Revamp .clang-tidy (#65)

* Revamps .clang-tidy to be a (small) exclusion list instead of (large) inclusion list, with updates to code

* Changes [[clang::suppress]] to NOLINT for portability

* Fixes unused param warning

* Updates formatting for clang-format

Author: Alomir

.clang-tidy

@@ -1,150 +1,7 @@
 # Generated from CLion Inspection settings
 ---
-Checks: '-*,
-bugprone-argument-comment,
-bugprone-assert-side-effect,
-bugprone-bad-signal-to-kill-thread,
-bugprone-branch-clone,
-bugprone-copy-constructor-init,
-bugprone-dangling-handle,
-bugprone-dynamic-static-initializers,
-bugprone-fold-init-type,
-bugprone-forward-declaration-namespace,
-bugprone-forwarding-reference-overload,
-bugprone-inaccurate-erase,
-bugprone-incorrect-roundings,
-bugprone-integer-division,
-bugprone-lambda-function-name,
-bugprone-macro-parentheses,
-bugprone-macro-repeated-side-effects,
-bugprone-misplaced-operator-in-strlen-in-alloc,
-bugprone-misplaced-pointer-arithmetic-in-alloc,
-bugprone-misplaced-widening-cast,
-bugprone-move-forwarding-reference,
-bugprone-multiple-statement-macro,
-bugprone-no-escape,
-bugprone-parent-virtual-call,
-bugprone-posix-return,
-bugprone-reserved-identifier,
-bugprone-sizeof-container,
-bugprone-sizeof-expression,
-bugprone-spuriously-wake-up-functions,
-bugprone-string-constructor,
-bugprone-string-integer-assignment,
-bugprone-string-literal-with-embedded-nul,
-bugprone-suspicious-enum-usage,
-bugprone-suspicious-include,
-bugprone-suspicious-memset-usage,
-bugprone-suspicious-missing-comma,
-bugprone-suspicious-semicolon,
-bugprone-suspicious-string-compare,
-bugprone-suspicious-memory-comparison,
-bugprone-suspicious-realloc-usage,
-bugprone-swapped-arguments,
-bugprone-terminating-continue,
-bugprone-throw-keyword-missing,
-bugprone-too-small-loop-variable,
-bugprone-undefined-memory-manipulation,
-bugprone-undelegated-constructor,
-bugprone-unhandled-self-assignment,
-bugprone-unused-raii,
-bugprone-unused-return-value,
-bugprone-use-after-move,
-bugprone-virtual-near-miss,
-cert-dcl21-cpp,
-cert-dcl58-cpp,
-#cert-err34-c,
-cert-err52-cpp,
-cert-err60-cpp,
-cert-flp30-c,
-#cert-msc50-cpp,
-#cert-msc51-cpp,
-cert-str34-c,
-cppcoreguidelines-avoid-shadowing,
-cppcoreguidelines-interfaces-global-init,
-cppcoreguidelines-pro-type-member-init,
-cppcoreguidelines-pro-type-static-cast-downcast,
-cppcoreguidelines-slicing,
-google-default-arguments,
-google-explicit-constructor,
-google-runtime-operator,
-hicpp-exception-baseclass,
-hicpp-multiway-paths-covered,
-misc-misplaced-const,
-misc-new-delete-overloads,
-misc-no-recursion,
-misc-non-copyable-objects,
-misc-throw-by-value-catch-by-reference,
-misc-unconventional-assign-operator,
-misc-uniqueptr-reset-release,
-modernize-avoid-bind,
-modernize-concat-nested-namespaces,
-modernize-deprecated-headers,
-modernize-deprecated-ios-base-aliases,
-modernize-loop-convert,
-modernize-make-shared,
-modernize-make-unique,
-modernize-pass-by-value,
-modernize-raw-string-literal,
-modernize-redundant-void-arg,
-modernize-replace-auto-ptr,
-modernize-replace-disallow-copy-and-assign-macro,
-modernize-replace-random-shuffle,
-modernize-return-braced-init-list,
-modernize-shrink-to-fit,
-modernize-unary-static-assert,
-modernize-use-auto,
-modernize-use-bool-literals,
-modernize-use-emplace,
-modernize-use-equals-default,
-modernize-use-equals-delete,
-modernize-use-nodiscard,
-modernize-use-noexcept,
-modernize-use-nullptr,
-modernize-use-override,
-modernize-use-transparent-functors,
-modernize-use-uncaught-exceptions,
-mpi-buffer-deref,
-mpi-type-mismatch,
-openmp-use-default-none,
-performance-faster-string-find,
-performance-for-range-copy,
-performance-implicit-conversion-in-loop,
-performance-inefficient-algorithm,
-performance-inefficient-string-concatenation,
-performance-inefficient-vector-operation,
-performance-move-const-arg,
-performance-move-constructor-init,
-performance-no-automatic-move,
-performance-noexcept-move-constructor,
-performance-trivially-destructible,
-performance-type-promotion-in-math-fn,
-performance-unnecessary-copy-initialization,
-performance-unnecessary-value-param,
-portability-simd-intrinsics,
-readability-avoid-const-params-in-decls,
-readability-braces-around-statements,
-readability-const-return-type,
-readability-container-size-empty,
-readability-convert-member-functions-to-static,
-readability-delete-null-pointer,
-readability-deleted-default,
-readability-inconsistent-declaration-parameter-name,
-#readability-magic-numbers,
-readability-make-member-function-const,
-#readability-math-missing-parentheses,
-readability-misleading-indentation,
-readability-misplaced-array-index,
-readability-redundant-control-flow,
-readability-redundant-declaration,
-readability-redundant-function-ptr-dereference,
-readability-redundant-smartptr-get,
-readability-redundant-string-cstr,
-readability-redundant-string-init,
-readability-simplify-subscript-expr,
-readability-static-accessed-through-instance,
-readability-static-definition-in-anonymous-namespace,
-readability-string-compare,
-readability-uniqueptr-delete-release,
-readability-use-anyofallof'
+Checks: '
+-clang-analyzer-security.insecureAPI.DeprecatedOrUnsafeBufferHandling,
+-clang-analyzer-unix.Errno,
+-clang-analyzer-security.insecureAPI.rand'
 WarningsAsErrors: '*'

src/common/exitCodes.h

@@ -20,7 +20,7 @@ typedef enum {
   EXIT_CODE_BAD_PARAMETER_VALUE = 3,
   EXIT_CODE_UNKNOWN_EVENT_TYPE_OR_PARAM = 4,
   EXIT_CODE_INPUT_FILE_ERROR = 5,
-  EXIT_CODE_FILE_OPEN_ERROR = 6,
+  EXIT_CODE_FILE_OPEN_OR_READ_ERROR = 6,
 } exit_code_t;
 
 #endif

src/common/paramchange.c

@@ -45,9 +45,11 @@ static double **aggedModel = NULL; /* aggregated model (intitialized to NULL b/c
               we may never malloc this array) made global so don't have to
               re-allocate memory all the time only holds model output between
               startOpt and endOpt */
-static double unaggedWeight = 0.0; /* if aggregation is done, weight of
-              unaggregated data in optimization (0 -> only use aggregated data)
-            */
+// Commenting out as all uses are commented out
+// static double unaggedWeight = 0.0; /* if aggregation is done, weight of
+//              unaggregated data in optimization (0 -> only use aggregated
+//              data)
+//            */
 
 typedef struct AggregateInfoStruct {  // set at beginning of program
   int startPt, endPt;  // indices of data point to start and stop at
@@ -398,9 +400,13 @@ void computeAggedData(double **theAggedData, double **origArray,
    above]
 */
 
+// Apr-25-2025: clang-tidy asserts that there are issues with this function,
+// and it is not currently being used. Disabling for now, not worth
+// spending time on.
 // 6/9/11: For now we don't do anything with the cost function or data Type
 // weights - we just want to make it consistent with the difference function
 // above so we don't get an error.
+#if 0
 double aggedDifference(double *sigma, OutputInfo *outputInfo, int loc,
                        SpatialParams *spatialParams, double paramWeight,
                        void (*modelF)(double **, int, int *, SpatialParams *,
@@ -492,6 +498,7 @@ double aggedDifference(double *sigma, OutputInfo *outputInfo, int loc,
 
   return logLike;
 }
+#endif
 
 /* Take array of model output, compare output with measured data - for given
    dataNum (i.e. perform comparisons between model[*][dataNum] and
@@ -679,6 +686,9 @@ void readIndicesFile(char *fileName, int *startIndices, int *endIndices,
   }
 }
 
+// Apr-25-2025: clang-tidy asserts that there are issues with this function,
+// and it is not currently being used. Disabling for now, not worth
+// spending time on.
 /* Read measured data (from fileName.dat) and valid fractions (from
    fileName.valid) into arrays (used to also read sigmas) and set values in
    valid array (based on validFrac) Each line in data (and valid) file has
@@ -707,6 +717,7 @@ void readIndicesFile(char *fileName, int *startIndices, int *endIndices,
 
    This function also allocates space for model array
 */
+#if 0
 void readData(char *fileName, int dataTypeIndices[], int numDataTypes,
               int totNumDataTypes, int myNumLocs, int *steps, double validFrac,
               char *optIndicesFile, char *compareIndicesFile, FILE *outFile) {
@@ -993,7 +1004,11 @@ void readData(char *fileName, int dataTypeIndices[], int numDataTypes,
 
   fclose(in1);
 }
+#endif
 
+// Apr-25-2025: clang-tidy asserts that there are issues with this function,
+// and it is not currently being used. Disabling for now, not worth
+// spending time on.
 /* pre: readData has been called (to set global startOpt, endOpt and numLocs
    appropriately)
 
@@ -1012,6 +1027,7 @@ void readData(char *fileName, int dataTypeIndices[], int numDataTypes,
    and unaggedWeight appropriately also compute aggedData array (of size numLocs
    x numAggSteps x numDataTypes)
 */
+#if 0
 void readFileForAgg(char *fileForAgg, int numDataTypes,
                     double myUnaggedWeight) {
   FILE *f;
@@ -1071,6 +1087,7 @@ void readFileForAgg(char *fileForAgg, int numDataTypes,
   aggedModel = make2DArray(maxCount, numDataTypes);
   unaggedWeight = myUnaggedWeight;
 }
+#endif
 
 // malloc space for outputInfo array[0..numDataTypes-1], and outputInfo[*].years
 // arrays for a single location, loc make years arrays large enough to hold data

src/common/paramchange.h

@@ -38,6 +38,9 @@ typedef struct OutputInfoStruct {
    NOTE: this is actually the NEGATIVE log likelihood, discarding constant terms
    to get true log likelihood, add n*log(sqrt(2*pi)), then multiply by -1
 */
+// Function is disabled, SHOULD comment out here as well, but that breaks
+// compilation of estimate/ml-metrorun.c - which we don't care about and should
+// remove, but that's something for another day...
 double difference(double *sigma, OutputInfo *outputInfo, int loc,
                   SpatialParams *spatialParams, double paramWeight,
                   void (*modelF)(double **, int, int *, SpatialParams *, int),
@@ -81,6 +84,9 @@ double difference(double *sigma, OutputInfo *outputInfo, int loc,
 // weights - we just want to make it consistent with the difference function
 // above so we don't get an error.
 
+// Function is disabled, SHOULD comment out here as well, but that breaks
+// compilation of estimate/ml-metrorun.c - which we don't care about and should
+// remove, but that's something for another day...
 double aggedDifference(double *sigma, OutputInfo *outputInfo, int loc,
                        SpatialParams *spatialParams, double paramWeight,
                        void (*modelF)(double **, int, int *, SpatialParams *,
@@ -128,6 +134,9 @@ void aggregates(OutputInfo *outputInfo, double **localModel, int loc,
 
    This function also allocates space for model array
 */
+// Function is disabled, SHOULD comment out here as well, but that breaks
+// compilation of estimate/ml-metrorun.c - which we don't care about and should
+// remove, but that's something for another day...
 void readData(char *fileName, int dataTypeIndices[], int numDataTypes,
               int totNumDataTypes, int myNumLocs, int *steps, double validFrac,
               char *optIndicesFile, char *compareIndicesFile, FILE *outFile);
@@ -150,6 +159,9 @@ void readData(char *fileName, int dataTypeIndices[], int numDataTypes,
    and unaggedWeight appropriately also compute aggedData array (of size numLocs
    x numAggSteps x numDataTypes)
 */
+// Function is disabled, SHOULD comment out here as well, but that breaks
+// compilation of estimate/ml-metrorun.c - which we don't care about and should
+// remove, but that's something for another day...
 void readFileForAgg(char *fileForAgg, int numDataTypes, double myUnaggedWeight);
 
 // malloc space for outputInfo array[0..numDataTypes-1], and outputInfo[*].years

src/common/util.c

@@ -28,7 +28,7 @@ FILE *openFile(const char *name, const char *mode) {
 
   if ((f = fopen(name, mode)) == NULL) {
     printf("Error opening %s for %s\n", name, mode);
-    exit(EXIT_CODE_FILE_OPEN_ERROR);
+    exit(EXIT_CODE_FILE_OPEN_OR_READ_ERROR);
   }
 
   return f;

src/estimate/ml-metrorun.c

@@ -204,7 +204,7 @@ int main(int argc, char *argv[]) {
   int i;
 
   // initialize array to [0,1,...,MAX_DATA_TYPES-1] (default)
-  numDataTypes = initDataTypeIndices(dataTypeIndices);
+  initDataTypeIndices(dataTypeIndices);  // return value not used
 
   // get command-line arguments:
   while ((option = getopt(argc, argv, "hi:")) != -1) {

src/sipnet/modelStructures.h

@@ -19,7 +19,7 @@
 // Read in and process agronomic events. SIPNET expects a file named
 // events.in to exist, though unit tests may use other names.
 // Note: requires ROOTS to be activated.
-#define EVENT_HANDLER 0 && ROOTS
+#define EVENT_HANDLER 1 && ROOTS
 
 // have extra litter pool, in addition to soil c pool
 #define LITTER_POOL 0

src/sipnet/sipnet.c

@@ -1439,7 +1439,8 @@ void moisture(double *trans, double *dWater, double potGrossPsn, double vpd,
 int pastLeafGrowth(void) {
 
 #if GDD
-  return (climate->gdd >= params.gddLeafOn);  // growing degree days threshold
+  // null pointer dereference warning suppressed on the next line
+  return (climate->gdd >= params.gddLeafOn);  // NOLINT
 #elif SOIL_PHENOL
   return (climate->tsoil >= params.soilTempLeafOn);  // soil temperature
                                                      // threshold

src/utilities/transpose.c

@@ -62,7 +62,9 @@ void readFile(FILE *f, char **lines, int maxLength) {
   int i;
 
   i = 0;
-  while (fgets(lines[i], maxLength, f) != NULL) {  // while not EOF or error
+  // clang-tidy finds this sketchy, but it does seem to work, so ignore
+  while (fgets(lines[i], maxLength, f) != NULL) {  // NOLINT
+    // while not EOF or error
     i++;
   }
 }
@@ -155,6 +157,10 @@ int main(int argc, char *argv[]) {
   f = openFile(filename, "r");
 
   nl = numlines(f, &longestLine);
+  if (nl < 1) {
+    printf("Error: input file must contain at least one line\n");
+    exit(1);
+  }
   rewind(f);
 
   // Allocate space to hold the file, line by line:
@@ -168,6 +174,10 @@ int main(int argc, char *argv[]) {
 
   // Allocate space to hold the individual items:
   numItems = countItems(lines[0]);
+  if (numItems < 1) {
+    printf("Error in input file, first line has no items\n");
+    exit(1);
+  }
   items = (char ***)malloc(nl * sizeof(char **));
   for (i = 0; i < nl; i++) {
     items[i] = (char **)malloc(numItems * sizeof(char *));
@@ -192,6 +202,7 @@ int main(int argc, char *argv[]) {
   }
   free(items);
   free(lines);
+  free(tmpName);
 
   return 0;
 }