ctsm5.3.063: b4b-dev merge 2025-07-10

.git-blame-ignore-revs

@@ -69,3 +69,4 @@ cdf40d265cc82775607a1bf25f5f527bacc97405
 742cfa606039ab89602fde5fef46458516f56fd4
 4ad46f46de7dde753b4653c15f05326f55116b73
 75db098206b064b8b7b2a0604d3f0bf8fdb950cc
+84609494b54ea9732f64add43b2f1dd035632b4c

.github/workflows/formatting_python.yml → .github/workflows/python-tests.yml

@@ -1,4 +1,4 @@
-name: Check Python formatting
+name: Run Python tests
 
 on:
   push:
@@ -18,7 +18,27 @@ on:
       - 'cime_config/buildnml/**'
 
 jobs:
-  lint-and-format-check:
+  python-unit-tests:
+    runs-on: ubuntu-latest
+    steps:
+      # Checkout the code
+      - uses: actions/checkout@v4
+
+      # Set up the conda environment
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: ctsm_pylib
+          environment-file: python/conda_env_ctsm_py.yml
+          channels: conda-forge
+          auto-activate-base: false
+
+      # Run Python unit tests check
+      - name: Run Python unit tests
+        run: |
+          cd python
+          conda run -n ctsm_pylib ./run_ctsm_py_tests -u
+
+  python-lint-and-black:
     runs-on: ubuntu-latest
     steps:
       # Checkout the code

bld/namelist_files/namelist_definition_ctsm.xml

@@ -3012,7 +3012,7 @@ snow melt of Brock et al. (2006)
        group="clm_initinterp_inparm" valid_values="" >
 If FALSE (which is the default): If an output type cannot be found in the input for initInterp,
 code aborts
-If TRUE: If an output type cannot be found in the input, fill with closest natural veg column
+If TRUE: If a non-urban output type cannot be found in the input, fill with closest natural veg column
 (using bare soil for patch-level variables)
 
 NOTE: Natural vegetation and crop landunits always behave as if this were true. e.g., if
@@ -3021,6 +3021,14 @@ always fill with the closest natural veg patch / column, regardless of the value
 flag. So interpolation from non-crop to crop cases can be done without setting this flag.
 </entry>
 
+<entry id="init_interp_fill_missing_urban_with_HD" type="logical" category="datasets"
+       group="clm_initinterp_inparm" valid_values="" >
+If FALSE (which is the default): If an urban output type cannot be found in the input for initInterp,
+code aborts
+If TRUE: If an urban output type cannot be found in the input, fill with closest urban high density
+(HD) landunit
+</entry>
+
 <entry id="init_interp_method" type="char*64" category="datasets"
        group="clm_initinterp_inparm"
        valid_values="general,use_finidat_areas" >

cime_config/SystemTests/lreprstruct.py

@@ -16,6 +16,8 @@
 
 """
 
+import re
+
 from CIME.SystemTests.system_tests_compare_two import SystemTestsCompareTwo
 from CIME.XML.standard_module_setup import *
 from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files
@@ -53,13 +55,16 @@ def _case_one_setup(self):
         user_nl_clm_path = os.path.join(self._get_caseroot(), "user_nl_clm")
         with open(user_nl_clm_path) as f:
             user_nl_clm_text = f.read()
-        for grain_output in re.findall("GRAIN\w*", user_nl_clm_text):
-            user_nl_clm_text = user_nl_clm_text.replace(
-                grain_output,
+
+        def replace_grain(match):
+            grain_output = match.group()
+            return (
                 grain_output.replace("GRAIN", "REPRODUCTIVE1")
                 + "', '"
-                + grain_output.replace("GRAIN", "REPRODUCTIVE2"),
+                + grain_output.replace("GRAIN", "REPRODUCTIVE2")
             )
+
+        user_nl_clm_text = re.sub(r"GRAIN\w*", replace_grain, user_nl_clm_text)
         with open(user_nl_clm_path, "w") as f:
             f.write(user_nl_clm_text)
 

cime_config/SystemTests/sspmatrixcn.py

@@ -14,6 +14,7 @@
 """
 
 import shutil, glob, os, sys
+from pathlib import Path
 from datetime import datetime
 
 if __name__ == "__main__":
@@ -205,9 +206,9 @@ def run_indv(self, nstep, st_archive=True):
             restdir = os.path.join(rest_r, rundate)
             os.mkdir(restdir)
             rpoint = os.path.join(restdir, "rpointer.clm." + rundate)
-            os.mknod(rpoint)
+            Path.touch(rpoint)
             rpoint = os.path.join(restdir, "rpointer.cpl." + rundate)
-            os.mknod(rpoint)
+            Path.touch(rpoint)
 
     def run_phase(self):
         "Run phase"