merge dev

Author: boulderdaze

.github/workflows/fortran_unit_tests.yml

@@ -0,0 +1,73 @@
+name: Fortran Unit Tests
+
+on:
+  push:
+    branches:
+      - development
+      - main
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  gcc-toolchain:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        version: [12, 13, 14]
+    env:
+      CC: gcc-${{ matrix.version }}
+      CXX: g++-${{ matrix.version }}
+      FC: gfortran-${{ matrix.version }}
+    steps:
+      - name: Checkout cam-sima
+        uses: actions/checkout@v4
+
+      - name: Build pFUnit
+        run: |
+          git clone --depth 1 --branch v4.10.0 https://github.com/Goddard-Fortran-Ecosystem/pFUnit.git
+          cd pFUnit
+          cmake -B./build -S.
+          cd build
+          make install
+
+      - name: Build cam-sima
+        run: |
+          cmake \
+            -DCMAKE_PREFIX_PATH=/home/runner/work/CAM-SIMA/CAM-SIMA/pFUnit/build/installed \
+            -DCAM_SIMA_ENABLE_CODE_COVERAGE=ON \
+            -B./build \
+            -S./test/unit/fortran
+          cd build
+          make
+      
+      - name: Run fortran unit tests
+        run: |
+          cd build && ctest -V --output-on-failure --output-junit test_results.xml
+
+      - name: Upload unit test results
+        uses: actions/upload-artifact@v4
+        with:
+          name: unit-test-results-${{ env.FC }}
+          path: build/test_results.xml
+
+      - name: Setup GCov
+        run: |
+          python3 -m venv venv
+          source venv/bin/activate
+          pip3 install gcovr
+
+      - name: Run Gcov
+        run: |
+          source venv/bin/activate
+          cd build
+          gcovr --gcov-executable gcov-${{ matrix.version }} -r .. --filter '\.\./src' --html cam_sima_code_coverage.html --txt
+
+      - name: Upload code coverage results
+        uses: actions/upload-artifact@v4
+        with:
+          name: code-coverage-results-${{ env.FC }}
+          path: build/cam_sima_code_coverage.html

.github/workflows/python_unit_tests.yml

@@ -1,6 +1,7 @@
 name: Python Unit Tests
 
 on:
+  workflow_dispatch:
   pull_request:
     types: [opened, synchronize, reopened]
   push:
@@ -16,12 +17,12 @@ jobs:
   #a PR is either opened or synced (i.e. additional commits are pushed
   #to branch involved in PR).
   python_unit_tests:
-    if: github.event_name == 'pull_request' || github.repository == 'ESCOMP/CAM-SIMA'
+    if: github.event_name == 'pull_request' || github.repository == 'ESCOMP/CAM-SIMA' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     strategy:
       matrix:
         #All of these python versions will be used to run tests:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
       fail-fast: false
     steps:
     # Acquire github action routines:
@@ -56,4 +57,4 @@ jobs:
         pytest src/data --doctest-modules
 
         # Run all python unit tests:
-        pytest test/unit
+        pytest test/unit/python

.gitignore

@@ -5,7 +5,7 @@ buildnmlc
 # Ignore test output
 test/include/*.mod
 test/include/*.o
-test/unit/tmp
+test/unit/python/tmp
 test/system/*.log
 test/system/cime-tests.o*
 test_driver_*.sh

.gitmodules

@@ -20,7 +20,7 @@
 [submodule "ncar-physics"]
         path          = src/physics/ncar_ccpp
 	url           = https://github.com/ESCOMP/atmospheric_physics
-	fxtag         = 60b71f3fd9f10b362caf64afffce12de10854d4d
+	fxtag         = 252b500a93c89f36ece7d8ba08fd8eb025279eaa
         fxrequired    = AlwaysRequired
         fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 [submodule "ccs_config"]

cime_config/atm_in_paramgen.py

@@ -1495,11 +1495,16 @@ def write(self, output_path):
                 # Write all variables within that group (sorted alphabetically):
                 for var in sorted(self._data[nml_group], key=var_sort_key):
                     #Extract variable value(s):
-                    val = self._data[nml_group][var]["values"].strip()
+                    val = self._data[nml_group][var]["values"]
 
-                    #If no value is set then move to the next variable:
+                    #Raise error if no value found:
                     if val is None:
-                        continue
+                        emsg = f"Namelist entry '{var}' is missing a "
+                        emsg += "valid/default 'value' element."
+                        raise AtmInParamGenError(emsg)
+                    else:
+                        #If value found then strip white space:
+                        val = val.strip()
                     #End if
 
                     #Extract variable type:

cime_config/buildlib

@@ -105,7 +105,8 @@ def _build_cam():
                  os.path.join(atm_root, "src", "history", "buffers", "src"),
                  os.path.join(atm_root, "src", "history", "buffers", "src", "hash"),
                  os.path.join(atm_root, "src", "history", "buffers", "src", "util"),
-                 os.path.join(atm_root, "src", "utils")]
+                 os.path.join(atm_root, "src", "utils"),
+                 os.path.join(atm_root, "src", "core_utils")]
         for path in phys_dirs:
             if path not in paths:
                 paths.append(path)

cime_config/cam_autogen.py

@@ -132,7 +132,7 @@ def _find_scheme_source(source_dirs, metadata_file_name):
     doctests:
 
     1.  Check that the function can correctly find source and namelist files:
-    >>> _find_scheme_source([os.path.join(_CAM_ROOT_DIR, "test", "unit", "sample_files", \
+    >>> _find_scheme_source([os.path.join(_CAM_ROOT_DIR, "test", "unit", "python", "sample_files", \
                             "autogen_files")], "two_scheme_banana") # doctest: +ELLIPSIS
     ('...two_scheme_banana.F90', '...two_scheme_banana_namelist.xml')
 

cime_config/testdefs/testlist_cam.xml

@@ -43,6 +43,15 @@
       <option name="comment">Test for Moist Held-Suarez (TJ2016) physics (physics_after_coupler group)</option>
     </options>
   </test>
+  <test compset="FPHYStest" grid="ne3pg3_ne3pg3_mg37" name="SMS_Ln2" testmods="cam/outfrq_zm_derecho">
+    <machines>
+      <machine name="derecho" compiler="gnu" category="aux_sima"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:10:00</option>
+      <option name="comment">Test for Zhang McFarlane physics</option>
+    </options>
+  </test>
 
   <!-- Derecho dycore tests -->
   <test compset="FKESSLER" grid="mpasa480_mpasa480" name="SMS_Ln9" testmods="cam/outfrq_kessler_mpas_derecho">

cime_config/testdefs/testmods_dirs/cam/outfrq_kessler_derecho/shell_commands

@@ -1 +1 @@
- ./xmlchange CAM_CONFIG_OPTS="--dyn none --physics-suites kessler"
+ ./xmlchange CAM_CONFIG_OPTS="--dyn none --physics-suites kessler_test"

cime_config/testdefs/testmods_dirs/cam/outfrq_zm_derecho/shell_commands

@@ -0,0 +1 @@
+ ./xmlchange CAM_CONFIG_OPTS="--dyn none --physics-suites zhang_mcfarlane"