Merge tag 'ctsm5.3.040' into alpha-ctsm5.4.CMIP7

Update ctsm_pylib to 3.13.2

Author: ekluzek

.git-blame-ignore-revs

@@ -1,4 +1,4 @@
-# Ran python directory through black python formatter
+# Reformat with black
 d89c86e7776bbf7451860b60038b4725fe7a0560
 b429b63824e09f82e95d2982f14311cbbd8e4a37
 d229b5c6689efc4c2a6cef077515c4ccd5c18ff6
@@ -29,7 +29,6 @@ e096358c832ab292ddfd22dd5878826c7c788968
 475831f0fb0e31e97f630eac4e078c886558b61c
 fd5f177131d63d39e79a13918390bdfb642d781e
 a51816e0de380300b69db9fc3e2c7fa83b267b64
-# Ran SystemTests and python/ctsm through black python formatter
 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
 8056ae649c1b37f5e10aaaac79005d6e3a8b2380
 0bc3f00115d86d026a977918661c93779b3b19f9
@@ -59,4 +58,7 @@ bd535c710db78420b8e8b9d71d88d8339e899c59
 cf433215b58ba8776ec5edfb0b0d80c0836ed3a0
 16d57ff37859b34dab005693e3085d64e2bcd95a
 e8fc526e0d7818d45f171488c78392c4ff63902a
+30d2682a0893f5620bfe37ca6e2614fa60c99f51
+890b4633c5477dc074f79c69c40d650196337591
+1972cef6bba0d97169b30a53f540d56bcbd97281
 cdf40d265cc82775607a1bf25f5f527bacc97405

.github/workflows/black.yml

@@ -18,20 +18,20 @@ jobs:
              options: "--check --config python/pyproject.toml"
              src: "./python"
              # Version should be coordinated with the ctsm_pylib conda environment under the python directory
-             version: "22.3.0"
+             version: "25.1.0"
           # Actions identical to above for each directory and source file we need to check (arrays aren't allowed for src: field)
         - uses: psf/black@stable
           with:
              options: "--check --config python/pyproject.toml"
              src: "./cime_config/SystemTests"
-             version: "22.3.0"
+             version: "25.1.0"
         - uses: psf/black@stable
           with:
              options: "--check --config python/pyproject.toml"
              src: "./cime_config/buildlib"
-             version: "22.3.0"
+             version: "25.1.0"
         - uses: psf/black@stable
           with:
              options: "--check --config python/pyproject.toml"
              src: "./cime_config/buildnml"
-             version: "22.3.0"
+             version: "25.1.0"

.gitignore

@@ -75,12 +75,11 @@ ctsm.input_data_list.previous
 /tools/mksurfdata_esmf/mksurfdata_in
 /tools/mksurfdata_esmf/surfdata_*.nc
 /tools/mksurfdata_esmf/landuse.timeseries_*.nc
-/tools/mksurfdata_esmf/mksurfdata_jobscript_multi.sh
-/tools/mksurfdata_esmf/mksurfdata_jobscript_single.sh
 /tools/mksurfdata_esmf/pio_iotype.txt
 /tools/mksurfdata_esmf/*.sh
 /tools/mksurfdata_esmf/tool_bld
 /tools/mksurfdata_esmf/pio_iotype.txt
+/tools/mksurfdata_esmf/mpibind*.log
 
 # mksurfdata unit tests
 unit_test_build

cime_config/SystemTests/mksurfdataesmf.py

@@ -10,6 +10,7 @@
 I added -C to the `git describe` in gen_mksurfdata_namelist for this
 system test to work.
 """
+
 import os
 import sys
 import subprocess

cime_config/SystemTests/pvt.py

@@ -9,6 +9,7 @@
 2) run a transient landuse case with use_fates_lupft
     - start from the restart file generated in (1)
 """
+
 from CIME.XML.standard_module_setup import *
 from CIME.SystemTests.system_tests_common import SystemTestsCommon
 from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files

cime_config/SystemTests/ssp.py

@@ -12,6 +12,7 @@
     - start from the restart files generated in (1)
     - turn MOSART off
 """
+
 from CIME.XML.standard_module_setup import *
 from CIME.SystemTests.system_tests_common import SystemTestsCommon
 import shutil, glob, os

cime_config/SystemTests/sspmatrixcn.py

@@ -12,6 +12,7 @@
 Step 3: Run a slow-mode spinup
 Step 4: matrix Spinup off
 """
+
 import shutil, glob, os, sys
 from datetime import datetime
 

cime_config/buildlib

@@ -20,6 +20,7 @@ from CIME.utils import run_cmd, expect
 
 logger = logging.getLogger(__name__)
 
+
 ###############################################################################
 def _write_ctsm_mk(gmake, gmake_opts, makefile, exeroot, libroot):
     """Writes a ctsm.mk file in exeroot.

cime_config/testdefs/ExpectedTestFails.xml

@@ -114,7 +114,7 @@
   </test>
 
   <test name="SMS_D.f10_f10_mg37.I2000Clm60BgcCrop.derecho_nvhpc.clm-crop">
-    <phase name="SHAREDLIB_BUILD">
+    <phase name="RUN">
       <status>FAIL</status>
       <issue>#1733</issue>
     </phase>

cime_config/testdefs/testlist_clm.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <!--
      CTSM test list. Test suites included:
-        ctsm_pymods: System tests for the python codes that also run CTSM cases (subset of aux_clm tests)
+        clm_pymods: System tests for the python code that also run CTSM cases (subset of aux_clm tests)
         clm_short: The short CLM test for basic testing of a few configurations
         aux_clm: Main workhorse test list to be run on main machines before most tags are made
         fates: The FATES testlist, run when FATES is updated