build: Optimize CI Pipeline Code

.github/workflows/ci.yml

@@ -82,13 +82,14 @@ jobs:
   # ----------------------------------------------------------------------
   # R CHECK
   # ----------------------------------------------------------------------
-  check_base:
+  check:
     if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build')
     runs-on: ubuntu-latest
 
     strategy:
       fail-fast: false
       matrix:
+        package: [check_base, check_modules, check_models]
         R:
           - "4.0"
           - "4.1"
@@ -130,128 +131,15 @@ jobs:
       run: Rscript scripts/generate_dependencies.R && Rscript docker/depends/pecan.depends.R
 
     # run PEcAn checks
+    # The package names of base, modules, and models are passed as matrix variables to avoid repeatability of code
     - name: check
-      run: make -j1 check_base
+      run: make -j1 ${{ matrix.package }}
       env:
         REBUILD_DOCS: "FALSE"
         RUN_TESTS: "FALSE"
 
     - name: check for out-of-date files
       uses: infotroph/tree-is-clean@v1
-
-  check_modules:
-    if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build')
-    runs-on: ubuntu-latest
-
-    strategy:
-      fail-fast: false
-      matrix:
-        R:
-          - "4.0"
-          - "4.1"
-
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      _R_CHECK_LENGTH_1_CONDITION_: true
-      _R_CHECK_LENGTH_1_LOGIC2_: true
-      # Avoid compilation check warnings that come from the system Makevars
-      # See https://stat.ethz.ch/pipermail/r-package-devel/2019q2/003898.html
-      _R_CHECK_COMPILATION_FLAGS_KNOWN_: -Wformat -Werror=format-security -Wdate-time
-      # Keep R checks from trying to consult the very flaky worldclockapi.com
-      _R_CHECK_SYSTEM_CLOCK_: 0
-
-    container: 
-      image: pecan/depends:R${{ matrix.R }}
-
-    steps:
-    # checkout source code
-    - name: work around https://github.com/actions/checkout/issues/766
-      run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
-    - uses: actions/checkout@v3
-      with:
-        set-safe-directory: false
-
-    # Forbid spaces in names. Yes, *we* know it's not 1980 anymore, but Make doesn't.
-    - name: check for filenames that would confuse Make
-      run: |
-        SPACENAMES=`find . -name '* *'`
-        if [ -n "$SPACENAMES" ]; then
-          echo "::error file=${SPACENAMES}::Spaces in filename(s): ${SPACENAMES}. Please rename these files by converting spaces to underscores."
-          exit 1
-        fi
-
-    # install additional tools needed
-    - name: install utils
-      run: apt-get update && apt-get install -y postgresql-client qpdf
-    - name: install new dependencies
-      run: Rscript scripts/generate_dependencies.R && Rscript docker/depends/pecan.depends.R
-
-    # run PEcAn checks
-    - name: check
-      run: make -j1 check_modules
-      env:
-        REBUILD_DOCS: "FALSE"
-        RUN_TESTS: "FALSE"
-
-    - name: check for out-of-date files
-      uses: infotroph/tree-is-clean@v1
-
-  check_models:
-    if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build')
-    runs-on: ubuntu-latest
-
-    strategy:
-      fail-fast: false
-      matrix:
-        R:
-          - "4.0"
-          - "4.1"
-
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      _R_CHECK_LENGTH_1_CONDITION_: true
-      _R_CHECK_LENGTH_1_LOGIC2_: true
-      # Avoid compilation check warnings that come from the system Makevars
-      # See https://stat.ethz.ch/pipermail/r-package-devel/2019q2/003898.html
-      _R_CHECK_COMPILATION_FLAGS_KNOWN_: -Wformat -Werror=format-security -Wdate-time
-      # Keep R checks from trying to consult the very flaky worldclockapi.com
-      _R_CHECK_SYSTEM_CLOCK_: 0
-
-    container: 
-      image: pecan/depends:R${{ matrix.R }}
-
-    steps:
-    # checkout source code
-    - name: work around https://github.com/actions/checkout/issues/766
-      run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
-    - uses: actions/checkout@v3
-      with:
-        set-safe-directory: false
-
-    # Forbid spaces in names. Yes, *we* know it's not 1980 anymore, but Make doesn't.
-    - name: check for filenames that would confuse Make
-      run: |
-        SPACENAMES=`find . -name '* *'`
-        if [ -n "$SPACENAMES" ]; then
-          echo "::error file=${SPACENAMES}::Spaces in filename(s): ${SPACENAMES}. Please rename these files by converting spaces to underscores."
-          exit 1
-        fi
-
-    # install additional tools needed
-    - name: install utils
-      run: apt-get update && apt-get install -y postgresql-client qpdf
-    - name: install new dependencies
-      run: Rscript scripts/generate_dependencies.R && Rscript docker/depends/pecan.depends.R
-
-    # run PEcAn checks
-    - name: check
-      run: make -j1 check_models
-      env:
-        REBUILD_DOCS: "FALSE"
-        RUN_TESTS: "FALSE"
-    - name: check for out-of-date files
-      uses: infotroph/tree-is-clean@v1
-
 
   # ----------------------------------------------------------------------
   # SIPNET TESTS