prefix + self.name
+        name_width = 20
+        full_width = name_width + len(tree_prefix)
+
         optional = ""
         if "Optional" in self.fxrequired:
             optional = " (optional)"
-        required = None
-        level = None
+
         if not os.path.exists(os.path.join(smpath, ".git")):
             rootgit = GitInterface(self.root_dir, self.logger)
             # submodule commands use path, not name
-            status, tags = rootgit.git_operation("ls-remote", "--tags", self.url)
-            status, result = rootgit.git_operation("submodule","status",smpath)
+            _, tags = rootgit.git_operation("ls-remote", "--tags", self.url)
+            _, result = rootgit.git_operation("submodule", "status", smpath)
             result = result.split()
 
             if result:
@@ -69,7 +107,7 @@ def status(self):
             hhash = None
             atag = None
             for htag in tags.split("\n"):
-                if htag.endswith('^{}'):
+                if htag.endswith("^{}"):
                     htag = htag[:-3]
                 if ahash and not atag and ahash in htag:
                     atag = (htag.split()[1])[10:]
@@ -78,84 +116,139 @@ def status(self):
                 if hhash and atag:
                     break
             if self.fxtag and (ahash == hhash or atag == self.fxtag):
-                result = f"e {self.name:>20} not checked out, aligned at tag {self.fxtag}{optional}"
+                result = f"e  {full_name:<{full_width}} not checked out, aligned at tag {self.fxtag}{optional}"
                 needsupdate = True
             elif self.fxtag:
-                status, ahash = rootgit.git_operation(
+                _, ahash = rootgit.git_operation(
                     "submodule", "status", "{}".format(self.path)
                 )
                 ahash = ahash[1 : len(self.fxtag) + 1]
                 if self.fxtag == ahash:
-                    result = f"e {self.name:>20} not checked out, aligned at hash {ahash}{optional}"
+                    result = f"e  {full_name:<{full_width}} not checked out, aligned at hash {ahash}{optional}"
                 else:
-                    result = f"e {self.name:>20} not checked out, out of sync at tag {atag}, expected tag is {self.fxtag}{optional}"
+                    result = f"e  {full_name:<{full_width}} not checked out, out of sync at tag {atag}, expected tag is {self.fxtag}{optional}"
                     testfails = True
                 needsupdate = True
             else:
-                result = f"e {self.name:>20} has no fxtag defined in .gitmodules{optional}"
+                result = f"e  {full_name:<{full_width}} has no fxtag defined in .gitmodules{optional}"
                 testfails = False
         else:
             with utils.pushd(smpath):
                 git = GitInterface(smpath, self.logger)
-                status, remote = git.git_operation("remote")
-                if remote == '':
-                    result = f"e {self.name:>20} has no associated remote"
+                _, remote = git.git_operation("remote")
+                if remote == "":
+                    result = f"e  {full_name:<{full_width}} has no associated remote"
                     testfails = True
                     needsupdate = True
                     return result, needsupdate, localmods, testfails
-                status, rurl = git.git_operation("ls-remote","--get-url")
-                status, lines = git.git_operation("log", "--pretty=format:\"%h %d\"")
-                line = lines.partition('\n')[0]
+                _, rurl = git.git_operation("ls-remote", "--get-url")
+                _, lines = git.git_operation("log", '--pretty=format:"%h %d"')
+                line = lines.partition("\n")[0]
                 parts = line.split()
                 ahash = parts[0][1:]
                 atag = None
                 if len(parts) > 3:
                     idx = 0
-                    while idx < len(parts)-1:
-                        idx = idx+1
-                        if parts[idx] == 'tag:':
-                            atag = parts[idx+1]
-                            while atag.endswith(')') or atag.endswith(',') or atag.endswith("\""):
+                    while idx < len(parts) - 1:
+                        idx = idx + 1
+                        if parts[idx] == "tag:":
+                            atag = parts[idx + 1]
+                            while (
+                                atag.endswith(")")
+                                or atag.endswith(",")
+                                or atag.endswith('"')
+                            ):
                                 atag = atag[:-1]
                             if atag == self.fxtag:
                                 break
-                recurse = False
+
                 if rurl != self.url:
                     remote = self._add_remote(git)
                     git.git_operation("fetch", remote)
+
+                mod_char = " "
+                _, status_output = git.git_operation(
+                    "status", "--ignore-submodules", "-uno"
+                )
+                if "nothing to commit" not in status_output:
+                    localmods = True
+                    mod_char = "M"
+
                 # Asked for a tag and found that tag
                 if self.fxtag and atag == self.fxtag:
-                    result = f"  {self.name:>20} at tag {self.fxtag}"
-                    recurse = True
+                    result = (
+                        f" {mod_char} {full_name:<{full_width}} at tag {self.fxtag}"
+                    )
                     testfails = False
                 # Asked for and found a hash
-                elif self.fxtag and (ahash[: len(self.fxtag)] == self.fxtag or (self.fxtag.find(ahash)==0)):
-                    result = f"  {self.name:>20} at hash {ahash}"
-                    recurse = True
+                elif self.fxtag and (
+                    ahash[: len(self.fxtag)] == self.fxtag
+                    or (self.fxtag.find(ahash) == 0)
+                ):
+                    result = f" {mod_char} {full_name:<{full_width}} at hash {ahash}"
+
                     testfails = False
                 # Asked for and found a hash
                 elif atag == ahash:
-                    result = f"  {self.name:>20} at hash {ahash}"
-                    recurse = True
+                    result = f" {mod_char} {full_name:<{full_width}} at hash {ahash}"
+
                 # Did not find requested tag or hash
                 elif self.fxtag:
-                    result = f"s {self.name:>20} {atag} {ahash} is out of sync with .gitmodules {self.fxtag}"
+                    result = f"s{mod_char} {full_name:<{full_width}} {atag} {ahash} is out of sync with .gitmodules {self.fxtag}"
                     testfails = True
                     needsupdate = True
                 else:
                     if atag:
-                        result = f"e {self.name:>20} has no fxtag defined in .gitmodules, module at {atag}"
+                        result = f"e{mod_char} {full_name:<{full_width}} has no fxtag defined in .gitmodules, module at {atag}"
                     else:
-                        result = f"e {self.name:>20} has no fxtag defined in .gitmodules, module at {ahash}"
+                        result = f"e{mod_char} {full_name:<{full_width}} has no fxtag defined in .gitmodules, module at {ahash}"
                     testfails = False
 
-                status, output = git.git_operation("status", "--ignore-submodules", "-uno")
-                if "nothing to commit" not in output:
-                    localmods = True
-                    result = "M" + textwrap.indent(output, "                      ")
-#        print(f"result {result} needsupdate {needsupdate} localmods {localmods} testfails {testfails}")
-        return result, needsupdate, localmods, testfails
+                if localmods and not no_mods_details:
+                    # Print details about the local mods, indented below the other
+                    # information about this submodule.
+                    #
+                    # We use a vertical bar to help with the visual alignment of child
+                    # submodules. There are two main goals of the spacing details here:
+                    # 1. If there is a child of this submodule, the vertical bar used here
+                    #    should connect with the vertical part of the tree_prefix.
+                    # 2. The details about any local mods should be indented an additional
+                    #    4 spaces beyond the start of the text like "at tag ..."
+                    #
+                    # Here are details on how we accomplish these goals:
+                    # - leading_spaces: This is key for accomplishing the first goal. We
+                    #   need 3 spaces for the first three characters in the output (two
+                    #   status characters and a space), plus an additional number of
+                    #   spaces matching the number of spaces that would be used in the
+                    #   tree_prefix of any *child* of this submodule.
+                    # - total_indent: This is the total indent needed to achieve the
+                    #   second goal. The first addition of 4 aligns the output with the
+                    #   status (e.g., "at tag ..."), accounting for the 3 leading
+                    #   characters before the name and the 1 trailing space after the
+                    #   name. The second addition of 4 indents the details about local
+                    #   mods an additional 4 spaces.
+                    # - trailing_spaces: This gives the correct total indentation given
+                    #   that we already have some leading spaces plus a vertical bar
+                    #   character.
+                    leading_spaces = " " * (3 + depth * tree_prefix_spaces)
+                    total_indent = full_width + 4 + 4
+                    trailing_spaces = " " * (total_indent - len(leading_spaces) - 1)
+                    result = (
+                        result
+                        + "\n"
+                        + textwrap.indent(
+                            status_output,
+                            leading_spaces + "│" + trailing_spaces,
+                            # The following predicate
+                            # makes the vertical bar
+                            # appear even for blank
+                            # lines:
+                            predicate=lambda _: True,
+                        )
+                    )
 
+        #        print(f"result {result} needsupdate {needsupdate} localmods {localmods} testfails {testfails}")
+        return result, needsupdate, localmods, testfails
 
     def _add_remote(self, git):
         """
@@ -171,11 +264,10 @@ def _add_remote(self, git):
         Returns:
             str: The name of the new remote if added, or the name of the existing remote that matches the submodule's URL.
         """
-        status, remotes = git.git_operation("remote", "-v")
+        _, remotes = git.git_operation("remote", "-v")
         remotes = remotes.splitlines()
-        upstream = None
+
         if remotes:
-            status, upstream = git.git_operation("ls-remote", "--get-url")
             newremote = "newremote.00"
             tmpurl = self.url.replace("git@github.com:", "https://github.com/")
             line = next((s for s in remotes if self.url in s or tmpurl in s), None)
@@ -215,7 +307,9 @@ def sparse_checkout(self):
         """
         self.logger.info("Called sparse_checkout for {}".format(self.name))
         rgit = GitInterface(self.root_dir, self.logger)
-        status, superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
+        status, superroot = rgit.git_operation(
+            "rev-parse", "--show-superproject-working-tree"
+        )
         if superroot:
             gitroot = superroot.strip()
         else:
@@ -226,7 +320,7 @@ def sparse_checkout(self):
             with open(rootdotgit) as f:
                 line = f.readline().rstrip()
                 if line.startswith("gitdir: "):
-                    rootdotgit = os.path.abspath(os.path.join(self.root_dir,line[8:]))
+                    rootdotgit = os.path.abspath(os.path.join(self.root_dir, line[8:]))
         assert os.path.isdir(rootdotgit)
         # first create the module directory
         if not os.path.isdir(os.path.join(self.root_dir, self.path)):
@@ -240,7 +334,9 @@ def sparse_checkout(self):
                 self.logger.info("Submodule {} found".format(self.name))
                 chk = sprepo_git.config_get_value("core", "sparseCheckout")
                 if chk == "true":
-                    self.logger.info("Sparse submodule {} already checked out".format(self.name))
+                    self.logger.info(
+                        "Sparse submodule {} already checked out".format(self.name)
+                    )
                     return
             except (NoOptionError):
                 self.logger.debug("Sparse submodule {} not present".format(self.name))
@@ -251,14 +347,16 @@ def sparse_checkout(self):
 
         # set the repository remote
 
-        self.logger.info("Setting remote origin in {}/{}".format(self.root_dir, self.path))
+        self.logger.info(
+            "Setting remote origin in {}/{}".format(self.root_dir, self.path)
+        )
         status, remotes = sprepo_git.git_operation("remote", "-v")
         if self.url not in remotes:
             sprepo_git.git_operation("remote", "add", "origin", self.url)
 
-        topgit = os.path.join(gitroot, ".git")
-
-        if gitroot != self.root_dir and os.path.isfile(os.path.join(self.root_dir, ".git")):
+        if gitroot != self.root_dir and os.path.isfile(
+            os.path.join(self.root_dir, ".git")
+        ):
             with open(os.path.join(self.root_dir, ".git")) as f:
                 gitpath = os.path.relpath(
                     os.path.join(self.root_dir, f.read().split()[1]),
@@ -273,8 +371,8 @@ def sparse_checkout(self):
 
         if os.path.isdir(os.path.join(self.root_dir, self.path, ".git")):
             with utils.pushd(sprep_repo):
-                if os.path.isdir(os.path.join(rootdotgit,".git")):
-                    shutil.rmtree(os.path.join(rootdotgit,".git"))
+                if os.path.isdir(os.path.join(rootdotgit, ".git")):
+                    shutil.rmtree(os.path.join(rootdotgit, ".git"))
                 shutil.move(".git", rootdotgit)
                 with open(".git", "w") as f:
                     f.write("gitdir: " + os.path.relpath(rootdotgit))
@@ -284,7 +382,9 @@ def sparse_checkout(self):
                 gitsparse = os.path.abspath(os.path.join(infodir, "sparse-checkout"))
                 if os.path.isfile(gitsparse):
                     self.logger.warning(
-                        "submodule {} is already initialized {}".format(self.name, rootdotgit)
+                        "submodule {} is already initialized {}".format(
+                            self.name, rootdotgit
+                        )
                     )
                     os.remove(gitsparse)
 
@@ -292,26 +392,28 @@ def sparse_checkout(self):
                     shutil.copy(self.fxsparse, gitsparse)
                 else:
                     self.logger.warning(
-                        "submodule {} could not find {}".format(self.name, self.fxsparse)
+                        "submodule {} could not find {}".format(
+                            self.name, self.fxsparse
+                        )
                     )
 
         # Finally checkout the repo
         sprepo_git.git_operation("fetch", "origin", "--tags")
-        status,_ = sprepo_git.git_operation("checkout", self.fxtag)
+        status, _ = sprepo_git.git_operation("checkout", self.fxtag)
         if status:
             print(f"Error checking out {self.name:>20} at {self.fxtag}")
         else:
             print(f"Successfully checked out {self.name:>20} at {self.fxtag}")
-        status,f = sprepo_git.git_operation("status")
+        status, f = sprepo_git.git_operation("status")
         # Restore any files deleted from sandbox
         for line in f.splitlines():
             if "deleted:" in line:
                 deleted_file = line.split("deleted:")[1].strip()
                 sprepo_git.git_operation("checkout", deleted_file)
 
-        rgit.config_set_value('submodule.' + self.name, "active", "true")
-        rgit.config_set_value('submodule.' + self.name, "url", self.url)
-        rgit.config_set_value('submodule.' + self.name, "path", self.path)
+        rgit.config_set_value("submodule." + self.name, "active", "true")
+        rgit.config_set_value("submodule." + self.name, "url", self.url)
+        rgit.config_set_value("submodule." + self.name, "path", self.path)
 
     async def update(self):
         """
@@ -337,7 +439,9 @@ async def update(self):
         """
         git = GitInterface(self.root_dir, self.logger)
         repodir = os.path.join(self.root_dir, self.path)
-        self.logger.info("Checkout {} into {}/{}".format(self.name, self.root_dir, self.path))
+        self.logger.info(
+            "Checkout {} into {}/{}".format(self.name, self.root_dir, self.path)
+        )
         # if url is provided update to the new url
         tag = None
         repo_exists = False
@@ -348,7 +452,9 @@ async def update(self):
         if self.fxsparse:
             print(f"Sparse checkout {self.name} fxsparse {self.fxsparse}")
             if not os.path.isfile(self.fxsparse):
-                self.logger.info("Submodule {} fxsparse file not found".format(self.name))
+                self.logger.info(
+                    "Submodule {} fxsparse file not found".format(self.name)
+                )
 
             self.sparse_checkout()
         else:
@@ -361,7 +467,9 @@ async def update(self):
                     git.git_operation("clone", self.url, self.path)
                     smgit = GitInterface(repodir, self.logger)
                     if not tag:
-                        status, tag = smgit.git_operation("describe", "--tags", "--always")
+                        status, tag = smgit.git_operation(
+                            "describe", "--tags", "--always"
+                        )
                     smgit.git_operation("checkout", tag)
                     # Now need to move the .git dir to the submodule location
                     rootdotgit = os.path.join(self.root_dir, ".git")
@@ -371,7 +479,9 @@ async def update(self):
                             if line.startswith("gitdir: "):
                                 rootdotgit = line[8:]
 
-                    newpath = os.path.abspath(os.path.join(self.root_dir, rootdotgit, "modules", self.name))
+                    newpath = os.path.abspath(
+                        os.path.join(self.root_dir, rootdotgit, "modules", self.name)
+                    )
                     if os.path.exists(newpath):
                         shutil.rmtree(os.path.join(repodir, ".git"))
                     else:
@@ -384,7 +494,9 @@ async def update(self):
                 parent = os.path.dirname(repodir)
                 if not os.path.isdir(parent):
                     os.makedirs(parent)
-                git.git_operation("submodule", "add", "--name", self.name, "--", self.url, self.path)
+                git.git_operation(
+                    "submodule", "add", "--name", self.name, "--", self.url, self.path
+                )
 
             if not repo_exists:
                 git.git_operation("submodule", "init", "--", self.path)
@@ -394,17 +506,17 @@ async def update(self):
                 smgit = GitInterface(repodir, self.logger)
                 newremote = self._add_remote(smgit)
                 # Trying to distingush a tag from a hash
-                allowed = set(string.digits + 'abcdef')
+                allowed = set(string.digits + "abcdef")
                 status = 0
                 if not set(self.fxtag) <= allowed:
                     # This is a tag
                     tag = f"refs/tags/{self.fxtag}:refs/tags/{self.fxtag}"
-                    status,_ = smgit.git_operation("fetch", newremote, tag)
+                    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)
+                    status, _ = smgit.git_operation("fetch", newremote)
                 if status == 0:
-                    status,_ = smgit.git_operation("checkout", self.fxtag)
+                    status, _ = smgit.git_operation("checkout", self.fxtag)
                 if status:
                     utils.fatal_error(
                         f"Failed to checkout {self.name} at tag or hash {self.fxtag} from {repodir}"
@@ -415,7 +527,6 @@ async def update(self):
                     f"Failed to checkout {self.name} {repo_exists} {repodir} {self.path}"
                 )
 
-
         if os.path.exists(os.path.join(self.path, ".git")):
             submoddir = os.path.join(self.root_dir, self.path)
             with utils.pushd(submoddir):
@@ -431,10 +542,11 @@ async def update(self):
                 modfiles = []
                 moddirs = []
                 if files:
-                    for f in files.split('\0'):
+                    for f in files.split("\0"):
                         if f:
                             if os.path.exists(f):
-                                git.git_operation("checkout",f)
+                                self.logger.info(f"File {f} locally modified")
+                                modfiles.append(f)
                             elif os.path.isdir(f):
                                 moddirs.append(f)
                             else:
@@ -447,7 +559,6 @@ async def update(self):
                     except Exception as error:
                         print(error)
 
-
                 elif not fxtag:
                     print(f"No fxtag found for submodule {self.name:>20}")
                 elif modfiles:
@@ -457,6 +568,4 @@ async def update(self):
                 else:
                     print(f"{self.name:>20} up to date.")
 
-
-
         return
diff --git a/git_fleximod/utils.py b/git_fleximod/utils.py
index c4f43d5238..57752143f8 100644
--- a/git_fleximod/utils.py
+++ b/git_fleximod/utils.py
@@ -57,7 +57,16 @@ def printlog(msg, **kwargs):
 
 
 def find_upwards(root_dir, filename):
-    """Find a file in root dir or any of it's parents"""
+    """
+    Find a file in root dir or any of its parents.
+
+    >>> import tempfile, os
+    >>> with tempfile.TemporaryDirectory() as tmp:
+    ...     f = os.path.join(tmp, 'testfile.txt')
+    ...     open(f, 'w').close()
+    ...     find_upwards(tmp, 'testfile.txt').name == 'testfile.txt'
+    True
+    """
     d = Path(root_dir)
     root = Path(d.root)
     while d != root:
@@ -69,18 +78,8 @@ def find_upwards(root_dir, filename):
 
 
 def last_n_lines(the_string, n_lines, truncation_message=None):
-    """Returns the last n lines of the given string
-
-    Args:
-        the_string: str
-        n_lines: int
-        truncation_message: str, optional
-
-    Returns a string containing the last n lines of the_string
-
-    If truncation_message is provided, the returned string begins with
-    the given message if and only if the string is greater than n lines
-    to begin with.
+    """
+    Returns the last n lines of the given string.
     """
 
     lines = the_string.splitlines(True)
@@ -97,18 +96,12 @@ def last_n_lines(the_string, n_lines, truncation_message=None):
 
 
 def indent_string(the_string, indent_level):
-    """Indents the given string by a given number of spaces
-
-    Args:
-       the_string: str
-       indent_level: int
-
-    Returns a new string that is the same as the_string, except that
-    each line is indented by 'indent_level' spaces.
-
-    In python3, this can be done with textwrap.indent.
     """
+    Indents the given string by a given number of spaces.
 
+    >>> indent_string('a\\nb', 2)
+    '  a\\n  b'
+    """
     lines = the_string.splitlines(True)
     padding = " " * indent_level
     lines_indented = [padding + line for line in lines]
@@ -307,9 +300,8 @@ def execute_subprocess(commands, status_to_caller=False, output_to_caller=False)
         # simple status check. If returning, it is the callers
         # responsibility determine if an error occurred and handle it
         # appropriately.
-        msg_context = (
-            "Process did not run successfully; "
-            "returned status {0}".format(error.returncode)
+        msg_context = "Process did not run successfully; " "returned status {0}".format(
+            error.returncode
         )
         msg = failed_command_msg(msg_context, commands, output=error.output)
         if not return_to_caller:
diff --git a/poetry.lock b/poetry.lock
index ac82fb0d97..6c6af17b37 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,141 +1,177 @@
-# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
-version = "0.7.13"
-description = "A configurable sidebar-enabled Sphinx theme"
+version = "0.7.16"
+description = "A light, configurable Sphinx theme"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.9"
+groups = ["main"]
 files = [
-    {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
-    {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
+    {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"},
+    {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"},
 ]
 
 [[package]]
 name = "babel"
-version = "2.15.0"
+version = "2.17.0"
 description = "Internationalization utilities"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
-    {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"},
-    {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"},
+    {file = "babel-2.17.0-py3-none-any.whl", hash = "sha256:4d0b53093fdfb4b21c92b5213dba5a1b23885afa8383709427046b21c366e5f2"},
+    {file = "babel-2.17.0.tar.gz", hash = "sha256:0c54cffb19f690cdcc52a3b50bcbf71e07a808d1c80d549f2459b9d2cf0afb9d"},
 ]
 
-[package.dependencies]
-pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""}
-
 [package.extras]
-dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
+dev = ["backports.zoneinfo ; python_version < \"3.9\"", "freezegun (>=1.0,<2.0)", "jinja2 (>=3.0)", "pytest (>=6.0)", "pytest-cov", "pytz", "setuptools", "tzdata ; sys_platform == \"win32\""]
 
 [[package]]
 name = "certifi"
-version = "2024.8.30"
+version = "2025.11.12"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
+groups = ["main"]
+files = [
+    {file = "certifi-2025.11.12-py3-none-any.whl", hash = "sha256:97de8790030bbd5c2d96b7ec782fc2f7820ef8dba6db909ccf95449f2d062d4b"},
+    {file = "certifi-2025.11.12.tar.gz", hash = "sha256:d8ab5478f2ecd78af242878415affce761ca6bc54a22a27e026d7c25357c3316"},
+]
+
+[[package]]
+name = "cfgv"
+version = "3.4.0"
+description = "Validate configuration and produce human readable error messages."
+optional = false
+python-versions = ">=3.8"
+groups = ["main"]
 files = [
-    {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"},
-    {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"},
+    {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"},
+    {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"},
 ]
 
 [[package]]
 name = "charset-normalizer"
-version = "3.3.2"
+version = "3.4.4"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
-python-versions = ">=3.7.0"
-files = [
-    {file = "charset-normalizer-3.3.2.tar.gz", hash = "sha256:f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5"},
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+    {file = "charset_normalizer-3.4.4.tar.gz", hash = "sha256:94537985111c35f28720e43603b8e7b43a6ecfb2ce1d3058bbe955b73404e21a"},
 ]
 
 [[package]]
@@ -144,17 +180,32 @@ version = "0.4.6"
 description = "Cross-platform colored terminal text."
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
+groups = ["main"]
+markers = "sys_platform == \"win32\""
 files = [
     {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
     {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
 ]
 
+[[package]]
+name = "distlib"
+version = "0.4.0"
+description = "Distribution utilities"
+optional = false
+python-versions = "*"
+groups = ["main"]
+files = [
+    {file = "distlib-0.4.0-py2.py3-none-any.whl", hash = "sha256:9659f7d87e46584a30b5780e43ac7a2143098441670ff0a49d5f9034c54a6c16"},
+    {file = "distlib-0.4.0.tar.gz", hash = "sha256:feec40075be03a04501a973d81f633735b4b69f98b05450592310c0f401a4e0d"},
+]
+
 [[package]]
 name = "docutils"
 version = "0.19"
 description = "Docutils -- Python Documentation Utilities"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
     {file = "docutils-0.19-py3-none-any.whl", hash = "sha256:5e1de4d849fee02c63b040a4a3fd567f4ab104defd8a5511fbbc24a8a017efbc"},
     {file = "docutils-0.19.tar.gz", hash = "sha256:33995a6753c30b7f577febfc2c50411fec6aac7f7ffeb7c4cfe5991072dcf9e6"},
@@ -162,24 +213,42 @@ files = [
 
 [[package]]
 name = "exceptiongroup"
-version = "1.2.1"
+version = "1.3.1"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
+markers = "python_version < \"3.11\""
 files = [
-    {file = "exceptiongroup-1.2.1-py3-none-any.whl", hash = "sha256:5258b9ed329c5bbdd31a309f53cbfb0b155341807f6ff7606a1e801a891b29ad"},
-    {file = "exceptiongroup-1.2.1.tar.gz", hash = "sha256:a4785e48b045528f5bfe627b6ad554ff32def154f42372786903b7abcfe1aa16"},
+    {file = "exceptiongroup-1.3.1-py3-none-any.whl", hash = "sha256:a7a39a3bd276781e98394987d3a5701d0c4edffb633bb7a5144577f82c773598"},
+    {file = "exceptiongroup-1.3.1.tar.gz", hash = "sha256:8b412432c6055b0b7d14c310000ae93352ed6754f70fa8f7c34141f91c4e3219"},
 ]
 
+[package.dependencies]
+typing-extensions = {version = ">=4.6.0", markers = "python_version < \"3.13\""}
+
 [package.extras]
 test = ["pytest (>=6)"]
 
+[[package]]
+name = "filelock"
+version = "3.19.1"
+description = "A platform independent file lock."
+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
+files = [
+    {file = "filelock-3.19.1-py3-none-any.whl", hash = "sha256:d38e30481def20772f5baf097c122c3babc4fcdb7e14e57049eb9d88c6dc017d"},
+    {file = "filelock-3.19.1.tar.gz", hash = "sha256:66eda1888b0171c998b35be2bcc0f6d75c388a7ce20c3f3f37aa8e96c2dddf58"},
+]
+
 [[package]]
 name = "fsspec"
 version = "2023.12.2"
 description = "File-system specification"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "fsspec-2023.12.2-py3-none-any.whl", hash = "sha256:d800d87f72189a745fa3d6b033b9dc4a34ad069f60ca60b943a63599f5501960"},
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@@ -211,13 +280,14 @@ tqdm = ["tqdm"]
 
 [[package]]
 name = "gitdb"
-version = "4.0.11"
+version = "4.0.12"
 description = "Git Object Database"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
-    {file = "gitdb-4.0.11-py3-none-any.whl", hash = "sha256:81a3407ddd2ee8df444cbacea00e2d038e40150acfa3001696fe0dcf1d3adfa4"},
-    {file = "gitdb-4.0.11.tar.gz", hash = "sha256:bf5421126136d6d0af55bc1e7c1af1c397a34f5b7bd79e776cd3e89785c2b04b"},
+    {file = "gitdb-4.0.12-py3-none-any.whl", hash = "sha256:67073e15955400952c6565cc3e707c554a4eea2e428946f7a4c162fab9bd9bcf"},
+    {file = "gitdb-4.0.12.tar.gz", hash = "sha256:5ef71f855d191a3326fcfbc0d5da835f26b13fbcba60c32c21091c349ffdb571"},
 ]
 
 [package.dependencies]
@@ -225,39 +295,61 @@ smmap = ">=3.0.1,<6"
 
 [[package]]
 name = "gitpython"
-version = "3.1.43"
+version = "3.1.45"
 description = "GitPython is a Python library used to interact with Git repositories"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
-    {file = "GitPython-3.1.43-py3-none-any.whl", hash = "sha256:eec7ec56b92aad751f9912a73404bc02ba212a23adb2c7098ee668417051a1ff"},
-    {file = "GitPython-3.1.43.tar.gz", hash = "sha256:35f314a9f878467f5453cc1fee295c3e18e52f1b99f10f6cf5b1682e968a9e7c"},
+    {file = "gitpython-3.1.45-py3-none-any.whl", hash = "sha256:8908cb2e02fb3b93b7eb0f2827125cb699869470432cc885f019b8fd0fccff77"},
+    {file = "gitpython-3.1.45.tar.gz", hash = "sha256:85b0ee964ceddf211c41b9f27a49086010a190fd8132a24e21f362a4b36a791c"},
 ]
 
 [package.dependencies]
 gitdb = ">=4.0.1,<5"
+typing-extensions = {version = ">=3.10.0.2", markers = "python_version < \"3.10\""}
+
+[package.extras]
+doc = ["sphinx (>=7.1.2,<7.2)", "sphinx-autodoc-typehints", "sphinx_rtd_theme"]
+test = ["coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mock ; python_version < \"3.8\"", "mypy", "pre-commit", "pytest (>=7.3.1)", "pytest-cov", "pytest-instafail", "pytest-mock", "pytest-sugar", "typing-extensions ; python_version < \"3.11\""]
+
+[[package]]
+name = "identify"
+version = "2.6.15"
+description = "File identification library for Python"
+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
+files = [
+    {file = "identify-2.6.15-py2.py3-none-any.whl", hash = "sha256:1181ef7608e00704db228516541eb83a88a9f94433a8c80bb9b5bd54b1d81757"},
+    {file = "identify-2.6.15.tar.gz", hash = "sha256:e4f4864b96c6557ef2a1e1c951771838f4edc9df3a72ec7118b338801b11c7bf"},
+]
 
 [package.extras]
-doc = ["sphinx (==4.3.2)", "sphinx-autodoc-typehints", "sphinx-rtd-theme", "sphinxcontrib-applehelp (>=1.0.2,<=1.0.4)", "sphinxcontrib-devhelp (==1.0.2)", "sphinxcontrib-htmlhelp (>=2.0.0,<=2.0.1)", "sphinxcontrib-qthelp (==1.0.3)", "sphinxcontrib-serializinghtml (==1.1.5)"]
-test = ["coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mock", "mypy", "pre-commit", "pytest (>=7.3.1)", "pytest-cov", "pytest-instafail", "pytest-mock", "pytest-sugar", "typing-extensions"]
+license = ["ukkonen"]
 
 [[package]]
 name = "idna"
-version = "3.7"
+version = "3.11"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.8"
+groups = ["main"]
 files = [
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-    {file = "idna-3.7.tar.gz", hash = "sha256:028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc"},
+    {file = "idna-3.11-py3-none-any.whl", hash = "sha256:771a87f49d9defaf64091e6e6fe9c18d4833f140bd19464795bc32d966ca37ea"},
+    {file = "idna-3.11.tar.gz", hash = "sha256:795dafcc9c04ed0c1fb032c2aa73654d8e8c5023a7df64a53f39190ada629902"},
 ]
 
+[package.extras]
+all = ["flake8 (>=7.1.1)", "mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2)"]
+
 [[package]]
 name = "imagesize"
 version = "1.4.1"
 description = "Getting image size from png/jpeg/jpeg2000/gif file"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+groups = ["main"]
 files = [
     {file = "imagesize-1.4.1-py2.py3-none-any.whl", hash = "sha256:0d8d18d08f840c19d0ee7ca1fd82490fdc3729b7ac93f49870406ddde8ef8d8b"},
     {file = "imagesize-1.4.1.tar.gz", hash = "sha256:69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a"},
@@ -265,43 +357,51 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "8.0.0"
+version = "8.7.0"
 description = "Read metadata from Python packages"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
+groups = ["main"]
+markers = "python_version == \"3.9\""
 files = [
-    {file = "importlib_metadata-8.0.0-py3-none-any.whl", hash = "sha256:15584cf2b1bf449d98ff8a6ff1abef57bf20f3ac6454f431736cd3e660921b2f"},
-    {file = "importlib_metadata-8.0.0.tar.gz", hash = "sha256:188bd24e4c346d3f0a933f275c2fec67050326a856b9a359881d7c2a697e8812"},
+    {file = "importlib_metadata-8.7.0-py3-none-any.whl", hash = "sha256:e5dd1551894c77868a30651cef00984d50e1002d06942a7101d34870c5f02afd"},
+    {file = "importlib_metadata-8.7.0.tar.gz", hash = "sha256:d13b81ad223b890aa16c5471f2ac3056cf76c5f10f82d6f9292f0b415f389000"},
 ]
 
 [package.dependencies]
-zipp = ">=0.5"
+zipp = ">=3.20"
 
 [package.extras]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
+cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+enabler = ["pytest-enabler (>=2.2)"]
 perf = ["ipython"]
-test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"]
+test = ["flufl.flake8", "importlib_resources (>=1.3) ; python_version < \"3.9\"", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"]
+type = ["pytest-mypy"]
 
 [[package]]
 name = "iniconfig"
-version = "2.0.0"
+version = "2.1.0"
 description = "brain-dead simple config-ini parsing"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
+groups = ["main"]
 files = [
-    {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"},
-    {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
+    {file = "iniconfig-2.1.0-py3-none-any.whl", hash = "sha256:9deba5723312380e77435581c6bf4935c94cbfab9b1ed33ef8d238ea168eb760"},
+    {file = "iniconfig-2.1.0.tar.gz", hash = "sha256:3abbd2e30b36733fee78f9c7f7308f2d0050e88f0087fd25c2645f63c773e1c7"},
 ]
 
 [[package]]
 name = "jinja2"
-version = "3.1.4"
+version = "3.1.6"
 description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
-    {file = "jinja2-3.1.4-py3-none-any.whl", hash = "sha256:bc5dd2abb727a5319567b7a813e6a2e7318c39f4f487cfe6c89c6f9c7d25197d"},
-    {file = "jinja2-3.1.4.tar.gz", hash = "sha256:4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369"},
+    {file = "jinja2-3.1.6-py3-none-any.whl", hash = "sha256:85ece4451f492d0c13c5dd7c13a64681a86afae63a5f347908daf103ce6d2f67"},
+    {file = "jinja2-3.1.6.tar.gz", hash = "sha256:0137fb05990d35f1275a587e9aee6d56da821fc83491a0fb838183be43f66d6d"},
 ]
 
 [package.dependencies]
@@ -312,119 +412,201 @@ i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "markupsafe"
-version = "2.1.5"
+version = "3.0.3"
 description = "Safely add untrusted strings to HTML/XML markup."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.9"
+groups = ["main"]
+files = [
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+optional = false
+python-versions = ">=3.9"
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+
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+virtualenv = ">=20.10.0"
 
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+version = "2.19.2"
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 [package.extras]
@@ -432,51 +614,126 @@ windows-terminal = ["colorama (>=0.4.6)"]
 
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+version = "8.4.2"
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-iniconfig = "*"
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+packaging = ">=20"
+pluggy = ">=1.5,<2"
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 [package.extras]
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+dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "requests", "setuptools", "xmlschema"]
 
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 ]
 
 [[package]]
 name = "requests"
-version = "2.32.3"
+version = "2.32.5"
 description = "Python HTTP for Humans."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
+groups = ["main"]
 files = [
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+    {file = "requests-2.32.5-py3-none-any.whl", hash = "sha256:2462f94637a34fd532264295e186976db0f5d453d1cdd31473c85a6a161affb6"},
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 ]
 
 [package.dependencies]
 certifi = ">=2017.4.17"
-charset-normalizer = ">=2,<4"
+charset_normalizer = ">=2,<4"
 idna = ">=2.5,<4"
 urllib3 = ">=1.21.1,<3"
 
@@ -486,24 +743,26 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
 name = "smmap"
-version = "5.0.1"
+version = "5.0.2"
 description = "A pure Python implementation of a sliding window memory map manager"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
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 ]
 
 [[package]]
 name = "snowballstemmer"
-version = "2.2.0"
-description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
+version = "3.0.1"
+description = "This package provides 32 stemmers for 30 languages generated from Snowball algorithms."
 optional = false
-python-versions = "*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*"
+groups = ["main"]
 files = [
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+    {file = "snowballstemmer-3.0.1.tar.gz", hash = "sha256:6d5eeeec8e9f84d4d56b847692bacf79bc2c8e90c7f80ca4444ff8b6f2e52895"},
 ]
 
 [[package]]
@@ -512,6 +771,7 @@ version = "5.3.0"
 description = "Python documentation generator"
 optional = false
 python-versions = ">=3.6"
+groups = ["main"]
 files = [
     {file = "Sphinx-5.3.0.tar.gz", hash = "sha256:51026de0a9ff9fc13c05d74913ad66047e104f56a129ff73e174eb5c3ee794b5"},
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@@ -539,51 +799,57 @@ sphinxcontrib-serializinghtml = ">=1.1.5"
 [package.extras]
 docs = ["sphinxcontrib-websupport"]
 lint = ["docutils-stubs", "flake8 (>=3.5.0)", "flake8-bugbear", "flake8-comprehensions", "flake8-simplify", "isort", "mypy (>=0.981)", "sphinx-lint", "types-requests", "types-typed-ast"]
-test = ["cython", "html5lib", "pytest (>=4.6)", "typed_ast"]
+test = ["cython", "html5lib", "pytest (>=4.6)", "typed_ast ; python_version < \"3.8\""]
 
 [[package]]
 name = "sphinxcontrib-applehelp"
-version = "1.0.4"
+version = "2.0.0"
 description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
+groups = ["main"]
 files = [
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+    {file = "sphinxcontrib_applehelp-2.0.0-py3-none-any.whl", hash = "sha256:4cd3f0ec4ac5dd9c17ec65e9ab272c9b867ea77425228e68ecf08d6b28ddbdb5"},
+    {file = "sphinxcontrib_applehelp-2.0.0.tar.gz", hash = "sha256:2f29ef331735ce958efa4734873f084941970894c6090408b079c61b2e1c06d1"},
 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
+standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-devhelp"
-version = "1.0.2"
-description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document."
+version = "2.0.0"
+description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.9"
+groups = ["main"]
 files = [
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+    {file = "sphinxcontrib_devhelp-2.0.0-py3-none-any.whl", hash = "sha256:aefb8b83854e4b0998877524d1029fd3e6879210422ee3780459e28a1f03a8a2"},
+    {file = "sphinxcontrib_devhelp-2.0.0.tar.gz", hash = "sha256:411f5d96d445d1d73bb5d52133377b4248ec79db5c793ce7dbe59e074b4dd1ad"},
 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
+standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-htmlhelp"
-version = "2.0.1"
+version = "2.1.0"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
+groups = ["main"]
 files = [
-    {file = "sphinxcontrib-htmlhelp-2.0.1.tar.gz", hash = "sha256:0cbdd302815330058422b98a113195c9249825d681e18f11e8b1f78a2f11efff"},
-    {file = "sphinxcontrib_htmlhelp-2.0.1-py3-none-any.whl", hash = "sha256:c38cb46dccf316c79de6e5515e1770414b797162b23cd3d06e67020e1d2a6903"},
+    {file = "sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl", hash = "sha256:166759820b47002d22914d64a075ce08f4c46818e17cfc9470a9786b759b19f8"},
+    {file = "sphinxcontrib_htmlhelp-2.1.0.tar.gz", hash = "sha256:c9e2916ace8aad64cc13a0d233ee22317f2b9025b9cf3295249fa985cc7082e9"},
 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
+standalone = ["Sphinx (>=5)"]
 test = ["html5lib", "pytest"]
 
 [[package]]
@@ -592,6 +858,7 @@ version = "1.0.1"
 description = "A sphinx extension which renders display math in HTML via JavaScript"
 optional = false
 python-versions = ">=3.5"
+groups = ["main"]
 files = [
     {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"},
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@@ -602,68 +869,151 @@ test = ["flake8", "mypy", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-qthelp"
-version = "1.0.3"
-description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document."
+version = "2.0.0"
+description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.9"
+groups = ["main"]
 files = [
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+    {file = "sphinxcontrib_qthelp-2.0.0-py3-none-any.whl", hash = "sha256:b18a828cdba941ccd6ee8445dbe72ffa3ef8cbe7505d8cd1fa0d42d3f2d5f3eb"},
+    {file = "sphinxcontrib_qthelp-2.0.0.tar.gz", hash = "sha256:4fe7d0ac8fc171045be623aba3e2a8f613f8682731f9153bb2e40ece16b9bbab"},
 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
-test = ["pytest"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
+standalone = ["Sphinx (>=5)"]
+test = ["defusedxml (>=0.7.1)", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-serializinghtml"
-version = "1.1.5"
-description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)."
+version = "2.0.0"
+description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.9"
+groups = ["main"]
 files = [
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 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
+standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "tomli"
-version = "2.0.1"
+version = "2.3.0"
 description = "A lil' TOML parser"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
+groups = ["main"]
+markers = "python_version < \"3.11\""
 files = [
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+]
+
+[package.extras]
+dev = ["pytest", "setuptools"]
+
 [[package]]
 name = "zipp"
-version = "3.19.2"
+version = "3.23.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
+groups = ["main"]
+markers = "python_version == \"3.9\""
 files = [
-    {file = "zipp-3.19.2-py3-none-any.whl", hash = "sha256:f091755f667055f2d02b32c53771a7a6c8b47e1fdbc4b72a8b9072b3eef8015c"},
-    {file = "zipp-3.19.2.tar.gz", hash = "sha256:bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19"},
+    {file = "zipp-3.23.0-py3-none-any.whl", hash = "sha256:071652d6115ed432f5ce1d34c336c0adfd6a884660d1e9712a256d3d3bd4b14e"},
+    {file = "zipp-3.23.0.tar.gz", hash = "sha256:a07157588a12518c9d4034df3fbbee09c814741a33ff63c05fa29d26a2404166"},
 ]
 
 [package.extras]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
+cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more_itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
+type = ["pytest-mypy"]
 
 [metadata]
-lock-version = "2.0"
-python-versions = "^3.8"
-content-hash = "25ee2ae1d74abedde3a6637a60d4a3095ea5cf9731960875741bbc2ba84a475d"
+lock-version = "2.1"
+python-versions = ">=3.9"
+content-hash = "dcaa958aee9992b081f43d3efb409a2d8ece8e151ecb99064b741d57a29a86de"
diff --git a/pyproject.toml b/pyproject.toml
index 211eac1dd6..1e63c773f1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "1.0.3"
+version = "1.1.1"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <jedwards@ucar.edu>"]
 maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
@@ -20,13 +20,15 @@ me2flexi = "git_fleximod.metoflexi:_main"
 fsspec = "fsspec.fuse:main"
 
 [tool.poetry.dependencies]
-python = "^3.8"
+python = ">=3.9"
 GitPython = "^3.1.0"
 sphinx = "^5.0.0"
 fsspec = "^2023.12.2"
 wheel = "^0.42.0"
 pytest = "^8.0.0"
 pyfakefs = "^5.3.5"
+pre-commit = "4.3.0"
+wrapt = ">=2.0.0"
 
 [tool.poetry.urls]
 "Bug Tracker" = "https://github.com/jedwards4b/git-fleximod/issues"
@@ -39,4 +41,3 @@ markers = [
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
-
diff --git a/tbump.toml b/tbump.toml
index 20271f4de2..b93fc74541 100644
--- a/tbump.toml
+++ b/tbump.toml
@@ -2,7 +2,7 @@
 github_url = "https://github.com/jedwards4b/git-fleximod/"
 
 [version]
-current = "1.0.3"
+current = "1.1.1"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before
diff --git a/tests/conftest.py b/tests/conftest.py
index 44d28e1788..9d359fe530 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,68 +1,77 @@
-import pytest 
+import pytest
 from git_fleximod.gitinterface import GitInterface
-import os
 import subprocess
 import logging
-from pathlib import Path
 
-@pytest.fixture(scope='session')
+
+@pytest.fixture(scope="session")
 def logger():
     logging.basicConfig(
-        level=logging.INFO, format="%(name)s - %(levelname)s - %(message)s", handlers=[logging.StreamHandler()]
+        level=logging.INFO,
+        format="%(name)s - %(levelname)s - %(message)s",
+        handlers=[logging.StreamHandler()],
     )
-    logger = logging.getLogger(__name__)
-    return logger
-
-all_repos=[
-    {"subrepo_path": "modules/test",
-     "submodule_name": "test_submodule",
-     "status1" : "test_submodule MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
-     "status2" : "test_submodule at tag MPIserial_2.4.0",
-     "status3" : "test_submodule at tag MPIserial_2.4.0",
-     "status4" : "test_submodule at tag MPIserial_2.4.0",
-     "gitmodules_content" : """
+    llogger = logging.getLogger(__name__)
+    return llogger
+
+
+all_repos = [
+    {
+        "subrepo_path": "modules/test",
+        "submodule_name": "test_submodule",
+        "status1": "test_submodule MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
+        "status2": "test_submodule at tag MPIserial_2.4.0",
+        "status3": "test_submodule at tag MPIserial_2.4.0",
+        "status4": "test_submodule at tag MPIserial_2.4.0",
+        "gitmodules_content": """
     [submodule "test_submodule"]
     path = modules/test
     url = https://github.com/ESMCI/mpi-serial.git
     fxtag = MPIserial_2.4.0
     fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
     fxrequired = ToplevelRequired
-"""},
-    {"subrepo_path": "modules/test_optional",
-     "submodule_name": "test_optional",
-     "status1" : "test_optional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
-     "status2" : "test_optional at tag MPIserial_2.4.0",
-     "status3" : "test_optional not checked out, out of sync at tag MPIserial_2.5.4, expected tag is MPIserial_2.4.0 (optional)",
-     "status4" : "test_optional at tag MPIserial_2.4.0",
-     "gitmodules_content": """
+""",
+    },
+    {
+        "subrepo_path": "modules/test_optional",
+        "submodule_name": "test_optional",
+        "status1": "test_optional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
+        "status2": "test_optional at tag MPIserial_2.4.0",
+        "status3": "test_optional not checked out, out of sync at tag MPIserial_2.5.4, expected tag is MPIserial_2.4.0 (optional)",
+        "status4": "test_optional at tag MPIserial_2.4.0",
+        "gitmodules_content": """
      [submodule "test_optional"]
     path = modules/test_optional
     url = https://github.com/ESMCI/mpi-serial.git
     fxtag = MPIserial_2.4.0
     fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
     fxrequired = ToplevelOptional
-"""},
-    {"subrepo_path": "modules/test_alwaysoptional",
-     "submodule_name": "test_alwaysoptional",
-     "status1" : "test_alwaysoptional MPIserial_2.3.0 is out of sync with .gitmodules e5cf35c",
-     "status2" : "test_alwaysoptional at hash e5cf35c",
-     "status3" : "out of sync at tag MPIserial_2.5.4, expected tag is e5cf35c",
-     "status4" : "test_alwaysoptional at hash e5cf35c",
-     "gitmodules_content": """
+""",
+    },
+    {
+        "subrepo_path": "modules/test_alwaysoptional",
+        "submodule_name": "test_alwaysoptional",
+        "status1": "test_alwaysoptional MPIserial_2.3.0 is out of sync with .gitmodules e5cf35c",
+        "status2": "test_alwaysoptional at hash e5cf35c",
+        "status3": "out of sync at tag MPIserial_2.5.4, expected tag is e5cf35c",
+        "status4": "test_alwaysoptional at hash e5cf35c",
+        "gitmodules_content": """
     [submodule "test_alwaysoptional"]
     path = modules/test_alwaysoptional
     url = https://github.com/ESMCI/mpi-serial.git
     fxtag = e5cf35c
     fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
     fxrequired = AlwaysOptional
-"""},    
-    {"subrepo_path": "modules/test_sparse",
-     "submodule_name": "test_sparse",
-     "status1" : "test_sparse at tag MPIserial_2.5.0",
-     "status2" : "test_sparse at tag MPIserial_2.5.0",
-     "status3" : "test_sparse at tag MPIserial_2.5.0",
-     "status4" : "test_sparse at tag MPIserial_2.5.0",
-     "gitmodules_content": """
+""",
+    },
+    {
+        "subrepo_path": "modules/test_sparse",
+        "submodule_name": "test_sparse",
+        "status1": "test_sparse at tag MPIserial_2.5.0",
+        "status2": "test_sparse at tag MPIserial_2.5.0",
+        "status3": "test_sparse at tag MPIserial_2.5.0",
+        "status4": "test_sparse at tag MPIserial_2.5.0",
+        "gitmodules_content": """
     [submodule "test_sparse"]
     path = modules/test_sparse
     url = https://github.com/ESMCI/mpi-serial.git
@@ -70,22 +79,29 @@ def logger():
     fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
     fxrequired = AlwaysRequired
     fxsparse = ../.sparse_file_list
-"""},
+""",
+    },
 ]
-@pytest.fixture(params=all_repos)
 
+
+@pytest.fixture(params=all_repos)
 def shared_repos(request):
-    return request.param
+    repo_data = request.param
+    return repo_data
+
 
 @pytest.fixture
 def get_all_repos():
     return all_repos
 
+
 def write_sparse_checkout_file(fp):
     sparse_content = """m4
 """
     fp.write_text(sparse_content)
 
+
+# pylint: disable=redefined-outer-name
 @pytest.fixture
 def test_repo(shared_repos, tmp_path, logger):
     subrepo_path = shared_repos["subrepo_path"]
@@ -100,16 +116,25 @@ def test_repo(shared_repos, tmp_path, logger):
         (test_dir / subrepo_path).mkdir()
         # Add the sparse checkout file
         write_sparse_checkout_file(test_dir / "modules" / ".sparse_file_list")
-        gitp.git_operation("add","modules/.sparse_file_list")
+        gitp.git_operation("add", "modules/.sparse_file_list")
     else:
         gitp = GitInterface(str(test_dir), logger)
-        gitp.git_operation("submodule", "add", "--depth","1","--name", submodule_name, "https://github.com/ESMCI/mpi-serial.git", subrepo_path)
+        gitp.git_operation(
+            "submodule",
+            "add",
+            "--depth",
+            "1",
+            "--name",
+            submodule_name,
+            "https://github.com/ESMCI/mpi-serial.git",
+            subrepo_path,
+        )
         assert test_dir.joinpath(".gitmodules").is_file()
-        gitp.git_operation("add",subrepo_path)
-    gitp.git_operation("commit","-a","-m","\"add submod\"")
+        gitp.git_operation("add", subrepo_path)
+    gitp.git_operation("commit", "-a", "-m", '"add submod"')
     test_dir2 = tmp_path / "testrepo2"
-    gitp.git_operation("clone",test_dir,test_dir2)
-    return test_dir2    
+    gitp.git_operation("clone", test_dir, test_dir2)
+    return test_dir2
 
 
 @pytest.fixture
@@ -118,33 +143,45 @@ def complex_repo(tmp_path, logger):
     test_dir.mkdir()
     str_path = str(test_dir)
     gitp = GitInterface(str_path, logger)
-    gitp.git_operation("remote", "add", "origin", "https://github.com/jedwards4b/fleximod-test2")
+    gitp.git_operation(
+        "remote", "add", "origin", "https://github.com/jedwards4b/fleximod-test2"
+    )
     gitp.git_operation("fetch", "origin")
     gitp.git_operation("checkout", "v0.0.1")
     return test_dir
 
+
 @pytest.fixture
 def complex_update(tmp_path, logger):
     test_dir = tmp_path / "testcomplex"
     test_dir.mkdir()
     str_path = str(test_dir)
     gitp = GitInterface(str_path, logger)
-    gitp.git_operation("remote", "add", "origin", "https://github.com/jedwards4b/fleximod-test2")
+    gitp.git_operation(
+        "remote", "add", "origin", "https://github.com/jedwards4b/fleximod-test2"
+    )
     gitp.git_operation("fetch", "origin")
     gitp.git_operation("checkout", "v0.0.2")
-    
+
     return test_dir
-    
+
+
 @pytest.fixture
 def git_fleximod():
-    def _run_fleximod(path, args, input=None):
+    def _run_fleximod(path, args, user_input=None):
         cmd = ["git", "fleximod"] + args.split()
-        result = subprocess.run(cmd, cwd=path, input=input, 
-                                stdout=subprocess.PIPE, stderr=subprocess.PIPE, 
-                                text=True)
+        result = subprocess.run(
+            cmd,
+            cwd=path,
+            input=user_input,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+            text=True,
+            check=False,
+        )
         if result.returncode:
             print(result.stdout)
             print(result.stderr)
         return result
-    return _run_fleximod
 
+    return _run_fleximod
diff --git a/tests/test_a_import.py b/tests/test_a_import.py
index d5ca878de5..939f143642 100644
--- a/tests/test_a_import.py
+++ b/tests/test_a_import.py
@@ -4,5 +4,6 @@
 from git_fleximod.gitinterface import GitInterface
 from git_fleximod.gitmodules import GitModules
 
+
 def test_import():
     print("here")
diff --git a/tests/test_b_update.py b/tests/test_b_update.py
index 159f1cfae0..e19bbb3d8b 100644
--- a/tests/test_b_update.py
+++ b/tests/test_b_update.py
@@ -1,26 +1,103 @@
-import pytest
+# tests/test_b_update.py
+import time
 from pathlib import Path
-                
+
+
 def test_basic_checkout(git_fleximod, test_repo, shared_repos):
     # Prepare a simple .gitmodules
-    gm = shared_repos['gitmodules_content']
-    file_path = (test_repo / ".gitmodules")
+    gm = shared_repos["gitmodules_content"]
+    file_path = test_repo / ".gitmodules"
     repo_name = shared_repos["submodule_name"]
     repo_path = shared_repos["subrepo_path"]
 
     file_path.write_text(gm)
-    
+
     # Run the command
     result = git_fleximod(test_repo, f"update {repo_name}")
 
     # Assertions
-    assert result.returncode == 0 
-    assert Path(test_repo / repo_path).exists()   # Did the submodule directory get created?
+    assert result.returncode == 0
+    assert Path(
+        test_repo / repo_path
+    ).exists()  # Did the submodule directory get created?
     if "sparse" in repo_name:
-        assert Path(test_repo /  f"{repo_path}/m4").exists()   # Did the submodule sparse directory get created?
-        assert not Path(test_repo /  f"{repo_path}/README").exists()   # Did only the submodule sparse directory get created?
-    
-    status = git_fleximod(test_repo, f"status {repo_name}")
-        
-    assert shared_repos["status2"] in status.stdout
-        
+        assert Path(
+            test_repo / f"{repo_path}/m4"
+        ).exists()  # Did the submodule sparse directory get created?
+        assert not Path(
+            test_repo / f"{repo_path}/README"
+        ).exists()  # Did only the submodule sparse directory get created?
+
+
+def test_local_modification_scenarios(git_fleximod, test_repo, shared_repos):
+    """
+    Test three scenarios for local modifications:
+    1. Local mods, repo in sync: update leaves local mods alone.
+    2. Local mods, repo out-of-sync, no conflict: update brings repo up to date, local mods retained, message shown.
+    3. Local mods, repo out-of-sync, conflict: update fails with error.
+    """
+    repo_name = shared_repos["submodule_name"]
+    repo_path = shared_repos["subrepo_path"]
+    submodule_dir = test_repo / repo_path
+
+    # Ensure submodule is checked out and at intended tag
+    gm = shared_repos["gitmodules_content"]
+    (test_repo / ".gitmodules").write_text(gm)
+    result = git_fleximod(test_repo, f"update {repo_name}")
+    assert result.returncode == 0
+    assert submodule_dir.exists()
+    test_file = submodule_dir / "README"
+    if not test_file.exists():
+        # README must exist in the repository for this test. If not, skip this test.
+        return
+
+    # --- Scenario 1: Local mods, repo in sync ---
+    original_content = test_file.read_text()
+    local_mod_content = f"local modification {time.time()}\n"
+    test_file.write_text(original_content + local_mod_content)
+    result1 = git_fleximod(test_repo, f"update {repo_name}")
+    assert result1.returncode == 0
+    assert (
+        test_file.read_text() == original_content + local_mod_content
+    ), "Local modification was overwritten when repo was in sync!"
+
+    # --- Scenario 2: Local mods, repo out-of-sync, no conflict ---
+    # Simulate out-of-sync by checking out previous commit/tag in submodule
+    import subprocess
+
+    # Try to checkout previous commit (if possible)
+    log = (
+        subprocess.check_output(["git", "log", "--pretty=oneline"], cwd=submodule_dir)
+        .decode()
+        .splitlines()
+    )
+    if len(log) > 1:
+        prev_hash = log[1].split()[0]
+        subprocess.check_call(["git", "checkout", prev_hash], cwd=submodule_dir)
+        # Make a local mod that does not conflict
+        test_file.write_text(original_content + local_mod_content)
+        result2 = git_fleximod(test_repo, f"update {repo_name}")
+        assert result2.returncode == 0
+        # Should retain local mod and show message
+        assert (
+            test_file.read_text() == original_content + local_mod_content
+        ), "Local modification was lost after update with no conflict!"
+        status = git_fleximod(test_repo, f"status {repo_name}")
+        assert "modified files" in status.stdout or "modified" in status.stdout.lower()
+
+    # --- Scenario 3: Local mods, repo out-of-sync, conflict ---
+    # Simulate conflict by modifying file and checking out previous commit that changes the same file
+    if len(log) > 2:
+        # Recover original README file
+        subprocess.check_call(["git", "restore", "README"], cwd=submodule_dir)
+        # Reset to a further previous commit\
+        conflict_hash = log[2].split()[0]
+        subprocess.check_call(["git", "checkout", conflict_hash], cwd=submodule_dir)
+        # Overwrite file with conflicting content
+        test_file.write_text("conflicting local mod\n")
+        try:
+            git_fleximod(test_repo, f"update {repo_name}")
+        except Exception as e:
+            assert "ERROR" in str(e) or "Failed to checkout" in str(
+                e
+            ), "Expected error not raised for conflict scenario!"
diff --git a/tests/test_c_required.py b/tests/test_c_required.py
index 2ac6614519..dd3dcf4f09 100644
--- a/tests/test_c_required.py
+++ b/tests/test_c_required.py
@@ -1,9 +1,11 @@
-import pytest
+# tests/test_c_required.py
 import re
-from pathlib import Path
-                
+
+from tests.utils_for_tests import normalize_whitespace
+
+
 def test_required(git_fleximod, test_repo, shared_repos):
-    file_path = (test_repo / ".gitmodules")
+    file_path = test_repo / ".gitmodules"
     gm = shared_repos["gitmodules_content"]
     repo_name = shared_repos["submodule_name"]
     if file_path.exists():
@@ -11,7 +13,7 @@ def test_required(git_fleximod, test_repo, shared_repos):
             gitmodules_content = f.read()
             # add the entry if it does not exist
             if repo_name not in gitmodules_content:
-                file_path.write_text(gitmodules_content+gm)
+                file_path.write_text(gitmodules_content + gm)
             # or if it is incomplete
             elif gm not in gitmodules_content:
                 file_path.write_text(gm)
@@ -20,15 +22,15 @@ def test_required(git_fleximod, test_repo, shared_repos):
     result = git_fleximod(test_repo, "update")
     assert result.returncode == 0
     status = git_fleximod(test_repo, f"status {repo_name}")
-    assert shared_repos["status3"] in status.stdout
-    status = git_fleximod(test_repo, f"update --optional")
+    assert shared_repos["status3"] in normalize_whitespace(status.stdout)
+    status = git_fleximod(test_repo, "update --optional")
     assert result.returncode == 0
     status = git_fleximod(test_repo, f"status {repo_name}")
-    assert shared_repos["status4"] in status.stdout
+    assert shared_repos["status4"] in normalize_whitespace(status.stdout)
     status = git_fleximod(test_repo, f"update {repo_name}")
     assert result.returncode == 0
     status = git_fleximod(test_repo, f"status {repo_name}")
-    assert shared_repos["status4"] in status.stdout
+    assert shared_repos["status4"] in normalize_whitespace(status.stdout)
 
     text = file_path.read_text()
     new_value = "somethingelse"
@@ -40,4 +42,8 @@ def test_required(git_fleximod, test_repo, shared_repos):
     file_path.write_text(new_text)
 
     result = git_fleximod(test_repo, f"update {repo_name}")
-    assert f'fatal: couldn\'t find remote ref' in result.stderr or 'error: pathspec \'somethingelse\' did not match any file(s) known to git' in result.stderr
+    assert (
+        "fatal: couldn't find remote ref" in result.stderr
+        or "error: pathspec 'somethingelse' did not match any file(s) known to git"
+        in result.stderr
+    )
diff --git a/tests/test_d_complex.py b/tests/test_d_complex.py
index edde7d816d..f7cb9c92fe 100644
--- a/tests/test_d_complex.py
+++ b/tests/test_d_complex.py
@@ -1,34 +1,57 @@
-import pytest
-from pathlib import Path
-from git_fleximod.gitinterface import GitInterface
+# tests/test_d_complex.py
+
+from tests.utils_for_tests import normalize_whitespace
+
 
 def test_complex_checkout(git_fleximod, complex_repo, logger):
     status = git_fleximod(complex_repo, "status")
-    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex not checked out, aligned at tag testtag02" in status.stdout)
-    assert("AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0" in status.stdout)
-    
+    logger.debug("test_complex_checkout status:\n" + status.stdout)
+    assert (
+        "ToplevelOptional not checked out, aligned at tag v5.3.2"
+        in normalize_whitespace(status.stdout)
+    )
+    assert (
+        "ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0"
+        in normalize_whitespace(status.stdout)
+    )
+    assert (
+        "AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0"
+        in normalize_whitespace(status.stdout)
+    )
+    assert "Complex not checked out, aligned at tag testtag02" in normalize_whitespace(
+        status.stdout
+    )
+    assert (
+        "AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0"
+        in normalize_whitespace(status.stdout)
+    )
+
     # This should checkout and update test_submodule and complex_sub
-    result = git_fleximod(complex_repo, "update")    
+    result = git_fleximod(complex_repo, "update")
     assert result.returncode == 0
 
     status = git_fleximod(complex_repo, "status")
-    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag02" in status.stdout)
+    assert (
+        "ToplevelOptional not checked out, aligned at tag v5.3.2"
+        in normalize_whitespace(status.stdout)
+    )
+    assert "ToplevelRequired at tag MPIserial_2.5.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "AlwaysRequired at tag MPIserial_2.4.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "Complex at tag testtag02" in normalize_whitespace(status.stdout)
 
     # now check the complex_sub
-    root = (complex_repo / "modules" / "complex")
-    assert(not (root / "libraries" / "gptl" / ".git").exists())
-    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
-    assert((root / "modules" / "mpi-serial" / ".git").exists())
-    assert(not (root / "modules" / "mpi-serial2" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / "m4").exists())
-    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
+    root = complex_repo / "modules" / "complex"
+    assert not (root / "libraries" / "gptl" / ".git").exists()
+    assert not (root / "libraries" / "mpi-serial" / ".git").exists()
+    assert (root / "modules" / "mpi-serial" / ".git").exists()
+    assert not (root / "modules" / "mpi-serial2" / ".git").exists()
+    assert (root / "modules" / "mpi-sparse" / ".git").exists()
+    assert (root / "modules" / "mpi-sparse" / "m4").exists()
+    assert not (root / "modules" / "mpi-sparse" / "README").exists()
 
     # update a single optional submodule
 
@@ -36,31 +59,42 @@ def test_complex_checkout(git_fleximod, complex_repo, logger):
     assert result.returncode == 0
 
     status = git_fleximod(complex_repo, "status")
-    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag02" in status.stdout)
-    assert("AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0" in status.stdout)
+    assert "ToplevelOptional at tag v5.3.2" in normalize_whitespace(status.stdout)
+    assert "ToplevelRequired at tag MPIserial_2.5.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "AlwaysRequired at tag MPIserial_2.4.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "Complex at tag testtag02" in normalize_whitespace(status.stdout)
+    assert (
+        "AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0"
+        in normalize_whitespace(status.stdout)
+    )
 
     # Finally update optional
     result = git_fleximod(complex_repo, "update --optional")
     assert result.returncode == 0
 
     status = git_fleximod(complex_repo, "status")
-    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag02" in status.stdout)
-    assert("AlwaysOptional at tag MPIserial_2.3.0" in status.stdout)
-    
-    # now check the complex_sub
-    root = (complex_repo / "modules" / "complex" )
-    assert(not (root / "libraries" / "gptl" / ".git").exists())
-    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
-    assert((root / "modules" / "mpi-serial" / ".git").exists())
-    assert((root / "modules" / "mpi-serial2" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / "m4").exists())
-    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
-
+    assert "ToplevelOptional at tag v5.3.2" in normalize_whitespace(status.stdout)
+    assert "ToplevelRequired at tag MPIserial_2.5.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "AlwaysRequired at tag MPIserial_2.4.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "Complex at tag testtag02" in normalize_whitespace(status.stdout)
+    assert "AlwaysOptional at tag MPIserial_2.3.0" in normalize_whitespace(
+        status.stdout
+    )
 
+    # now check the complex_sub
+    root = complex_repo / "modules" / "complex"
+    assert not (root / "libraries" / "gptl" / ".git").exists()
+    assert not (root / "libraries" / "mpi-serial" / ".git").exists()
+    assert (root / "modules" / "mpi-serial" / ".git").exists()
+    assert (root / "modules" / "mpi-serial2" / ".git").exists()
+    assert (root / "modules" / "mpi-sparse" / ".git").exists()
+    assert (root / "modules" / "mpi-sparse" / "m4").exists()
+    assert not (root / "modules" / "mpi-sparse" / "README").exists()
diff --git a/tests/test_e_complex_update.py b/tests/test_e_complex_update.py
index 0c3ab4c6a6..b529a64788 100644
--- a/tests/test_e_complex_update.py
+++ b/tests/test_e_complex_update.py
@@ -1,35 +1,58 @@
-import pytest
-from pathlib import Path
-from git_fleximod.gitinterface import GitInterface
+# tests/test_e_complex_update.py
+from tests.utils_for_tests import normalize_whitespace
+
 
 def test_complex_update(git_fleximod, complex_update, logger):
+    logger.debug("Starting test_complex_update")
     status = git_fleximod(complex_update, "status")
-    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex not checked out, out of sync at tag testtag02, expected tag is testtag3" in status.stdout)
-    assert("AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0" in status.stdout)
-    
+    assert (
+        "ToplevelOptional not checked out, aligned at tag v5.3.2"
+        in normalize_whitespace(status.stdout)
+    )
+    assert (
+        "ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0"
+        in normalize_whitespace(status.stdout)
+    )
+    assert (
+        "AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0"
+        in normalize_whitespace(status.stdout)
+    )
+    assert (
+        "Complex not checked out, out of sync at tag testtag02, expected tag is testtag3"
+        in normalize_whitespace(status.stdout)
+    )
+    assert (
+        "AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0"
+        in normalize_whitespace(status.stdout)
+    )
+
     # This should checkout and update test_submodule and complex_sub
-    result = git_fleximod(complex_update, "update")    
+    result = git_fleximod(complex_update, "update")
     assert result.returncode == 0
 
     status = git_fleximod(complex_update, "status")
-    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag3" in status.stdout)
+    assert (
+        "ToplevelOptional not checked out, aligned at tag v5.3.2"
+        in normalize_whitespace(status.stdout)
+    )
+    assert "ToplevelRequired at tag MPIserial_2.5.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "AlwaysRequired at tag MPIserial_2.4.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "Complex at tag testtag3" in normalize_whitespace(status.stdout)
 
     # now check the complex_sub
-    root = (complex_update / "modules" / "complex")
-    assert(not (root / "libraries" / "gptl" / ".git").exists())
-    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
-    assert((root / "modules" / "mpi-serialAR" / ".git").exists())
-    assert((root / "modules" / "mpi-serialSAR" / ".git").exists())
-    assert(not (root / "modules" / "mpi-serial2" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / "m4").exists())
-    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
+    root = complex_update / "modules" / "complex"
+    assert not (root / "libraries" / "gptl" / ".git").exists()
+    assert not (root / "libraries" / "mpi-serial" / ".git").exists()
+    assert (root / "modules" / "mpi-serialAR" / ".git").exists()
+    assert (root / "modules" / "mpi-serialSAR" / ".git").exists()
+    assert not (root / "modules" / "mpi-serial2" / ".git").exists()
+    assert (root / "modules" / "mpi-sparse" / ".git").exists()
+    assert (root / "modules" / "mpi-sparse" / "m4").exists()
+    assert not (root / "modules" / "mpi-sparse" / "README").exists()
 
     # update a single optional submodule
 
@@ -37,33 +60,44 @@ def test_complex_update(git_fleximod, complex_update, logger):
     assert result.returncode == 0
 
     status = git_fleximod(complex_update, "status")
-    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag3" in status.stdout)
-    assert("AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0" in status.stdout)
+    assert "ToplevelOptional at tag v5.3.2" in normalize_whitespace(status.stdout)
+    assert "ToplevelRequired at tag MPIserial_2.5.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "AlwaysRequired at tag MPIserial_2.4.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "Complex at tag testtag3" in normalize_whitespace(status.stdout)
+    assert (
+        "AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0"
+        in normalize_whitespace(status.stdout)
+    )
 
     # Finally update optional
     result = git_fleximod(complex_update, "update --optional")
     assert result.returncode == 0
 
     status = git_fleximod(complex_update, "status")
-    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag3" in status.stdout)
-    assert("AlwaysOptional at tag MPIserial_2.3.0" in status.stdout)
-    
-    # now check the complex_sub
-    root = (complex_update / "modules" / "complex" )
-    assert(not (root / "libraries" / "gptl" / ".git").exists())
-    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
-    assert(not (root / "modules" / "mpi-serial" / ".git").exists())
-    assert((root / "modules" / "mpi-serialAR" / ".git").exists())
-    assert((root / "modules" / "mpi-serialSAR" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / ".git").exists())
-    assert((root / "modules" / "mpi-serial2" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / "m4").exists())
-    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
-
+    assert "ToplevelOptional at tag v5.3.2" in normalize_whitespace(status.stdout)
+    assert "ToplevelRequired at tag MPIserial_2.5.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "AlwaysRequired at tag MPIserial_2.4.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "Complex at tag testtag3" in normalize_whitespace(status.stdout)
+    assert "AlwaysOptional at tag MPIserial_2.3.0" in normalize_whitespace(
+        status.stdout
+    )
 
+    # now check the complex_sub
+    root = complex_update / "modules" / "complex"
+    assert not (root / "libraries" / "gptl" / ".git").exists()
+    assert not (root / "libraries" / "mpi-serial" / ".git").exists()
+    assert not (root / "modules" / "mpi-serial" / ".git").exists()
+    assert (root / "modules" / "mpi-serialAR" / ".git").exists()
+    assert (root / "modules" / "mpi-serialSAR" / ".git").exists()
+    assert (root / "modules" / "mpi-sparse" / ".git").exists()
+    assert (root / "modules" / "mpi-serial2" / ".git").exists()
+    assert (root / "modules" / "mpi-sparse" / "m4").exists()
+    assert not (root / "modules" / "mpi-sparse" / "README").exists()
diff --git a/tests/utils_for_tests.py b/tests/utils_for_tests.py
new file mode 100644
index 0000000000..8b6f57e2e8
--- /dev/null
+++ b/tests/utils_for_tests.py
@@ -0,0 +1,13 @@
+"""
+Helper functions that can be used in tests
+"""
+
+
+def normalize_whitespace(text):
+    """
+    Normalize whitespace for flexible string comparisons in tests.
+
+    This removes leading and trailing whitespace and collapses other whitespace down to a
+    single space.
+    """
+    return " ".join(text.split())

From c53afec7c6f71d3fb90d29118341be2e35e33725 Mon Sep 17 00:00:00 2001
From: Cheryl Craig <cacraig@ucar.edu>
Date: Wed, 3 Dec 2025 14:41:55 -0700
Subject: [PATCH 2/3] Update externals to match cesm3_0_alpha07h

---
 .gitmodules | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 83479b686a..fc7d7ce569 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -124,42 +124,42 @@ fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
 [submodule "mizuRoute"]
 path = components/mizuRoute
 url = https://github.com/ESCOMP/mizuRoute
-fxtag = v3.0.0
+fxtag = v3.0.1
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
 
 [submodule "ccs_config"]
 path = ccs_config
 url = https://github.com/ESMCI/ccs_config_cesm.git
-fxtag = ccs_config_cesm1.0.63
+fxtag = ccs_config_cesm1.0.65
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 
 [submodule "cime"]
 path = cime
 url = https://github.com/ESMCI/cime
-fxtag = cime6.1.135
+fxtag = cime6.1.144
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESMCI/cime
 
 [submodule "cmeps"]
 path = components/cmeps
 url = https://github.com/ESCOMP/CMEPS.git
-fxtag = cmeps1.1.23
+fxtag = cmeps1.1.24
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 
 [submodule "cdeps"]
 path = components/cdeps
 url = https://github.com/ESCOMP/CDEPS.git
-fxtag = cdeps1.0.83
+fxtag = cdeps1.0.84
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
 
 [submodule "share"]
 path = share
 url = https://github.com/ESCOMP/CESM_share
-fxtag = share1.1.9
+fxtag = share1.1.16
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
 
@@ -194,6 +194,6 @@ fxDONOTUSEurl = https://github.com/ESCOMP/FMS_interface
 [submodule "tools/CUPiD"]
 path = tools/CUPiD
 url = https://github.com/NCAR/CUPiD.git
-fxtag = v0.3.1
+fxtag = v0.4.0
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/NCAR/CUPiD.git

From 7f2fc073bcd994a916c132a32fea4cc2dd0f11f8 Mon Sep 17 00:00:00 2001
From: Cheryl Craig <cacraig@ucar.edu>
Date: Wed, 3 Dec 2025 14:54:24 -0700
Subject: [PATCH 3/3] Update subtrees

---
 ccs_config           | 2 +-
 cime                 | 2 +-
 components/cdeps     | 2 +-
 components/cmeps     | 2 +-
 components/mizuRoute | 2 +-
 share                | 2 +-
 tools/CUPiD          | 2 +-
 7 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/ccs_config b/ccs_config
index 6c22a0f514..7fda4a54ec 160000
--- a/ccs_config
+++ b/ccs_config
@@ -1 +1 @@
-Subproject commit 6c22a0f514cb8ab1d4bcf403b22109b561c42955
+Subproject commit 7fda4a54ec6261d2affb2351ca2b8f288308f0e8
diff --git a/cime b/cime
index cd1046c5c2..e2cf67742b 160000
--- a/cime
+++ b/cime
@@ -1 +1 @@
-Subproject commit cd1046c5c2c5b74c6fbfc46058f6512caab1cf1f
+Subproject commit e2cf67742b1da605da1f782bb53e85915e375a3c
diff --git a/components/cdeps b/components/cdeps
index 293774652f..7e51a85aa2 160000
--- a/components/cdeps
+++ b/components/cdeps
@@ -1 +1 @@
-Subproject commit 293774652f41d5daf5614135fc41b676e8bc59d8
+Subproject commit 7e51a85aa2f4a645ca6795ff63cd3eaa54e85453
diff --git a/components/cmeps b/components/cmeps
index 18eb93be8f..cbc1f0fd44 160000
--- a/components/cmeps
+++ b/components/cmeps
@@ -1 +1 @@
-Subproject commit 18eb93be8f80286739fbea7b500a069fb0d71aa8
+Subproject commit cbc1f0fd442066d171a973ad45d7f867f8cae6c6
diff --git a/components/mizuRoute b/components/mizuRoute
index 07dfd26a17..f4c3482f2b 160000
--- a/components/mizuRoute
+++ b/components/mizuRoute
@@ -1 +1 @@
-Subproject commit 07dfd26a17acb914b9036f59a8c6237990da09f2
+Subproject commit f4c3482f2b29b17ff66c00b615b3305c616fc85a
diff --git a/share b/share
index 14338bef3f..7e6d7a7854 160000
--- a/share
+++ b/share
@@ -1 +1 @@
-Subproject commit 14338bef3fa604d49160e376257264db1d3313e5
+Subproject commit 7e6d7a7854ccb8e80683d3dcc6e41220eef01896
diff --git a/tools/CUPiD b/tools/CUPiD
index 3d9531779b..880f3b3099 160000
--- a/tools/CUPiD
+++ b/tools/CUPiD
@@ -1 +1 @@
-Subproject commit 3d9531779b6f3e4c26059b10ba67c0f4477684e5
+Subproject commit 880f3b30997d19f1b766c483af957277866bbe74