Initial pFUnit Integration (#326)

Tag name (required for release branches): Originator(s): @mwaxmonsky Description (include the issue title, and the keyword ['closes', 'fixes', 'resolves'] followed by the issue number): Describe any changes made to build system: None Describe any changes made to the namelist: None List any changes to the defaults for the input datasets (e.g. boundary datasets): None List all files eliminated and why: None List all files added and what they do: A .github/workflows/fortran_unit_tests.yml - Initial workflow file to support unit testing in CI A src/core_utils/CMakeLists.txt A test/unit-fortran/CMakeLists.txt A test/unit-fortran/src/core_utils/CMakeLists.txt - Initial unit test build infrastructure. A src/core_utils/string_core_utils.F90 A test/unit-fortran/src/core_utils/test_string_core_utils.pf - Refactored string utils and unit tests without dependencies List all existing files that have been modified, and describe the changes: (Helpful git command: `git diff --name-status development...<your_branch_name>`) R085 test/run_unit_tests.sh test/run_python_unit_tests.sh R100 test/unit/.coveragerc test/unit/python/.coveragerc R100 test/unit/sample_files/atm_in_files/test_attr_in test/unit/python/sample_files/atm_in_files/test_attr_in R100 test/unit/sample_files/atm_in_files/test_cmplx_array_atm_in test/unit/python/sample_files/atm_in_files/test_cmplx_array_atm_in R100 test/unit/sample_files/atm_in_files/test_extra_nml_def.xml test/unit/python/sample_files/atm_in_files/test_extra_nml_def.xml R100 test/unit/sample_files/atm_in_files/test_extra_nml_same_group.xml test/unit/python/sample_files/atm_in_files/test_extra_nml_same_group.xml R100 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test/unit/python/test_hist_config.py R099 test/unit/test_registry.py test/unit/python/test_registry.py R099 test/unit/test_write_init_files.py test/unit/python/test_write_init_files.py - Moved python tests and associated files from top level test directory to python specific directory to allow other language based tests. M src/utils/string_utils.F90 - Removed unused code (`last_sig_char`, `lower_to_upper`, `upper_to_lower`, `last_index`, and `increment_string`), made formatting consistent, and refactored portable string util code to core equivalent so this layer handles non-portable code and then calls core util code. M .github/workflows/python_unit_tests.yml M .gitignore M cime_config/cam_autogen.py - Updated python test paths to new directory. M cime_config/buildlib - Adding `core_utils` directory to list of source directories. If there are new failures (compared to the `test/existing-test-failures.txt` file), have them OK'd by the gatekeeper, note them here, and add them to the file. If there are baseline differences, include the test and the reason for the diff. What is the nature of the change? Roundoff? derecho/intel/aux_sima: derecho/gnu/aux_sima: If this changes climate describe any run(s) done to evaluate the new climate in enough detail that it(they) could be reproduced: CAM-SIMA date used for the baseline comparison tests if different than latest:
ESCOMP · Feb 11, 2025 · 74b935d · 74b935d
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diff --git a/.github/workflows/fortran_unit_tests.yml b/.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
diff --git a/.github/workflows/python_unit_tests.yml b/.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
diff --git a/.gitignore b/.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

diff --git a/cime_config/buildlib b/cime_config/buildlib
@@ -101,7 +101,8 @@ 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)

diff --git a/cime_config/cam_autogen.py b/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')
 

diff --git a/src/core_utils/CMakeLists.txt b/src/core_utils/CMakeLists.txt
@@ -0,0 +1,9 @@
+set(CORE_UTILS_SRC string_core_utils.F90)
+
+# core_utils is not integrated into the CMake build of any top level
+# project yet and this CMake is for testing purposes only.
+# Making a change to this project's CMake will not impact the build of
+# a parent project at this time.
+add_library(core_utils ${CORE_UTILS_SRC})
+target_include_directories(core_utils PUBLIC ${CMAKE_CURRENT_BINARY_DIR})
+
diff --git a/src/core_utils/string_core_utils.F90 b/src/core_utils/string_core_utils.F90
@@ -0,0 +1,162 @@
+module string_core_utils
+
+    implicit none
+    private
+
+    public :: core_to_str                ! Convert integer to left justified string
+    public :: core_int_date_to_yyyymmdd  ! Convert encoded date integer to "yyyy-mm-dd" format
+    public :: core_int_seconds_to_hhmmss ! Convert integer seconds past midnight to "hh:mm:ss" format
+    public :: core_stringify             ! Convert one or more values of any intrinsic data types to a character string for pretty printing
+
+CONTAINS
+
+    character(len=10) pure function core_to_str(n)
+        ! return default integer as a left justified string
+
+        integer, intent(in) :: n
+
+        write(core_to_str,'(i0)') n
+
+    end function core_to_str
+
+    character(len=10) pure function core_int_date_to_yyyymmdd (date)
+        ! Undefined behavior if date <= 0
+
+        ! Input arguments
+        integer, intent(in) :: date
+
+        ! Local variables
+        integer :: year    ! year of yyyy-mm-dd
+        integer :: month   ! month of yyyy-mm-dd
+        integer :: day     ! day of yyyy-mm-dd
+
+        year  = date / 10000
+        month = (date - year*10000) / 100
+        day   = date - year*10000 - month*100
+
+        write(core_int_date_to_yyyymmdd, '(i4.4,A,i2.2,A,i2.2)') &
+                                           year,'-',month,'-',day
+
+    end function core_int_date_to_yyyymmdd
+
+    character(len=8) pure function core_int_seconds_to_hhmmss (seconds)
+        ! Undefined behavior if seconds outside [0, 86400]
+
+        ! Input arguments
+        integer, intent(in) :: seconds
+
+        ! Local variables
+        integer :: hours     ! hours of hh:mm:ss
+        integer :: minutes   ! minutes of hh:mm:ss
+        integer :: secs      ! seconds of hh:mm:ss
+
+        hours   = seconds / 3600
+        minutes = (seconds - hours*3600) / 60
+        secs    = (seconds - hours*3600 - minutes*60)
+
+        write(core_int_seconds_to_hhmmss,'(i2.2,A,i2.2,A,i2.2)') &
+                                        hours,':',minutes,':',secs
+
+    end function core_int_seconds_to_hhmmss
+
+    !> Convert one or more values of any intrinsic data types to a character string for pretty printing.
+    !> If `value` contains more than one element, the elements will be stringified, delimited by `separator`, then concatenated.
+    !> If `value` contains exactly one element, the element will be stringified without using `separator`.
+    !> If `value` contains zero element or is of unsupported data types, an empty character string is produced.
+    !> If `separator` is not supplied, it defaults to `, ` (i.e., a comma and a space).
+    !> (KCW, 2024-02-04)
+    pure function core_stringify(value, separator)
+        use, intrinsic :: iso_fortran_env, only: int32, int64, real32, real64
+
+        class(*), intent(in) :: value(:)
+        character(*), optional, intent(in) :: separator
+        character(:), allocatable :: core_stringify
+
+        integer, parameter :: sizelimit = 1024
+
+        character(:), allocatable :: buffer, delimiter, format
+        integer :: i, n, offset
+
+        if (present(separator)) then
+            delimiter = separator
+        else
+            delimiter = ', '
+        end if
+
+        n = min(size(value), sizelimit)
+
+        if (n == 0) then
+            core_stringify = ''
+            return
+        end if
+
+        select type (value)
+            type is (character(*))
+                allocate(character(len(value) * n + len(delimiter) * (n - 1)) :: buffer)
+
+                buffer(:) = ''
+                offset = 0
+
+                do i = 1, n
+                    if (len(delimiter) > 0 .and. i > 1) then
+                        buffer(offset + 1:offset + len(delimiter)) = delimiter
+                        offset = offset + len(delimiter)
+                    end if
+
+                    if (len_trim(adjustl(value(i))) > 0) then
+                        buffer(offset + 1:offset + len_trim(adjustl(value(i)))) = trim(adjustl(value(i)))
+                        offset = offset + len_trim(adjustl(value(i)))
+                    end if
+                end do
+            type is (integer(int32))
+                allocate(character(11 * n + len(delimiter) * (n - 1)) :: buffer)
+                allocate(character(17 + len(delimiter) + floor(log10(real(n))) + 1) :: format)
+
+                write(format, '(a, i0, 3a)') '(ss, ', n, '(i0, :, "', delimiter, '"))'
+                write(buffer, format) value
+            type is (integer(int64))
+                allocate(character(20 * n + len(delimiter) * (n - 1)) :: buffer)
+                allocate(character(17 + len(delimiter) + floor(log10(real(n))) + 1) :: format)
+
+                write(format, '(a, i0, 3a)') '(ss, ', n, '(i0, :, "', delimiter, '"))'
+                write(buffer, format) value
+            type is (logical)
+                allocate(character(1 * n + len(delimiter) * (n - 1)) :: buffer)
+                allocate(character(13 + len(delimiter) + floor(log10(real(n))) + 1) :: format)
+
+                write(format, '(a, i0, 3a)') '(', n, '(l1, :, "', delimiter, '"))'
+                write(buffer, format) value
+            type is (real(real32))
+                allocate(character(13 * n + len(delimiter) * (n - 1)) :: buffer)
+
+                if (maxval(abs(value)) < 1.0e5_real32) then
+                    allocate(character(20 + len(delimiter) + floor(log10(real(n))) + 1) :: format)
+                    write(format, '(a, i0, 3a)') '(ss, ', n, '(f13.6, :, "', delimiter, '"))'
+                else
+                    allocate(character(23 + len(delimiter) + floor(log10(real(n))) + 1) :: format)
+                    write(format, '(a, i0, 3a)') '(ss, ', n, '(es13.6e2, :, "', delimiter, '"))'
+                end if
+
+                write(buffer, format) value
+            type is (real(real64))
+                allocate(character(13 * n + len(delimiter) * (n - 1)) :: buffer)
+
+                if (maxval(abs(value)) < 1.0e5_real64) then
+                    allocate(character(20 + len(delimiter) + floor(log10(real(n))) + 1) :: format)
+                    write(format, '(a, i0, 3a)') '(ss, ', n, '(f13.6, :, "', delimiter, '"))'
+                else
+                    allocate(character(23 + len(delimiter) + floor(log10(real(n))) + 1) :: format)
+                    write(format, '(a, i0, 3a)') '(ss, ', n, '(es13.6e2, :, "', delimiter, '"))'
+                end if
+
+                write(buffer, format) value
+            class default
+            core_stringify = ''
+                return
+        end select
+
+        core_stringify = trim(buffer)
+
+    end function core_stringify
+
+end module string_core_utils