reformat code using clang-format

.clang-format

@@ -1,66 +1,5 @@
 ---
-Language:        Cpp
-# BasedOnStyle:  LLVM
-AccessModifierOffset: -2
-AlignAfterOpenBracket: true
-AlignEscapedNewlinesLeft: false
-AlignOperands:   true
-AlignTrailingComments: true
-AlignConsecutiveAssignments: false
-AllowAllParametersOfDeclarationOnNextLine: true
-AllowShortBlocksOnASingleLine: false
-AllowShortCaseLabelsOnASingleLine: false
-AllowShortIfStatementsOnASingleLine: false
-AllowShortLoopsOnASingleLine: false
-AllowShortFunctionsOnASingleLine: All
-AlwaysBreakAfterDefinitionReturnType: false
-AlwaysBreakTemplateDeclarations: false
-AlwaysBreakBeforeMultilineStrings: false
-BreakBeforeBinaryOperators: None
-BreakBeforeTernaryOperators: true
-BreakConstructorInitializersBeforeComma: false
-BinPackParameters: true
-BinPackArguments: true
-ColumnLimit:     80
-ConstructorInitializerAllOnOneLineOrOnePerLine: false
-ConstructorInitializerIndentWidth: 4
-DerivePointerAlignment: false
-ExperimentalAutoDetectBinPacking: false
-IndentCaseLabels: false
-IndentWrappedFunctionNames: false
-IndentFunctionDeclarationAfterType: false
-MaxEmptyLinesToKeep: 1
-KeepEmptyLinesAtTheStartOfBlocks: true
-NamespaceIndentation: None
-ObjCBlockIndentWidth: 2
-ObjCSpaceAfterProperty: false
-ObjCSpaceBeforeProtocolList: true
-PenaltyBreakBeforeFirstCallParameter: 19
-PenaltyBreakComment: 300
-PenaltyBreakString: 1000
-PenaltyBreakFirstLessLess: 120
-PenaltyExcessCharacter: 1000000
-PenaltyReturnTypeOnItsOwnLine: 60
-PointerAlignment: Right
-SpacesBeforeTrailingComments: 1
-Cpp11BracedListStyle: true
-Standard:        Cpp11
-IndentWidth:     2
-TabWidth:        8
-UseTab:          Never
-BreakBeforeBraces: Attach
-SpacesInParentheses: false
-SpacesInSquareBrackets: false
-SpacesInAngles:  false
-SpaceInEmptyParentheses: false
-SpacesInCStyleCastParentheses: false
-SpaceAfterCStyleCast: false
-SpacesInContainerLiterals: true
-SpaceBeforeAssignmentOperators: true
-ContinuationIndentWidth: 4
-CommentPragmas:  '^ IWYU pragma:'
-ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
-SpaceBeforeParens: ControlStatements
-DisableFormat:   false
+Language: Cpp
+BasedOnStyle: LLVM
+DisableFormat: false
 ...
-

src/examples/algorithms/HelloSP_TP.cpp

@@ -20,31 +20,33 @@
  * ---------------------------------------------------------------------
  */
 
+#include <algorithm> // std::generate
+#include <cmath>     // pow
+#include <cstdlib>   // std::rand, std::srand
+#include <ctime>     // std::time
 #include <iostream>
 #include <vector>
-#include <algorithm>    // std::generate
-#include <ctime>        // std::time
-#include <cstdlib>      // std::rand, std::srand
-#include <cmath> 	// pow
 
-#include "nupic/algorithms/SpatialPooler.hpp"
 #include "nupic/algorithms/Cells4.hpp"
+#include "nupic/algorithms/SpatialPooler.hpp"
 #include "nupic/os/Timer.hpp"
 
 using namespace std;
 using namespace nupic;
-using nupic::algorithms::spatial_pooler::SpatialPooler;
 using nupic::algorithms::Cells4::Cells4;
+using nupic::algorithms::spatial_pooler::SpatialPooler;
 
 // function generator:
-int RandomNumber01 () { return (rand()%2); } // returns random (binary) numbers from {0,1}
+int RandomNumber01() {
+  return (rand() % 2);
+} // returns random (binary) numbers from {0,1}
 
-int main(int argc, const char * argv[])
-{
-const UInt DIM = 2048; // number of columns in SP, TP
-const UInt DIM_INPUT = 10000;
-const UInt TP_CELLS_PER_COL = 10; // cells per column in TP
-const UInt EPOCHS = pow(10, 4); // number of iterations (calls to SP/TP compute() )
+int main(int argc, const char *argv[]) {
+  const UInt DIM = 2048; // number of columns in SP, TP
+  const UInt DIM_INPUT = 10000;
+  const UInt TP_CELLS_PER_COL = 10; // cells per column in TP
+  const UInt EPOCHS =
+      pow(10, 4); // number of iterations (calls to SP/TP compute() )
 
   vector<UInt> inputDim = {DIM_INPUT};
   vector<UInt> colDim = {DIM};
@@ -53,18 +55,19 @@ const UInt EPOCHS = pow(10, 4); // number of iterations (calls to SP/TP compute(
   vector<UInt> input(DIM_INPUT);
   vector<UInt> outSP(DIM); // active array, output of SP/TP
   const int _CELLS = DIM * TP_CELLS_PER_COL;
-  vector<UInt> outTP(_CELLS);   
+  vector<UInt> outTP(_CELLS);
   Real rIn[DIM] = {}; // input for TP (must be Reals)
   Real rOut[_CELLS] = {};
 
   // initialize SP, TP
   SpatialPooler sp(inputDim, colDim);
-  Cells4 tp(DIM, TP_CELLS_PER_COL, 12, 8, 15, 5, .5, .8, 1.0, .1, .1, 0.0, false, 42, true, false);
+  Cells4 tp(DIM, TP_CELLS_PER_COL, 12, 8, 15, 5, .5, .8, 1.0, .1, .1, 0.0,
+            false, 42, true, false);
 
   // Start a stopwatch timer
   Timer stopwatch(true);
 
-  //run
+  // run
   for (UInt e = 0; e < EPOCHS; e++) {
     generate(input.begin(), input.end(), RandomNumber01);
     fill(outSP.begin(), outSP.end(), 0);
@@ -77,20 +80,21 @@ const UInt EPOCHS = pow(10, 4); // number of iterations (calls to SP/TP compute(
 
     tp.compute(rIn, rOut, true, true);
 
-    for (UInt i=0; i< _CELLS; i++) {
+    for (UInt i = 0; i < _CELLS; i++) {
       outTP[i] = (UInt)rOut[i];
     }
 
     // print
-    if (e == EPOCHS-1) {
+    if (e == EPOCHS - 1) {
       cout << "Epoch = " << e << endl;
       cout << "SP=" << outSP << endl;
       cout << "TP=" << outTP << endl;
     }
   }
 
   stopwatch.stop();
-  cout << "Total elapsed time = " << stopwatch.getElapsed() << " seconds" << endl;
+  cout << "Total elapsed time = " << stopwatch.getElapsed() << " seconds"
+       << endl;
 
   return 0;
 }

src/examples/prototest.cpp

@@ -20,8 +20,8 @@
  * ---------------------------------------------------------------------
  */
 
-#include <iostream>
 #include <fstream>
+#include <iostream>
 #include <stdio.h>
 #include <time.h>
 #include <vector>
@@ -38,8 +38,7 @@ using namespace std;
 using namespace nupic;
 using namespace nupic::algorithms::spatial_pooler;
 
-void testSP()
-{
+void testSP() {
   Random random(10);
 
   const UInt inputSize = 500;
@@ -53,30 +52,25 @@ void testSP()
   sp1.initialize(inputDims, colDims);
 
   UInt input[inputSize];
-  for (UInt i = 0; i < inputSize; ++i)
-  {
-    if (i < w)
-    {
+  for (UInt i = 0; i < inputSize; ++i) {
+    if (i < w) {
       input[i] = 1;
     } else {
       input[i] = 0;
     }
   }
   UInt output[numColumns];
 
-  for (UInt i = 0; i < 10000; ++i)
-  {
+  for (UInt i = 0; i < 10000; ++i) {
     random.shuffle(input, input + inputSize);
     sp1.compute(input, true, output);
   }
 
   // Now we reuse the last input to test after serialization
 
   vector<UInt> activeColumnsBefore;
-  for (UInt i = 0; i < numColumns; ++i)
-  {
-    if (output[i] == 1)
-    {
+  for (UInt i = 0; i < numColumns; ++i) {
+    if (output[i] == 1) {
       activeColumnsBefore.push_back(i);
     }
   }
@@ -94,8 +88,7 @@ void testSP()
 
   Real64 timeA = 0.0, timeC = 0.0;
 
-  for (UInt i = 0; i < 100; ++i)
-  {
+  for (UInt i = 0; i < 100; ++i) {
     // Create new input
     random.shuffle(input, input + inputSize);
 
@@ -128,8 +121,7 @@ void testSP()
       timeA = timeA + testTimer.getElapsed();
     }
 
-    for (UInt i = 0; i < numColumns; ++i)
-    {
+    for (UInt i = 0; i < numColumns; ++i) {
       NTA_CHECK(outputBaseline[i] == outputA[i]);
     }
 
@@ -158,11 +150,9 @@ void testSP()
       timeC = timeC + testTimer.getElapsed();
     }
 
-    for (UInt i = 0; i < numColumns; ++i)
-    {
+    for (UInt i = 0; i < numColumns; ++i) {
       NTA_CHECK(outputBaseline[i] == outputC[i]);
     }
-
   }
 
   remove("outA.proto");
@@ -173,15 +163,13 @@ void testSP()
   cout << "Manual: " << timeC << endl;
 }
 
-void testRandomIOStream(UInt n)
-{
+void testRandomIOStream(UInt n) {
   Random r1(7);
   Random r2;
 
   nupic::Timer testTimer;
   testTimer.start();
-  for (UInt i = 0; i < n; ++i)
-  {
+  for (UInt i = 0; i < n; ++i) {
     r1.getUInt32();
 
     // Serialize
@@ -209,15 +197,13 @@ void testRandomIOStream(UInt n)
   cout << "Cap'n Proto: " << testTimer.getElapsed() << endl;
 }
 
-void testRandomManual(UInt n)
-{
+void testRandomManual(UInt n) {
   Random r1(7);
   Random r2;
 
   nupic::Timer testTimer;
   testTimer.start();
-  for (UInt i = 0; i < n; ++i)
-  {
+  for (UInt i = 0; i < n; ++i) {
     r1.getUInt32();
 
     // Serialize
@@ -245,8 +231,7 @@ void testRandomManual(UInt n)
   cout << "Manual: " << testTimer.getElapsed() << endl;
 }
 
-int main(int argc, const char * argv[])
-{
+int main(int argc, const char *argv[]) {
   UInt n = 1000;
   cout << "Timing for Random serialization (smaller is better):" << endl;
   testRandomIOStream(n);