Merge remote-tracking branch 'origin/develop'

.github/workflows/ci.yml

@@ -14,7 +14,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [windows-latest, ubuntu-latest] 
-        python-version: [3.9] # , 3.7, 3.6]
+        python-version: [3.10] # , 3.7, 3.6]
         run-type: [std]
         # test_repo: [""]
         # test_dir: [""]
@@ -46,7 +46,7 @@ jobs:
 
     steps:
 
-    - uses:  actions/checkout@v2.3.4 
+    - uses:  actions/checkout@v4
     # - name: Setup Ninja
       # if: ${{ runner.os == 'Windows' }} 
     - uses: seanmiddleditch/gha-setup-ninja@master
@@ -179,9 +179,15 @@ jobs:
         
         ls -l
         cd ${{ env.test_dir }}
-        nosetests --nocapture -v ${{ env.test_script }}
-        cd
-    
+        nosetests -v ${{ env.test_script }}
+        status=$?
+        echo $status
+
+        if [ $status -eq 0 ]; then
+            exit 0
+        else
+            exit 127
+        fi
         
 
 

benchmarks/basic_tests.py

@@ -821,6 +821,7 @@ def ext_stdcol_test():
     par.loc[pst.adj_par_names,"standard_deviation"] = (par.loc[pst.adj_par_names,"parubnd_trans"] - par.loc[pst.adj_par_names,"parlbnd_trans"]) / 4.0
     #par.loc[pst.adj_par_names[0],"mean"] = par.loc[pst.adj_par_names[0],"parubnd"]
     pst.pestpp_options["ies_num_reals"] = 10
+    pst.pestpp_options["ies_no_noise"] = False
     pst.control_data.noptmax = -1
     pst.write(os.path.join(m_d,"pest_base.pst"))
     pyemu.os_utils.run("{0} pest_base.pst".format(exe_path),cwd=m_d)
@@ -1481,14 +1482,16 @@ def sweep_bin_test():
     print(np.abs(diff).max())
     assert np.abs(diff).max() < 1e-7
 
-
+#def fail_test():
+#    raise Exception("fail please")
 
 if __name__ == "__main__":
     #run()
     #mf6_v5_ies_test()
     #prep_ends()
-    sweep_bin_test()
+    #sweep_bin_test()
     #mf6_v5_sen_test()
+    #ext_stdcol_test()
     #shutil.copy2(os.path.join("..","exe","windows","x64","Debug","pestpp-glm.exe"),os.path.join("..","bin","win","pestpp-glm.exe"))
     #shutil.copy2(os.path.join("..", "exe", "windows", "x64", "Debug", "pestpp-ies.exe"),
     #             os.path.join("..", "bin", "win", "pestpp-ies.exe"))
@@ -1526,7 +1529,7 @@ def sweep_bin_test():
     #shutil.copy2(os.path.join("..","exe","windows","x64","Debug","pestpp-ies.exe"),os.path.join("..","bin","win","pestpp-ies.exe"))
     #tplins1_test()
 
-    #fr_timeout_test()
+    fr_timeout_test()
     #mf6_v5_ies_test()
     #mf6_v5_sen_test()
 

src/libs/common/config_os.h

@@ -2,7 +2,7 @@
 #define CONFIG_OS_H_
 
 
-#define PESTPP_VERSION "5.2.10";
+#define PESTPP_VERSION "5.2.11";
 
 #if defined(_WIN32) || defined(_WIN64)
 #define OS_WIN

src/libs/common/system_variables.cpp

@@ -165,7 +165,7 @@ int start(string &cmd_string)
 	//  argv[icmd] = cmds[icmd].data();
 	//}
 	//argv[cmds.size() + 1] = NULL; //last arg must be NULL
-
+   
 	arg_v.push_back(NULL);
 	pid_t pid = fork();
 	if (pid == 0)

src/libs/common/utilities.cpp

@@ -1127,12 +1127,14 @@ void read_dense_binary(const string& filename, vector<string>& row_names, vector
 		cout << "reading 'dense' format matrix with " << n_obs_and_pi << " columns" << endl;
 		//first read the names of the columns and the rows
         col_names = read_dense_binary_col_names(in,n_obs_and_pi);
+        streampos first_record = in.tellg();
         row_names = read_dense_binary_remaining_row_names(in,col_names);
 
 
 		in.close();
-		in.open(filename.c_str(), ifstream::binary);
 
+		in.open(filename.c_str(), ifstream::binary);
+        in.seekg(first_record);
 		//resize the matrix now that we know big it should be
 		matrix.resize(row_names.size(), col_names.size());
 

src/libs/pestpp_common/Ensemble.cpp

@@ -2166,10 +2166,18 @@ ParameterEnsemble ParameterEnsemble::zeros_like(int nrows)
 	if (nrows < 0)
 		nrows = real_names.size();
 	Eigen::MatrixXd new_reals = Eigen::MatrixXd::Zero(nrows, var_names.size());
-
+	stringstream ss;
 	vector<string> new_real_names;
 	for (int i = 0; i < nrows; i++)
-		new_real_names.push_back(real_names[i]);
+        if (i < real_names.size())
+		    new_real_names.push_back(real_names[i]);
+        else
+        {
+            ss.str("");
+            ss << "zeros_like_real_" << i;
+            new_real_names.push_back(ss.str());
+        }
+
 
 	ParameterEnsemble new_en(pest_scenario_ptr, rand_gen_ptr);
 	new_en.from_eigen_mat(new_reals, new_real_names, var_names);