From noreply at nexusformat.org  Wed Jun 15 00:32:29 2011
From: noreply at nexusformat.org (NeXus Data Format Library and Applications)
Date: Tue, 14 Jun 2011 23:32:29 -0000
Subject: [NeXus-code-tickets] [NeXusCode] #270: make configure accept a HDF5
 version greater than 1.8
Message-ID: <052.c0ed3257d2cfc2e875479045de8c75c9@nexusformat.org>

#270: make configure accept a HDF5 version greater than 1.8
---------------------------+------------------------------------------------
 Reporter:  Pedro.vicente  |       Owner:  Pedro.vicente
     Type:  defect         |      Status:  new          
 Priority:  major          |   Milestone:               
Component:  napi           |     Version:  trunk        
 Keywords:                 |  
---------------------------+------------------------------------------------
 while trying to use a HDF5 version 1.9 with --with-hdf5 configure issues
 an error

 configure: WARNING: The HDF 5 installation has not the right version
 (1.9.81-FA_a5). You need at least 1.6

 HDF5 support:  no
                 found version 1.9.81-FA_a5 (1.9.81-FA_a5)

 This is because of this check in configure.ac

 if test "$H5ROOT"; then
     H5VERSION=`grep H5_VERS_INFO ${H5ROOT}/include/H5public.h | cut -d '"'
 -f 2 | cut -d ' ' -f 4`
     case $H5VERSION in
         1.[[68]]*)

 Solution:

 change to

  case $H5VERSION in
         1.[[689]]*)

-- 
Ticket URL: <http://trac.nexusformat.org/code/ticket/270>
NeXus Data Format Library and Applications <http://www.nexusformat.org/>
NeXus Data Format Library and Applications


From noreply at nexusformat.org  Wed Jun 15 00:47:50 2011
From: noreply at nexusformat.org (NeXus Data Format Library and Applications)
Date: Tue, 14 Jun 2011 23:47:50 -0000
Subject: [NeXus-code-tickets] [NeXusCode] #271: NX5putslab: use
	H5Dset_extent instead of H5Dextend
Message-ID: <052.3c881513850226f3ca2f20322e592cfd@nexusformat.org>

#271: NX5putslab: use H5Dset_extent instead of H5Dextend
---------------------------+------------------------------------------------
 Reporter:  Pedro.vicente  |       Owner:  Pedro.vicente
     Type:  enhancement    |      Status:  new          
 Priority:  major          |   Milestone:               
Component:  napi           |     Version:  trunk        
 Keywords:                 |  
---------------------------+------------------------------------------------
 H5Dextend is a deprecated function that does not allow reducing a
 dataset's dimension;

 replace with H5Dset_extent

 http://www.hdfgroup.org/HDF5/doc/RM/RM_H5D.html

-- 
Ticket URL: <http://trac.nexusformat.org/code/ticket/271>
NeXus Data Format Library and Applications <http://www.nexusformat.org/>
NeXus Data Format Library and Applications


From noreply at nexusformat.org  Thu Jun 16 17:52:41 2011
From: noreply at nexusformat.org (NeXus Data Format Library and Applications)
Date: Thu, 16 Jun 2011 16:52:41 -0000
Subject: [NeXus-code-tickets] [NeXusCode] #272: NeXus thread safety
Message-ID: <054.59db9da884e481ad0b9a389978790d2b@nexusformat.org>

#272: NeXus thread safety
-----------------------------+----------------------------------------------
 Reporter:  Freddie Akeroyd  |       Owner:  Freddie Akeroyd
     Type:  enhancement      |      Status:  new            
 Priority:  major            |   Milestone:                 
Component:  napi             |     Version:  trunk          
 Keywords:                   |  
-----------------------------+----------------------------------------------
 HDF5 on windows is not thread safe out of the box. Previous
 implementations needed a recompile with an additional  Win32 ptheads
 library and while the latest HDF5 uses native Windows locks, it seem to
 use some features only available on Vista and above.

-- 
Ticket URL: <http://trac.nexusformat.org/code/ticket/272>
NeXus Data Format Library and Applications <http://www.nexusformat.org/>
NeXus Data Format Library and Applications


From noreply at nexusformat.org  Thu Jun 16 17:55:40 2011
From: noreply at nexusformat.org (NeXus Data Format Library and Applications)
Date: Thu, 16 Jun 2011 16:55:40 -0000
Subject: [NeXus-code-tickets] [NeXusCode] #272: NeXus thread safety
In-Reply-To: <054.59db9da884e481ad0b9a389978790d2b@nexusformat.org>
References: <054.59db9da884e481ad0b9a389978790d2b@nexusformat.org>
Message-ID: <063.ffc641a72634717439acd82a2c620afb@nexusformat.org>

#272: NeXus thread safety
-----------------------------+----------------------------------------------
 Reporter:  Freddie Akeroyd  |       Owner:  Freddie Akeroyd
     Type:  enhancement      |      Status:  new            
 Priority:  major            |   Milestone:                 
Component:  napi             |     Version:  trunk          
 Keywords:                   |  
-----------------------------+----------------------------------------------

Comment(by Freddie Akeroyd):

 (In [1591]) Add global locking aroud all calls to underlying data routines
 from
 the NeXus API on windows (on linux HDF5 seems to have pthreads locks
 already enabled). This should allow NeXus to be thread safe with
 standard HDF5 windows binaries.
 refs #272

-- 
Ticket URL: <http://trac.nexusformat.org/code/ticket/272#comment:1>
NeXus Data Format Library and Applications <http://www.nexusformat.org/>
NeXus Data Format Library and Applications


From noreply at nexusformat.org  Thu Jun 16 18:03:24 2011
From: noreply at nexusformat.org (NeXus Data Format Library and Applications)
Date: Thu, 16 Jun 2011 17:03:24 -0000
Subject: [NeXus-code-tickets] [NeXusCode] #272: NeXus thread safety
In-Reply-To: <054.59db9da884e481ad0b9a389978790d2b@nexusformat.org>
References: <054.59db9da884e481ad0b9a389978790d2b@nexusformat.org>
Message-ID: <063.2d2adb2c3fc2682e4d5036b4d7657dc3@nexusformat.org>

#272: NeXus thread safety
-----------------------------+----------------------------------------------
 Reporter:  Freddie Akeroyd  |       Owner:  Freddie Akeroyd
     Type:  enhancement      |      Status:  new            
 Priority:  major            |   Milestone:                 
Component:  napi             |     Version:  trunk          
 Keywords:                   |  
-----------------------------+----------------------------------------------

Comment(by Freddie Akeroyd):

 (In [1592]) Missed header file. Refs #272

-- 
Ticket URL: <http://trac.nexusformat.org/code/ticket/272#comment:2>
NeXus Data Format Library and Applications <http://www.nexusformat.org/>
NeXus Data Format Library and Applications


From noreply at nexusformat.org  Thu Jun 16 18:22:59 2011
From: noreply at nexusformat.org (NeXus Data Format Library and Applications)
Date: Thu, 16 Jun 2011 17:22:59 -0000
Subject: [NeXus-code-tickets] [NeXusCode] #273: NXsummary fails to compile
Message-ID: <054.e4ffbea697512dd7f41ea0d4f343d730@nexusformat.org>

#273: NXsummary fails to compile
-----------------------------+----------------------------------------------
 Reporter:  Freddie Akeroyd  |       Owner:  Freddie Akeroyd
     Type:  defect           |      Status:  new            
 Priority:  major            |   Milestone:                 
Component:  napi             |     Version:  trunk          
 Keywords:                   |  
-----------------------------+----------------------------------------------


-- 
Ticket URL: <http://trac.nexusformat.org/code/ticket/273>
NeXus Data Format Library and Applications <http://www.nexusformat.org/>
NeXus Data Format Library and Applications


From noreply at nexusformat.org  Thu Jun 16 18:24:00 2011
From: noreply at nexusformat.org (NeXus Data Format Library and Applications)
Date: Thu, 16 Jun 2011 17:24:00 -0000
Subject: [NeXus-code-tickets] [NeXusCode] #273: NXsummary fails to
	compile
In-Reply-To: <054.e4ffbea697512dd7f41ea0d4f343d730@nexusformat.org>
References: <054.e4ffbea697512dd7f41ea0d4f343d730@nexusformat.org>
Message-ID: <063.9bfae1d65959bf0a4a33cb7a0341a05e@nexusformat.org>

#273: NXsummary fails to compile
------------------------------+---------------------------------------------
  Reporter:  Freddie Akeroyd  |       Owner:  Freddie Akeroyd
      Type:  defect           |      Status:  closed         
  Priority:  major            |   Milestone:                 
 Component:  napi             |     Version:  trunk          
Resolution:  fixed            |    Keywords:                 
------------------------------+---------------------------------------------
Changes (by Freddie Akeroyd):

  * status:  new => closed
  * resolution:  => fixed


Comment:

 (In [1593]) Add back nxconfig.h - it is needed for the HAVE_STDINT_H test
 fixes #273

-- 
Ticket URL: <http://trac.nexusformat.org/code/ticket/273#comment:1>
NeXus Data Format Library and Applications <http://www.nexusformat.org/>
NeXus Data Format Library and Applications


From noreply at nexusformat.org  Tue Jun 28 16:52:51 2011
From: noreply at nexusformat.org (NeXus Data Format Library and Applications)
Date: Tue, 28 Jun 2011 15:52:51 -0000
Subject: [NeXus-code-tickets] [NeXusCode] #274: make external links to
	datasets work
Message-ID: <053.581083864f5feb0dfa2f11c4e2236f3c@nexusformat.org>

#274: make external links to datasets work
----------------------------+-----------------------------------------------
 Reporter:  Tobias Richter  |       Owner:  Tobias Richter
     Type:  defect          |      Status:  new           
 Priority:  major           |   Milestone:                
Component:  napi            |     Version:  4.2.0         
 Keywords:                  |  
----------------------------+-----------------------------------------------
 The current NAPI only supports links to groups. We suspect a main use case
 for linking to an external file is writing data into two files from an
 acquisition system and directly from a detector (for obvious performance
 reasons) but having them as a single logical unit for data analysis by the
 user. This use case has two main problems with linking to groups:
  * The detector needs to write the entire NXdetector group and hence has
 to know the entire metadata you might want there. With the level of
 control you have over detector file writing that is a major drawback.
  * It is not possible to link the detector data into an /entry/nxdata from
 /entry/instrument/detector/data as that needs to cross file boundaries
 (correct me if I'm wrong there).
 If it was possible to link to an SDS, these limitations would not exist.

-- 
Ticket URL: <http://trac.nexusformat.org/code/ticket/274>
NeXus Data Format Library and Applications <http://www.nexusformat.org/>
NeXus Data Format Library and Applications


From noreply at nexusformat.org  Tue Jun 28 17:03:54 2011
From: noreply at nexusformat.org (NeXus Data Format Library and Applications)
Date: Tue, 28 Jun 2011 16:03:54 -0000
Subject: [NeXus-code-tickets] [NeXusCode] #274: make external links to
	datasets work
In-Reply-To: <053.581083864f5feb0dfa2f11c4e2236f3c@nexusformat.org>
References: <053.581083864f5feb0dfa2f11c4e2236f3c@nexusformat.org>
Message-ID: <062.d10a83b2cfaf8e1197d26f3c1db34d0e@nexusformat.org>

#274: make external links to datasets work
----------------------------+-----------------------------------------------
 Reporter:  Tobias Richter  |       Owner:  Tobias Richter
     Type:  defect          |      Status:  new           
 Priority:  major           |   Milestone:                
Component:  napi            |     Version:  4.2.0         
 Keywords:                  |  
----------------------------+-----------------------------------------------

Comment(by Tobias Richter):

 (In [1594]) make externallinks for datasets work (reading)

 refs #274
 this change is transparent on the API level

 that means there is no API method to query the external link
 status for datasets and there is no gold plated way of creating
 link to datasets, but all that is required is a dummy dataset
 with the napimount attribute set

-- 
Ticket URL: <http://trac.nexusformat.org/code/ticket/274#comment:1>
NeXus Data Format Library and Applications <http://www.nexusformat.org/>
NeXus Data Format Library and Applications


From noreply at nexusformat.org  Tue Jun 28 17:17:02 2011
From: noreply at nexusformat.org (NeXus Data Format Library and Applications)
Date: Tue, 28 Jun 2011 16:17:02 -0000
Subject: [NeXus-code-tickets] [NeXusCode] #275: files opened while following
 external links are opened read-write
Message-ID: <053.e4e3c7c89170af8ea6f6f06739608cfe@nexusformat.org>

#275: files opened while following external links are opened read-write
----------------------------+-----------------------------------------------
 Reporter:  Tobias Richter  |       Owner:  Unassigned
     Type:  defect          |      Status:  new       
 Priority:  major           |   Milestone:            
Component:  napi            |     Version:  4.2.0     
 Keywords:                  |  
----------------------------+-----------------------------------------------
 Even if the 'main' file was opened read only, files subsequently visited
 while following external links are opened in read/write mode potentially
 opening them up for corruption.

-- 
Ticket URL: <http://trac.nexusformat.org/code/ticket/275>
NeXus Data Format Library and Applications <http://www.nexusformat.org/>
NeXus Data Format Library and Applications


From noreply at nexusformat.org  Tue Jun 28 19:43:54 2011
From: noreply at nexusformat.org (NeXus Data Format Library and Applications)
Date: Tue, 28 Jun 2011 18:43:54 -0000
Subject: [NeXus-code-tickets] [NeXusCode] #186: RPM build errors on
	Fedora 11
In-Reply-To: <054.fa0fb7395893de6fd3dce886ec1a00f0@nexusformat.org>
References: <054.fa0fb7395893de6fd3dce886ec1a00f0@nexusformat.org>
Message-ID: <063.22f69c2e4050375b307ad2c3737c9d31@nexusformat.org>

#186: RPM build errors on Fedora 11
------------------------------+---------------------------------------------
 Reporter:  Stuart Campbell   |       Owner:  Freddie Akeroyd
     Type:  defect            |      Status:  new            
 Priority:  minor             |   Milestone:  4.3.0          
Component:  Installation kit  |     Version:  4.2.0          
 Keywords:  RPM               |  
------------------------------+---------------------------------------------
Changes (by Peter Peterson):

  * milestone:  4.2.1 => 4.3.0


Old description:

> When building the RPM on Fedora 11 (x86_64) I get the following errors...
> {{{
> RPM build errors:
>     Installed (but unpackaged) file(s) found:
>    /usr/lib/python2.6/site-packages/nxs/__init__.py
>    /usr/lib/python2.6/site-packages/nxs/__init__.pyc
>    /usr/lib/python2.6/site-packages/nxs/__init__.pyo
>    /usr/lib/python2.6/site-packages/nxs/napi.py
>    /usr/lib/python2.6/site-packages/nxs/napi.pyc
>    /usr/lib/python2.6/site-packages/nxs/napi.pyo
> }}}

New description:

 When building the RPM on Fedora 11 (x86_64) I get the following errors...
 {{{
 RPM build errors:
     Installed (but unpackaged) file(s) found:
    /usr/lib/python2.6/site-packages/nxs/__init__.py
    /usr/lib/python2.6/site-packages/nxs/__init__.pyc
    /usr/lib/python2.6/site-packages/nxs/__init__.pyo
    /usr/lib/python2.6/site-packages/nxs/napi.py
    /usr/lib/python2.6/site-packages/nxs/napi.pyc
    /usr/lib/python2.6/site-packages/nxs/napi.pyo
 }}}

--

Comment:

 4.2.1 is closed.

-- 
Ticket URL: <http://trac.nexusformat.org/code/ticket/186#comment:1>
NeXus Data Format Library and Applications <http://www.nexusformat.org/>
NeXus Data Format Library and Applications


From noreply at nexusformat.org  Tue Jun 28 19:44:46 2011
From: noreply at nexusformat.org (NeXus Data Format Library and Applications)
Date: Tue, 28 Jun 2011 18:44:46 -0000
Subject: [NeXus-code-tickets] [NeXusCode] #276: NXsummary does not escape
	xml entities
Message-ID: <053.28ef0440eba49abd35c5c95a3326ce4b@nexusformat.org>

#276: NXsummary does not escape xml entities
----------------------------+-----------------------------------------------
 Reporter:  Peter Peterson  |       Owner:  Peter Peterson
     Type:  defect          |      Status:  new           
 Priority:  major           |   Milestone:  4.3.0         
Component:  napi            |     Version:  4.2.0         
 Keywords:                  |  
----------------------------+-----------------------------------------------
 When writing out xml entities the content is not properly escaped.

-- 
Ticket URL: <http://trac.nexusformat.org/code/ticket/276>
NeXus Data Format Library and Applications <http://www.nexusformat.org/>
NeXus Data Format Library and Applications


From noreply at nexusformat.org  Tue Jun 28 19:44:53 2011
From: noreply at nexusformat.org (NeXus Data Format Library and Applications)
Date: Tue, 28 Jun 2011 18:44:53 -0000
Subject: [NeXus-code-tickets] [NeXusCode] #276: NXsummary does not
	escape xml entities
In-Reply-To: <053.28ef0440eba49abd35c5c95a3326ce4b@nexusformat.org>
References: <053.28ef0440eba49abd35c5c95a3326ce4b@nexusformat.org>
Message-ID: <062.1a8c183cc725e9d53d0dca2a7e8fc4cc@nexusformat.org>

#276: NXsummary does not escape xml entities
----------------------------+-----------------------------------------------
 Reporter:  Peter Peterson  |       Owner:  Peter Peterson
     Type:  defect          |      Status:  assigned      
 Priority:  major           |   Milestone:  4.3.0         
Component:  napi            |     Version:  4.2.0         
 Keywords:                  |  
----------------------------+-----------------------------------------------
Changes (by Peter Peterson):

  * status:  new => assigned


-- 
Ticket URL: <http://trac.nexusformat.org/code/ticket/276#comment:1>
NeXus Data Format Library and Applications <http://www.nexusformat.org/>
NeXus Data Format Library and Applications


From noreply at nexusformat.org  Tue Jun 28 19:46:17 2011
From: noreply at nexusformat.org (NeXus Data Format Library and Applications)
Date: Tue, 28 Jun 2011 18:46:17 -0000
Subject: [NeXus-code-tickets] [NeXusCode] #276: NXsummary does not
	escape xml entities
In-Reply-To: <053.28ef0440eba49abd35c5c95a3326ce4b@nexusformat.org>
References: <053.28ef0440eba49abd35c5c95a3326ce4b@nexusformat.org>
Message-ID: <062.010ab8c8df986b0607d1243a6188f870@nexusformat.org>

#276: NXsummary does not escape xml entities
-----------------------------+----------------------------------------------
  Reporter:  Peter Peterson  |       Owner:  Peter Peterson
      Type:  defect          |      Status:  closed        
  Priority:  major           |   Milestone:  4.3.0         
 Component:  napi            |     Version:  4.2.0         
Resolution:  fixed           |    Keywords:                
-----------------------------+----------------------------------------------
Changes (by Peter Peterson):

  * status:  assigned => closed
  * resolution:  => fixed


Comment:

 (In [1595]) Dealt with xml entities. Fixes #276.

-- 
Ticket URL: <http://trac.nexusformat.org/code/ticket/276#comment:2>
NeXus Data Format Library and Applications <http://www.nexusformat.org/>
NeXus Data Format Library and Applications


From noreply at nexusformat.org  Thu Jun 30 14:53:23 2011
From: noreply at nexusformat.org (NeXus Data Format Library and Applications)
Date: Thu, 30 Jun 2011 13:53:23 -0000
Subject: [NeXus-code-tickets] [NeXusCode] #277: Add methods that get data
 and coerce to a vector of ints or doubles
Message-ID: <053.58983ec815f8e3a6a8c713809bc4bf62@nexusformat.org>

#277: Add methods that get data and coerce to a vector of ints or doubles
----------------------------+-----------------------------------------------
 Reporter:  Janik Zikovsky  |       Owner:  Janik Zikovsky
     Type:  defect          |      Status:  new           
 Priority:  major           |   Milestone:                
Component:  other bindings  |     Version:  trunk         
 Keywords:                  |  
----------------------------+-----------------------------------------------


-- 
Ticket URL: <http://trac.nexusformat.org/code/ticket/277>
NeXus Data Format Library and Applications <http://www.nexusformat.org/>
NeXus Data Format Library and Applications


From noreply at nexusformat.org  Thu Jun 30 14:53:50 2011
From: noreply at nexusformat.org (NeXus Data Format Library and Applications)
Date: Thu, 30 Jun 2011 13:53:50 -0000
Subject: [NeXus-code-tickets] [NeXusCode] #277: Add methods that get
 data and coerce to a vector of ints or doubles
In-Reply-To: <053.58983ec815f8e3a6a8c713809bc4bf62@nexusformat.org>
References: <053.58983ec815f8e3a6a8c713809bc4bf62@nexusformat.org>
Message-ID: <062.6d1a750149dac4f755fbdb4b9aa06d4a@nexusformat.org>

#277: Add methods that get data and coerce to a vector of ints or doubles
----------------------------+-----------------------------------------------
 Reporter:  Janik Zikovsky  |       Owner:  Janik Zikovsky
     Type:  defect          |      Status:  assigned      
 Priority:  major           |   Milestone:                
Component:  other bindings  |     Version:  trunk         
 Keywords:                  |  
----------------------------+-----------------------------------------------
Changes (by Janik Zikovsky):

  * status:  new => assigned


-- 
Ticket URL: <http://trac.nexusformat.org/code/ticket/277#comment:1>
NeXus Data Format Library and Applications <http://www.nexusformat.org/>
NeXus Data Format Library and Applications


From noreply at nexusformat.org  Thu Jun 30 14:54:14 2011
From: noreply at nexusformat.org (NeXus Data Format Library and Applications)
Date: Thu, 30 Jun 2011 13:54:14 -0000
Subject: [NeXus-code-tickets] [NeXusCode] #277: Add methods that get
 data and coerce to a vector of ints or doubles
In-Reply-To: <053.58983ec815f8e3a6a8c713809bc4bf62@nexusformat.org>
References: <053.58983ec815f8e3a6a8c713809bc4bf62@nexusformat.org>
Message-ID: <062.7e593917c7963707f9a980524ff92809@nexusformat.org>

#277: Add methods that get data and coerce to a vector of ints or doubles
-----------------------------+----------------------------------------------
  Reporter:  Janik Zikovsky  |       Owner:  Janik Zikovsky
      Type:  defect          |      Status:  closed        
  Priority:  major           |   Milestone:                
 Component:  other bindings  |     Version:  trunk         
Resolution:  fixed           |    Keywords:                
-----------------------------+----------------------------------------------
Changes (by Janik Zikovsky):

  * status:  assigned => closed
  * resolution:  => fixed


Comment:

 (In [1596]) Added methods to C++ API called getDataCoerce() to convert
 from differently-sized ints or doubles to a vector of doubles or a vector
 of ints. Added tests for those methods. Fixes #277.

-- 
Ticket URL: <http://trac.nexusformat.org/code/ticket/277#comment:2>
NeXus Data Format Library and Applications <http://www.nexusformat.org/>
NeXus Data Format Library and Applications


