redo logic for -i flag

src/cmdstan/stansummary.cpp

@@ -150,22 +150,35 @@ Example:  stansummary model_chain_1.csv model_chain_2.csv
 
   bool reorder_params = true;
   if (requested_params_vec.size() > 0) {
-    reorder_params = false;
-    std::set<std::string> requested_params(requested_params_vec.begin(),
-                                           requested_params_vec.end());
-    std::set<std::string> check_requested_params(requested_params_vec.begin(),
-                                                 requested_params_vec.end());
-    for (size_t i = 0; i < param_names.size(); ++i) {
-      check_requested_params.erase(param_names[i]);
+    auto num_requested = requested_params_vec.size();
+    std::vector<std::string> valid_params;
+    std::vector<std::string> invalid_params;
+
+    std::set<std::string> pnames(param_names.begin(), param_names.end());
+    for (std::string request : requested_params_vec) {
+      auto it = pnames.find(request);
+      if (it == pnames.end()) {
+	auto find_dups = std::find(invalid_params.begin(), invalid_params.end(), request);
+	if (find_dups == invalid_params.end()) {
+	  invalid_params.emplace_back(request);
+	}
+      } else {
+	valid_params.emplace_back(request);
+	auto find_dups = std::find(valid_params.begin(), valid_params.end(), request);
+	if (find_dups == valid_params.end()) {
+	  valid_params.emplace_back(request);
+	}
+      }
     }
-    if (check_requested_params.size() == 0) {
+    if (invalid_params.empty()) {
+      reorder_params = false;
       param_names.clear();
-      std::copy(requested_params.begin(), requested_params.end(),
+      std::copy(valid_params.begin(), valid_params.end(),
                 std::back_inserter(param_names));
     } else {
       std::cout << "--include_param: Unrecognized parameter(s): ";
-      for (auto param : requested_params) {
-        std::cout << "'" << param << "' ";
+      for (size_t i = 0; i < invalid_params.size(); ++i) {
+        std::cout << "'" << invalid_params[i] << "' ";
       }
       std::cout << std::endl;
       return return_codes::NOT_OK;

src/test/interface/stansummary_test.cpp

@@ -589,3 +589,37 @@ TEST(CommandStansummary, check_csv_output_include_param) {
     FAIL();
   }
 }
+
+TEST(CommandStansummary, check_csv_output_include_param_order) {
+  std::vector<std::string> expect_names = {"y[1,1]", "y[2,2]", "y[2,1]", "y[1,3]"};
+  std::string path_separator;
+  path_separator.push_back(get_path_separator());
+  std::string csv_file = "src" + path_separator + "test" + path_separator
+    + "interface" + path_separator + "matrix_output.csv";
+  std::stringstream ss_command;
+  ss_command << "bin" << path_separator << "stansummary "
+             << " -i y.1.1 -i y.2.2 -i y.2.1 -i y.1.3 "
+	     << csv_file;
+  run_command_output out = run_command(ss_command.str());
+  ASSERT_FALSE(out.hasError);
+  std::istringstream target_stream(out.output);
+  std::string line;
+
+  std::getline(target_stream, line);  // model name
+  std::getline(target_stream, line);  // chain info
+  std::getline(target_stream, line);  // blank
+  std::getline(target_stream, line);  // warmup time
+  std::getline(target_stream, line);  // sample time
+  std::getline(target_stream, line);  // blank
+  std::getline(target_stream, line);  // header
+  std::getline(target_stream, line);  // blank
+  boost::char_separator<char> sep(" \t\n");
+  for (size_t i = 0; i < expect_names.size(); ++i) {
+    std::getline(target_stream, line);
+    boost::tokenizer<boost::char_separator<char>> line_tok(line, sep);
+    for (const auto& token : line_tok) {
+      EXPECT_EQ(token, expect_names[i]);
+      break;
+    }
+  }
+}