From b42d3140a50051efd4e097df0e605943502148e0 Mon Sep 17 00:00:00 2001
From: jajhall <jajhall@ed.ac.uk>
Date: Mon, 9 Sep 2024 00:39:38 +0100
Subject: [PATCH 1/6] Now reading rvb-sub, but need to add the comment trim to
 other MPS read methods to pass unit test

---
 check/TestFilereader.cpp | 15 ++++++++++++++-
 src/io/HMpsFF.cpp        |  5 +++++
 src/util/stringutil.cpp  |  9 +++++++++
 src/util/stringutil.h    | 17 ++++++++++-------
 4 files changed, 38 insertions(+), 8 deletions(-)

diff --git a/check/TestFilereader.cpp b/check/TestFilereader.cpp
index 14ad114b6e..98c0ecae26 100644
--- a/check/TestFilereader.cpp
+++ b/check/TestFilereader.cpp
@@ -10,7 +10,7 @@
 #include "lp_data/HighsLp.h"
 #include "lp_data/HighsLpUtils.h"
 
-const bool dev_run = false;
+const bool dev_run = true;
 
 TEST_CASE("filereader-edge-cases", "[highs_filereader]") {
   std::string model = "";
@@ -343,3 +343,16 @@ TEST_CASE("filereader-dD2e", "[highs_filereader]") {
   objective_value = highs.getInfo().objective_function_value;
   REQUIRE(objective_value == optimal_objective_value);
 }
+
+TEST_CASE("filereader-comment", "[highs_filereader]") {
+  // Check that comments - either whole line with * in first column,
+  // or rest of line following */$ are handled correctly
+  const double optimal_objective_value = -4;
+  std::string model_file = std::string(HIGHS_DIR) + "/check/instances/comment.mps";
+  Highs highs;
+  highs.setOptionValue("output_flag", dev_run);
+  REQUIRE(highs.readModel(model_file) == HighsStatus::kOk);
+  REQUIRE(highs.run() == HighsStatus::kOk);
+  double objective_value = highs.getInfo().objective_function_value;
+  REQUIRE(objective_value == optimal_objective_value);
+}
diff --git a/src/io/HMpsFF.cpp b/src/io/HMpsFF.cpp
index 14f0bf5dc0..823109a6e5 100644
--- a/src/io/HMpsFF.cpp
+++ b/src/io/HMpsFF.cpp
@@ -534,6 +534,9 @@ HMpsFF::Parsekey HMpsFF::parseRows(const HighsLogOptions& log_options,
   assert(row_upper.size() == 0);
   while (getline(file, strline)) {
     if (is_empty(strline) || strline[0] == '*') continue;
+    printf("HMpsFF::parseRows before rtrim: strline = \"%s\"\n", strline.c_str());
+    mpsCommentTrim(strline);
+    printf("HMpsFF::parseRows  after rtrim: strline = \"%s\"\n", strline.c_str());
     double current = getWallTime();
     if (time_limit > 0 && current - start_time > time_limit)
       return HMpsFF::Parsekey::kTimeout;
@@ -588,7 +591,9 @@ HMpsFF::Parsekey HMpsFF::parseRows(const HighsLogOptions& log_options,
     }
 
     std::string rowname = first_word(strline, start + 1);
+    printf("HMpsFF::parseRows rowname = \"%s\"; strline = \"%s\"\n", rowname.c_str(), strline.c_str());
     size_t rowname_end = first_word_end(strline, start + 1);
+    printf("HMpsFF::parseRows rowname_end = %d\n", int(rowname_end));
 
     // Detect if file is in fixed format.
     if (!is_end(strline, rowname_end)) {
diff --git a/src/util/stringutil.cpp b/src/util/stringutil.cpp
index 5b0de58e73..5a4fef80a5 100644
--- a/src/util/stringutil.cpp
+++ b/src/util/stringutil.cpp
@@ -126,3 +126,12 @@ std::string first_word(std::string& str, size_t start) {
   assert(next_word_start != std::string::npos);
   return str.substr(next_word_start, next_word_end - next_word_start);
 }
+
+std::string& mpsCommentTrim(std::string& str) {
+  const size_t p = str.find_first_of(mps_comment_chars);
+  printf("In rTrimAt, First of \"%s\" in \"%s\" is %zu\n", mps_comment_chars.c_str(), str.c_str(), p);
+  if (p > str.length()) return str;
+  str.erase(p);
+  return str;
+}
+
diff --git a/src/util/stringutil.h b/src/util/stringutil.h
index 4fa072485b..95b71e17e1 100644
--- a/src/util/stringutil.h
+++ b/src/util/stringutil.h
@@ -27,18 +27,21 @@ void strTrim(char* str);
 
 void tolower(std::string& str);
 
-const std::string non_chars = "\t\n\v\f\r ";
-std::string& ltrim(std::string& str, const std::string& chars = non_chars);
-std::string& rtrim(std::string& str, const std::string& chars = non_chars);
-std::string& trim(std::string& str, const std::string& chars = non_chars);
+const std::string default_non_chars = "\t\n\v\f\r ";
+const std::string mps_comment_chars = "*$";
+std::string& ltrim(std::string& str, const std::string& chars = default_non_chars);
+std::string& rtrim(std::string& str, const std::string& chars = default_non_chars);
+std::string& trim(std::string& str, const std::string& chars = default_non_chars);
 
-bool is_empty(std::string& str, const std::string& chars = non_chars);
-bool is_empty(char c, const std::string& chars = non_chars);
-bool is_end(std::string& str, size_t end, const std::string& chars = non_chars);
+bool is_empty(std::string& str, const std::string& chars = default_non_chars);
+bool is_empty(char c, const std::string& chars = default_non_chars);
+bool is_end(std::string& str, size_t end, const std::string& chars = default_non_chars);
 
 // todo: replace with pair of references rather than string ret value to avoid
 // copy and also using function below. or do it properly with iterators.
 std::string first_word(std::string& str, size_t start);
 size_t first_word_end(std::string& str, size_t start);
 
+std::string& mpsCommentTrim(std::string& str);
+
 #endif

From 1556a6ed2161ef4d98b6f9b7a6650f1fc300fd3c Mon Sep 17 00:00:00 2001
From: jajhall <jajhall@ed.ac.uk>
Date: Wed, 11 Sep 2024 23:17:43 +0100
Subject: [PATCH 2/6] Added comment.mps

---
 check/instances/comment.mps | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 check/instances/comment.mps

diff --git a/check/instances/comment.mps b/check/instances/comment.mps
new file mode 100644
index 0000000000..96d7c80985
--- /dev/null
+++ b/check/instances/comment.mps
@@ -0,0 +1,23 @@
+* Optimal objective is -4
+NAME          Comment
+* Comment
+ROWS
+ N  COST $Comment
+ G  R0
+ G  R1 *Comment
+ G  R2 $Comment
+COLUMNS
+    C0        R0            1.0        COST       -1.0 $Comment
+    C0        R1           -1.0 $Comment
+    C0        R2           -1.0 $Comment
+    C1        R0            1.0        COST       -2.0 *Comment
+    C1        R1           -1.0 *Comment
+    C1        R2           -1.0 *Comment
+RHS
+    DEMANDS   R0            1.0        R1         -2.0 $Comment
+    DEMANDS   R2           -2.0 $Comment
+RANGES
+    test      R0        1  $Comment
+BOUNDS
+ UP SERVINGS  C0            1.0 $Comment
+ENDATA

From 1ec433b3caee9dd65fd4534eff88a067c0c0e8c4 Mon Sep 17 00:00:00 2001
From: JAJHall <jajhall@ed.ac.uk>
Date: Thu, 12 Sep 2024 09:03:44 +0100
Subject: [PATCH 3/6] Introduced HMpsFF::getMpsLine, eliminating mpsCommentTrim

---
 src/io/HMpsFF.cpp       | 25 ++++++++++++++++++++-----
 src/io/HMpsFF.h         |  4 ++++
 src/util/stringutil.cpp |  9 ---------
 src/util/stringutil.h   |  3 ---
 4 files changed, 24 insertions(+), 17 deletions(-)

diff --git a/src/io/HMpsFF.cpp b/src/io/HMpsFF.cpp
index 823109a6e5..e7bd94e1d9 100644
--- a/src/io/HMpsFF.cpp
+++ b/src/io/HMpsFF.cpp
@@ -210,6 +210,22 @@ HighsInt HMpsFF::fillHessian(const HighsLogOptions& log_options) {
   return 0;
 }
 
+bool HMpsFF::getMpsLine(std::istream& file, std::string& strline, bool& skip) {
+  skip = false;
+  if (!getline(file, strline)) return false;
+  if (is_empty(strline) || strline[0] == '*') {
+    skip = true;
+  } else {
+    // Remove any trailing comment
+    const size_t p = strline.find_first_of(mps_comment_chars);
+    printf("In rTrimAt, First of \"%s\" in \"%s\" is %zu\n", mps_comment_chars.c_str(), strline.c_str(), p);
+    // If a comment character has been found, then erase from it to
+    // the end of the line
+    if (p <= strline.length()) strline.erase(p);
+  }
+  return true;
+}
+
 FreeFormatParserReturnCode HMpsFF::parse(const HighsLogOptions& log_options,
                                          const std::string& filename) {
   HMpsFF::Parsekey keyword = HMpsFF::Parsekey::kNone;
@@ -525,6 +541,7 @@ HMpsFF::Parsekey HMpsFF::parseObjsense(const HighsLogOptions& log_options,
 HMpsFF::Parsekey HMpsFF::parseRows(const HighsLogOptions& log_options,
                                    std::istream& file) {
   std::string strline, word;
+  bool skip;
   bool hasobj = false;
   // Assign a default objective name
   objective_name = "Objective";
@@ -532,11 +549,9 @@ HMpsFF::Parsekey HMpsFF::parseRows(const HighsLogOptions& log_options,
   assert(num_row == 0);
   assert(row_lower.size() == 0);
   assert(row_upper.size() == 0);
-  while (getline(file, strline)) {
-    if (is_empty(strline) || strline[0] == '*') continue;
-    printf("HMpsFF::parseRows before rtrim: strline = \"%s\"\n", strline.c_str());
-    mpsCommentTrim(strline);
-    printf("HMpsFF::parseRows  after rtrim: strline = \"%s\"\n", strline.c_str());
+  while (getMpsLine(file, strline, skip)) {
+    if (skip) continue;
+    printf("HMpsFF::parseRows: strline = \"%s\"\n", strline.c_str());
     double current = getWallTime();
     if (time_limit > 0 && current - start_time > time_limit)
       return HMpsFF::Parsekey::kTimeout;
diff --git a/src/io/HMpsFF.h b/src/io/HMpsFF.h
index 6c17e0c7ef..cd5dc5c22b 100644
--- a/src/io/HMpsFF.h
+++ b/src/io/HMpsFF.h
@@ -38,6 +38,8 @@
 
 using Triplet = std::tuple<HighsInt, HighsInt, double>;
 
+const std::string mps_comment_chars = "*$";
+
 enum class FreeFormatParserReturnCode {
   kSuccess,
   kParserError,
@@ -189,6 +191,8 @@ class HMpsFF {
 
   mutable std::string section_args;
 
+  bool getMpsLine(std::istream& file, std::string& strline, bool& skip);
+
   FreeFormatParserReturnCode parse(const HighsLogOptions& log_options,
                                    const std::string& filename);
   // Checks first word of strline and wraps it by it_begin and it_end
diff --git a/src/util/stringutil.cpp b/src/util/stringutil.cpp
index 5a4fef80a5..5b0de58e73 100644
--- a/src/util/stringutil.cpp
+++ b/src/util/stringutil.cpp
@@ -126,12 +126,3 @@ std::string first_word(std::string& str, size_t start) {
   assert(next_word_start != std::string::npos);
   return str.substr(next_word_start, next_word_end - next_word_start);
 }
-
-std::string& mpsCommentTrim(std::string& str) {
-  const size_t p = str.find_first_of(mps_comment_chars);
-  printf("In rTrimAt, First of \"%s\" in \"%s\" is %zu\n", mps_comment_chars.c_str(), str.c_str(), p);
-  if (p > str.length()) return str;
-  str.erase(p);
-  return str;
-}
-
diff --git a/src/util/stringutil.h b/src/util/stringutil.h
index 95b71e17e1..3c0a9c819d 100644
--- a/src/util/stringutil.h
+++ b/src/util/stringutil.h
@@ -28,7 +28,6 @@ void strTrim(char* str);
 void tolower(std::string& str);
 
 const std::string default_non_chars = "\t\n\v\f\r ";
-const std::string mps_comment_chars = "*$";
 std::string& ltrim(std::string& str, const std::string& chars = default_non_chars);
 std::string& rtrim(std::string& str, const std::string& chars = default_non_chars);
 std::string& trim(std::string& str, const std::string& chars = default_non_chars);
@@ -42,6 +41,4 @@ bool is_end(std::string& str, size_t end, const std::string& chars = default_non
 std::string first_word(std::string& str, size_t start);
 size_t first_word_end(std::string& str, size_t start);
 
-std::string& mpsCommentTrim(std::string& str);
-
 #endif

From 49c6aa4b1ff62cc0b6d9aa8ba04f49ef50cb2d70 Mon Sep 17 00:00:00 2001
From: JAJHall <jajhall@ed.ac.uk>
Date: Thu, 12 Sep 2024 09:34:00 +0100
Subject: [PATCH 4/6] Start replacing use of getline by getMpsLine

---
 src/io/HMpsFF.cpp | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/src/io/HMpsFF.cpp b/src/io/HMpsFF.cpp
index e7bd94e1d9..9aa9bbe952 100644
--- a/src/io/HMpsFF.cpp
+++ b/src/io/HMpsFF.cpp
@@ -218,10 +218,12 @@ bool HMpsFF::getMpsLine(std::istream& file, std::string& strline, bool& skip) {
   } else {
     // Remove any trailing comment
     const size_t p = strline.find_first_of(mps_comment_chars);
-    printf("In rTrimAt, First of \"%s\" in \"%s\" is %zu\n", mps_comment_chars.c_str(), strline.c_str(), p);
-    // If a comment character has been found, then erase from it to
-    // the end of the line
-    if (p <= strline.length()) strline.erase(p);
+    if (p <= strline.length()) {
+    // A comment character has been found, so erase from it to the end
+    // of the line and check whether the line is now empty
+      strline.erase(p);
+      skip = is_empty(strline);
+    }
   }
   return true;
 }
@@ -541,7 +543,6 @@ HMpsFF::Parsekey HMpsFF::parseObjsense(const HighsLogOptions& log_options,
 HMpsFF::Parsekey HMpsFF::parseRows(const HighsLogOptions& log_options,
                                    std::istream& file) {
   std::string strline, word;
-  bool skip;
   bool hasobj = false;
   // Assign a default objective name
   objective_name = "Objective";
@@ -549,9 +550,9 @@ HMpsFF::Parsekey HMpsFF::parseRows(const HighsLogOptions& log_options,
   assert(num_row == 0);
   assert(row_lower.size() == 0);
   assert(row_upper.size() == 0);
+  bool skip;
   while (getMpsLine(file, strline, skip)) {
     if (skip) continue;
-    printf("HMpsFF::parseRows: strline = \"%s\"\n", strline.c_str());
     double current = getWallTime();
     if (time_limit > 0 && current - start_time > time_limit)
       return HMpsFF::Parsekey::kTimeout;

From aeb80d5d53ca9cb593ac94efa141ad44cff901c6 Mon Sep 17 00:00:00 2001
From: JAJHall <jajhall@ed.ac.uk>
Date: Thu, 12 Sep 2024 09:51:53 +0100
Subject: [PATCH 5/6] Now using getMpsLine rather than getline

---
 check/TestFilereader.cpp |   7 +-
 src/io/HMpsFF.cpp        | 163 ++++++++++++++++-----------------------
 src/io/HMpsFF.h          |   1 -
 src/util/stringutil.h    |  12 ++-
 4 files changed, 79 insertions(+), 104 deletions(-)

diff --git a/check/TestFilereader.cpp b/check/TestFilereader.cpp
index 98c0ecae26..bd6c709c1e 100644
--- a/check/TestFilereader.cpp
+++ b/check/TestFilereader.cpp
@@ -10,7 +10,7 @@
 #include "lp_data/HighsLp.h"
 #include "lp_data/HighsLpUtils.h"
 
-const bool dev_run = true;
+const bool dev_run = false;
 
 TEST_CASE("filereader-edge-cases", "[highs_filereader]") {
   std::string model = "";
@@ -348,9 +348,10 @@ TEST_CASE("filereader-comment", "[highs_filereader]") {
   // Check that comments - either whole line with * in first column,
   // or rest of line following */$ are handled correctly
   const double optimal_objective_value = -4;
-  std::string model_file = std::string(HIGHS_DIR) + "/check/instances/comment.mps";
+  std::string model_file =
+      std::string(HIGHS_DIR) + "/check/instances/comment.mps";
   Highs highs;
-  highs.setOptionValue("output_flag", dev_run);
+  //  highs.setOptionValue("output_flag", dev_run);
   REQUIRE(highs.readModel(model_file) == HighsStatus::kOk);
   REQUIRE(highs.run() == HighsStatus::kOk);
   double objective_value = highs.getInfo().objective_function_value;
diff --git a/src/io/HMpsFF.cpp b/src/io/HMpsFF.cpp
index 9aa9bbe952..9f9b3fbb55 100644
--- a/src/io/HMpsFF.cpp
+++ b/src/io/HMpsFF.cpp
@@ -219,8 +219,8 @@ bool HMpsFF::getMpsLine(std::istream& file, std::string& strline, bool& skip) {
     // Remove any trailing comment
     const size_t p = strline.find_first_of(mps_comment_chars);
     if (p <= strline.length()) {
-    // A comment character has been found, so erase from it to the end
-    // of the line and check whether the line is now empty
+      // A comment character has been found, so erase from it to the end
+      // of the line and check whether the line is now empty
       strline.erase(p);
       skip = is_empty(strline);
     }
@@ -466,7 +466,8 @@ HighsInt HMpsFF::getColIdx(const std::string& colname, const bool add_if_new) {
 HMpsFF::Parsekey HMpsFF::parseDefault(const HighsLogOptions& log_options,
                                       std::istream& file) {
   std::string strline, word;
-  if (getline(file, strline)) {
+  bool skip;
+  if (getMpsLine(file, strline, skip)) {
     strline = trim(strline);
     if (strline.empty()) return HMpsFF::Parsekey::kComment;
     size_t s, e;
@@ -513,8 +514,9 @@ HMpsFF::Parsekey HMpsFF::parseObjsense(const HighsLogOptions& log_options,
                                        std::istream& file) {
   std::string strline, word;
 
-  while (getline(file, strline)) {
-    if (is_empty(strline) || strline[0] == '*') continue;
+  bool skip;
+  while (getMpsLine(file, strline, skip)) {
+    if (skip) continue;
 
     size_t start = 0;
     size_t end = 0;
@@ -607,9 +609,7 @@ HMpsFF::Parsekey HMpsFF::parseRows(const HighsLogOptions& log_options,
     }
 
     std::string rowname = first_word(strline, start + 1);
-    printf("HMpsFF::parseRows rowname = \"%s\"; strline = \"%s\"\n", rowname.c_str(), strline.c_str());
     size_t rowname_end = first_word_end(strline, start + 1);
-    printf("HMpsFF::parseRows rowname_end = %d\n", int(rowname_end));
 
     // Detect if file is in fixed format.
     if (!is_end(strline, rowname_end)) {
@@ -691,22 +691,18 @@ typename HMpsFF::Parsekey HMpsFF::parseCols(const HighsLogOptions& log_options,
       assert(-1 == rowidx || -2 == rowidx);
   };
 
-  while (getline(file, strline)) {
+  bool skip;
+  while (getMpsLine(file, strline, skip)) {
     double current = getWallTime();
     if (time_limit > 0 && current - start_time > time_limit)
       return HMpsFF::Parsekey::kTimeout;
 
-    if (kAnyFirstNonBlankAsStarImpliesComment) {
-      trim(strline);
-      if (strline.size() == 0 || strline[0] == '*') continue;
-    } else {
-      if (strline.size() > 0) {
-        // Just look for comment character in column 1
-        if (strline[0] == '*') continue;
-      }
-      trim(strline);
-      if (strline.size() == 0) continue;
+    if (strline.size() > 0) {
+      // Just look for comment character in column 1
+      if (strline[0] == '*') continue;
     }
+    trim(strline);
+    if (strline.size() == 0) continue;
 
     HMpsFF::Parsekey key = checkFirstWord(strline, start, end, word);
 
@@ -998,22 +994,18 @@ HMpsFF::Parsekey HMpsFF::parseRhs(const HighsLogOptions& log_options,
   has_obj_entry_ = false;
   bool has_entry = false;
 
-  while (getline(file, strline)) {
+  bool skip;
+  while (getMpsLine(file, strline, skip)) {
     double current = getWallTime();
     if (time_limit > 0 && current - start_time > time_limit)
       return HMpsFF::Parsekey::kTimeout;
 
-    if (kAnyFirstNonBlankAsStarImpliesComment) {
-      trim(strline);
-      if (strline.size() == 0 || strline[0] == '*') continue;
-    } else {
-      if (strline.size() > 0) {
-        // Just look for comment character in column 1
-        if (strline[0] == '*') continue;
-      }
-      trim(strline);
-      if (strline.size() == 0) continue;
+    if (strline.size() > 0) {
+      // Just look for comment character in column 1
+      if (strline[0] == '*') continue;
     }
+    trim(strline);
+    if (strline.size() == 0) continue;
 
     size_t begin = 0;
     size_t end = 0;
@@ -1164,22 +1156,18 @@ HMpsFF::Parsekey HMpsFF::parseBounds(const HighsLogOptions& log_options,
   has_lower.assign(num_col, false);
   has_upper.assign(num_col, false);
 
-  while (getline(file, strline)) {
+  bool skip;
+  while (getMpsLine(file, strline, skip)) {
     double current = getWallTime();
     if (time_limit > 0 && current - start_time > time_limit)
       return HMpsFF::Parsekey::kTimeout;
 
-    if (kAnyFirstNonBlankAsStarImpliesComment) {
-      trim(strline);
-      if (strline.size() == 0 || strline[0] == '*') continue;
-    } else {
-      if (strline.size() > 0) {
-        // Just look for comment character in column 1
-        if (strline[0] == '*') continue;
-      }
-      trim(strline);
-      if (strline.size() == 0) continue;
+    if (strline.size() > 0) {
+      // Just look for comment character in column 1
+      if (strline[0] == '*') continue;
     }
+    trim(strline);
+    if (strline.size() == 0) continue;
 
     size_t begin = 0;
     size_t end = 0;
@@ -1443,22 +1431,18 @@ HMpsFF::Parsekey HMpsFF::parseRanges(const HighsLogOptions& log_options,
   // Initialise tracking for duplicate entries
   has_row_entry_.assign(num_row, false);
 
-  while (getline(file, strline)) {
+  bool skip;
+  while (getMpsLine(file, strline, skip)) {
     double current = getWallTime();
     if (time_limit > 0 && current - start_time > time_limit)
       return HMpsFF::Parsekey::kTimeout;
 
-    if (kAnyFirstNonBlankAsStarImpliesComment) {
-      trim(strline);
-      if (strline.size() == 0 || strline[0] == '*') continue;
-    } else {
-      if (strline.size() > 0) {
-        // Just look for comment character in column 1
-        if (strline[0] == '*') continue;
-      }
-      trim(strline);
-      if (strline.size() == 0) continue;
+    if (strline.size() > 0) {
+      // Just look for comment character in column 1
+      if (strline[0] == '*') continue;
     }
+    trim(strline);
+    if (strline.size() == 0) continue;
 
     size_t begin, end;
     std::string word;
@@ -1596,21 +1580,18 @@ typename HMpsFF::Parsekey HMpsFF::parseHessian(
   size_t end_coeff_name;
   HighsInt colidx, rowidx;
 
-  while (getline(file, strline)) {
+  bool skip;
+  while (getMpsLine(file, strline, skip)) {
     double current = getWallTime();
     if (time_limit > 0 && current - start_time > time_limit)
       return HMpsFF::Parsekey::kTimeout;
-    if (kAnyFirstNonBlankAsStarImpliesComment) {
-      trim(strline);
-      if (strline.size() == 0 || strline[0] == '*') continue;
-    } else {
-      if (strline.size() > 0) {
-        // Just look for comment character in column 1
-        if (strline[0] == '*') continue;
-      }
-      trim(strline);
-      if (strline.size() == 0) continue;
+
+    if (strline.size() > 0) {
+      // Just look for comment character in column 1
+      if (strline[0] == '*') continue;
     }
+    trim(strline);
+    if (strline.size() == 0) continue;
 
     size_t begin = 0;
     size_t end = 0;
@@ -1723,7 +1704,8 @@ typename HMpsFF::Parsekey HMpsFF::parseQuadRows(
                    "Row name \"%s\" in %s section is not defined: ignored\n",
                    rowname.c_str(), section_name.c_str());
     // read lines until start of new section
-    while (getline(file, strline)) {
+    bool skip;
+    while (getMpsLine(file, strline, skip)) {
       size_t begin = 0;
       size_t end = 0;
       HMpsFF::Parsekey key = checkFirstWord(strline, begin, end, col_name);
@@ -1746,21 +1728,18 @@ typename HMpsFF::Parsekey HMpsFF::parseQuadRows(
 
   auto& qentries = (rowidx == -1 ? q_entries : qrows_entries[rowidx]);
 
-  while (getline(file, strline)) {
+  bool skip;
+  while (getMpsLine(file, strline, skip)) {
     double current = getWallTime();
     if (time_limit > 0 && current - start_time > time_limit)
       return HMpsFF::Parsekey::kTimeout;
-    if (kAnyFirstNonBlankAsStarImpliesComment) {
-      trim(strline);
-      if (strline.size() == 0 || strline[0] == '*') continue;
-    } else {
-      if (strline.size() > 0) {
-        // Just look for comment character in column 1
-        if (strline[0] == '*') continue;
-      }
-      trim(strline);
-      if (strline.size() == 0) continue;
+
+    if (strline.size() > 0) {
+      // Just look for comment character in column 1
+      if (strline[0] == '*') continue;
     }
+    trim(strline);
+    if (strline.size() == 0) continue;
 
     size_t begin = 0;
     size_t end = 0;
@@ -1899,22 +1878,18 @@ typename HMpsFF::Parsekey HMpsFF::parseCones(const HighsLogOptions& log_options,
 
   // now parse the cone entries: one column per line
   std::string strline;
-  while (getline(file, strline)) {
+  bool skip;
+  while (getMpsLine(file, strline, skip)) {
     double current = getWallTime();
     if (time_limit > 0 && current - start_time > time_limit)
       return HMpsFF::Parsekey::kTimeout;
 
-    if (kAnyFirstNonBlankAsStarImpliesComment) {
-      trim(strline);
-      if (strline.size() == 0 || strline[0] == '*') continue;
-    } else {
-      if (strline.size() > 0) {
-        // Just look for comment character in column 1
-        if (strline[0] == '*') continue;
-      }
-      trim(strline);
-      if (strline.size() == 0) continue;
+    if (strline.size() > 0) {
+      // Just look for comment character in column 1
+      if (strline[0] == '*') continue;
     }
+    trim(strline);
+    if (strline.size() == 0) continue;
 
     size_t begin;
     std::string colname;
@@ -1942,22 +1917,18 @@ typename HMpsFF::Parsekey HMpsFF::parseSos(const HighsLogOptions& log_options,
                                            const HMpsFF::Parsekey keyword) {
   std::string strline, word;
 
-  while (getline(file, strline)) {
+  bool skip;
+  while (getMpsLine(file, strline, skip)) {
     double current = getWallTime();
     if (time_limit > 0 && current - start_time > time_limit)
       return HMpsFF::Parsekey::kTimeout;
 
-    if (kAnyFirstNonBlankAsStarImpliesComment) {
-      trim(strline);
-      if (strline.size() == 0 || strline[0] == '*') continue;
-    } else {
-      if (strline.size() > 0) {
-        // Just look for comment character in column 1
-        if (strline[0] == '*') continue;
-      }
-      trim(strline);
-      if (strline.size() == 0) continue;
+    if (strline.size() > 0) {
+      // Just look for comment character in column 1
+      if (strline[0] == '*') continue;
     }
+    trim(strline);
+    if (strline.size() == 0) continue;
 
     size_t begin, end;
     std::string word;
diff --git a/src/io/HMpsFF.h b/src/io/HMpsFF.h
index cd5dc5c22b..b5c86ae177 100644
--- a/src/io/HMpsFF.h
+++ b/src/io/HMpsFF.h
@@ -126,7 +126,6 @@ class HMpsFF {
   HighsInt fillMatrix(const HighsLogOptions& log_options);
   HighsInt fillHessian(const HighsLogOptions& log_options);
 
-  const bool kAnyFirstNonBlankAsStarImpliesComment = false;
   /// how to treat variables that appear in COLUMNS section first
   /// assume them to be binary as in the original IBM interpretation
   /// or integer with default bounds
diff --git a/src/util/stringutil.h b/src/util/stringutil.h
index 3c0a9c819d..25ac72c0ef 100644
--- a/src/util/stringutil.h
+++ b/src/util/stringutil.h
@@ -28,13 +28,17 @@ void strTrim(char* str);
 void tolower(std::string& str);
 
 const std::string default_non_chars = "\t\n\v\f\r ";
-std::string& ltrim(std::string& str, const std::string& chars = default_non_chars);
-std::string& rtrim(std::string& str, const std::string& chars = default_non_chars);
-std::string& trim(std::string& str, const std::string& chars = default_non_chars);
+std::string& ltrim(std::string& str,
+                   const std::string& chars = default_non_chars);
+std::string& rtrim(std::string& str,
+                   const std::string& chars = default_non_chars);
+std::string& trim(std::string& str,
+                  const std::string& chars = default_non_chars);
 
 bool is_empty(std::string& str, const std::string& chars = default_non_chars);
 bool is_empty(char c, const std::string& chars = default_non_chars);
-bool is_end(std::string& str, size_t end, const std::string& chars = default_non_chars);
+bool is_end(std::string& str, size_t end,
+            const std::string& chars = default_non_chars);
 
 // todo: replace with pair of references rather than string ret value to avoid
 // copy and also using function below. or do it properly with iterators.

From cd69aea9efb7339636003b24c5aee905b56bf3ff Mon Sep 17 00:00:00 2001
From: JAJHall <jajhall@ed.ac.uk>
Date: Thu, 12 Sep 2024 10:51:41 +0100
Subject: [PATCH 6/6] getMpsLine now trims lines and the checks is_empty

---
 check/TestFilereader.cpp |   2 +-
 src/io/HMpsFF.cpp        | 116 +++++++++++----------------------------
 src/io/HMpsFF.h          |   1 +
 3 files changed, 33 insertions(+), 86 deletions(-)

diff --git a/check/TestFilereader.cpp b/check/TestFilereader.cpp
index bd6c709c1e..a1b420d316 100644
--- a/check/TestFilereader.cpp
+++ b/check/TestFilereader.cpp
@@ -351,7 +351,7 @@ TEST_CASE("filereader-comment", "[highs_filereader]") {
   std::string model_file =
       std::string(HIGHS_DIR) + "/check/instances/comment.mps";
   Highs highs;
-  //  highs.setOptionValue("output_flag", dev_run);
+  highs.setOptionValue("output_flag", dev_run);
   REQUIRE(highs.readModel(model_file) == HighsStatus::kOk);
   REQUIRE(highs.run() == HighsStatus::kOk);
   double objective_value = highs.getInfo().objective_function_value;
diff --git a/src/io/HMpsFF.cpp b/src/io/HMpsFF.cpp
index 9f9b3fbb55..414e1fcbbb 100644
--- a/src/io/HMpsFF.cpp
+++ b/src/io/HMpsFF.cpp
@@ -210,6 +210,10 @@ HighsInt HMpsFF::fillHessian(const HighsLogOptions& log_options) {
   return 0;
 }
 
+bool HMpsFF::timeout() {
+  return time_limit > 0 && getWallTime() - start_time > time_limit;
+}
+
 bool HMpsFF::getMpsLine(std::istream& file, std::string& strline, bool& skip) {
   skip = false;
   if (!getline(file, strline)) return false;
@@ -223,7 +227,10 @@ bool HMpsFF::getMpsLine(std::istream& file, std::string& strline, bool& skip) {
       // of the line and check whether the line is now empty
       strline.erase(p);
       skip = is_empty(strline);
+      if (skip) return true;
     }
+    strline = trim(strline);
+    skip = is_empty(strline);
   }
   return true;
 }
@@ -468,8 +475,9 @@ HMpsFF::Parsekey HMpsFF::parseDefault(const HighsLogOptions& log_options,
   std::string strline, word;
   bool skip;
   if (getMpsLine(file, strline, skip)) {
-    strline = trim(strline);
-    if (strline.empty()) return HMpsFF::Parsekey::kComment;
+    if (skip) return HMpsFF::Parsekey::kComment;
+    if (timeout()) return HMpsFF::Parsekey::kTimeout;
+
     size_t s, e;
     HMpsFF::Parsekey key = checkFirstWord(strline, s, e, word);
     if (key == HMpsFF::Parsekey::kName) {
@@ -517,6 +525,7 @@ HMpsFF::Parsekey HMpsFF::parseObjsense(const HighsLogOptions& log_options,
   bool skip;
   while (getMpsLine(file, strline, skip)) {
     if (skip) continue;
+    if (timeout()) return HMpsFF::Parsekey::kTimeout;
 
     size_t start = 0;
     size_t end = 0;
@@ -555,9 +564,7 @@ HMpsFF::Parsekey HMpsFF::parseRows(const HighsLogOptions& log_options,
   bool skip;
   while (getMpsLine(file, strline, skip)) {
     if (skip) continue;
-    double current = getWallTime();
-    if (time_limit > 0 && current - start_time > time_limit)
-      return HMpsFF::Parsekey::kTimeout;
+    if (timeout()) return HMpsFF::Parsekey::kTimeout;
 
     bool isobj = false;
     bool isFreeRow = false;
@@ -693,16 +700,8 @@ typename HMpsFF::Parsekey HMpsFF::parseCols(const HighsLogOptions& log_options,
 
   bool skip;
   while (getMpsLine(file, strline, skip)) {
-    double current = getWallTime();
-    if (time_limit > 0 && current - start_time > time_limit)
-      return HMpsFF::Parsekey::kTimeout;
-
-    if (strline.size() > 0) {
-      // Just look for comment character in column 1
-      if (strline[0] == '*') continue;
-    }
-    trim(strline);
-    if (strline.size() == 0) continue;
+    if (skip) continue;
+    if (timeout()) return HMpsFF::Parsekey::kTimeout;
 
     HMpsFF::Parsekey key = checkFirstWord(strline, start, end, word);
 
@@ -996,16 +995,8 @@ HMpsFF::Parsekey HMpsFF::parseRhs(const HighsLogOptions& log_options,
 
   bool skip;
   while (getMpsLine(file, strline, skip)) {
-    double current = getWallTime();
-    if (time_limit > 0 && current - start_time > time_limit)
-      return HMpsFF::Parsekey::kTimeout;
-
-    if (strline.size() > 0) {
-      // Just look for comment character in column 1
-      if (strline[0] == '*') continue;
-    }
-    trim(strline);
-    if (strline.size() == 0) continue;
+    if (skip) continue;
+    if (timeout()) return HMpsFF::Parsekey::kTimeout;
 
     size_t begin = 0;
     size_t end = 0;
@@ -1158,16 +1149,8 @@ HMpsFF::Parsekey HMpsFF::parseBounds(const HighsLogOptions& log_options,
 
   bool skip;
   while (getMpsLine(file, strline, skip)) {
-    double current = getWallTime();
-    if (time_limit > 0 && current - start_time > time_limit)
-      return HMpsFF::Parsekey::kTimeout;
-
-    if (strline.size() > 0) {
-      // Just look for comment character in column 1
-      if (strline[0] == '*') continue;
-    }
-    trim(strline);
-    if (strline.size() == 0) continue;
+    if (skip) continue;
+    if (timeout()) return HMpsFF::Parsekey::kTimeout;
 
     size_t begin = 0;
     size_t end = 0;
@@ -1433,16 +1416,8 @@ HMpsFF::Parsekey HMpsFF::parseRanges(const HighsLogOptions& log_options,
 
   bool skip;
   while (getMpsLine(file, strline, skip)) {
-    double current = getWallTime();
-    if (time_limit > 0 && current - start_time > time_limit)
-      return HMpsFF::Parsekey::kTimeout;
-
-    if (strline.size() > 0) {
-      // Just look for comment character in column 1
-      if (strline[0] == '*') continue;
-    }
-    trim(strline);
-    if (strline.size() == 0) continue;
+    if (skip) continue;
+    if (timeout()) return HMpsFF::Parsekey::kTimeout;
 
     size_t begin, end;
     std::string word;
@@ -1582,16 +1557,8 @@ typename HMpsFF::Parsekey HMpsFF::parseHessian(
 
   bool skip;
   while (getMpsLine(file, strline, skip)) {
-    double current = getWallTime();
-    if (time_limit > 0 && current - start_time > time_limit)
-      return HMpsFF::Parsekey::kTimeout;
-
-    if (strline.size() > 0) {
-      // Just look for comment character in column 1
-      if (strline[0] == '*') continue;
-    }
-    trim(strline);
-    if (strline.size() == 0) continue;
+    if (skip) continue;
+    if (timeout()) return HMpsFF::Parsekey::kTimeout;
 
     size_t begin = 0;
     size_t end = 0;
@@ -1706,6 +1673,9 @@ typename HMpsFF::Parsekey HMpsFF::parseQuadRows(
     // read lines until start of new section
     bool skip;
     while (getMpsLine(file, strline, skip)) {
+      if (skip) continue;
+      if (timeout()) return HMpsFF::Parsekey::kTimeout;
+
       size_t begin = 0;
       size_t end = 0;
       HMpsFF::Parsekey key = checkFirstWord(strline, begin, end, col_name);
@@ -1730,16 +1700,8 @@ typename HMpsFF::Parsekey HMpsFF::parseQuadRows(
 
   bool skip;
   while (getMpsLine(file, strline, skip)) {
-    double current = getWallTime();
-    if (time_limit > 0 && current - start_time > time_limit)
-      return HMpsFF::Parsekey::kTimeout;
-
-    if (strline.size() > 0) {
-      // Just look for comment character in column 1
-      if (strline[0] == '*') continue;
-    }
-    trim(strline);
-    if (strline.size() == 0) continue;
+    if (skip) continue;
+    if (timeout()) return HMpsFF::Parsekey::kTimeout;
 
     size_t begin = 0;
     size_t end = 0;
@@ -1880,16 +1842,8 @@ typename HMpsFF::Parsekey HMpsFF::parseCones(const HighsLogOptions& log_options,
   std::string strline;
   bool skip;
   while (getMpsLine(file, strline, skip)) {
-    double current = getWallTime();
-    if (time_limit > 0 && current - start_time > time_limit)
-      return HMpsFF::Parsekey::kTimeout;
-
-    if (strline.size() > 0) {
-      // Just look for comment character in column 1
-      if (strline[0] == '*') continue;
-    }
-    trim(strline);
-    if (strline.size() == 0) continue;
+    if (skip) continue;
+    if (timeout()) return HMpsFF::Parsekey::kTimeout;
 
     size_t begin;
     std::string colname;
@@ -1919,16 +1873,8 @@ typename HMpsFF::Parsekey HMpsFF::parseSos(const HighsLogOptions& log_options,
 
   bool skip;
   while (getMpsLine(file, strline, skip)) {
-    double current = getWallTime();
-    if (time_limit > 0 && current - start_time > time_limit)
-      return HMpsFF::Parsekey::kTimeout;
-
-    if (strline.size() > 0) {
-      // Just look for comment character in column 1
-      if (strline[0] == '*') continue;
-    }
-    trim(strline);
-    if (strline.size() == 0) continue;
+    if (skip) continue;
+    if (timeout()) return HMpsFF::Parsekey::kTimeout;
 
     size_t begin, end;
     std::string word;
diff --git a/src/io/HMpsFF.h b/src/io/HMpsFF.h
index b5c86ae177..2426273ec2 100644
--- a/src/io/HMpsFF.h
+++ b/src/io/HMpsFF.h
@@ -190,6 +190,7 @@ class HMpsFF {
 
   mutable std::string section_args;
 
+  bool timeout();
   bool getMpsLine(std::istream& file, std::string& strline, bool& skip);
 
   FreeFormatParserReturnCode parse(const HighsLogOptions& log_options,