ORG81 Add automatic formatting/linting github checks

.github/workflows/cpp-linter.yaml

@@ -0,0 +1,28 @@
+name: cpp-linter
+
+on:
+  pull_request:
+    # This is overkill, but why not
+    paths: ['**.c', '**.cpp', '**.h', '**.hpp', '**.cxx', '**.hxx', '**.cc', '**.hh', '**CMakeLists.txt', 'meson.build', '**.cmake']
+
+jobs:
+  cpp-linter:
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
+    steps:
+      - uses: actions/checkout@v4
+      - uses: cpp-linter/cpp-linter-action@v2
+        id: linter
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          style: 'file'  # Use .clang-format config file
+          tidy-checks: '' # Use .clang-tidy config file
+          # only 'update' a single comment in a pull request thread.
+          thread-comments: ${{ github.event_name == 'pull_request' && 'update' }}
+      - name: Fail fast
+        if: steps.linter.outputs.checks-failed > 0
+        run: |
+            echo "Some linter checks failed. ${{ steps.linter.outputs.checks-failed }}" |
+            exit 1

sipnet.c

@@ -1,4 +1,4 @@
 /* SiPnET: Simplified PnET
 
    Author: Bill Sacks  wsacks@wisc.edu
    modified by...
@@ -2456,13 +2456,13 @@
 
 // ensure that all the allocation parameters sum up to something less than one:
   #if ROOTS
-  	ensureAllocation();
+    ensureAllocation();
   #endif
 
 // If we aren't explicitly modeling microbe pool, then do not have a pulse to microbes,
 // exudates go directly to the soil
 #if !MICROBES
-	params.microbePulseEff=0;
+  params.microbePulseEff=0;
 #endif
 
   // change units of parameters:
@@ -2479,49 +2479,49 @@
  #if ROOTS
   envi.plantWoodC = (1-params.coarseRootFrac-params.fineRootFrac)*params.plantWoodInit;
  #else
- 	envi.plantWoodC = params.plantWoodInit;
+  envi.plantWoodC = params.plantWoodInit;
  #endif
 
   envi.plantLeafC = params.laiInit * params.leafCSpWt;
   envi.litter = params.litterInit;
 
 
 // If SOIL_QUALITY, split initial soilCarbon equally among all the pools
- 	#if SOIL_MULTIPOOL
- 		int counter;
+  #if SOIL_MULTIPOOL
+    int counter;
 
-		for( counter=0; counter <NUMBER_SOIL_CARBON_POOLS; counter++) {
+    for( counter=0; counter <NUMBER_SOIL_CARBON_POOLS; counter++) {
 
-			envi.soil[counter]=params.soilInit/NUMBER_SOIL_CARBON_POOLS;
+      envi.soil[counter]=params.soilInit/NUMBER_SOIL_CARBON_POOLS;
 
-		}
-		trackers.totSoilC=params.soilInit;
-	#else
-  		envi.soil = params.soilInit;
+    }
+    trackers.totSoilC=params.soilInit;
+  #else
+      envi.soil = params.soilInit;
 
-	#endif
+  #endif
 
-	#if SOIL_QUALITY
-		params.maxIngestionRate = params.maxIngestionRate*24*params.microbeInit/1000;
-			// change from per hour to per day rate, and then multiply by microbial concentration (mg C / g soil).
+  #if SOIL_QUALITY
+    params.maxIngestionRate = params.maxIngestionRate*24*params.microbeInit/1000;
+      // change from per hour to per day rate, and then multiply by microbial concentration (mg C / g soil).
 
-	#else
-		params.maxIngestionRate = params.maxIngestionRate*24;	// change from per hour to per day rate
-	#endif
+  #else
+    params.maxIngestionRate = params.maxIngestionRate*24; // change from per hour to per day rate
+  #endif
 
 
 
-  envi.microbeC = params.microbeInit*params.soilInit/1000;		// convert to gC m-2
+  envi.microbeC = params.microbeInit*params.soilInit/1000;    // convert to gC m-2
 
 
-  params.totNitrogen = params.totNitrogen*params.soilInit;	// convert to gC m-2
+  params.totNitrogen = params.totNitrogen*params.soilInit;  // convert to gC m-2
 
   params.fineRootTurnoverRate /= 365.0;
   params.coarseRootTurnoverRate /= 365.0;
 
   params.baseCoarseRootResp /= 365.0;
   params.baseFineRootResp /= 365.0;
-  params.baseMicrobeResp = params.baseMicrobeResp*24;		// change from per hour to per day rate
+  params.baseMicrobeResp = params.baseMicrobeResp*24;   // change from per hour to per day rate
 
 
   envi.coarseRootC = params.coarseRootFrac*params.plantWoodInit;