From 30a1a86a6c41cdb725c91b61f797267be7947a31 Mon Sep 17 00:00:00 2001
From: Stefan Grosshauser <Stefan.Grosshauser@uni-bayreuth.de>
Date: Tue, 12 Jan 2016 10:49:17 +0100
Subject: [PATCH 01/10] add script to update version, and fix version in octave
 package description

---
 increment_version.sh | 6 ++++++
 package/DESCRIPTION  | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)
 create mode 100755 increment_version.sh

diff --git a/increment_version.sh b/increment_version.sh
new file mode 100755
index 0000000..6c05e51
--- /dev/null
+++ b/increment_version.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+echo -n "Enter new version: "
+read vers
+sed -i "s/VERSION=.*/VERSION=$vers/" makefile
+sed -i "s/Version:.*/Version: $vers/" package/DESCRIPTION
diff --git a/package/DESCRIPTION b/package/DESCRIPTION
index b27cc8b..f92ff13 100644
--- a/package/DESCRIPTION
+++ b/package/DESCRIPTION
@@ -1,5 +1,5 @@
 Name: hdf5oct
-Version: 0.2.0
+Version: 0.4.0
 Date: 2015-10-02
 Author: Tom Mullins, Anton Starikov, Thorsten Liebig, Stefan Großhauser
 Maintainer: Stefan Großhauser <Stefan.Grosshauser@uni-bayreuth.de>

From d55aef2fc513f4c5735ae21f6ea89bee77ca6add Mon Sep 17 00:00:00 2001
From: Stefan Grosshauser <Stefan.Grosshauser@uni-bayreuth.de>
Date: Mon, 15 Feb 2016 15:17:20 +0100
Subject: [PATCH 02/10] minor to README

---
 README | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/README b/README
index 4ab73f5..c872354 100644
--- a/README
+++ b/README
@@ -34,12 +34,16 @@ Note that only few of the HDF5 datatypes are supported by each of the
 functions hdf5oct at the moment, typically one or several of double,
 integer and string.
 
+# REQUIREMENTS #########################
+
+The wrapper h5c++ provided by the HDF5 library must be available.
+
 # INSTALLATION #########################
 
-To install, just use
+To compile this package, use
 
     make
-    
+
 This will produce a package file named "hdf5oct-*.tar.gz" .  Then
 you may either install the package with
 
@@ -50,7 +54,7 @@ the correct file name) with the command
 
     pkg install hdf5oct-0.2.0.tar.gz
 
-This will put the *.oct files somewhere where Octave will find them.
+Both will put the *.oct files somewhere where Octave will find them.
 You can try running
 
     make test
@@ -62,6 +66,10 @@ To uninstall the package you may want to use
 
    make uninstall
 
+or on the GNU Octave prompt
+
+   pkg uninstall hdf5oct
+
 # TODO #################################
 
 - write h5info, h5disp

From cd8ed9dd060670c5d3b1c83baa35895363008133 Mon Sep 17 00:00:00 2001
From: Stefan Grosshauser <Stefan.Grosshauser@uni-bayreuth.de>
Date: Mon, 15 Feb 2016 15:18:22 +0100
Subject: [PATCH 03/10] check for NULL and minors

---
 h5read.cc | 65 ++++++++++++++++++++++++++++++++++++++++++++++---------
 1 file changed, 55 insertions(+), 10 deletions(-)

diff --git a/h5read.cc b/h5read.cc
index f346fd5..ad94566 100644
--- a/h5read.cc
+++ b/h5read.cc
@@ -722,7 +722,7 @@ H5File::read_dset_complete (const char *dsetname)
     return octave_value_list ();
 
   mat_dims.resize (max (rank, 2));
-  // .resize(1) still leaves mat_dims with a length of 2 for some reason, so
+  // .resize(1) still leaves mat_dims with a length of 2, so
   // we need at least 2 filled
   mat_dims(0) = mat_dims(1) = 1;
   for (int i = 0; i < rank; i++)
@@ -782,8 +782,8 @@ H5File::read_dset_hyperslab (const char *dsetname,
       error ("block must be a vector of length %d, the dataset rank", rank);
       return octave_value_list ();
     }
-  
-  // .resize(1) still leaves mat_dims with a length of 2 for some reason, so
+
+  // .resize(1) still leaves mat_dims with a length of 2, so
   // we need at least 2 filled
   mat_dims.resize (max (rank, 2));
   mat_dims(0) = mat_dims(1) = 1;
@@ -815,24 +815,45 @@ H5File::read_dset_hyperslab (const char *dsetname,
     }
 
   hsize_t *hstart = alloc_hsize (start, ALLOC_HSIZE_DEFAULT, true);
+  if(hstart == NULL)
+    {
+      error ("error when allocating hstart array, for %s", dsetname);
+      return octave_value_list ();
+    }
   hsize_t *hstride = alloc_hsize (_stride, ALLOC_HSIZE_DEFAULT, true);
+  if(hstride == NULL)
+    {
+      error ("error when allocating hstride array, for %s", dsetname);
+      return octave_value_list ();
+    }
   hsize_t *hcount = alloc_hsize (_count, ALLOC_HSIZE_DEFAULT, true);
+  if(hcount == NULL)
+    {
+      error ("error when allocating hcount array, for %s", dsetname);
+      return octave_value_list ();
+    }
   hsize_t *hblock = alloc_hsize (_block, ALLOC_HSIZE_DEFAULT, true);
-  // TODO check these (and hmem) for NULLs
-
+  if(hblock == NULL)
+    {
+      error ("error when allocating hblock array, for %s", dsetname);
+      return octave_value_list ();
+    }
+  
   herr_t sel_result = H5Sselect_hyperslab (dspace_id, H5S_SELECT_SET, hstart,
                                            hstride, hcount, hblock);
-
   free (hstart);
   free (hstride);
   free (hcount);
   free (hblock);
-
   if (sel_result < 0)
-    return octave_value_list ();
-
+    {
+      error ("error when selecting the hyperslab of dataset %s to read from", dsetname);
+      return octave_value_list ();
+    }
+  
   octave_value retval = read_dset ();
   return retval;
+  
 }
 
 octave_value
@@ -1178,10 +1199,29 @@ H5File::write_dset_hyperslab (const char *dsetname,
         h5_dims[rank-i-1] = end;
     }
   hsize_t *hstart = alloc_hsize (start, ALLOC_HSIZE_DEFAULT, true);
+  if(hstart == NULL)
+    {
+      error ("error when allocating hstart array, for %s", dsetname);
+      return;
+    }
   hsize_t *hstride = alloc_hsize (_stride, ALLOC_HSIZE_DEFAULT, true);
+  if(hstride == NULL)
+    {
+      error ("error when allocating hstride array, for %s", dsetname);
+      return;
+    }
   hsize_t *hcount = alloc_hsize (count, ALLOC_HSIZE_DEFAULT, true);
+  if(hcount == NULL)
+    {
+      error ("error when allocating hcount array, for %s", dsetname);
+      return;
+    }
   hsize_t *hblock = alloc_hsize (_block, ALLOC_HSIZE_DEFAULT, true);
-  // TODO check these (and hmem) for NULLs
+  if(hblock == NULL)
+    {
+      error ("error when allocating hblock array, for %s", dsetname);
+      return;
+    }
   
   // make the current size of the dataset bigger
   H5Sclose (dspace_id);
@@ -1211,6 +1251,11 @@ H5File::write_dset_hyperslab (const char *dsetname,
     }
   
   hsize_t *hmem = alloc_hsize (data.dims (), ALLOC_HSIZE_DEFAULT, false);
+  if(hmem == NULL)
+    {
+      error ("error when allocating hmem array, for %s", dsetname);
+      return;
+    }
   hid_t memspace_id = H5Screate_simple (rank, hmem, hmem);
   if (memspace_id < 0)
     {

From 658ea719ee9ff6cb29207b69ab9ba92d62d31a80 Mon Sep 17 00:00:00 2001
From: Stefan Grosshauser <Stefan.Grosshauser@uni-bayreuth.de>
Date: Mon, 15 Feb 2016 15:20:08 +0100
Subject: [PATCH 04/10] fix a memory issue when reading hyperslabs

---
 h5read.cc | 42 ++++++++++++++++++------------------------
 1 file changed, 18 insertions(+), 24 deletions(-)

diff --git a/h5read.cc b/h5read.cc
index ad94566..111553c 100644
--- a/h5read.cc
+++ b/h5read.cc
@@ -862,12 +862,23 @@ H5File::read_dset ()
   bool is_cmplx = false;
   type_id = H5Dget_type (dset_id);
   hid_t complex_type_id = hdf5_make_complex_type (H5T_NATIVE_DOUBLE);
+  
+  hsize_t *hmem = alloc_hsize (mat_dims, ALLOC_HSIZE_DEFAULT, false);
+  hid_t memspace_id = H5Screate_simple (rank, hmem, hmem);
+  free (hmem);
+  if (memspace_id < 0)
+    {
+      return octave_value_list ();
+    }
 
-  // hsize_t *hmem = alloc_hsize (mat_dims, ALLOC_HSIZE_DEFAULT, false);
-  // hid_t memspace_id = H5Screate_simple (rank, hmem, hmem);
-  // free (hmem);
+  if (H5Sselect_valid (dspace_id) <= 0)
+    {
+      error ("selected dataspace is not valid");
+      return octave_value_list ();
+    }
 
   octave_value retval;
+  herr_t read_result;
   if (H5Tget_class (type_id) == H5T_COMPOUND &&
       H5Tget_class (complex_type_id) == H5T_COMPOUND &&
       hdf5_types_compatible (type_id, complex_type_id) > 0)
@@ -875,27 +886,10 @@ H5File::read_dset ()
       ComplexNDArray ret (mat_dims);
       // macro begin
 #define HDF5_READ_DATA(type)                                            \
-      if (H5Sselect_valid (dspace_id) <= 0)                             \
-        {                                                               \
-          error ("selected dataspace is not valid");                    \
-          return octave_value_list ();                                  \
-        }                                                               \
-                                                                        \
-      int mdc_nelem = -1;                                               \
-      size_t rdcc_nelem = -1;                                           \
-      size_t rdcc_nbytes = -1;                                          \
-      double rdcc_w0 = -1;                                              \
-      if (H5Pget_cache (H5Fget_access_plist (file), &mdc_nelem,         \
-                        &rdcc_nelem, &rdcc_nbytes, &rdcc_w0 ) < 0)      \
-        {                                                               \
-          error ("could not determine raw data chunk cache parameters."); \
-          return octave_value_list ();                                  \
-        }                                                               \
-      /*cout << "cache params:" << rdcc_nelem << "," << rdcc_nbytes << endl;*/ \
-      herr_t read_result = H5Dread (dset_id,                            \
-                                    type,                               \
-                                    H5S_ALL, dspace_id,                 \
-                                    H5P_DEFAULT, ret.fortran_vec ());   \
+      read_result = H5Dread (dset_id,                                   \
+                             type,                                      \
+                             memspace_id, dspace_id,                    \
+                             H5P_DEFAULT, ret.fortran_vec ());          \
       if (read_result < 0)                                              \
         {                                                               \
           error ("error when reading dataset");                         \

From ecfa73b023b4841233c04f506d1f700ada7b78e3 Mon Sep 17 00:00:00 2001
From: Stefan Grosshauser <Stefan.Grosshauser@uni-bayreuth.de>
Date: Mon, 22 Feb 2016 10:06:05 +0100
Subject: [PATCH 05/10] comment on h5delete and diskspace

---
 h5read.cc | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/h5read.cc b/h5read.cc
index 111553c..982944f 100644
--- a/h5read.cc
+++ b/h5read.cc
@@ -529,7 +529,10 @@ DEFUN_DLD (h5delete, args, nargout,
 @deftypefnx {Loadable Function} h5delete (@var{filename}, @var{objname}, @var{attname})\n\
 \n\
 In the first form, delete a dataset or group with name @var{objname}\n\
-in the HDF5 file specified by @var{filename}.\n\
+in the HDF5 file specified by @var{filename}. Note that hdf5 is like a\n\
+filesystem: the library does not free the used space when a dataset is\n\
+deleted. One can use the tool h5repack afterwards to actually reduce the \n\
+filesize.\n                                                             \
 \n\
 In the second form, delete an attribute with name @var{attname} associated\n\
 to a dataset or group with name @var{objname}\n\

From 867b58a46c547c84c29baef73421054dc2284c37 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Christian=20H=C3=A4ggstr=C3=B6m?= <kalvdans@gmail.com>
Date: Fri, 4 Nov 2016 16:49:18 +0100
Subject: [PATCH 06/10] Open files in read-only mode when they should only be
 read from

---
 h5read.cc | 21 ++++++++++++---------
 h5read.h  |  3 ++-
 2 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/h5read.cc b/h5read.cc
index f346fd5..00b634e 100644
--- a/h5read.cc
+++ b/h5read.cc
@@ -170,7 +170,7 @@ the appropriate size for the given HDF5 type.\n\
     return octave_value_list ();
 
   //open the hdf5 file
-  H5File file (filename.c_str (), false);
+  H5File file (filename.c_str (), false, false);
   if (error_state)
     return octave_value_list ();
 
@@ -244,7 +244,7 @@ is to read.\n\
     return octave_value_list ();
   
   //open the hdf5 file
-  H5File file (filename.c_str (), false);
+  H5File file (filename.c_str (), false, false);
   if (error_state)
     return octave_value_list ();
         
@@ -318,7 +318,7 @@ the appropriate size for the given Octave type.\n\
   if (nargin == 3)
     {
       //open the hdf5 file, create it if it does not exist
-      H5File file (filename.c_str (), true);
+      H5File file (filename.c_str (), true, true);
       if (error_state)
         return octave_value_list ();
       file.write_dset (location.c_str (),
@@ -327,7 +327,7 @@ the appropriate size for the given Octave type.\n\
   else  
     {
       //open the hdf5 file, complain if it does not exist
-      H5File file (filename.c_str (), false);
+      H5File file (filename.c_str (), false, true);
       if (error_state)
         return octave_value_list ();
 
@@ -397,7 +397,7 @@ the object named @var{objectname} in the HDF5 file specified by @var{filename}.\
     return octave_value_list ();
     
   //open the hdf5 file
-  H5File file (filename.c_str (), false);
+  H5File file (filename.c_str (), false, true);
   if (error_state)
     return octave_value_list ();
 
@@ -513,7 +513,7 @@ setting is not @sc{matlab} compatible.\n\
   
   
   //open the hdf5 file
-  H5File file (filename.c_str (), true);
+  H5File file (filename.c_str (), true, true);
   if (error_state)
     return octave_value_list ();
   file.create_dset (location.c_str (), size, datatype.c_str (), chunksize);
@@ -568,7 +568,7 @@ Note that this function is not @sc{matlab} compliant.\n\
     return octave_value_list ();
 
   //open the hdf5 file
-  H5File file (filename.c_str (), true);
+  H5File file (filename.c_str (), true, true);
   if (error_state)
     return octave_value_list ();
   if (nargin == 2)
@@ -586,7 +586,8 @@ Note that this function is not @sc{matlab} compliant.\n\
 
 #if defined (HAVE_HDF5) && defined (HAVE_HDF5_18)
 
-H5File::H5File (const char *filename, const bool create_if_nonexisting)
+H5File::H5File (const char *filename, const bool create_if_nonexisting,
+		const bool write_access)
 {
   H5E_auto_t oef;
   void *olderr;
@@ -606,7 +607,9 @@ H5File::H5File (const char *filename, const bool create_if_nonexisting)
         error ("The file is not in the HDF5 format, %s: %s", filename, strerror (errno));
       else
         {
-          file = H5Fopen (filename, H5F_ACC_RDWR, H5P_DEFAULT);
+          file = H5Fopen (filename,
+			  write_access ? H5F_ACC_RDWR : H5F_ACC_RDONLY,
+			  H5P_DEFAULT);
           if (file < 0)
             error ("Opening the file failed, %s: %s", filename, strerror (errno));
         }
diff --git a/h5read.h b/h5read.h
index ba5361d..813ba4d 100644
--- a/h5read.h
+++ b/h5read.h
@@ -39,7 +39,8 @@ class H5File
   
  public:
   
-  H5File (const char *filename, const bool create_if_nonexisting);
+  H5File (const char *filename, const bool create_if_nonexisting,
+	  const bool write_access);
   
   ~H5File ();
   

From a6119481d61b924c93b1d7c61ba2ead3ab3a6ab1 Mon Sep 17 00:00:00 2001
From: Greg Thomsen <gthomsen@gmail.com>
Date: Mon, 30 Jan 2017 15:42:35 -0600
Subject: [PATCH 07/10] create intermediate groups during dataset creation. 
 supports creation of non-floating point datasets within a group hierarchy.

---
 h5read.cc     | 11 ++++++++---
 test/h5test.m |  3 +++
 2 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/h5read.cc b/h5read.cc
index f346fd5..f4fa82d 100644
--- a/h5read.cc
+++ b/h5read.cc
@@ -414,7 +414,8 @@ DEFUN_DLD (h5create, args, nargout,
 @deftypefn {Loadable Function} h5create (@var{filename}, @var{dsetname}, @var{size}, @var{key}, @var{val},...)\n\
 \n\
 Create a dataset with name @var{dsetname} and size @var{size} \n\
-in the HDF5 file specified by @var{filename}.\n\
+in the HDF5 file specified by @var{filename}.  Intermediate groups\n\
+are created as necessary.\n\
 \n\
 The vector @var{size} may contain one or several Inf (or \n\
 equivalently: zero) values.\n\
@@ -1555,15 +1556,19 @@ H5File::create_dset (const char *location, const Matrix& size,
         }
       free (dims_chunk);
     }
-  
+
+  // create non-existent intermediate groups.
+  hid_t lcpl_list = H5Pcreate (H5P_LINK_CREATE);
+  H5Pset_create_intermediate_group (lcpl_list, 1);
   dset_id = H5Dcreate (file, location, type_id, dspace_id,
-                       H5P_DEFAULT, crp_list, H5P_DEFAULT);
+                       lcpl_list, crp_list, H5P_DEFAULT);
   if (dset_id < 0)
     {
       error ("Could not create dataset %s", location);
       return;
     }
   H5Pclose (crp_list);
+  H5Pclose (lcpl_list);
 
 }
 
diff --git a/test/h5test.m b/test/h5test.m
index 5338634..b614546 100644
--- a/test/h5test.m
+++ b/test/h5test.m
@@ -110,6 +110,9 @@ function read_write_chunk_at(filename, dsetname, chunk, start)
 %%%%%%%%
 h5create("test.h5","created_dset_inf23",[ 2 3 4],'Datatype','int8', 'ChunkSize', [2 3 2])
 
+%%%%%%%%
+h5create("test.h5","/nonexistent/groups/created_dset_single",[1],'Datatype','single')
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 disp("Test h5write and h5read...")
 

From 620f871c9296e3f82bbbcea1bb0b65c5a9fb205b Mon Sep 17 00:00:00 2001
From: Stefan Grosshauser <Stefan.Grosshauser@uni-bayreuth.de>
Date: Mon, 15 May 2017 18:08:17 +0200
Subject: [PATCH 08/10] replace deprecated function gripe_disabled_feature

---
 h5read.cc | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/h5read.cc b/h5read.cc
index 173ea50..396fba8 100644
--- a/h5read.cc
+++ b/h5read.cc
@@ -148,7 +148,7 @@ the appropriate size for the given HDF5 type.\n\
 @end deftypefn")
 {
 #if ! (defined (HAVE_HDF5) && defined (HAVE_HDF5_18))
-  gripe_disabled_feature ("h5read", "HDF5 IO");
+  err_disabled_feature ("h5read", "HDF5 IO");
   return octave_value_list ();
 #else
   int nargin = args.length ();
@@ -222,7 +222,7 @@ is to read.\n\
 {
   octave_value retval;
 #if ! (defined (HAVE_HDF5) && defined (HAVE_HDF5_18))
-  gripe_disabled_feature ("h5readatt", "HDF5 IO");
+  err_disabled_feature ("h5readatt", "HDF5 IO");
   return octave_value_list ();
 #else
   int nargin = args.length ();
@@ -293,7 +293,7 @@ the appropriate size for the given Octave type.\n\
 @end deftypefn")
 {
 #if ! (defined (HAVE_HDF5) && defined (HAVE_HDF5_18))
-  gripe_disabled_feature ("h5write", "HDF5 IO");
+  err_disabled_feature ("h5write", "HDF5 IO");
   return octave_value_list ();
 #else
   int nargin = args.length ();
@@ -373,7 +373,7 @@ the object named @var{objectname} in the HDF5 file specified by @var{filename}.\
 @end deftypefn")
 {
 #if ! (defined (HAVE_HDF5) && defined (HAVE_HDF5_18))
-  gripe_disabled_feature ("h5writeatt", "HDF5 IO");
+  err_disabled_feature ("h5writeatt", "HDF5 IO");
   return octave_value_list ();
 #else
   int nargin = args.length ();
@@ -443,7 +443,7 @@ setting is not @sc{matlab} compatible.\n\
 @end deftypefn")
 {
 #if ! (defined (HAVE_HDF5) && defined (HAVE_HDF5_18))
-  gripe_disabled_feature("h5create", "HDF5 IO");
+  err_disabled_feature("h5create", "HDF5 IO");
   return octave_value_list ();
 #else
   int nargin = args.length ();
@@ -545,7 +545,7 @@ Note that this function is not @sc{matlab} compliant.\n\
 @end deftypefn")
 {
 #if ! (defined (HAVE_HDF5) && defined (HAVE_HDF5_18))
-  gripe_disabled_feature("h5delete", "HDF5 IO");
+  err_disabled_feature("h5delete", "HDF5 IO");
   return octave_value_list ();
 #else
   int nargin = args.length ();

From 62098f7e82eab88059f7d104895f7bfb84d37850 Mon Sep 17 00:00:00 2001
From: Stefan Grosshauser <Stefan.Grosshauser@uni-bayreuth.de>
Date: Mon, 15 May 2017 18:10:23 +0200
Subject: [PATCH 09/10] fix makefile, to compile with recent GNU Octave sources
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

The preprocessor macros à la HAVE_HDF5 which used to be inherited from config.log
via oct.h, are not available anymore. This is a dirty hack, to find out if
octave was compiled with HDF5 or not.
---
 makefile | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/makefile b/makefile
index 7d3cd8b..0e9584c 100644
--- a/makefile
+++ b/makefile
@@ -3,7 +3,11 @@ src= h5read.cc
 headers=h5read.h
 octs=$(src:.cc=.oct)
 objs=$(src:.cc=.o)
-MKOCTFILE=CXX=$(CXX) mkoctfile -g
+
+H5FLAGS=$(shell octave --eval 'exit(__octave_config_info__ ("build_features").HDF5 != 1)' &> /dev/null && echo "-DHAVE_HDF5") \
+$(shell octave --eval 'exit(__octave_config_info__ ("build_features").HDF5_18 != 1)' &> /dev/null && echo "-DHAVE_HDF5_18")
+
+MKOCTFILE=CXX="$(CXX)" CXXFLAGS="-ansi" mkoctfile -v -std=c++11 $(H5FLAGS)
 
 VERSION=0.4.0
 PACKAGEFILE=hdf5oct-$(VERSION).tar.gz
@@ -13,6 +17,7 @@ PACKAGEFILE=hdf5oct-$(VERSION).tar.gz
 all: $(octs) package
 
 %.oct: $(objs)
+	echo $(MKOCTFILE) -o $@ $(objs)
 	$(MKOCTFILE) -o $@ $(objs)
 
 %.o: %.cc $(headers)

From 346dbfbdbca00642f52e7b29da91847a009a6f13 Mon Sep 17 00:00:00 2001
From: Stefan Grosshauser <Stefan.Grosshauser@uni-bayreuth.de>
Date: Mon, 8 Jan 2018 20:16:23 +0100
Subject: [PATCH 10/10] fixes to compile with GNU octave version 4.3.0

---
 h5read.cc           | 178 ++++++++++++++++++++++----------------------
 makefile            |   2 +-
 package/DESCRIPTION |   2 +-
 3 files changed, 91 insertions(+), 91 deletions(-)

diff --git a/h5read.cc b/h5read.cc
index 396fba8..26304a2 100644
--- a/h5read.cc
+++ b/h5read.cc
@@ -58,7 +58,7 @@ using namespace std;
 bool
 any_int_leq_zero (const Matrix& mat)
 {
-  for (int i = 0; i < mat.length (); i++)
+  for (int i = 0; i < mat.numel (); i++)
     {
       if (mat(i) < 0.5)
         return true;
@@ -76,7 +76,7 @@ check_vec (const octave_value& val, Matrix& mat/*out*/,
   if (error_state)
     return 0;
 
-  if (! mat.is_vector ())
+  if (! mat.isvector ())
     {
       error ("%s must be a vector", name);
       return 0;
@@ -85,7 +85,7 @@ check_vec (const octave_value& val, Matrix& mat/*out*/,
   double mind, maxd;
   if (allow_zeros)
     {
-      for (int i = 0; i < mat.nelem (); i++)
+      for (int i = 0; i < mat.numel (); i++)
         {
           if (mat(i) == octave_Inf)
             mat(i) = 0;
@@ -149,30 +149,30 @@ the appropriate size for the given HDF5 type.\n\
 {
 #if ! (defined (HAVE_HDF5) && defined (HAVE_HDF5_18))
   err_disabled_feature ("h5read", "HDF5 IO");
-  return octave_value_list ();
+  return octave_value ();
 #else
   int nargin = args.length ();
 
   if (nargin < 2 || nargin == 3 || nargin > 6 || nargout > 1)
     {
       print_usage ();
-      return octave_value_list ();
+      return octave_value ();
     }
   if (! (args(0).is_string () && args (1).is_string ()))
     {
       print_usage ();
-      return octave_value_list ();
+      return octave_value ();
     }
 
   string filename = args(0).string_value ();
   string dsetname = args(1).string_value ();
   if (error_state)
-    return octave_value_list ();
+    return octave_value ();
 
   //open the hdf5 file
   H5File file (filename.c_str (), false, false);
   if (error_state)
-    return octave_value_list ();
+    return octave_value ();
 
   if (nargin < 4)
     {
@@ -200,7 +200,7 @@ the appropriate size for the given HDF5 type.\n\
         err = err || ! check_vec (args(5), block, "BLOCK", false);
 
       if (err)
-        return octave_value_list ();
+        return octave_value ();
 
       return file.read_dset_hyperslab (dsetname.c_str (),
                                        start, count, stride, block, nargin-2);
@@ -223,7 +223,7 @@ is to read.\n\
   octave_value retval;
 #if ! (defined (HAVE_HDF5) && defined (HAVE_HDF5_18))
   err_disabled_feature ("h5readatt", "HDF5 IO");
-  return octave_value_list ();
+  return octave_value ();
 #else
   int nargin = args.length ();
   if (nargin != 3)
@@ -241,12 +241,12 @@ is to read.\n\
   string objname = args(1).string_value ();
   string attname = args(2).string_value ();
   if (error_state)
-    return octave_value_list ();
+    return octave_value ();
   
   //open the hdf5 file
   H5File file (filename.c_str (), false, false);
   if (error_state)
-    return octave_value_list ();
+    return octave_value ();
         
   retval = file.read_att (objname.c_str (), attname.c_str ());
   return retval;
@@ -294,25 +294,25 @@ the appropriate size for the given Octave type.\n\
 {
 #if ! (defined (HAVE_HDF5) && defined (HAVE_HDF5_18))
   err_disabled_feature ("h5write", "HDF5 IO");
-  return octave_value_list ();
+  return octave_value ();
 #else
   int nargin = args.length ();
 
   if (! (nargin == 3 || nargin == 5 || nargin  == 6 || nargin == 7) || nargout != 0)
     {
       print_usage ();
-      return octave_value_list ();
+      return octave_value ();
     }
   if (! (args(0).is_string () && args(1).is_string ()))
     {
       print_usage ();
-      return octave_value_list ();
+      return octave_value ();
     }
   string filename = args(0).string_value ();
   string location = args(1).string_value ();
   
   if (error_state)
-    return octave_value_list ();
+    return octave_value ();
     
 
   if (nargin == 3)
@@ -320,7 +320,7 @@ the appropriate size for the given Octave type.\n\
       //open the hdf5 file, create it if it does not exist
       H5File file (filename.c_str (), true, true);
       if (error_state)
-        return octave_value_list ();
+        return octave_value ();
       file.write_dset (location.c_str (),
                        args(2));
     }
@@ -329,7 +329,7 @@ the appropriate size for the given Octave type.\n\
       //open the hdf5 file, complain if it does not exist
       H5File file (filename.c_str (), false, true);
       if (error_state)
-        return octave_value_list ();
+        return octave_value ();
 
       Matrix start, count, stride, block;
       int err = 0;
@@ -350,14 +350,14 @@ the appropriate size for the given Octave type.\n\
         err = err || ! check_vec (args(6), block, "BLOCK", false);
 
       if (err)
-        return octave_value_list ();
+        return octave_value ();
 
       file.write_dset_hyperslab (location.c_str (),
                                  args(2),
                                  start, count, stride, block, nargin-3);
     }
 
-  return octave_value_list ();
+  return octave_value ();
 #endif
 }
 
@@ -374,19 +374,19 @@ the object named @var{objectname} in the HDF5 file specified by @var{filename}.\
 {
 #if ! (defined (HAVE_HDF5) && defined (HAVE_HDF5_18))
   err_disabled_feature ("h5writeatt", "HDF5 IO");
-  return octave_value_list ();
+  return octave_value ();
 #else
   int nargin = args.length ();
 
   if (nargin != 4 || nargout != 0)
     {
       print_usage ();
-      return octave_value_list ();
+      return octave_value ();
     }
   if (! (args(0).is_string () && args(1).is_string () && args(2).is_string ()))
     {
       print_usage ();
-      return octave_value_list ();
+      return octave_value ();
     }
 
   string filename = args(0).string_value ();
@@ -394,17 +394,17 @@ the object named @var{objectname} in the HDF5 file specified by @var{filename}.\
   string attname = args(2).string_value ();
   
   if (error_state)
-    return octave_value_list ();
+    return octave_value ();
     
   //open the hdf5 file
   H5File file (filename.c_str (), false, true);
   if (error_state)
-    return octave_value_list ();
+    return octave_value ();
 
   file.write_att (location.c_str (), attname.c_str (),
                   args(3));
 
-  return octave_value_list ();
+  return octave_value ();
 #endif
 }
 
@@ -444,34 +444,34 @@ setting is not @sc{matlab} compatible.\n\
 {
 #if ! (defined (HAVE_HDF5) && defined (HAVE_HDF5_18))
   err_disabled_feature("h5create", "HDF5 IO");
-  return octave_value_list ();
+  return octave_value ();
 #else
   int nargin = args.length ();
 
   if (! (nargin ==  3 || nargin == 5 || nargin == 7) || nargout != 0)
     {
       print_usage ();
-      return octave_value_list ();
+      return octave_value ();
     }
   if (! (args(0).is_string () && args(1).is_string ()))
     {
       print_usage ();
-      return octave_value_list ();
+      return octave_value ();
     }
   if ((nargin == 5 && ! args(3).is_string ())
       || (nargin == 7 && ! args(5).is_string ()))
     {
       print_usage ();
-      return octave_value_list ();
+      return octave_value ();
     }
   string filename = args(0).string_value ();
   string location = args(1).string_value ();
   if (error_state)
-    return octave_value_list ();
+    return octave_value ();
   
   Matrix size;
   if (! check_vec (args(2), size, "SIZE", true))
-    return octave_value_list ();
+    return octave_value ();
 
 
   // loop over the key-value pairs and see what is given
@@ -485,7 +485,7 @@ setting is not @sc{matlab} compatible.\n\
           if (error_state)
             {
               error ("Datatype argument must be a string");
-              return octave_value_list ();
+              return octave_value ();
             }
         }
       else if (args(i).string_value () == "ChunkSize")
@@ -495,19 +495,19 @@ setting is not @sc{matlab} compatible.\n\
 	      if(args(i+1).string_value () != "auto")
 		{
 		  error ("ChunkSize argument must be either a vector, or the string 'auto'.");
-		  return octave_value_list ();
+		  return octave_value ();
 		}
 	      chunksize = args(2).matrix_value ();
 	      chunksize(0) = 0;
 
 	    }
           else if (! check_vec (args(i+1), chunksize, "ChunkSize", false))
-            return octave_value_list ();
+            return octave_value ();
         }
       else
         {
           error ("unknown parameter name %s", args(i).string_value ().c_str ());
-          return octave_value_list ();
+          return octave_value ();
         }
     }
 
@@ -516,10 +516,10 @@ setting is not @sc{matlab} compatible.\n\
   //open the hdf5 file
   H5File file (filename.c_str (), true, true);
   if (error_state)
-    return octave_value_list ();
+    return octave_value ();
   file.create_dset (location.c_str (), size, datatype.c_str (), chunksize);
   
-  return octave_value_list ();
+  return octave_value ();
 #endif
 }
 
@@ -546,35 +546,35 @@ Note that this function is not @sc{matlab} compliant.\n\
 {
 #if ! (defined (HAVE_HDF5) && defined (HAVE_HDF5_18))
   err_disabled_feature("h5delete", "HDF5 IO");
-  return octave_value_list ();
+  return octave_value ();
 #else
   int nargin = args.length ();
 
   if (! (nargin ==  2 || nargin == 3) || nargout != 0)
     {
       print_usage ();
-      return octave_value_list ();
+      return octave_value ();
     }
   if (! (args(0).is_string () && args(1).is_string ()))
     {
       print_usage ();
-      return octave_value_list ();
+      return octave_value ();
     }
   if (nargin == 3 && ! args(2).is_string ())
     {
       print_usage ();
-      return octave_value_list ();
+      return octave_value ();
     }
   
   string filename = args(0).string_value ();
   string location = args(1).string_value ();
   if (error_state)
-    return octave_value_list ();
+    return octave_value ();
 
   //open the hdf5 file
   H5File file (filename.c_str (), true, true);
   if (error_state)
-    return octave_value_list ();
+    return octave_value ();
   if (nargin == 2)
     file.delete_link (location.c_str ());
   else if (nargin == 3)
@@ -584,7 +584,7 @@ Note that this function is not @sc{matlab} compliant.\n\
 	file.delete_att (location.c_str (), attname.c_str ());
     }
   
-  return octave_value_list ();
+  return octave_value ();
 #endif
 }
 
@@ -599,7 +599,7 @@ H5File::H5File (const char *filename, const bool create_if_nonexisting,
   //suppress hdf5 error output
   H5Eset_auto (H5E_DEFAULT,0,0);
 
-  file_stat fs (filename);
+  octave::sys::file_stat fs (filename);
   if (! fs.exists () && create_if_nonexisting)
     file = H5Fcreate (filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
   else if (! fs.exists () && ! create_if_nonexisting)
@@ -666,7 +666,7 @@ template <typename T>
 hsize_t*
 H5File::alloc_hsize (const T& dim, const int mode, const bool reverse)
 {
-  int rank = dim.length ();
+  int rank = dim.numel ();
   hsize_t *hsize = (hsize_t*)malloc (rank * sizeof (hsize_t));
   for (int i = 0; i < rank; i++)
     {
@@ -726,7 +726,7 @@ octave_value
 H5File::read_dset_complete (const char *dsetname)
 {
   if (open_dset (dsetname) < 0)
-    return octave_value_list ();
+    return octave_value ();
 
   mat_dims.resize (max (rank, 2));
   // .resize(1) still leaves mat_dims with a length of 2, so
@@ -739,7 +739,7 @@ H5File::read_dset_complete (const char *dsetname)
   if (H5Sselect_all (dspace_id) < 0)
     {
       error ("Error selecting complete dataset %s", dsetname);
-      return octave_value_list ();
+      return octave_value ();
     }
 
   octave_value retval = read_dset ();
@@ -753,41 +753,41 @@ H5File::read_dset_hyperslab (const char *dsetname,
                              int nargin)
 {
   if (open_dset (dsetname) < 0)
-    return octave_value_list ();
+    return octave_value ();
 
-  if (rank == 0 && ! (start.is_empty () && count.is_empty ()
-                      && stride.is_empty () && block.is_empty ()))
+  if (rank == 0 && ! (start.isempty () && count.isempty ()
+                      && stride.isempty () && block.isempty ()))
     {
       error ("Cannot specify hyperslab for scalar datasets (rank 0)");
-      return octave_value_list ();
+      return octave_value ();
     }
 
-  if (start.nelem () != rank)
+  if (start.numel () != rank)
     {
       error ("start must be a vector of length %d, the dataset rank", rank);
-      return octave_value_list ();
+      return octave_value ();
     }
-  if (count.nelem () != rank)
+  if (count.numel () != rank)
     {
       error ("count must be a vector of length %d, the dataset rank", rank);
-      return octave_value_list ();
+      return octave_value ();
     }
   
   Matrix _stride = stride;
   if (nargin < 3)
     _stride = Matrix (dim_vector(1, rank), 1);
-  if (_stride.nelem () != rank)
+  if (_stride.numel () != rank)
     {
       error ("stride must be a vector of length %d, the dataset rank", rank);
-      return octave_value_list ();
+      return octave_value ();
     }
   Matrix _block = block;
   if (nargin < 4)
     _block = Matrix (dim_vector(1, rank), 1);
-  if (_block.nelem () != rank)
+  if (_block.numel () != rank)
     {
       error ("block must be a vector of length %d, the dataset rank", rank);
-      return octave_value_list ();
+      return octave_value ();
     }
 
   // .resize(1) still leaves mat_dims with a length of 2, so
@@ -802,7 +802,7 @@ H5File::read_dset_hyperslab (const char *dsetname,
         {
           error ("In dimension %d, requested stride %d smaller than block size %d",
                  i+1, (int)_stride(i), (int)_block(i));
-          return octave_value_list ();
+          return octave_value ();
         }
       if (_count(i) == 0)
         {
@@ -817,7 +817,7 @@ H5File::read_dset_hyperslab (const char *dsetname,
           error ("In dimension %d, dataset only has %d elements, but at least %d"
                  " are required for requested hyperslab", i+1, (int)h5_dims[rank-i-1],
                  end);
-          return octave_value_list ();
+          return octave_value ();
         }
     }
 
@@ -825,25 +825,25 @@ H5File::read_dset_hyperslab (const char *dsetname,
   if(hstart == NULL)
     {
       error ("error when allocating hstart array, for %s", dsetname);
-      return octave_value_list ();
+      return octave_value ();
     }
   hsize_t *hstride = alloc_hsize (_stride, ALLOC_HSIZE_DEFAULT, true);
   if(hstride == NULL)
     {
       error ("error when allocating hstride array, for %s", dsetname);
-      return octave_value_list ();
+      return octave_value ();
     }
   hsize_t *hcount = alloc_hsize (_count, ALLOC_HSIZE_DEFAULT, true);
   if(hcount == NULL)
     {
       error ("error when allocating hcount array, for %s", dsetname);
-      return octave_value_list ();
+      return octave_value ();
     }
   hsize_t *hblock = alloc_hsize (_block, ALLOC_HSIZE_DEFAULT, true);
   if(hblock == NULL)
     {
       error ("error when allocating hblock array, for %s", dsetname);
-      return octave_value_list ();
+      return octave_value ();
     }
   
   herr_t sel_result = H5Sselect_hyperslab (dspace_id, H5S_SELECT_SET, hstart,
@@ -855,7 +855,7 @@ H5File::read_dset_hyperslab (const char *dsetname,
   if (sel_result < 0)
     {
       error ("error when selecting the hyperslab of dataset %s to read from", dsetname);
-      return octave_value_list ();
+      return octave_value ();
     }
   
   octave_value retval = read_dset ();
@@ -875,13 +875,13 @@ H5File::read_dset ()
   free (hmem);
   if (memspace_id < 0)
     {
-      return octave_value_list ();
+      return octave_value ();
     }
 
   if (H5Sselect_valid (dspace_id) <= 0)
     {
       error ("selected dataspace is not valid");
-      return octave_value_list ();
+      return octave_value ();
     }
 
   octave_value retval;
@@ -900,7 +900,7 @@ H5File::read_dset ()
       if (read_result < 0)                                              \
         {                                                               \
           error ("error when reading dataset");                         \
-          return octave_value_list ();                                  \
+          return octave_value ();                                  \
         }                                                               \
       retval = octave_value (ret)
       // macro end
@@ -989,7 +989,7 @@ void
 H5File::write_dset (const char *dsetname,
                     const octave_value ov_data)
 {
-  int rank = ov_data.dims ().length ();
+  int rank = ov_data.dims ().numel ();
 
   hsize_t *dims = alloc_hsize (ov_data.dims(), ALLOC_HSIZE_DEFAULT, true);
   dspace_id = H5Screate_simple (rank, dims, NULL);
@@ -1019,7 +1019,7 @@ H5File::write_dset (const char *dsetname,
 
   herr_t status;
   // find the right type
-  if (ov_data.is_complex_type ())
+  if (ov_data.iscomplex ())
     {
       //check if the data set already exists. if it does, open it,
       //otherwise, create it.  Furthermore check if the datatype is
@@ -1045,7 +1045,7 @@ H5File::write_dset (const char *dsetname,
       ComplexNDArray data = ov_data.complex_array_value ();
       OPEN_AND_WRITE;
     }
-  else if (ov_data.is_integer_type ())
+  else if (ov_data.isinteger ())
     {
       if (ov_data.is_uint64_type ())
         {
@@ -1137,19 +1137,19 @@ H5File::write_dset_hyperslab (const char *dsetname,
     return;
 
   // check if the given hyperslab settings are reasonable
-  if (rank == 0 && ! (start.is_empty () && count.is_empty ()
-                      && stride.is_empty () && block.is_empty ()))
+  if (rank == 0 && ! (start.isempty () && count.isempty ()
+                      && stride.isempty () && block.isempty ()))
     {
       error ("Cannot specify hyperslab for scalar datasets (rank 0)");
       return;
     }
 
-  if (start.nelem () != rank)
+  if (start.numel () != rank)
     {
       error ("start must be a vector of length %d, the dataset rank", rank);
       return;
     }
-  if (count.nelem () != rank)
+  if (count.numel () != rank)
     {
       error ("count must be a vector of length %d, the dataset rank", rank);
       return;
@@ -1157,7 +1157,7 @@ H5File::write_dset_hyperslab (const char *dsetname,
   Matrix _stride = stride;
   if (nargin < 3)
     _stride = Matrix (dim_vector(1, rank), 1);
-  if (_stride.nelem () != rank)
+  if (_stride.numel () != rank)
     {
       error ("stride must be a vector of length %d, the dataset rank", rank);
       return;
@@ -1165,7 +1165,7 @@ H5File::write_dset_hyperslab (const char *dsetname,
   Matrix _block = block;
   if (nargin < 4)
     _block = Matrix (dim_vector(1, rank), 1);
-  if (_block.nelem () != rank)
+  if (_block.numel () != rank)
     {
       error ("block must be a vector of length %d, the dataset rank", rank);
       return;
@@ -1411,7 +1411,7 @@ H5File::write_att (const char *location, const char *attname,
       error ("matrix type attributes are not yet supported.");
       return;
       // dims = alloc_hsize (attvalue.dims (), ALLOC_HSIZE_DEFAULT, true);
-      // dspace_id = H5Screate_simple (attvalue.dims ().length (), dims, NULL);
+      // dspace_id = H5Screate_simple (attvalue.dims ().numel (), dims, NULL);
       // free (dims);
     }
   else
@@ -1463,7 +1463,7 @@ H5File::write_att (const char *location, const char *attname,
       
       buf = (void *) attvalue.string_value ().c_str ();
     }
-  else if (attvalue.is_integer_type ())
+  else if (attvalue.isinteger ())
     {
       //type_id = H5Tcopy (H5T_STD_I64LE); //cannot read this back in then, don't know why
       type_id = H5Tcopy (H5T_NATIVE_INT);
@@ -1471,14 +1471,14 @@ H5File::write_att (const char *location, const char *attname,
       attval_int = attvalue.int_value ();
       buf = (void *) &attval_int;
     }
-  else if (attvalue.is_real_type ())
+  else if (attvalue.isreal ())
     {
       type_id = H5Tcopy (H5T_NATIVE_DOUBLE);
       mem_type_id = H5Tcopy (H5T_NATIVE_DOUBLE);
       attval_double = attvalue.double_value ();
       buf = (void *) &attval_double;
     }
-  else if (attvalue.is_complex_type ())
+  else if (attvalue.iscomplex ())
     {
       error ("complex values are not supported by the HDF5 format. \
 You have to save real and imag part separately.");
@@ -1571,18 +1571,18 @@ H5File::create_dset (const char *location, const Matrix& size,
   hsize_t *dims = alloc_hsize (size, ALLOC_HSIZE_INF_TO_ZERO, true);
   // and produce unlimited maximum extent for..
   hsize_t *maxdims = alloc_hsize (size, ALLOC_HSIZE_INFZERO_TO_UNLIMITED, true);
-  dspace_id = H5Screate_simple (size.nelem (), dims, maxdims);
+  dspace_id = H5Screate_simple (size.numel (), dims, maxdims);
   free (dims);
   free (maxdims);
 
-  if (any_int_leq_zero (size) && chunksize.is_empty ())
+  if (any_int_leq_zero (size) && chunksize.isempty ())
     {
       error ("If the size argument contains an Inf or zero element, then ChunkSize must be specified.");
       return;
     }
   // get a dataset creation property list
   hid_t crp_list = H5Pcreate (H5P_DATASET_CREATE);
-  if (! chunksize.is_empty ())
+  if (! chunksize.isempty ())
     {
       // a dataset with an unlimited dimension must be chunked.
       if (chunksize(0) == 0)
@@ -1594,7 +1594,7 @@ H5File::create_dset (const char *location, const Matrix& size,
           error ("Could not set chunked layout of %s", location);
           return;
         }
-      if (H5Pset_chunk (crp_list, size.nelem (), dims_chunk) < 0)
+      if (H5Pset_chunk (crp_list, size.numel (), dims_chunk) < 0)
         {
           error ("Could not set chunk size of %s", location);
           return;
@@ -1655,7 +1655,7 @@ H5File::get_auto_chunksize(const Matrix& dset_shape, int typesize)
   const int CHUNK_MAX = 1024*1024; // Hard upper limit (1M)
 
   Matrix chunksize = dset_shape;
-  int ndims = chunksize.length ();
+  int ndims = chunksize.numel ();
   for (int i = 0; i < ndims; i++)
     {
       //For unlimited dimensions we have to guess 1024
diff --git a/makefile b/makefile
index 0e9584c..6d617b3 100644
--- a/makefile
+++ b/makefile
@@ -9,7 +9,7 @@ $(shell octave --eval 'exit(__octave_config_info__ ("build_features").HDF5_18 !=
 
 MKOCTFILE=CXX="$(CXX)" CXXFLAGS="-ansi" mkoctfile -v -std=c++11 $(H5FLAGS)
 
-VERSION=0.4.0
+VERSION=0.5.0
 PACKAGEFILE=hdf5oct-$(VERSION).tar.gz
 
 .PHONY: test clean install uninstall package
diff --git a/package/DESCRIPTION b/package/DESCRIPTION
index f92ff13..3f311ff 100644
--- a/package/DESCRIPTION
+++ b/package/DESCRIPTION
@@ -1,5 +1,5 @@
 Name: hdf5oct
-Version: 0.4.0
+Version: 0.5.0
 Date: 2015-10-02
 Author: Tom Mullins, Anton Starikov, Thorsten Liebig, Stefan Großhauser
 Maintainer: Stefan Großhauser <Stefan.Grosshauser@uni-bayreuth.de>