Merge pull request #3578 from ekluzek/merge-b4bdev-20251030

ctsm5.3.084: Merge b4bdev 20251030

Author: ekluzek

.github/workflows/docs-build-and-deploy.yml

@@ -33,6 +33,10 @@ concurrency:
 jobs:
 
   build-and-deploy:
+
+    # Only run on upstream repository
+    if: ${{ github.repository == 'ESCOMP/CTSM' }}
+
     environment:
       name: github-pages
       url: ${{ steps.deployment.outputs.page_url }}

doc/ChangeLog

@@ -1,4 +1,90 @@
 ===============================================================
+Tag name: ctsm5.3.084
+Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Date: Fri 31 Oct 2025 01:12:26 PM MDT
+One-line Summary: Merge b4b-dev to master
+
+Purpose and description of changes
+----------------------------------
+
+Bring changes on b4b-dev to master
+
+- Fix FUNIT testing on Mac's
+- Some fixes to set_paramfile
+- Don't auto build documentation on personal forks, only on ESCOMP
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+  Fixes #3571 -- set_paramfile ordering of PFT's from user doesn't have to match paramfile order
+  Fixes #3559 -- Correct Ndims error
+  Fixes #3369 -- Docs build and deploy only runs on ESCOMP not personal forks
+
+Notes of particular relevance for users
+---------------------------------------
+
+Changes to documentation:
+   Some changes to set_paramfile documentation
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Testing summary: regular
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - OK
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: No bit-for-bit
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+
+  -- #3577 unit testing on Mac
+  -- #3572 set_paramfile ordering
+  -- #3560 Fix Ndim error in set_paramfile
+  -- #3557 doc/build/run/deploy only on ESCOMP
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.083
 Originator(s): rgknox (Ryan Knox,LAWRENCE BERKELEY NATIONAL LABORATORY,510-495-2153)
 Date: Wed 29 Oct 2025 03:35:50 PM MDT

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.084     erik 10/31/2025 Merge b4b-dev to master
        ctsm5.3.083   rgknox 10/29/2025 Changes to coupling of supplementation status with FATES.
        ctsm5.3.082   slevis 10/24/2025 Update to CMIP7 population density file for non-SSP cases
        ctsm5.3.081     erik 10/22/2025 Change defaults for when Carbon isotopes are turned on, and turn on irrigate for Sp/Bgc cases for clm6_0 historical transient cases

doc/source/users_guide/using-clm-tools/paramfile-tools.md

@@ -57,9 +57,14 @@ Change a one-dimensional parameter (`mimics_fmet` has the `segment` dimension, l
 tools/param_utils/set_paramfile -i paramfile.nc -o output.nc mimics_fmet=0.1,0.2,0.3,0.4
 ```
 
+Change a one-dimensional parameter to be all one value (`mxmat` has the `pft` dimension, length 79):
+```bash
+tools/param_utils/set_paramfile -i paramfile.nc -o output.nc mxmat=360
+```
+
 Change a parameter for specific PFTs:
 ```bash
-tools/param_utils/set_paramfile -i paramfile.nc -o output.nc -p needleleaf_evergreen_temperate_tree,c4_grass medlynintercept=99.9,100.1 medlynslope=2.99,1.99
+tools/param_utils/set_paramfile -i paramfile.nc -o output.nc -p needleleaf_evergreen_temperate_tree,c4_grass medlynintercept=99.9,100.1 medlynslope=2.99,1.99 mxmat=199
 ```
 
 Set a parameter to the fill value:

python/ctsm/param_utils/paramfile_shared.py

@@ -85,7 +85,9 @@ def get_selected_pft_indices(selected_pfts, pft_names):
     list of int
         Indices of selected PFTs.
     """
-    indices = [i for i, name in enumerate(pft_names) if name in selected_pfts]
+    if isinstance(selected_pfts, str):
+        selected_pfts = [selected_pfts]
+    indices = [pft_names.index(pft) for pft in selected_pfts]
     return indices
 
 

python/ctsm/param_utils/set_paramfile.py

@@ -130,7 +130,7 @@ def check_correct_ndims(da, new_value, throw_error=False):
     """
     expected = da.ndim
     actual = np.array(new_value).ndim
-    is_ndim_correct = expected == actual
+    is_ndim_correct = actual in (0, expected)  # If actual 0, apply it to all
     if throw_error and not is_ndim_correct:
         raise RuntimeError(f"Incorrect N dims: Expected {expected}, got {actual}")
     return is_ndim_correct
@@ -323,11 +323,12 @@ def apply_new_value_to_parameter(args, ds_out, var, new_value, var_encoding, *,
     # Ensure that any NaNs are replaced with the fill value
     new_value = _replace_nans_with_fill(var_encoding, new_value, chg=chg)
 
-    # This can be needed if, e.g., you're selecting and changing just one PFT
+    # This can be needed if, (a) you're selecting and changing just one PFT or (b) you're changing
+    # all values in a dimensioned parameter to match one value.
     if ds_out[var].values.ndim > 0 and new_value.ndim == 0:
-        new_value = np.atleast_1d(new_value)
-
-    ds_out[var].values = new_value
+        ds_out[var].values[:] = new_value
+    else:
+        ds_out[var].values = new_value
     return ds_out
 
 

python/ctsm/test/test_sys_set_paramfile.py

@@ -121,19 +121,65 @@ def test_set_paramfile_changeparams_scalar_errors_given_list(self):
         with self.assertRaisesRegex(RuntimeError, "Incorrect N dims"):
             sp.main()
 
-    def test_set_paramfile_changeparam_1d_errors_given_scalar(self):
-        """Test that set_paramfile errors if given a scalar for a 1-d parameter"""
+    def test_set_paramfile_changeparam_1d_given_scalar(self):
+        """
+        Test that set_paramfile works correctly if given a scalar for a 1-d parameter. We want it
+        to set all members of the 1d array to the given scalar.
+        """
         output_path = os.path.join(self.tempdir, "output.nc")
         sys.argv = [
             "set_paramfile",
             "-i",
             PARAMFILE,
             "-o",
             output_path,
-            "xl=0.724",
+            "mxmat=1987",
         ]
-        with self.assertRaisesRegex(RuntimeError, "Incorrect N dims"):
-            sp.main()
+        sp.main()
+        self.assertTrue(os.path.exists(output_path))
+        ds_in = open_paramfile(PARAMFILE)
+        ds_out = open_paramfile(output_path)
+
+        for var in ds_in.variables:
+            # Check that all variables/coords are equal except the ones we changed, which should be
+            # set to what we asked
+            if var == "mxmat":
+                self.assertTrue(np.all(ds_out[var].values == 1987))
+            else:
+                self.assertTrue(are_paramfile_dataarrays_identical(ds_in[var], ds_out[var]))
+
+    def test_set_paramfile_changeparam_1d_given_scalar_and_pftlist(self):
+        """
+        Test that set_paramfile works correctly if given a scalar for a 1-d parameter. We want it
+        to set all members of the 1d array to the given scalar. As
+        test_set_paramfile_changeparam_1d_given_scalar, but here we give a pft list.
+        """
+        output_path = os.path.join(self.tempdir, "output.nc")
+        sys.argv = [
+            "set_paramfile",
+            "-i",
+            PARAMFILE,
+            "-o",
+            output_path,
+            "-p",
+            "temperate_corn,irrigated_temperate_corn",
+            "mxmat=1987",
+        ]
+        sp.main()
+        self.assertTrue(os.path.exists(output_path))
+        ds_in = open_paramfile(PARAMFILE)
+        ds_out = open_paramfile(output_path)
+
+        for var in ds_in.variables:
+            # Check that all variables/coords are equal except the ones we changed, which should be
+            # set to what we asked
+            if var == "mxmat":
+                # First, check that they weren't 1987 before
+                self.assertFalse(np.any(ds_in[var].values[17:18] == 1987))
+                # Now check that they are 1987
+                self.assertTrue(np.all(ds_out[var].values[17:18] == 1987))
+            else:
+                self.assertTrue(are_paramfile_dataarrays_identical(ds_in[var], ds_out[var]))
 
     def test_set_paramfile_changeparams_scalar_double(self):
         """Test that set_paramfile can copy to a new file with some scalar double params changed"""
@@ -732,6 +778,46 @@ def test_set_paramfile_double_ok_given_int(self):
         ds_out = open_paramfile(output_path)
         self.assertFalse(sp.is_integer(ds_out[param_name].values))
 
+    def test_set_paramfile_pft_order(self):
+        """
+        Test that set_paramfile gives the same result regardless of the order you specify the PFTs
+        """
+
+        # First order
+        pfts_to_include = ["rice", "irrigated_rice"]
+        output0_path = os.path.join(self.tempdir, "output0.nc")
+        sys.argv = [
+            "set_paramfile",
+            "-i",
+            PARAMFILE,
+            "-o",
+            output0_path,
+            "-p",
+            ",".join(pfts_to_include),
+            "mxmat=100,200",
+        ]
+        sp.main()
+
+        # Reverse order
+        pfts_to_include.reverse()
+        output1_path = os.path.join(self.tempdir, "output1.nc")
+        sys.argv = [
+            "set_paramfile",
+            "-i",
+            PARAMFILE,
+            "-o",
+            output1_path,
+            "-p",
+            ",".join(pfts_to_include),
+            "mxmat=200,100",
+        ]
+        sp.main()
+
+        # These files should be identical
+        ds0 = open_paramfile(output0_path)
+        ds1 = open_paramfile(output1_path)
+        self.assertTrue(ds0.equals(ds1))
+
 
 if __name__ == "__main__":
     unit_testing.setup_for_tests()

python/ctsm/test/test_unit_paramfile_shared.py

@@ -0,0 +1,57 @@
+#!/usr/bin/env python3
+
+"""Unit tests for paramfile_shared"""
+
+import unittest
+
+from ctsm import unit_testing
+
+from ctsm.param_utils import paramfile_shared as ps
+
+# Allow names that pylint doesn't like, because otherwise I find it hard
+# to make readable unit test names
+# pylint: disable=invalid-name
+
+
+class TestUnitGetSelectedPftIndices(unittest.TestCase):
+    """Unit tests of get_selected_pft_indices"""
+
+    def test_get_selected_pft_indices_1strselected_onlyinlist(self):
+        """Check get_selected_pft_indices() given the only one in the list, as a string"""
+        selected_pfts = "rice"
+        pft_names = ["rice"]
+        result = ps.get_selected_pft_indices(selected_pfts=selected_pfts, pft_names=pft_names)
+        self.assertListEqual(result, [0])
+
+    def test_get_selected_pft_indices_1selected_onlyinlist(self):
+        """Check get_selected_pft_indices() given the only one in the list, as a list"""
+        selected_pfts = ["rice"]
+        pft_names = ["rice"]
+        result = ps.get_selected_pft_indices(selected_pfts=selected_pfts, pft_names=pft_names)
+        self.assertListEqual(result, [0])
+
+    def test_get_selected_pft_indices_2selected_sameorder(self):
+        """Check get_selected_pft_indices() given 2 selected in the same order as the list"""
+        pft_names = ["rice", "irrigated_rice"]
+        result = ps.get_selected_pft_indices(selected_pfts=pft_names, pft_names=pft_names)
+        self.assertListEqual(result, [0, 1])
+
+    def test_get_selected_pft_indices_2selected_difforder(self):
+        """Check get_selected_pft_indices() given 2 selected NOT in the same order as the list"""
+        pft_names = ["rice", "irrigated_rice"]
+        result = ps.get_selected_pft_indices(
+            selected_pfts=list(reversed(pft_names)), pft_names=pft_names
+        )
+        self.assertListEqual(result, [1, 0])
+
+    def test_get_selected_pft_indices_missing_valueerror(self):
+        """Check get_selected_pft_indices() given selected pft NOT in the list"""
+        selected_pfts = ["wheat"]
+        pft_names = ["rice", "irrigated_rice"]
+        with self.assertRaises(ValueError):
+            ps.get_selected_pft_indices(selected_pfts=selected_pfts, pft_names=pft_names)
+
+
+if __name__ == "__main__":
+    unit_testing.setup_for_tests()
+    unittest.main()

python/ctsm/test/test_unit_set_paramfile.py

@@ -65,14 +65,14 @@ def test_checkcorrectndims_0d_int_np(self):
         self.assertTrue(sp.check_correct_ndims(da, np.int32(1)))
 
     def test_checkcorrectndims_1d_int(self):
-        """Check False when given a standard int for a 0d parameter"""
+        """Check True when given a standard int for a 0d parameter"""
         da = xr.DataArray(data=[1, 2])
-        self.assertFalse(sp.check_correct_ndims(da, 1))
+        self.assertTrue(sp.check_correct_ndims(da, 1))
 
     def test_checkcorrectndims_1d_int_np(self):
-        """Check False when given a numpy int for a 0d parameter"""
+        """Check True when given a numpy int for a 0d parameter"""
         da = xr.DataArray(data=[1, 2])
-        self.assertFalse(sp.check_correct_ndims(da, np.int32(1)))
+        self.assertTrue(sp.check_correct_ndims(da, np.int32(1)))
 
     def test_checkcorrectndims_0d_list(self):
         """Check False when given a list for a 0d parameter"""

src/CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8)
+cmake_minimum_required(VERSION 3.10)
 
 list(APPEND CMAKE_MODULE_PATH ${CIME_CMAKE_MODULE_DIRECTORY})
 include(CIME_initial_setup)
@@ -93,7 +93,7 @@ add_library(csm_share ${share_sources} ${drv_sources_needed})
 declare_generated_dependencies(csm_share "${share_genf90_sources}")
 add_library(clm ${clm_sources})
 declare_generated_dependencies(clm "${clm_genf90_sources}")
-add_dependencies(clm csm_share esmf)
+add_dependencies(clm csm_share ESMF)
 
 # We need to look for header files here, in order to pick up shr_assert.h
 include_directories(${CLM_ROOT}/share/include)