Hi! I cleaned up your code for you!

SConstruct

@@ -15,7 +15,7 @@ if sys.platform == 'darwin':
 elif sys.platform == 'linux2':
     libname = 'libarac.so'
     frameworksflags = ''
-    linkflags = '' 
+    linkflags = ''
 else:
     raise SystemExit("Cannot build on %s." % sys.platform)
 
@@ -27,15 +27,15 @@ NUMPYPATH = numpy.distutils.misc_util.get_numpy_include_dirs()
 # First compile and link the library.
 libenv = Environment(LIBS=['m', 'blas'], CPPPATH=CPPPATH, LIBPATH=LIBPATH,
                      SHLIBPREFIX="", CCFLAGS=CCFLAGS)
-library_globs = ['src/cpp/*.cpp', 
-                 'src/cpp/common/*.cpp', 
-                 'src/cpp/utilities/*.cpp', 
-                 'src/cpp/datasets/*.cpp', 
-                 'src/cpp/optimization/*.cpp', 
-                 'src/cpp/optimization/descent/*.cpp', 
-                 'src/cpp/structure/*.cpp',  
-                 'src/cpp/structure/connections/*.cpp',  
-                 'src/cpp/structure/modules/*.cpp',  
+library_globs = ['src/cpp/*.cpp',
+                 'src/cpp/common/*.cpp',
+                 'src/cpp/utilities/*.cpp',
+                 'src/cpp/datasets/*.cpp',
+                 'src/cpp/optimization/*.cpp',
+                 'src/cpp/optimization/descent/*.cpp',
+                 'src/cpp/structure/*.cpp',
+                 'src/cpp/structure/connections/*.cpp',
+                 'src/cpp/structure/modules/*.cpp',
                  'src/cpp/structure/networks/*.cpp',
                  'src/cpp/structure/networks/mdrnns/*.cpp']
 lib = libenv.SharedLibrary(libname, sum([Glob(i) for i in library_globs], []))
@@ -51,10 +51,10 @@ swigenv = Environment(SWIGFLAGS=['-python', '-c++', '-outdir', 'src/python/arac'
                       FRAMEWORKSFLAGS=frameworksflags,
                       LINKFLAGS=linkflags,
                       LIBPATH=LIBPATH,
-                      LDMODULEPREFIX='src/python/arac/_', 
+                      LDMODULEPREFIX='src/python/arac/_',
                       LDMODULESUFFIX = '.so',
                       )
-swig = swigenv.LoadableModule('cppbridge', 
+swig = swigenv.LoadableModule('cppbridge',
                              ['src/swig/cppbridge.i'])
 
 # Declare some dependencies.

examples/mdrnn/mnist.cpp

@@ -22,10 +22,10 @@ SupervisedDataset<double*, double*> make_dataset()
     SupervisedDataset<double*, double*> ds(insize, insize * outsize);
     double* sample_p = new double[insize];
     double* target_p = new double[outsize];
-    
+
     memset(sample_p, 0, sizeof(double) * insize);
     memset(target_p, 0, sizeof(double) * outsize * insize);
-    
+
     ds.append(sample_p, target_p);
     return ds;
 }
@@ -35,15 +35,15 @@ Network make_network()
 {
     int hidden = 5;
     Network net;
-    
+
     Mdrnn<MdlstmLayer>* inlayer_p = new Mdrnn<MdlstmLayer>(2, hidden);
-    
+
     inlayer_p->set_sequence_shape(0, 28);
     inlayer_p->set_sequence_shape(1, 28);
     inlayer_p->set_block_shape(0, 1);
     inlayer_p->set_block_shape(1, 1);
     inlayer_p->sort();
-    
+
     PartialSoftmaxLayer* outlayer_p = \
         new PartialSoftmaxLayer(insize * outsize, outsize);
 
@@ -55,16 +55,16 @@ Network make_network()
               << std::endl;
 
     WeightShareConnection* con_p = new WeightShareConnection(
-                                        inlayer_p, outlayer_p, 
+                                        inlayer_p, outlayer_p,
                                         hidden, outsize);
 
     net.add_module(inlayer_p, Network::InputModule);
     net.add_module(outlayer_p, Network::OutputModule);
 
     net.add_connection(con_p);
-    
+
     net.randomize();
-    
+
     return net;
 }
 

examples/xor/xor.cpp

@@ -19,7 +19,7 @@ SupervisedDataset<double*, double*> make_dataset()
     data_p[0] = 0;
     data_p[1] = 0;
     data_p[2] = 0;
-    
+
     data_p[3] = 0;
     data_p[4] = 1;
     data_p[5] = 1;
@@ -31,12 +31,12 @@ SupervisedDataset<double*, double*> make_dataset()
     data_p[9] = 1;
     data_p[10] = 1;
     data_p[11] = 0;
-    
+
     ds.append(data_p, data_p + 2);
     ds.append(data_p + 3, data_p + 5);
     ds.append(data_p + 6, data_p + 8);
     ds.append(data_p + 9, data_p + 11);
-    
+
     return ds;
 }
 
@@ -51,17 +51,17 @@ Network make_network()
     FullConnection* con1_p = new FullConnection(inlayer_p, hidden_p);
     FullConnection* con2_p = new FullConnection(hidden_p, outlayer_p);
     FullConnection* con3_p = new FullConnection(bias_p, hidden_p);
-    
+
     net.add_module(inlayer_p, Network::InputModule);
     net.add_module(hidden_p);
     net.add_module(bias_p);
     net.add_module(outlayer_p, Network::OutputModule);
     net.add_connection(con1_p);
     net.add_connection(con2_p);
     net.add_connection(con3_p);
-    
+
     net.randomize();
-    
+
     return net;
 }
 

src/cpp/common/buffer.h

@@ -16,35 +16,35 @@ namespace arac {
 namespace common {
 
 ///
-/// Buffer objects hold pointers to arrays which are serving as 
-/// inputs/outputs/errors/etc. to modules. 
+/// Buffer objects hold pointers to arrays which are serving as
+/// inputs/outputs/errors/etc. to modules.
 ///
 /// A buffer is organized in different rows which are held as a vector of double
-/// pointers. 
-/// A buffer may either "own" its arrays or not own them. In the first case, the 
-/// buffer frees the memory of the arrays on destruction. 
+/// pointers.
+/// A buffer may either "own" its arrays or not own them. In the first case, the
+/// buffer frees the memory of the arrays on destruction.
 ///
 
 class Buffer
 {
     public:
-        
+
         Buffer(size_t rowsize, bool owner=true);
         virtual ~Buffer();
-        
+
         ///
         /// Add the contents at the given pointer to the last buffer row. If an
         /// index is given, the content will be added to that buffer row.
         ///
         void add(double* addend_p, int index=-1);
-        
+
         ///
         /// Append an empty  row to the buffer's contents.
         ///
         void expand();
-        
+
         ///
-        /// Set all the contents to zero. 
+        /// Set all the contents to zero.
         ///
         void clear();
 
@@ -58,9 +58,9 @@ class Buffer
         /// does not own the memory.
         ///
         void free_memory();
-        
+
         ///
-        /// Add the given pointer as a row. Attention: This removes ownership 
+        /// Add the given pointer as a row. Attention: This removes ownership
         /// for all buffers.
         ///
         void append(double* row);
@@ -112,7 +112,7 @@ class Buffer
         bool _contmemory;
 
         // Index that says up to which row the buffer has been used recently. Is
-        // being reset by .clear() and clear_at(). Is updated by append(), 
+        // being reset by .clear() and clear_at(). Is updated by append(),
         // add and operator [].
         // The index is an exclusive upper bound.
         size_t _dirtyindex;
@@ -128,7 +128,7 @@ Buffer::rowsize()
 }
 
 
-inline 
+inline
 void
 Buffer::set_rowsize(size_t value)
 {
@@ -137,13 +137,13 @@ Buffer::set_rowsize(size_t value)
 
 
 inline
-size_t 
+size_t
 Buffer::size()
 {
     return _content.size();
 }
 
-    
+
 inline
 double*
 Buffer::operator[] (size_t index)

src/cpp/common/common.h

@@ -14,7 +14,7 @@
 namespace arac {
 namespace common {
 
-    
+
 typedef std::vector<double*> DoublePtrVec;
 
 

src/cpp/datasets/datasets.h

@@ -12,13 +12,13 @@
 
 namespace arac {
 namespace datasets {
-    
+
 typedef SupervisedDataset<arac::datasets::Sequence, arac::datasets::Sequence> SupervisedSequentialDataset;
 typedef SupervisedDataset<arac::datasets::Sequence, double*> SupervisedSemiSequentialDataset;
 typedef SupervisedDataset<double*, double*> SupervisedSimpleDataset;
 typedef UnsupervisedDataset<double*> UnsupervisedSimpleDataset;
 typedef UnsupervisedDataset<arac::datasets::Sequence> UnsupervisedSequenceDataset;
-    
+
 } } // Namespace
 
 

src/cpp/datasets/sequence.cpp

@@ -12,11 +12,11 @@ Sequence::Sequence(int length, int itemsize, double* data_p) :
     _length(length),
     _itemsize(itemsize),
     _data_p(data_p)
-{    
+{
 }
 
 
-Sequence::~Sequence()                  
+Sequence::~Sequence()
 {
-    
+
 }

src/cpp/datasets/sequence.h

@@ -12,27 +12,27 @@
 
 namespace arac {
 namespace datasets {
-
 
-class Sequence 
+
+class Sequence
 {
     public:
-        
+
         Sequence(int length, int itemsize, double* data_p);
         virtual ~Sequence();
-        
+
         int length() const;
         int itemsize() const;
         double* operator[](int index);
-        
+
     private:
         int _length;
         int _itemsize;
         double* _data_p;
 };
 
 
-inline 
+inline
 int
 Sequence::length() const
 {