Merge branch 'develop' of https://github.com/dtcenter/MET into develop

.readthedocs.yaml

@@ -9,10 +9,14 @@ version: 2
 #formats: all
 formats: [pdf]
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
 # Optionally set the version of Python and requirements required to build your
 # docs
 python:
-   version: 3.8
    install:
    - requirements: docs/requirements.txt
 

configure.ac

@@ -1086,6 +1086,9 @@ AM_CONDITIONAL([ENABLE_DEVELOPMENT], [test -n "$MET_DEVELOPMENT"])
 
 CPPFLAGS=$CPPFLAGS' -DMET_BASE="\"$(pkgdatadir)\""'
 
+# Add -std=c++11 to CXXFLAGS                                                                                                                                                 
+CXXFLAGS=$CXXFLAGS' -std=c++11'
+
 # Define other variables for the makefiles
 
 AC_SUBST(FC_LIBS, [-lgfortran])

docs/Users_Guide/installation.rst

@@ -21,6 +21,8 @@ Programming Languages
 
 The MET package, including MET-TC, is written primarily in C/C++ in order to be compatible with an extensive verification code base in C/C++ already in existence. In addition, the object-based MODE and MODE-TD verification tools rely heavily on the object-oriented aspects of C++. Knowledge of C/C++ is not necessary to use the MET package. The MET package has been designed to be highly configurable through the use of ASCII configuration files, enabling a great deal of flexibility without the need for source code modifications.
 
+With the release of MET-11.1.0, C++11 is now the minimum required version of the C++ programming language standard.
+
 NCEP's BUFRLIB is written entirely in Fortran. The portion of MET that handles the interface to the BUFRLIB for reading PrepBUFR point observation files is also written in Fortran.
 
 The MET package is intended to be a tool for the modeling community to use and adapt. As users make upgrades and improvements to the tools, they are encouraged to offer those upgrades to the broader community by offering feedback to the developers.

src/libcode/vx_grid/goes_grid.cc

@@ -493,13 +493,13 @@ void GoesImagerData::compute_lat_lon()
                 mlog << Error << method_name << " index=" << index
                      << "  too big than " << buf_len << "\n";
             else {
-               if (isnan(lat_rad)) lat = bad_data_float;
+	       if (std::isnan(lat_rad)) lat = bad_data_float;
                else {
                   lat = lat_rad * deg_per_rad;
                   if (lat > lat_max) {lat_max = lat; idx_lat_max = index; }
                   if (lat < lat_min) {lat_min = lat; idx_lat_min = index; }
                }
-               if (isnan(lon_rad)) lon = bad_data_float;
+	       if (std::isnan(lon_rad)) lon = bad_data_float;
                else {
                   lon = lon_of_projection_origin - (lon_rad * deg_per_rad);
                   if (lon > lon_max) {lon_max = lon; idx_lon_max = index; }

src/libcode/vx_python3_utils/python3_script.h

@@ -64,7 +64,7 @@ class Python3_Script {
 
       ConcatString filename() const;
 
-      PyObject * module();
+      PyObject * get_module();
       PyObject * dict();
       PyObject * module_ascii();
       PyObject * dict_ascii();
@@ -92,7 +92,7 @@ class Python3_Script {
 ////////////////////////////////////////////////////////////////////////
 
 
-inline PyObject * Python3_Script::module() { return ( Module ); }
+inline PyObject * Python3_Script::get_module() { return ( Module ); }
 
 inline PyObject * Python3_Script::dict() { return ( Dict ); }
 

src/libcode/vx_statistics/compute_stats.cc

@@ -1596,7 +1596,7 @@ void compute_aggregated_seeps_grid(const DataPlane &fcst_dp, const DataPlane &ob
                   else count_diagonal++;
                }
                seeps_score = seeps_mpr->score;
-               if (isnan(seeps_score)) {
+               if (std::isnan(seeps_score)) {
                   nan_count++;
                   seeps_score = bad_data_double;
                }

src/libcode/vx_statistics/contable_stats.cc

@@ -1146,7 +1146,7 @@ for (j=0; j<Nrows; ++j)  {
    //  replace nan with bad data
    //
 
-if (isnan(sum))  sum = bad_data_double;
+ if (std::isnan(sum))  sum = bad_data_double;
 
    //
    //  done

src/tools/other/madis2nc/madis2nc.cc

@@ -85,12 +85,13 @@ static void setup_netcdf_out(int nhdr);
 
 static bool get_filtered_nc_data(NcVar var, float *data, const long dim,
                                  const long cur, const char *var_name, bool required=true);
+// Added data_len for SonarQube
 static bool get_filtered_nc_data_2d(NcVar var, int *data, const LongArray &dim,
                                     const LongArray &cur, const char *var_name,
-                                    bool count_bad=false);
+                                    int data_len=0, bool count_bad=false);
 static bool get_filtered_nc_data_2d(NcVar var, float *data, const LongArray &dim,
                                     const LongArray &cur, const char *var_name,
-                                    bool count_bad=false);
+                                    int data_len=0, bool count_bad=false);
 
 static void check_quality_control_flag(int &value, const char qty, const char *var_name);
 static void check_quality_control_flag(float &value, const char qty, const char *var_name);
@@ -459,12 +460,12 @@ static bool get_filtered_nc_data(NcVar var, float *data,
 
 static bool get_filtered_nc_data_2d(NcVar var, int *data, const LongArray &dim,
                                     const LongArray &cur, const char *var_name,
-                                    bool count_bad) {
+                                    int data_len, bool count_bad) {
 
    bool status = false;
-   int data_len = dim[0] * dim[1];
    const char *method_name = "get_filtered_nc_data_2d(int) ";
 
+   if (data_len <= 0) data_len = dim[0] * dim[1];
    for (int offset=0; offset<data_len; offset++) {
       data[offset] = bad_data_int;
    }
@@ -503,12 +504,12 @@ static bool get_filtered_nc_data_2d(NcVar var, int *data, const LongArray &dim,
 
 static bool get_filtered_nc_data_2d(NcVar var, float *data, const LongArray &dim,
                                     const LongArray &cur, const char *var_name,
-                                    bool count_bad) {
+                                    int data_len, bool count_bad) {
 
    bool status = false;
-   int data_len = dim[0] * dim[1];
    const char *method_name = "get_filtered_nc_data_2d(float) ";
 
+   if (data_len <= 0) data_len = dim[0] * dim[1];
    for (int offset=0; offset<data_len; offset++) {
       data[offset] = bad_data_float;
    }
@@ -2135,8 +2136,8 @@ void process_madis_profiler(NcFile *&f_in) {
       if (IS_VALID_NC(in_vComponentQty_var)) get_nc_data(&in_vComponentQty_var, (char *)vComponentQty_arr, dim, cur);
       else memset(vComponentQty_arr, 0, data_cnt*sizeof(char));
 
-      get_filtered_nc_data_2d(in_uComponent_var, (float *)uComponent_arr, dim, cur, "uComponent");
-      get_filtered_nc_data_2d(in_vComponent_var, (float *)vComponent_arr, dim, cur, "vComponent");
+      get_filtered_nc_data_2d(in_uComponent_var, (float *)uComponent_arr, dim, cur, "uComponent", data_cnt);
+      get_filtered_nc_data_2d(in_vComponent_var, (float *)vComponent_arr, dim, cur, "vComponent", data_cnt);
 
       for (int i_idx=0; i_idx<buf_size; i_idx++) {
 
@@ -3354,13 +3355,14 @@ void process_madis_acarsProfiles(NcFile *&f_in) {
       cur[0] = i_hdr_s;
       dim[0] = buf_size;
       dim[1] = maxLevels;
+      data_cnt = buf_size * maxLevels;
+
       get_nc_data(&in_hdr_vld_var, tmp_dbl_arr, dim, cur);
       get_nc_data(&in_hdr_lat_var, (float *)hdr_lat_arr, dim, cur);
       get_nc_data(&in_hdr_lon_var, (float *)hdr_lon_arr, dim, cur);
-      get_filtered_nc_data_2d(in_hdr_elv_var, (float *)hdr_elv_arr, dim, cur, "elevation");
+      get_filtered_nc_data_2d(in_hdr_elv_var, (float *)hdr_elv_arr, dim, cur, "elevation", data_cnt);
 
 
-      data_cnt = buf_size * maxLevels;
       if (IS_VALID_NC(in_temperatureQty_var)) get_nc_data(&in_temperatureQty_var, (char *)&temperatureQty_arr, dim, cur);
       else memset(temperatureQty_arr, 0, data_cnt*sizeof(char));
       if (IS_VALID_NC(in_dewpointQty_var))    get_nc_data(&in_dewpointQty_var, (char *)&dewpointQty_arr, dim, cur);
@@ -3372,11 +3374,11 @@ void process_madis_acarsProfiles(NcFile *&f_in) {
       if (IS_VALID_NC(in_altitudeQty_var))    get_nc_data(&in_altitudeQty_var, (char *)&altitudeQty_arr, dim, cur);
       else memset(altitudeQty_arr, 0, data_cnt*sizeof(char));
 
-      get_filtered_nc_data_2d(in_hdr_tob_var,     (int *)&obsTimeOfDay_arr,  dim, cur, "obsTimeOfDay");
-      get_filtered_nc_data_2d(in_temperature_var, (float *)&temperature_arr, dim, cur, "temperature");
-      get_filtered_nc_data_2d(in_dewpoint_var,    (float *)&dewpoint_arr,    dim, cur, "dewpoint");
-      get_filtered_nc_data_2d(in_windDir_var,     (float *)&windDir_arr,     dim, cur, "windDir");
-      get_filtered_nc_data_2d(in_windSpeed_var,   (float *)&windSpeed_arr,   dim, cur, "windSpeed");
+      get_filtered_nc_data_2d(in_hdr_tob_var,     (int *)&obsTimeOfDay_arr,  dim, cur, "obsTimeOfDay", data_cnt);
+      get_filtered_nc_data_2d(in_temperature_var, (float *)&temperature_arr, dim, cur, "temperature", data_cnt);
+      get_filtered_nc_data_2d(in_dewpoint_var,    (float *)&dewpoint_arr,    dim, cur, "dewpoint", data_cnt);
+      get_filtered_nc_data_2d(in_windDir_var,     (float *)&windDir_arr,     dim, cur, "windDir", data_cnt);
+      get_filtered_nc_data_2d(in_windSpeed_var,   (float *)&windSpeed_arr,   dim, cur, "windSpeed", data_cnt);
 
       dim[1] = hdr_sid_len;
       get_nc_data(&in_hdr_sid_var, (char *)hdr_sid_arr, dim, cur);

src/tools/other/mode_time_domain/interest_calc.cc

@@ -143,7 +143,7 @@ void InterestCalculator::assign(const InterestCalculator & i)
 
 clear();
 
-if ( i.Nelements == 0 )  return;
+if ( i.Nelements <= 0 )  return;
 
 extend(i.Nelements);
 
@@ -256,6 +256,7 @@ if ( _weight < 0.0 )  {
 
 }
 
+if (Nelements < 0) Nelements = 0;   // SonarQube findings
 
 extend(Nelements + 1);
 

src/tools/other/mode_time_domain/mtd_file_int.cc

@@ -832,7 +832,7 @@ void MtdIntFile::fatten()
 int x, y, n;
 const int nxy = Nx*Ny;
 int * u = new int [nxy];
-int * a = 0;
+int * a = nullptr;
 
 a = u;
 
@@ -899,7 +899,9 @@ for (y = 0; y<(Ny - 2); ++y)  {
 
    for (x=0; x<(Nx - 2); ++x)  {
 
-      if ( *a )  {
+      if (n >= (nxy-1)) break;  // For SonarQube findings
+
+      if (n >=0 &&  *a )  {
 
          Data[n + 1]      = 1;   //  (x + 1, y)
          Data[n + Nx]     = 1;   //  (x, y + 1)
@@ -1719,11 +1721,14 @@ s.set_to_zeroes();
 
 int * in  =   Data;
 int * out = s.Data;
+int out_size = s.nxyt();
 
 v = 0;
 
 for (j=0; j<n3; ++j)  {
 
+   if (j >= out_size) break;    // For SonarQube findings
+
    if ( yesno[*in] )  { *out = 1;  ++v; }
 
    ++in;

src/tools/other/mode_time_domain/mtd_partition.cc

@@ -230,6 +230,8 @@ void EquivalenceClass::add_no_repeat(int k)
 
 if ( has(k) )  return;
 
+if (Nelements < 0) Nelements = 0;
+
 extend(Nelements + 1);
 
 E[Nelements++] = k;
@@ -685,6 +687,8 @@ void Mtd_Partition::add_no_repeat(int k)
 
 if ( has(k) )  return;
 
+if (Nelements < 0) Nelements = 0;
+
 extend(Nelements + 1);
 
 C[Nelements] = new EquivalenceClass;