Merge branch 'b4b-dev' into cmake_use_function

Author: ekluzek

.git-blame-ignore-revs

@@ -75,3 +75,4 @@ cdf40d265cc82775607a1bf25f5f527bacc97405
 49ad0f7ebe0b07459abc00a5c33c55a646f1e7e0
 ac03492012837799b7111607188acff9f739044a
 d858665d799690d73b56bcb961684382551193f4
+c0c6da391ee359f2765439426f3a2a4593a95343

.gitmodules

@@ -28,15 +28,15 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.88.0_api.42.0.0
+fxtag = sci.1.89.0_api.43.0.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NGEET/fates
 
 [submodule "cism"]
 path = components/cism
 url = https://github.com/ESCOMP/CISM-wrapper
-fxtag = cismwrap_2_2_010
+fxtag = cismwrap_2_2_011
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
@@ -60,47 +60,47 @@ fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
 [submodule "mizuRoute"]
 	path = components/mizuroute
 	url = https://github.com/ESCOMP/mizuRoute
-fxtag = cesm-coupling.n03_v2.2.0
+fxtag = v3.0.1
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
 
 [submodule "ccs_config"]
 path = ccs_config
 url = https://github.com/ESMCI/ccs_config_cesm.git
-fxtag = ccs_config_cesm1.0.61
+fxtag = ccs_config_cesm1.0.66
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 
 [submodule "cime"]
 path = cime
 url = https://github.com/ESMCI/cime
-fxtag = cime6.1.128
+fxtag = cime6.1.144
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/cime
 
 [submodule "cmeps"]
 path = components/cmeps
 url = https://github.com/ESCOMP/CMEPS.git
-fxtag = cmeps1.1.20
+fxtag = cmeps1.1.24
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 
 [submodule "cdeps"]
 path = components/cdeps
 url = https://github.com/ESCOMP/CDEPS.git
-fxtag = cdeps1.0.81
+fxtag = cdeps1.0.84
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
 
 [submodule "share"]
 path = share
 url = https://github.com/ESCOMP/CESM_share
-fxtag = share1.1.9
+fxtag = share1.1.15
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share

.lib/git-fleximod/.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

.lib/git-fleximod/.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

.lib/git-fleximod/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

.lib/git-fleximod/README.md

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

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

@@ -1,8 +1,8 @@
 from pathlib import Path
 import argparse, os, sys
-from git_fleximod import utils
 
-__version__ = "1.0.2"
+__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",