Introduce source code linting to CAM-SIMA Fortran CI

.github/workflows/cam_sima_fortran_ci.yml

@@ -29,27 +29,35 @@ jobs:
     name: Check if jobs should run
     runs-on: ubuntu-slim
     outputs:
-      should-run: ${{ steps.conditional.outputs.result }}
+      # Encoded in base64 to preserve the matched paths exactly.
+      matched-paths: ${{ steps.conditional.outputs.matched-paths }}
+      should-run: ${{ steps.conditional.outputs.should-run }}
     timeout-minutes: 1
     steps:
       - name: Checkout CAM-SIMA
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Check if there are changes to Fortran source code
         id: conditional
         run: |
           set -euo pipefail
 
           write_result_and_exit() {
+            if [ -f matched-paths.txt ]; then
+              echo "matched-paths=$(base64 -w 0 < matched-paths.txt)" >> "$GITHUB_OUTPUT"
+            else
+              echo "matched-paths=" >> "$GITHUB_OUTPUT"
+            fi
+
             case "$1" in
               false)
                 echo "Result: Skip jobs."
-                echo "result=$1" >> "$GITHUB_OUTPUT"
+                echo "should-run=$1" >> "$GITHUB_OUTPUT"
                 exit 0
                 ;;
               true)
                 echo "Result: Run jobs."
-                echo "result=$1" >> "$GITHUB_OUTPUT"
+                echo "should-run=$1" >> "$GITHUB_OUTPUT"
                 exit 0
                 ;;
               error|*)
@@ -114,7 +122,7 @@ jobs:
           echo "Finding changed paths between $BASE_COMMIT..$HEAD_COMMIT..."
           git diff --name-only "$BASE_COMMIT..$HEAD_COMMIT" | tee changed-paths.txt || write_result_and_exit error
 
-          if grep -E -q '(^\.github\/workflows\/cam_sima_fortran_ci\.yml$|^share$|^src\/.+$|^test\/unit\/.+$)' changed-paths.txt; then
+          if grep -E '^\.github/workflows/cam_sima_fortran_ci\.yml$|^share$|^src/.+$|^test/unit/.+$' changed-paths.txt > matched-paths.txt; then
             write_result_and_exit true
           else
             write_result_and_exit false
@@ -129,6 +137,7 @@ jobs:
     name: Overall status (CAM-SIMA Fortran CI)
     needs:
       - conditional-check
+      - source-code-linting
       - unit-tests
     if: ${{ always() }}
     runs-on: ubuntu-slim
@@ -167,6 +176,18 @@ jobs:
               ;;
           esac
 
+          case "${{ needs.source-code-linting.result }}" in
+            skipped|success)
+              :
+              ;;
+            cancelled|failure)
+              write_result_and_exit false
+              ;;
+            *)
+              write_result_and_exit error
+              ;;
+          esac
+
           case "${{ needs.unit-tests.result }}" in
             skipped|success)
               :
@@ -180,6 +201,73 @@ jobs:
           esac
 
           write_result_and_exit true
+  source-code-linting:
+    name: Lint Fortran source code
+    needs: conditional-check
+    if: ${{ needs.conditional-check.outputs.should-run == 'true' }}
+    runs-on: ubuntu-slim
+    env:
+      FORTITUDE_VERSION: 0.9.*
+      SOURCE_CODE_PATH: ${{ github.workspace }}
+    timeout-minutes: 10
+    steps:
+      - name: Checkout CAM-SIMA
+        uses: actions/checkout@v7
+
+      - name: Setup Python
+        uses: actions/setup-python@v7
+        with:
+          cache: pip
+          python-version: 3.12
+
+      - name: Install Fortitude
+        run: |
+          python3 -m venv venv-fortitude
+          source venv-fortitude/bin/activate
+          python3 -m pip install --upgrade pip
+          python3 -m pip install "fortitude-lint==$FORTITUDE_VERSION"
+
+      - name: Lint Fortran source code
+        run: |
+          # Retrieve the matched paths.
+          echo "${{ needs.conditional-check.outputs.matched-paths }}" | base64 -d > matched-paths.txt
+
+          # Filter Fortran files for Fortitude.
+          # Fortitude will choke if it encounters non-Fortran files in the command line arguments.
+          if grep -E '[^/]+\.(F|f|F90|f90|pf)$' matched-paths.txt > filtered-paths.txt; then
+            set --
+            while IFS="" read -r LINE || [ -n "$LINE" ]; do
+              [ -f "$LINE" ] && set -- "$@" "$LINE"
+            done < filtered-paths.txt
+
+            # Fortitude will still choke if there are no command line arguments.
+            if [ "$#" -gt 0 ]; then
+              source venv-fortitude/bin/activate
+              # First run: Annotated output for GitHub Actions.
+              fortitude \
+                --config-file "$SOURCE_CODE_PATH/test/fortitude.toml" \
+                check \
+                --exit-zero \
+                --output-format github \
+                "$@" | sed -e "s|file=$SOURCE_CODE_PATH/|file=|g"
+              # Second run: Output to a log file for uploading.
+              fortitude \
+                --config-file "$SOURCE_CODE_PATH/test/fortitude.toml" \
+                check \
+                --exit-zero \
+                --output-file "$SOURCE_CODE_PATH/source-code-linting.log" \
+                "$@"
+            fi
+          fi
+
+      - name: Upload Fortran source code linting log
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v7
+        with:
+          if-no-files-found: ignore
+          name: source-code-linting-log
+          path: ${{ env.SOURCE_CODE_PATH }}/source-code-linting.log
+          retention-days: 7
   unit-tests:
     name: Build and run unit tests (${{ matrix.compiler }})
     needs: conditional-check
@@ -218,14 +306,14 @@ jobs:
     timeout-minutes: 10
     steps:
       - name: Checkout CAM-SIMA
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Checkout dependencies
         run: |
           ./bin/git-fleximod update ncar-physics share
 
       - name: Checkout rrtmgp-data for PIO file reader tests
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
         with:
           repository: earth-system-radiation/rrtmgp-data
           ref: ${{ env.RRTMGP_DATA_REFERENCE }}

.github/workflows/mpas_dynamical_core_ci.yml

@@ -29,27 +29,35 @@ jobs:
     name: Check if jobs should run
     runs-on: ubuntu-slim
     outputs:
-      should-run: ${{ steps.conditional.outputs.result }}
+      # Encoded in base64 to preserve the matched paths exactly.
+      matched-paths: ${{ steps.conditional.outputs.matched-paths }}
+      should-run: ${{ steps.conditional.outputs.should-run }}
     timeout-minutes: 1
     steps:
       - name: Checkout CAM-SIMA
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Check if there are changes to MPAS dynamical core
         id: conditional
         run: |
           set -euo pipefail
 
           write_result_and_exit() {
+            if [ -f matched-paths.txt ]; then
+              echo "matched-paths=$(base64 -w 0 < matched-paths.txt)" >> "$GITHUB_OUTPUT"
+            else
+              echo "matched-paths=" >> "$GITHUB_OUTPUT"
+            fi
+
             case "$1" in
               false)
                 echo "Result: Skip jobs."
-                echo "result=$1" >> "$GITHUB_OUTPUT"
+                echo "should-run=$1" >> "$GITHUB_OUTPUT"
                 exit 0
                 ;;
               true)
                 echo "Result: Run jobs."
-                echo "result=$1" >> "$GITHUB_OUTPUT"
+                echo "should-run=$1" >> "$GITHUB_OUTPUT"
                 exit 0
                 ;;
               error|*)
@@ -114,7 +122,7 @@ jobs:
           echo "Finding changed paths between $BASE_COMMIT..$HEAD_COMMIT..."
           git diff --name-only "$BASE_COMMIT..$HEAD_COMMIT" | tee changed-paths.txt || write_result_and_exit error
 
-          if grep -E -q '(^\.github\/workflows\/mpas_dynamical_core_ci\.yml$|^src\/dynamics\/mpas\/.+$)' changed-paths.txt; then
+          if grep -E '^\.github/workflows/mpas_dynamical_core_ci\.yml$|^src/dynamics/mpas/.+$' changed-paths.txt > matched-paths.txt; then
             write_result_and_exit true
           else
             write_result_and_exit false
@@ -199,15 +207,15 @@ jobs:
     if: ${{ needs.conditional-check.outputs.should-run == 'true' }}
     runs-on: ubuntu-slim
     env:
-      FORTITUDE_VERSION: 0.7.*
+      FORTITUDE_VERSION: 0.9.*
       SOURCE_CODE_PATH: ${{ github.workspace }}/src/dynamics/mpas
     timeout-minutes: 10
     steps:
       - name: Checkout CAM-SIMA
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Setup Python
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           cache: pip
           python-version: 3.12
@@ -216,6 +224,7 @@ jobs:
         run: |
           python3 -m venv venv-fortitude
           source venv-fortitude/bin/activate
+          python3 -m pip install --upgrade pip
           python3 -m pip install "fortitude-lint==$FORTITUDE_VERSION"
 
       - name: Lint Fortran source code
@@ -226,7 +235,6 @@ jobs:
             check \
             --exit-zero \
             --output-file "$SOURCE_CODE_PATH/source-code-linting.log" \
-            --preview \
             "$SOURCE_CODE_PATH"
           cat "$SOURCE_CODE_PATH/source-code-linting.log"
 
@@ -267,7 +275,7 @@ jobs:
     timeout-minutes: 10
     steps:
       - name: Checkout CAM-SIMA
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Build unit tests
         run: |

src/control/cam_logfile.F90

@@ -12,12 +12,13 @@ module cam_logfile
 !-----------------------------------------------------------------------
 !- use statements ------------------------------------------------------
 !-----------------------------------------------------------------------
+   use, intrinsic :: iso_fortran_env, only: output_unit
+
 !-----------------------------------------------------------------------
 !- module boilerplate --------------------------------------------------
 !-----------------------------------------------------------------------
    implicit none
    private
-   save
 
 !-----------------------------------------------------------------------
 ! Public interfaces ----------------------------------------------------
@@ -35,7 +36,7 @@ module cam_logfile
    integer, public, protected :: debug_output = DEBUGOUT_NONE
    !> \section arg_table_cam_logfile  Argument Table
    !! \htmlinclude cam_logfile.html
-   integer, public, protected :: iulog = 6
+   integer, public, protected :: iulog = output_unit
    logical, public, protected :: log_output = .false.
 
 !-----------------------------------------------------------------------
@@ -48,7 +49,7 @@ module cam_logfile
       module procedure cam_log_multiwrite_nr8 ! Multiple 8-byte reals
    end interface cam_log_multiwrite
 
-CONTAINS
+contains
 
 !-----------------------------------------------------------------------
 ! Subroutines and functions --------------------------------------------
@@ -72,13 +73,15 @@ end subroutine cam_set_log_unit
 
    subroutine cam_logfile_readnl(nlfile)
       use mpi,        only: mpi_integer
+      use shr_kind_mod, only: cx => shr_kind_cx
       use shr_nl_mod, only: find_group_name => shr_nl_find_group_name
       use spmd_utils, only: mpicom, masterprocid, masterproc
 
       ! nlfile: filepath for file containing namelist input
       character(len=*), intent(in) :: nlfile
 
       ! Local variables
+      character(len=cx)            :: cerr
       integer                      :: unitn
       integer                      :: ierr
 
@@ -92,13 +95,14 @@ subroutine cam_logfile_readnl(nlfile)
       log_output = masterproc
 
       if (masterproc) then
-         open(newunit=unitn, file=trim(nlfile), status='old')
+         open(newunit=unitn, action='read', file=trim(nlfile), status='old')
          call find_group_name(unitn, 'cam_logfile_nl', status=ierr)
          if (ierr == 0) then
-            read(unitn, cam_logfile_nl, iostat=ierr)
+            read(unitn, cam_logfile_nl, iomsg=cerr, iostat=ierr)
             if (ierr /= 0) then
                ! Can't call endrun because of dependency loop
-               write(iulog, *) subname, ': ERROR: reading namelist'
+               write(iulog, *) subname, ': ERROR: reading namelist' // new_line('') // &
+                  trim(adjustl(cerr))
             end if
          end if
          close(unitn)
@@ -123,16 +127,16 @@ subroutine cam_logfile_readnl(nlfile)
       if (ierr /= 0) then
          ! Can't call endrun because of dependency loop
          ! But MPI usually crashes in Fortran
-         write(iulog, *) subname, ": ERROR: mpi_bcast: debug_output"
+         write(iulog, *) subname, ': ERROR: mpi_bcast: debug_output'
       end if
 
    end subroutine cam_logfile_readnl
 
    subroutine cam_log_multiwrite_ni(subname, headers, fmt_string, values)
       ! Print out values from every task
+      use mpi,          only: mpi_integer
       use shr_sys_mod,  only: shr_sys_flush
       use spmd_utils,   only: mpicom, masterprocid, masterproc, npes
-      use mpi,          only: mpi_integer
 
       ! Dummy arguments
       character(len=*), intent(in) :: subname
@@ -165,10 +169,10 @@ end subroutine cam_log_multiwrite_ni
 
    subroutine cam_log_multiwrite_nr8(subname, headers, fmt_string, values)
       ! Print out values from every task
-      use iso_fortran_env, only: r8 => REAL64
+      use, intrinsic :: iso_fortran_env, only: r8 => REAL64
+      use mpi,             only: mpi_real8
       use shr_sys_mod,     only: shr_sys_flush
       use spmd_utils,      only: mpicom, masterprocid, masterproc, npes
-      use mpi,             only: mpi_real8
 
       ! Dummy arguments
       character(len=*), intent(in) :: subname