Containerize CAM-SIMA unit tests and clean up CI infrastructure

.github/workflows/branch_push_workflow.yml

@@ -17,10 +17,10 @@ jobs:
   #in the body of a pull request merged into a non-default branch.
   issue_closer:
     if: github.repository == 'ESCOMP/CAM-SIMA' # Only run on main repo
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-slim
     steps:
     # Acquire github action routines
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
     # Acquire specific version of python
     - name: Set up Python 3.11
       uses: actions/setup-python@v6

.github/workflows/build_and_run_cirrus.yml

@@ -19,6 +19,7 @@ concurrency:
 jobs:
   build-and-run-on-CIRRUS:
     name: Run ${{ matrix.image }} on ${{ matrix.runner }}
+    if: ${{ github.repository == 'ESCOMP/CAM-SIMA' }}
     env:
       TMP_DIR: tmp
       TMP_OUTPUT: case_output.log
@@ -84,7 +85,7 @@ jobs:
           fi
 
       - name: Upload logs to GitHub artifacts when the CI test fails
-        if: failure() 
+        if: failure()
         uses: actions/upload-artifact@v7
         with:
           name: logs.${{ matrix.test_type }}.${{ matrix.compset }}.${{ matrix.compiler }}.${{ matrix.runner }}

.github/workflows/cam_sima_fortran_ci.yml

@@ -0,0 +1,300 @@
+name: CAM-SIMA Fortran CI
+
+permissions:
+  contents: read
+
+on:
+  pull_request:
+    types:
+      - opened
+      - reopened
+      - synchronize
+  push:
+    branches:
+      - staging/**
+      - development
+  workflow_dispatch:
+
+concurrency:
+  cancel-in-progress: true
+  group: ${{ github.workflow }} - ${{ github.ref }}
+
+jobs:
+  # This check is the stepped leader to determine if the rest of jobs should run. We unfortunately cannot use path filtering
+  # due to the peculiar limitations of GitHub Actions, quoted below for reference:
+  #
+  # "If a workflow is skipped due to path filtering, then checks associated with that workflow will remain in a "Pending" state.
+  # A pull request that requires those checks to be successful will be blocked from merging."
+  conditional-check:
+    name: Check if jobs should run
+    runs-on: ubuntu-slim
+    outputs:
+      should-run: ${{ steps.conditional.outputs.result }}
+    timeout-minutes: 1
+    steps:
+      - name: Checkout CAM-SIMA
+        uses: actions/checkout@v6
+
+      - name: Check if there are changes to Fortran source code
+        id: conditional
+        run: |
+          set -euo pipefail
+
+          write_result_and_exit() {
+            case "$1" in
+              false)
+                echo "Result: Skip jobs."
+                echo "result=$1" >> "$GITHUB_OUTPUT"
+                exit 0
+                ;;
+              true)
+                echo "Result: Run jobs."
+                echo "result=$1" >> "$GITHUB_OUTPUT"
+                exit 0
+                ;;
+              error|*)
+                echo "Error occurred!"
+                exit 1
+                ;;
+            esac
+          }
+
+          case "${{ github.event_name }}" in
+            pull_request)
+              echo "Event is pull request."
+
+              HEAD_COMMIT="${{ github.sha }}"
+
+              if [ -z "$HEAD_COMMIT" ]; then
+                echo "HEAD_COMMIT is empty."
+                write_result_and_exit false
+              fi
+
+              echo "Fetching $HEAD_COMMIT with parents..."
+              git fetch --depth=2 origin "$HEAD_COMMIT" || write_result_and_exit error
+
+              BASE_COMMIT="$(git rev-parse $HEAD_COMMIT^1)" || write_result_and_exit error
+              ;;
+            push)
+              echo "Event is push."
+
+              BASE_COMMIT="${{ github.event.before }}"
+              HEAD_COMMIT="${{ github.event.after }}"
+
+              if [ -z "$BASE_COMMIT" ] || [ -z "$HEAD_COMMIT" ]; then
+                echo "BASE_COMMIT or HEAD_COMMIT is empty."
+                write_result_and_exit false
+              fi
+
+              if [ -z "${BASE_COMMIT//0/}" ] || [ -z "${HEAD_COMMIT//0/}" ]; then
+                echo "BASE_COMMIT or HEAD_COMMIT is null."
+                write_result_and_exit false
+              fi
+
+              echo "Fetching $BASE_COMMIT..."
+              git fetch --depth=1 origin "$BASE_COMMIT" || write_result_and_exit error
+
+              echo "Fetching $HEAD_COMMIT..."
+              git fetch --depth=1 origin "$HEAD_COMMIT" || write_result_and_exit error
+              ;;
+            workflow_dispatch)
+              echo "Event is workflow dispatch."
+
+              # Always run jobs when triggered manually.
+              write_result_and_exit true
+              ;;
+            *)
+              echo "Event is unknown."
+
+              # Always skip jobs for any other events.
+              write_result_and_exit false
+              ;;
+          esac
+
+          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
+            write_result_and_exit true
+          else
+            write_result_and_exit false
+          fi
+  # This job evaluates the overall status of CAM-SIMA Fortran CI for the purpose of inclusion as a required status check.
+  # It exists solely due to, again, the peculiar limitations of GitHub Actions, quoted below for reference:
+  #
+  # "The `jobs.<job_id>.if` conditional is evaluated before `jobs.<job_id>.strategy.matrix` is applied." This implies that
+  # when a matrix job is set as a required status check, skipping it due to the conditional will cause a pull request to be
+  # blocked from merging.
+  overall-status:
+    name: Overall status (CAM-SIMA Fortran CI)
+    needs:
+      - conditional-check
+      - unit-tests
+    if: ${{ always() }}
+    runs-on: ubuntu-slim
+    timeout-minutes: 1
+    steps:
+      - name: Evaluate overall status
+        run: |
+          set -euo pipefail
+
+          write_result_and_exit() {
+            case "$1" in
+              false)
+                echo "Result: Failure."
+                exit 1
+                ;;
+              true)
+                echo "Result: Success."
+                exit 0
+                ;;
+              error|*)
+                echo "Error occurred!"
+                exit 1
+                ;;
+            esac
+          }
+
+          case "${{ needs.conditional-check.result }}" in
+            success)
+              :
+              ;;
+            cancelled|failure|skipped)
+              write_result_and_exit false
+              ;;
+            *)
+              write_result_and_exit error
+              ;;
+          esac
+
+          case "${{ needs.unit-tests.result }}" in
+            skipped|success)
+              :
+              ;;
+            cancelled|failure)
+              write_result_and_exit false
+              ;;
+            *)
+              write_result_and_exit error
+              ;;
+          esac
+
+          write_result_and_exit true
+  unit-tests:
+    name: Build and run unit tests (${{ matrix.compiler }})
+    needs: conditional-check
+    if: ${{ needs.conditional-check.outputs.should-run == 'true' }}
+    runs-on: ubuntu-24.04
+    container:
+      image: ghcr.io/kuanchihwang/atm-sci-container:2026-06-12_${{ matrix.compiler }}_${{ matrix.mpi }}
+    env:
+      CONTAINER_PRESET: cesm
+      CONTAINER_ENVIRONMENT: pfunit
+      RRTMGP_DATA_REFERENCE: v1.9
+      UNIT_TESTS_BUILD_TYPE: Debug
+      UNIT_TESTS_PATH: ${{ github.workspace }}/test/unit/fortran
+    strategy:
+      fail-fast: false
+      matrix:
+        compiler:
+          - gnu-11
+          - gnu-12
+          - gnu-13
+          - gnu-14
+          - gnu-15
+          - intel-2024
+          - intel-2025
+        # Uncomment the following lines to test with more MPI implementations. Currently only `open-mpi-5`
+        # (Open MPI 5.0.x series) is enabled. We may expand this matrix as our test coverage grows in the future.
+        mpi:
+          # - mpich-4
+          # - open-mpi-4
+          - open-mpi-5
+        # include:
+        #   - compiler: intel-2024
+        #     mpi: intel-mpi
+        #   - compiler: intel-2025
+        #     mpi: intel-mpi
+    timeout-minutes: 10
+    steps:
+      - name: Checkout CAM-SIMA
+        uses: actions/checkout@v6
+
+      - name: Checkout dependencies
+        run: |
+          ./bin/git-fleximod update ncar-physics share
+
+      - name: Checkout rrtmgp-data for PIO file reader tests
+        uses: actions/checkout@v6
+        with:
+          repository: earth-system-radiation/rrtmgp-data
+          ref: ${{ env.RRTMGP_DATA_REFERENCE }}
+          path: ${{ env.UNIT_TESTS_PATH }}/rrtmgp-data
+
+      - name: Build unit tests
+        run: |
+          source "$(command -v container-entrypoint-hook.sh)"
+          cmake \
+            -D CMAKE_BUILD_TYPE="$UNIT_TESTS_BUILD_TYPE" \
+            -D CAM_SIMA_ENABLE_CODE_COVERAGE=ON \
+            -D CAM_SIMA_ENABLE_IO_TESTS=ON \
+            -D CAM_SIMA_ENABLE_TESTS=ON \
+            -B "$UNIT_TESTS_PATH/build" \
+            -S "$UNIT_TESTS_PATH"
+          cmake \
+            --build "$UNIT_TESTS_PATH/build" \
+            --config "$UNIT_TESTS_BUILD_TYPE"
+
+      - name: Run unit tests
+        run: |
+          source "$(command -v container-entrypoint-hook.sh)"
+          ctest \
+            --build-config "$UNIT_TESTS_BUILD_TYPE" \
+            --output-junit "$UNIT_TESTS_PATH/build/unit-tests.xml" \
+            --output-on-failure \
+            --test-dir "$UNIT_TESTS_PATH/build" \
+            --test-output-size-failed 524288 \
+            --test-output-size-passed 524288 \
+            --verbose
+
+      - name: Upload unit test results
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v7
+        with:
+          if-no-files-found: ignore
+          name: unit-tests-xml-${{ matrix.compiler }}
+          path: ${{ env.UNIT_TESTS_PATH }}/build/unit-tests.xml
+          retention-days: 7
+
+      # Code coverage analysis only works reliably with the GNU Compiler Collection.
+      # Do it only with the latest version to save CI time.
+
+      - name: Install Gcovr
+        if: ${{ matrix.compiler == 'gnu-15' }}
+        run: |
+          python3 -m venv venv-gcovr
+          source venv-gcovr/bin/activate
+          python3 -m pip install --upgrade pip
+          python3 -m pip install gcovr
+
+      - name: Run Gcovr
+        if: ${{ matrix.compiler == 'gnu-15' }}
+        run: |
+          source venv-gcovr/bin/activate
+          export SOURCE_PATH="$PWD"
+          cd "$UNIT_TESTS_PATH/build"
+          gcovr \
+            --filter "$SOURCE_PATH/src" \
+            --html code-coverage.html \
+            --root "$SOURCE_PATH" \
+            --verbose \
+            .
+
+      - name: Upload code coverage results
+        if: ${{ always() && matrix.compiler == 'gnu-15' }}
+        uses: actions/upload-artifact@v7
+        with:
+          if-no-files-found: ignore
+          name: code-coverage-html
+          path: ${{ env.UNIT_TESTS_PATH }}/build/code-coverage.html
+          retention-days: 7

.github/workflows/fleximod_test.yaml

@@ -2,15 +2,15 @@ on:
   pull_request:
 jobs:
   fleximod-test:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-slim
     strategy:
       fail-fast: false
       matrix:
         # oldest supported and latest supported
         python-version: ["3.8", "3.x"]
     steps:
       - id: checkout-CESM
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
       - id: run-fleximod
         run: |
           $GITHUB_WORKSPACE/bin/git-fleximod update -o