Merge pull request #614 from votca/fix_readers_on_windows

readers: getline() -> tools::getline()
votca · Nov 16, 2020 · 7165e42 · 7165e42
2 parents 4d86424 + f64940a
commit 7165e42
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Showing 12 changed files with 72 additions and 68 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,7 @@ For more detailed information about the changes see the history of the
 * add gmx2021 builds to CI (#607)
 * remove set-env call from CI (#608)
 * use master .clang-format in format action (#610)
+* strip windows line endings in readers (#614)
 
 ## Version 1.6.2 _SuperGitta_ (released 22.08.20)
 * move CI to GitHub Actions (#563, #567, #569)

diff --git a/CMakeModules/CheckFunctionExists.cpp b/CMakeModules/CheckFunctionExists.cpp
@@ -2,22 +2,21 @@
 
 char CHECK_FUNCTION_EXISTS();
 #ifdef __CLASSIC_C__
-int main(){
+int main() {
   int ac;
-  char*av[];
+  char* av[];
 #else
-int main(int ac, char*av[]){
+int main(int ac, char* av[]) {
 #endif
   CHECK_FUNCTION_EXISTS();
-  if(ac > 1000)
-    {
+  if (ac > 1000) {
     return *av[0];
-    }
+  }
   return 0;
 }
 
-#else  /* CHECK_FUNCTION_EXISTS */
+#else /* CHECK_FUNCTION_EXISTS */
 
-#  error "CHECK_FUNCTION_EXISTS has to specify the function"
+#error "CHECK_FUNCTION_EXISTS has to specify the function"
 
 #endif /* CHECK_FUNCTION_EXISTS */
diff --git a/include/votca/csg/xyzreader.h b/include/votca/csg/xyzreader.h
@@ -1,5 +1,5 @@
 /*
- * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org)
+ * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org)
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -24,6 +24,7 @@
 #include <votca/csg/topologyreader.h>
 #include <votca/csg/trajectoryreader.h>
 #include <votca/tools/constants.h>
+#include <votca/tools/getline.h>
 
 #include <type_traits>
 namespace votca {
@@ -104,7 +105,7 @@ class XYZReader : public TrajectoryReader, public TopologyReader {
 template <bool topology, class T>
 inline bool XYZReader::ReadFrame(T &container) {
   std::string line;
-  std::getline(_fl, line);
+  tools::getline(_fl, line);
   ++_line;
   if (!_fl.eof()) {
     // read the number of atoms
@@ -121,11 +122,11 @@ inline bool XYZReader::ReadFrame(T &container) {
           "number of beads in topology and trajectory differ");
     }
     // the title line
-    getline(_fl, line);
+    tools::getline(_fl, line);
     ++_line;
     // read atoms
     for (Index i = 0; i < natoms; ++i) {
-      getline(_fl, line);
+      tools::getline(_fl, line);
       ++_line;
       if (_fl.eof()) {
         throw std::runtime_error("unexpected end of file in xyz file");

diff --git a/src/csg_boltzmann/main.cc b/src/csg_boltzmann/main.cc
@@ -1,5 +1,5 @@
 /*
- * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org)
+ * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org)
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -29,6 +29,7 @@
 #include <math.h>
 #include <string>
 #include <votca/csg/csgapplication.h>
+#include <votca/tools/getline.h>
 #include <votca/tools/rangeparser.h>
 #include <votca/tools/tokenizer.h>
 
@@ -181,7 +182,7 @@ void CsgBoltzmann::InteractiveMode() {
   while (1) {
     string line;
     cout << "> ";
-    getline(cin, line);
+    votca::tools::getline(cin, line);
 
     boost::trim(line);
 

diff --git a/src/libcsg/imcio.cc b/src/libcsg/imcio.cc
@@ -1,5 +1,5 @@
 /*
- * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org)
+ * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org)
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -115,7 +115,7 @@ Eigen::MatrixXd imcio_read_matrix(const std::string &filename) {
   std::vector<double> result;
   Index numrows = 0;
   size_t numcols = 0;
-  while (getline(intt, line)) {
+  while (tools::getline(intt, line)) {
     if (line[0] == '#') {
       continue;
     }
@@ -148,7 +148,7 @@ std::vector<std::pair<std::string, tools::RangeParser> > imcio_read_index(
   std::vector<std::pair<std::string, tools::RangeParser> > indeces;
   string line;
   // read till the first data line
-  while (getline(in, line)) {
+  while (tools::getline(in, line)) {
     // remove comments and xmgrace stuff
     line = line.substr(0, line.find("#"));
     line = line.substr(0, line.find("@"));

diff --git a/src/libcsg/modules/io/dlpolytopologyreader.cc b/src/libcsg/modules/io/dlpolytopologyreader.cc
@@ -1,5 +1,5 @@
 /*
- * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org)
+ * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org)
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -47,7 +47,7 @@ string DLPOLYTopologyReader::_NextKeyline(ifstream &fs, const char *wspace)
   size_t i_nws = 0;
 
   do {
-    getline(fs, line);
+    tools::getline(fs, line);
 
     if (fs.eof()) {
       throw std::runtime_error("Error: unexpected end of dlpoly file '" +
@@ -374,7 +374,7 @@ bool DLPOLYTopologyReader::ReadTopology(string file, Topology &top) {
   }
 
 #ifdef DEBUG
-  getline(fl, line);  // is "close" found?
+  tools::getline(fl, line);  // is "close" found?
   if (line == "close") {
     cout << "Read from dlpoly file '" << _fname << "' : '" << line
          << "' - done with topology" << endl;

diff --git a/src/libcsg/modules/io/dlpolytrajectoryreader.cc b/src/libcsg/modules/io/dlpolytrajectoryreader.cc
@@ -1,5 +1,5 @@
 /*
- * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org)
+ * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org)
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -102,14 +102,14 @@ bool DLPOLYTrajectoryReader::NextFrame(Topology &conf) {
 
   if (_first_frame) {
 
-    getline(_fl, line);  // title
+    tools::getline(_fl, line);  // title
 
 #ifdef DEBUG
     cout << "Read from dlpoly file '" << _fname << "' : '" << line
          << "' - header" << endl;
 #endif
 
-    getline(_fl, line);  // 2nd header line
+    tools::getline(_fl, line);  // 2nd header line
 
 #ifdef DEBUG
     cout << "Read from dlpoly file '" << _fname << "' : '" << line
@@ -179,8 +179,8 @@ bool DLPOLYTrajectoryReader::NextFrame(Topology &conf) {
   // read normal frame
 
   if (!_isConfig) {
-    getline(_fl, line);  // timestep line - only present in HISTORY, and not in
-                         // CONFIG
+    tools::getline(_fl, line);  // timestep line - only present in HISTORY, and
+                                // not in CONFIG
 #ifdef DEBUG
     cout << "Read from dlpoly file '" << _fname << "' : '" << line << "'"
          << endl;
@@ -283,7 +283,7 @@ bool DLPOLYTrajectoryReader::NextFrame(Topology &conf) {
     Eigen::Matrix3d box = Eigen::Matrix3d::Zero();
     for (Index i = 0; i < 3; i++) {  // read 3 box/cell lines
 
-      getline(_fl, line);
+      tools::getline(_fl, line);
 
 #ifdef DEBUG
       cout << "Read from dlpoly file '" << _fname << "' : '" << line
@@ -308,7 +308,7 @@ bool DLPOLYTrajectoryReader::NextFrame(Topology &conf) {
     for (Index i = 0; i < natoms; i++) {
 
       {
-        getline(_fl, line);  // atom header line
+        tools::getline(_fl, line);  // atom header line
 
 #ifdef DEBUG
         cout << "Read from dlpoly file '" << _fname << "' : '" << line << "'"
@@ -336,7 +336,7 @@ bool DLPOLYTrajectoryReader::NextFrame(Topology &conf) {
       Eigen::Matrix3d atom_vecs = Eigen::Matrix3d::Zero();
       for (Index j = 0; j < std::min(navecs, Index(2)) + 1; j++) {
 
-        getline(_fl, line);  // read atom positions
+        tools::getline(_fl, line);  // read atom positions
 
 #ifdef DEBUG
         cout << "Read from dlpoly file '" << _fname << "' : '" << line << "'"

diff --git a/src/libcsg/modules/io/groreader.cc b/src/libcsg/modules/io/groreader.cc
@@ -1,5 +1,5 @@
 /*
- * Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org)
+ * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org)
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -61,11 +61,11 @@ bool GROReader::FirstFrame(Topology &top) {
 
 bool GROReader::NextFrame(Topology &top) {
   string tmp;
-  getline(_fl, tmp);  // title
+  tools::getline(_fl, tmp);  // title
   if (_fl.eof()) {
     return !_fl.eof();
   }
-  getline(_fl, tmp);  // number atoms
+  tools::getline(_fl, tmp);  // number atoms
   Index natoms = std::stoi(tmp);
   if (!_topology && natoms != top.BeadCount()) {
     throw std::runtime_error(
@@ -74,7 +74,7 @@ bool GROReader::NextFrame(Topology &top) {
 
   for (Index i = 0; i < natoms; i++) {
     string line;
-    getline(_fl, line);
+    tools::getline(_fl, line);
     string resNum, resName, atName, x, y, z;
     try {
       resNum = string(line, 0, 5);   // %5i
@@ -142,7 +142,7 @@ bool GROReader::NextFrame(Topology &top) {
     }
   }
 
-  getline(_fl, tmp);  // read box line
+  tools::getline(_fl, tmp);  // read box line
   if (_fl.eof()) {
     throw std::runtime_error(
         "unexpected end of file in poly file, when boxline");