and replace it with new url for COPYING file.
Fix 2 lines in java error test expected output file where messages
include line numbers changed by reducing the copyright header by 2
lines.
Removed obsolet macros from C++ API:
H5_NO_NAMESPACE, H5_NO_STD, __cplusplus
Leave OLD_HEADER_FILENAME because iostream.h might still be in use,
until further checking is done.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Jelly
Description:
Removed deprecated functions in previous releases due to missing const.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Description:
- Removed many warnings:
warning: use of old-style cast
warning: enumeration value ‘H5D_VIRTUAL’ not handled in switch
warning: comparison between signed and unsigned
There are others of the same warnings and they will be taken care of
in the next release.
- Made some code reuse between overloads
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Description:
Removed obsolete functions from the documentation. They are still
in the code, however, until the next two releases, just in case.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Description:
Added member function ArrayType::operator= because ArrayType has
pointer data members.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Description:
Merged from hdf5_CppAPI_Constants
r27942:
------
Description:
- Added H5dont_atexit() to getPredType and all the getConstant's to prevent
the C library from terminating before the C++ library cleanup.
- More cleanup and added more comments
r27923:
------
- Updated more comments and moved some things around for consistency
- Removed check for "new" failure, exceptions would be thrown
r27922:
------
Description:
Added function headers and more comments for clarity.
r27917:
------
Description:
The C++ library has several types of global constants from different
classes, such as PropList, PredType, DataSpace, etc... Previously,
these global constants were declared statically and the C++ library used
a constant, called PredType::AtExit, to detect when all the global
contants are destroyed then close the C library (H5close). This method
relied on the order of the constants being created and destroyed and
that PredType constants be the last to be destroyed. In September 2015,
it was recognized that the order in which the global constants were
created and destroyed was actually undefined, thus can be different
between different compilers. This resulted in failure when compilers
destroy PredType constants before others because when PredType::AtExit
was destroyed, the C library was closed, so when the constants of other
classes such as PropList or DataSpace were being deleted, the C library
would not be available.
Solution:
The static approach is changed to dynamic. In order to avoid an impact
on existing applications, the static global constants are changed to
constant references to the dynamically allocated objects.
A detailed explanation of the new method and a description of the
changes are in a Design Notes at the end of the file H5PredType.cpp.
New functions added to support the new methods are listed below.
class H5Library:
// Returns a singleton H5Library to initialize the global
// constants, invoked in IdComponent default constructor
static H5Library* getInstance(); // public
// Registers cleanup and terminating functions with atexit(),
// called in IdComponent default constructor
static void initH5cpp(void); // public
// Calls H5close to terminate the library, registered with
// atexit(), as the last thing to be done.
static void termH5cpp(void); // public
class PredType:
// Creates the constants
static void makePredTypes(); // private
// Calls makePredTypes to create the constants and returns
// the dummy constant PREDTYPE_CONST;
static PredType* getPredTypes(); // private
class DataSpace:
// Creates the constant
static DataSpace* getConstant(); // private
class PropList:
// Creates the constant
static PropList* getConstant(); // private
class DSetCreatPropList:
// Creates the constant
static DSetCreatPropList* getConstant(); // private
class DSetMemXferPropList:
// Creates the constant
static DSetMemXferPropList* getConstant(); // private
class FileCreatPropList:
// Creates the constant
static FileCreatPropList* getConstant(); // private
class FileAccPropList:
// Creates the constant
static FileAccPropList* getConstant(); // private
This function is added to PredType, DataSpace, PropList, and the four
subclasses of PropList:
// Deletes the constant
static void deleteConstants(); // public
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Description:
- Put back the UNUSED parameters in dsets test because the change to remove
the warning last time caused failure in setting filter, in turn, caused
failure in the test with such obscure/unrelated errors!
- Added incRefCount() to other constructors that missed from last time.
Platforms tested:
Linux/64 (platypus)
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
Description:
The following two constructors of classes: AbstractDs, IdComponent,
H5Location, and H5Object are no longer appropriate after the data member
"id" had been moved from IdComponent to the sub-classes.
The copy constructors are noop and will be generated by the compilers if
needed so they can be removed in 1.8.15 without effecting applications. The
other constructors will be removed from 1.10 release, and then from 1.8 if
their removal does not raise any problems in at least two 1.10 releases.
<Classname>(const hid_t h5_id);
<Classname>(const <Classname>& original);
Deprecation warnings are added to each of these classes.
The other classes are changed to call the default constructor instead of
one of the constructors above.
Platforms tested:
Linux/64 (platypus)
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
Description:
- Used H5I_INVALID_HID instead of 0 to initialized member "id" in classes
that represent HDF5 objects. For PropList, H5P_DEFAULT has to be used
instead of H5I_INVALID_HID.
- Added try/catch block to some dynamically allocating memory code and
re-throw the bad_alloc exception with a message informing the location of
the failure.
Platforms tested:
Linux/ppc64 (ostrich)
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
Put back overloaded functions for backward compatibility:
- were replaced by better prototyped versions, such as Attribute::getName.
- were modified to add const to constant arguments.
Added notes for future removal in documentation.
Platforms tested:
Linux/ppc64 (ostrich)
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
Description:
- The failure in daily test was caused by missing initialization of member
"id" in a few constructors. This is now fixed.
- Added two overloaded H5Location::setComment
- Improved some error reporting in H5Location
- Improved error reporting in tests
Platforms tested:
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
Linux/64 2.6 (koala)/PGI compilers
Description:
- Improved the changes in revisions r22836 and r23438, mainly on the
wrappers of reference, dereference, get region, and set/getcomment.
- Added more tests.
Platforms tested:
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
Linux/ppc64 (ostrich)
Description:
- Completed the changes in revisions r22836 and r23438 with improvement
on wrappers such as reference, dereference, get region, and set/getcomment.
- Added more tests.
Platforms tested:
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
Linux/ppc64 (ostrich)
Description:
- Replaced PredType::NotAtexit() with PredType::AtExit(H5CPP_EXITED);
and used PredType::AtExit as a flag to detect when all predefined
types have been destroyed. Then, H5close will be called to terminate
the library after its being re-initiated when the PredType destructors
were activated. This change removed the memory leaks shown by the
user's sample program.
- Added H5CPP_EXITED for PredType::AtExit to use as a flag
- Updated some inaccurate comments
- Removed stream functions from FileAccPropList
- Replaced H5_VMS with appropriate macro in H5IdComponent.cpp
- Corrected many URLs (hdfgroup vs. ncsa) in comments
- Replaced std::string with H5std_string in comments
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 2.6 (amani)
SunOS 5.10 (linew)
Description:
After a C++ API object is closed, its id should be reset regardless
of the reference count of the underlying HDF5 object. User reported
the bug for Group, but it's applicable to all other objects. Fixed.
Platforms tested:
Linux/32 2.6 (jam)
FreeBSD/64 6.3 (liberty)
SunOS 5.10 (linew)
Description:
Changed all subclasses' setId to protected p_setId and put back setId
in IdComponent. p_setId is used in the library where the id provided
by a C API passed on to user's application in the form of a C++ API
object, which will be destroyed properly, and so p_setId does not
call incRefCount. On the other hand, the public version setId is
used by other applications, in which the id passed to setId needs
to be closed properly by the application, so setId must call incRefCount
for the new object to prevent prematurely closing of the id.
Platforms tested:
Linux 2.6 (kagiso)
SunOS 5.10 (linew)
FreeBSD (duty)
the file didn't have the data. It happened because each handle had its own
object structure, and the empty one overwrote the data with fill value. This is
fixed by making some attribute information like the data be shared in the
attribute structure.
Tested on smirom, kagiso, and linew.
Description:
The class hierarchy was revised to address the problem reported in
bugzilla #1068. Classes AbstractDS and Attribute are moved out of
H5Object. Class Attribute now multiply inherits from IdComponent and
AbstractDs and class DataSet from H5Object and AbstractDs.
In addition, data member IdComponent::id was moved into subclasses:
Attribute, DataSet, DataSpace, DataType, H5File, Group, and PropList.
Platforms tested:
SunOS 5.10 (linew)
Linux 2.6 (kagiso)
FreeBSD (duty)
Correct the prototype for H5Sselect_elements() to take an 'hsize_t *' for
the coordinates, instead of 'hsize_t **'.
Tested on:
Mac OS X/32 10.5.1 (amazon)
Tested platform:
Kagiso only since it is only a comment block change. If it works in one
machine, it should work in all, I hope. Still need to check the parallel
build on copper.
Description:
- Added overloaded function DataType::copy to take a DataSet
- Added overloaded DataType::commit
- Fixed bugzilla 797
- Fixed a warning in DataSpace::operator=
- Set PropList parameter to default in DataType::convert
Platforms tested
AIX 5.1 (copper)
SunOS 5.8 64-bit (sol)
HPUX 11.00 (kelgia)
Description:
Fixed typos and re-arranged some functions to be in sync with 1.6.
Platforms tested:
Linux 2.4 (heping)
SunOS 5.9 (shanti)
AIX 5.1 (copper)
Description:
Shanti compiler destroy unnamed objects later than others, which caused
some reference counting test fail. Revised the test so that destructors
are called at the same time, regardless the differences of compiler
implementation.
Revised some constructors, close, operator=, and destructors to make
sure that all the object ids are handled properly.
Platforms tested:
Linux 2.4 (heping)
SunOS 5.9 (shanti)
HPUX 11.00 (kelgia)
AIX 5.1 (copper)
Description:
Added alias H5_std so either the global or std namespace can be
used, depending on H5_NO_STD.
Platforms tested:
Linux 2.4 (heping)
SunOS 5.8 64-bit (sol)
AIX 5.1 (copper)
Description:
There was a workaround for predefined types, in the C++ library,
implemented when the C++ library was handling the reference
counting of the object ids on its own. Currently, the C++ library
is using the available APIs from the C library for that purpose,
and there were bugs reported involving that part of the C++ library.
So, I decided to remove the workaround completely.
Also, improved the use of std members.
Platforms tested:
Linux 2.4 (heping)
SunOS 5.8 64-bit (sol)
Linux 2.4 w/PGI (colonelk)
Code cleanup
Description:
Trim trailing whitespace, which is making 'diff'ing the two branches
difficult.
Solution:
Ran this script in each directory:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
Description:
PropList::copyProp has incorrect prototype; although it works,
it does cause users inconvenience.
Solution:
Added another overloaded function with correct prototype. The
old version will be removed in a future release. In the meantime,
"Obsolete" will be displayed in its RM page.
Also, changed several checks on the returned value of a C API from
non-positive to negative because id = 0 is no longer significant,
now that the C++ reference counting had been removed.
Platforms tested:
Linux 2.4 (heping)
IRIX64 with -n32 (modi4)
Linux 2.4 w/PGI (colonelk)
Description:
The use of FileCreatPropList::DEFAULT sometimes caused failure
in the reference counting area. This occurs to all the default
property lists, which also include FileAccPropList::DEFAULT,
DSetCreatPropList::DEFAULT, and DSetMemXferPropList::DEFAULT.
H5P_DEFAULT was used to create these default prop lists and
because its value is 0, the id of these prop lists are 0, which
is rejected by the H5I functions during the reference counting.
Solution:
The main action to fix the above problem was to use
H5P_FILE_CREATE
H5P_FILE_ACCESS
H5P_DATASET_CREATE
H5P_DATASET_XFER
to define the default property lists accordingly. Yet, when this
fix was applied, some bug in reference counting was revealed.
It appeared that some ids were not incremented but were passed in
for decrementing. The following actions were then taken to fix and
improve the current use of reference counting H5I functions.
* added private func IdComponent::p_valid_id to verify that the
id is a valid id and can be passed into an H5I function
* used p_valid_id to validate an id before calling an H5I functions
in the reference-counting member functions incRefCount,
decRefCount, and getCounter
* changed to use member function incRefCount, decRefCount, and
getCounter instead of the C APIs H5Iinc_ref, H5Idec_ref, and
H5Iget_ref throughout IdComponent.
In addition, overloadings were added for incRefCount, decRefCount,
and getCounter to take an id different than the id of the current
instance; they can be convenient during debugging.
Platforms tested:
Linux 2.4 (heping)
SunOS 5.8 64-bit (sol)
AIX 5.1 (copper)
Description:
Doxygen 1.4.2 has a bug that when an \exception immediately
follows a \brief, the exception will be displayed prominently
in the brief section.
Solution:
Temporarily added /// to after \brief to work around this
problem and notified the Doxygen's author.
Platforms tested:
Linux 2.4 (heping) - only in documentation sections
Description:
Added the following to the C++ library
+ overloaded functions:
string CommonFG::getObjnameByIdx(hsize_t idx)
H5T_order_t AtomType::getOrder()
+ wrappers for H5*close
+ wrappers for H5Arename, H5Aget_storage_size, and H5Dget_storage_size
Platforms tested:
Linux 2.4 (heping)
AIX 5.1 (copper)
SunOS 5.8 64-bit (sol)
Description:
Checked return value from C API for failure condition.
Added/Modified some comments appropriately.
Platforms tested:
Linux 2.4 (heping)
AIX 5.1 (copper) - tests passed but there were some old warnings about
duplicate symbols on std::string; I'll check on that.
Bug Fix/Code Cleanup/Doc Cleanup/Optimization/Branch Sync :-)
Description:
Generally speaking, this is the "signed->unsigned" change to selections.
However, in the process of merging code back, things got stickier and stickier
until I ended up doing a big "sync the two branches up" operation. So... I
brought back all the "infrastructure" fixes from the development branch to the
release branch (which I think were actually making some improvement in
performance) as well as fixed several bugs which had been fixed in one branch,
but not the other.
I've also tagged the repository before making this checkin with the label
"before_signed_unsigned_changes".
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel & fphdf5
FreeBSD 4.10 (sleipnir) w/threadsafe
FreeBSD 4.10 (sleipnir) w/backward compatibility
Solaris 2.7 (arabica) w/"purify options"
Solaris 2.8 (sol) w/FORTRAN & C++
AIX 5.x (copper) w/parallel & FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN
Linux 2.4 (heping) w/FORTRAN & C++
Misc. update:
Description:
Updated various function headers for the RM as reviewing progresses.
Rearranged functions in header files for more sensible look of the RM.
Platforms tested:
SunOS 5.7 (arabica)
Linux 2.4 (eirene)
Description:
H5IdComponent.cpp: initialized a pointer to NULL
H5Object.cpp: removed functions being added by mistake
Update function headers for the rest.
Platforms tested:
SunOS 5.7 (arabica)
Linux 2.4 (eirene)
Code update
Description:
Update C++ wrappers to use new ID reference counting mechanisms.
Platforms tested:
FreeBSD 4.9 (sleipnir) w/C++
Too focused to require h5committest
Add/Improve documentation
Description
Added doxygen documentation to H5PredType.cpp and made minor changes
to the others for either correction or clarification.
Platforms:
SunOS 5.7 (arabica)
Linux 2.4 (eirene)
Misc. update:
Add more C++ wrapper and documentation - incrementally check-in
Description:
Added doxygen documentation to:
H5DataSet.cpp
H5DataSpace.cpp
H5CommonFG.cpp
and a wrapper for H5Rcreate to H5Object.* with tests will be added
later.
There are more documentation need to be added to these files but
to preserve the changes, I check them in now.
Platforms:
SunOS 5.7 (arabica)
Linux 2.4 (eirene)
Misc. update:
Bug fix and minor code enhancement
Description:
Missing methods to read/write C++ String for an attribute and
a dataset.
Solution:
Added overloaded functions read and write to H5::Attribute and
H5::DataSet.
Also, added another constructor StrType so the need to separately
set the length of the string type can be eliminated. It's minor
but convenient.
Made some minor changes to make error messages more readable.
Platforms:
SunOS 5.7 (arabica)
Linux 2.4 (eirene)
IRIX 6.5.11 (modi4)
HPUX 11.00 (kelgia)
API tweak.
Description:
The H5Sget_select_bounds() API call was using hsize_t arrays for retrieving
the 'start' and 'end' coordinates, which is counter to the rest of the dataspace
API.
Solution:
Change the arrays to be hssize_t instead.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
FreeBSD 4.8 (sleipnir) w/parallel
h5committested
Misc. update:
Updated all docs for this change.
Added 1.4 compatibility #ifdef's
