Merge branch 'b4b-dev' into anping-lecture-2024

# Conflicts:
#	python/ctsm/site_and_regional/run_tower.py

.git-blame-ignore-revs

@@ -1,4 +1,5 @@
 # Ran python directory through black python formatter
+d89c86e7776bbf7451860b60038b4725fe7a0560
 b429b63824e09f82e95d2982f14311cbbd8e4a37
 d229b5c6689efc4c2a6cef077515c4ccd5c18ff6
 4cd83cb3ee6d85eb909403487abf5eeaf4d98911
@@ -27,6 +28,7 @@ d866510188d26d51bcd6d37239283db690af7e82
 e096358c832ab292ddfd22dd5878826c7c788968
 475831f0fb0e31e97f630eac4e078c886558b61c
 fd5f177131d63d39e79a13918390bdfb642d781e
+a51816e0de380300b69db9fc3e2c7fa83b267b64
 # Ran SystemTests and python/ctsm through black python formatter
 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
 8056ae649c1b37f5e10aaaac79005d6e3a8b2380
@@ -52,3 +54,7 @@ aa04d1f7d86cc2503b98b7e2b2d84dbfff6c316b
 045d90f1d80f713eb3ae0ac58f6c2352937f1eb0
 753fda3ff0147837231a73c9c728dd9ce47b5997
 f112ba0bbf96a61d5a4d354dc0dcbd8b0c68145c
+bd535c710db78420b8e8b9d71d88d8339e899c59
+4b20bbd7003e6f77dab4e3268cc4a43f9b5a3b5d
+cf433215b58ba8776ec5edfb0b0d80c0836ed3a0
+16d57ff37859b34dab005693e3085d64e2bcd95a

.gitignore

@@ -89,8 +89,18 @@ unit_test_build
 /tools/site_and_regional/listing.csv
 /tools/site_and_regional/????/
 /tools/site_and_regional/????.ad/
+/tools/site_and_regional/????.*.ad/
 /tools/site_and_regional/????.postad/
+/tools/site_and_regional/????.*.postad/
 /tools/site_and_regional/????.transient/
+/tools/site_and_regional/????.*.transient/
+/tools/site_and_regional/??-???/
+/tools/site_and_regional/??-???.ad/
+/tools/site_and_regional/??-???.*.ad/
+/tools/site_and_regional/??-???.postad/
+/tools/site_and_regional/??-???.*.postad/
+/tools/site_and_regional/??-???.transient/
+/tools/site_and_regional/??-???.*.transient/
 /tools/site_and_regional/archive/
 
 # build output

.gitmodules

@@ -28,99 +28,99 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.79.3_api.37.0.0
+fxtag = sci.1.80.11_api.37.0.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/fates-release
 
 [submodule "cism"]
 path = components/cism
 url = https://github.com/ESCOMP/CISM-wrapper
-fxtag = cismwrap_2_2_002
+fxtag = cismwrap_2_2_005
 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
 
 [submodule "rtm"]
 path = components/rtm
 url = https://github.com/ESCOMP/RTM
-fxtag = rtm1_0_80
+fxtag = rtm1_0_86
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/RTM
 
 [submodule "mosart"]
 path = components/mosart
 url = https://github.com/ESCOMP/MOSART
-fxtag = mosart1.1.02
+fxtag = mosart1.1.08
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
 
 [submodule "mizuRoute"]
 path = components/mizuRoute
 url = https://github.com/ESCOMP/mizuRoute
-fxtag = cesm-coupling.n02_v2.1.2
+fxtag = cesm-coupling.n03_v2.2.0
 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_cesm1.0.0
+fxtag = ccs_config_cesm1.0.20
 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 = cime6.0.246
+fxtag = cime6.1.59
 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 = cmeps0.14.77
+fxtag = cmeps1.0.33
 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 = cdeps1.0.48
+fxtag = cdeps1.0.61
 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 = share1.0.19
+fxtag = share1.1.7
 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
 
-[submodule "mct"]
-path = libraries/mct
-url = https://github.com/MCSclimate/MCT
-fxtag = MCT_2.11.0
-fxrequired = ToplevelRequired
-# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
-fxDONOTUSEurl = https://github.com/MCSclimate/MCT
-
 [submodule "parallelio"]
 path = libraries/parallelio
 url = https://github.com/NCAR/ParallelIO
-fxtag = pio2_6_2
+fxtag = pio2_6_3
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/ParallelIO
 
+[submodule "mpi-serial"]
+path = libraries/mpi-serial
+url = https://github.com/ESMCI/mpi-serial
+fxtag = MPIserial_2.5.1
+fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
+fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial
+
 [submodule "doc-builder"]
 path = doc/doc-builder
 url = https://github.com/ESMCI/doc-builder

.lib/git-fleximod/.github/workflows/pytest.yaml

@@ -18,7 +18,7 @@ jobs:
       # reference the matrixe python version here.
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.9'
+          python-version: '3.12'
 
       # Cache the installation of Poetry itself, e.g. the next step. This prevents the workflow
       # from installing Poetry every time, which can be slow. Note the use of the Poetry version
@@ -29,7 +29,7 @@ jobs:
         uses: actions/cache@v4
         with:
           path: ~/.local
-          key: poetry-1.7.1
+          key: poetry-1.8.2
 
       # Install Poetry. You could do this manually, or there are several actions that do this.
       # `snok/install-poetry` seems to be minimal yet complete, and really just calls out to
@@ -42,7 +42,7 @@ jobs:
       # cache it.
       - uses: snok/install-poetry@v1
         with:
-          version: 1.7.1
+          version: 1.8.2
           virtualenvs-create: true
           virtualenvs-in-project: true
 
@@ -74,4 +74,7 @@ jobs:
           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
 

CODE_OF_CONDUCT.md → .lib/git-fleximod/CODE_OF_CONDUCT.md

@@ -2,7 +2,7 @@
 _The Contributor Code of Conduct is for participants in our software projects and community._
 
 ## Our Pledge
-We, as contributors, creators, stewards, and maintainers (participants), of **Community Terrestrial Systems Model (CTSM)** pledge to make participation in
+We, as contributors, creators, stewards, and maintainers (participants), of **git-fleximod** pledge to make participation in
 our software, system or hardware project and community a safe, productive, welcoming and inclusive experience for everyone.
 All participants are required to abide by this Code of Conduct.
 This includes respectful treatment of everyone regardless of age, body size, disability, ethnicity, gender identity or expression,

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

@@ -2,27 +2,31 @@
 import argparse
 from git_fleximod import utils
 
-__version__ = "0.7.8"
+__version__ = "0.9.3"
 
 def find_root_dir(filename=".gitmodules"):
     """ finds the highest directory in tree
     which contains a file called filename """
-    d = Path.cwd()
-    root = Path(d.root)
-    dirlist = []
-    dl = d
-    while dl != root:
-        dirlist.append(dl)
-        dl = dl.parent
-    dirlist.append(root)
-    dirlist.reverse()
-
-    for dl in dirlist:
-        attempt = dl / filename
-        if attempt.is_file():
-            return str(dl)
-    return None
-
+    try:
+        root = utils.execute_subprocess(["git","rev-parse", "--show-toplevel"],
+                                        output_to_caller=True ).rstrip()
+    except:
+        d = Path.cwd()
+        root = Path(d.root)
+        dirlist = []
+        dl = d
+        while dl != root:
+            dirlist.append(dl)
+            dl = dl.parent
+        dirlist.append(root)
+        dirlist.reverse()
+
+        for dl in dirlist:
+            attempt = dl / filename
+            if attempt.is_file():
+                return str(dl)
+        return None
+    return Path(root)
 
 def get_parser():
     description = """