| Commit message (Collapse) | Author | Age | Files | Lines |
|
|
|
|
| |
* Updated source file copyright headers to remove "Copyright by the Board of Trustees
of the University of Illinois", which is kept in the top-level COPYING file.
|
|
|
|
|
|
|
| |
* Fixes sign-conversion warnings w/ clang 14
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
|
| |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
* fixed missed closing of a dataset
* fixed missed closing of a dataset
* fixed typo in error return
* Committing clang-format changes
* minor edits
* code format
* Committing clang-format changes
* code format
* minor edit
* switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging
* Committing clang-format changes
* changed size_i in printf to reflect the I/O.
* Committing clang-format changes
* Fixed seg fault with xlf on BE with -qintsize=8
* fixed error function string
* spelling corrections via codespell, added new spell check github actions
* Committing clang-format changes
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* Committing clang-format changes
* misc
* misc
* misc
* misc
* misc
* misc
* Committing clang-format changes
* misc
* work around for https://github.com/codespell-project/codespell/issues/2137
* misc
* added missing file
* misc
* misc.
* misc
* switch to using Codespell with GitHub Actions
* misc.
* misc.
* fixed more sp errors
* Fix new typos found by codespell.
* fixed proceed with precede
* fixed variable in fortran test
* fixed minnum
* updated spelling list
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
|
|
|
|
|
|
|
|
|
|
|
| |
* Removes C++ dependency on H5private.h
Most C API calls have been removed, aside from a few uses of free,
where we just dropped the 'HD'. A couple of H5_ATTR_UNUSED macros
were also replaced with (void) statements.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
* BUG: DataSet assignment operator is missing
* Some compilers complain if the copy constructor is given explicitly
but the assignment operator is implicitly set to default.
* Explicitly defining the assignment operator allows us to properly
handle reference counters for shared resources.
* BUG: DataSet assignment operator is missing.
* Mimicking code of H5DataType::operator() as suggested by @bmribler.
* Added test
Description:
Added test for DataSet::operator= that Leengit added
Platform tested:
Linux/64 (jelly)
* Removed Author field.
* Commit clang format changes.
* Entry for Leengit's github PR #503
* Removed lines left by mistake
Co-authored-by: Binh-Minh Ribler <bmribler@hdfgroup.org>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
|
|
|
|
|
|
|
| |
* Update clang config to put H5E_BEGIN_TRY / H5E_END_TRY on separate lines, empty C++ methods on separate lines, understand that ALL_MEMBERS / UNIQUE_MEMBERS are foreach macros, and properly skip the 'config' directory in the find command without emiting a warning
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
|
|
|
|
|
|
|
|
| |
After 30+ years, just assume that the following exist:
- extension-less includes
- namespaces
- std::
- static_cast
- bool
|
|
|
|
|
|
| |
* Modify temporary rpath for testing in java example scripts.
* Update URL in source file Copyright headers for web copy of COPYING
file - files not in src or test.
|
| |
|
| |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Description:
- Added class DSetAccPropList for the dataset access property list.
- Added wrapper for H5Dget_access_plist to class DataSet
// Gets the access property list of this dataset.
DSetAccPropList getAccessPlist() const;
- Added wrappers for H5Pset_chunk_cache and H5Pget_chunk_cache to class
DSetAccPropList
// Sets the raw data chunk cache parameters.
void setChunkCache(size_t rdcc_nslots, size_t rdcc_nbytes, double rdcc_w0)
// Retrieves the raw data chunk cache parameters.
void getChunkCache(size_t &rdcc_nslots, size_t &rdcc_nbytes, double &rdcc_w0)
- Added two more arguments to H5Location::createDataSet:
const DSetAccPropList& dapl = DSetAccPropList::DEFAULT
const LinkCreatPropList& lcpl = LinkCreatPropList::DEFAULT
- Added one more argument to H5Location::openDataSet:
const DSetAccPropList& dapl = DSetAccPropList::DEFAULT
Platforms tested:
Linux/64 (jelly)
Linux/32 (jam)
Darwin (osx1010test)
|
|
|
|
|
|
|
|
| |
Description:
- Updated the description of copy constructor for clarification.
- Removed unnecessary comments.
Platforms tested:
Linux/64 (jelly)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Description:
- Moved the new wrappers committed on Mar 9:
43158f3bb352f374c31556a5d0dc463a09e0b32e
to H5Location and renamed some of them for overloading.
This is because the loc_id in the C APIs can be file, group, dataset,
named datatype, and attribute. Previous implementation was wrong
following some inaccurate C API reference manual.
- Only the following wrappers are modified or added:
+ H5Lcreate_soft: changed name from newLink to link
// Creates a soft link from link_name to target_name.
void link(const char *target_name, const char *link_name,...)
void link(const H5std_string& target_name,...)
+ H5Lcreate_hard: changed name from newLink to link
// Creates a hard link from new_name to curr_name.
void link(const char *curr_name, const Group& new_loc,...)
void link(const H5std_string& curr_name, const Group& new_loc,...)
// Creates a hard link from new_name to curr_name in same location.
void link(const char *curr_name, const hid_t same_loc,...)
void link(const H5std_string& curr_name, const hid_t same_loc,...)
+ H5Ldelete: modified existing functions to add 2nd argument
// Removes the specified link from this location.
void unlink(const char *link_name,
const LinkAccPropList& lapl = LinkAccPropList::DEFAULT)
void unlink(const H5std_string& link_name,
const LinkAccPropList& lapl = LinkAccPropList::DEFAULT)
- copyLink and moveLink were only moved from Group to H5Location, no change
- Added class LinkCreatPropList
- Added overloaded functions H5Location::createGroup to take a link creation
property list
Group createGroup(const char* name, const LinkCreatPropList& lcpl)
Group createGroup(const H5std_string& name, const LinkCreatPropList& lcpl)
- Added wrapper for H5Lget_info() to H5Location
H5L_info_t getLinkInfo(const H5std_string& link_name,...)
Platforms tested:
Linux/64 (jelly)
Linux/ppc64 (ostrich)
Darwin (osx1010test)
|
|
|
|
|
|
|
|
|
|
| |
Description:
- Replaced external links with text including the C API name
- Removed links of copyright at the bottom of each page
- Removed logo at top
- Removed document name and version number
Platforms tested:
Linux/32 2.6 (jam) - only documentation
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Description:
- Removed two inadvertently-added Group constructors in the header file.
There was no implementation.
- Removed deprecated H5Location and H5Object constructors that take an
existing ID.
- Miscellaneous improvements in comments, including updating URLs.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (jelly)
Darwin (osx1010test)
|
|
|
|
|
|
|
|
|
|
| |
hdf5_1_10
* commit '54957d37f5aa73912763dbb6e308555e863c43f4':
Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes.
Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh.
Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1
Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
|
|
|
|
|
|
| |
Only format changes: mostly tabs vs. spaces
Platforms tested:
Linux/64 (jelly) - very minor
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Description:
Added wrappers H5Location::exists() for H5Lexists.
Added wrapper H5Object::objVersion() to return the header version
of an HDF5 object.
Added new class LinkAccPropList to be used by H5Location::exists()
Added new exception: ObjHeaderIException for H5Object::objVersion()
Rearranged source files in Makefile.am
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Description:
When adding wrappers for H5Lexists, a new class, LinkAccPropList, was
added to the C++ API, triggered complicated circular dependencies. Thus,
some improvement was made to resolve the problems.
- Replaced existing functions openXxxType with individual type constructors
+ Added individual XxxType constructors to replace the existing functions
openXxxType because it's rather awkward to use these functions.
+ Moved openXxxType from H5Location back to CommonFG
+ Put back CommonFG as a baseclass of Group for openXxxType functions.
+ This replacement should improve usability and prevent the problem of
circular dependencies.
- Removed overloaded constructor that takes an Attribute when there is
already one that takes H5Location because Attribute inherits from
H5Location now.
Platforms tested:
Linux/32 2.6 (jam)
Darwin (osx1010test)
Linux/64 (platypus)
|
|
|
|
|
|
|
|
|
|
|
|
| |
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:
Adding user's test revealed a flaw in the fix.
Moved CommonFG's functions in Group to H5Location, so that they
could be called by objects that can be used to specify a location
Also, rearranged many "#include" header files to resolve conflicts.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
trunk:
Description:
Continued rearranging the classes to model the relationship of HDF5
objects more accurately. The changes included:
- in the baseclass list of Attribute, changed "public IdComponent" to
"public H5Location", because location sometime can be specified with
attribute
- moved H5A wrappers in H5Location to H5Object because H5A functions
can't be called on attribute id
- removed the stubs Attribute::iterateAttrs and Attribute::renameAttr
- removed Attribute::getFileName and Attribute::flush, because
H5Location has them
- result of the modified partial class diagram, regarding Attribute
IdComponent
|
H5Location AbstractDs
/ \ /
H5Object Attribute
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Description:
Rearranged the classes to model the relationship of HDF5 objects more
accurately. The changes included:
- moved CommonFG's methods to Group
- removed CommonFG from Group's base class list
- removed CommonFG from H5File's base class list and changed
"public H5Location" to "public Group" in the base class list
- CommonFG became unused
- result of the modified partial class diagram:
IdComponent
|
H5Location
/
H5Object
|
/ / \
DadaType Group DataSet
|
H5File
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
|
|
|
|
|
|
|
|
|
| |
Description:
Removed deprecated functions in previous releases due to missing const.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
|
|
|
|
|
|
|
|
|
|
|
|
| |
Description:
- Changed object in catch statements to reference
- Replaced old-style casts or reinterpret_cast with static_cast
- Removed unused name H5Library::need_cleanup
- Removed Exception::printError from documentation
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
|
|
|
|
|
|
| |
Removed another left-over commented-out line.
Platforms tested:
Linux/64 (platypus) - very minor
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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:
- Implemented the friend function
void f_PropList_setId(PropList* plist, hid_t new_id)
to work around the same problem described in trunk r26655, for the
API DataSet::getCreatePlist()
- Cleaned up some comments and obsolete functions
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Description:
Added wrappers for H5P[s/g]et_attr_phase_change and H5P[s/g]et_attr_creation_order
// Sets attribute storage phase change thresholds.
void setAttrPhaseChange(unsigned max_compact = 8, unsigned min_dense = 6)
// Gets attribute storage phase change thresholds.
void getAttrPhaseChange(unsigned& max_compact, unsigned& min_dense)
// Sets tracking and indexing of attribute creation order.
void setAttrCrtOrder(unsigned crt_order_flags)
// Gets tracking and indexing settings for attribute creation order.
unsigned getAttrCrtOrder()
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:
When copy constructor or constructor that takes an existing id is invoked,
the C ref counter stays the same but there is an extra C++ object which
later is destroyed and may cause the HDF5 id to be closed prematurely. The
C++ library needs to increment the ref counter in these situations, so that
the C library will not close the id when it is still being referenced.
However, the incrementing of ref count left some objects opened at the end
of the program, perhaps, due to compiler's optimization on cons/destructors. The constructor, that takes an existing id, needs to increment the counter
but it seems that the matching destructor wasn't invoked. The workaround
is to have a function for each class that has "id" that only sets the id
and not increment the ref count for the library to use in these situations.
These functions are "friend" and not public.
The friend functions are:
void f_Attribute_setId(Attribute *, hid_t)
void f_DataSet_setId(DataSet *, hid_t)
void f_DataSpace_setId(DataSpace *, hid_t)
void f_DataType_setId(DataType *, hid_t)
Platforms tested:
Linux/64 (platypus)
Linux/32 2.6 (jam gnu and Intel 15.0)
SunOS 5.11 (emu)
|
|
|
|
|
|
|
|
|
|
| |
Description:
Fixed base classes that were in wrong order on the prototype lines and
some misc. warnings.
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)
|
|
|
|
|
|
|
|
| |
Fixed some minor documentation mistakes.
Updated configuration file for Doxygen.
Platforms tested:
Linux/ppc64 (ostrich)
Linux/32 2.6 (jam)
|
|
|
|
|
|
|
|
|
|
| |
Description:
- Added const to const arguments
- Fixed miscellaneous comments
Platforms tested:
Linux/ppc64 (ostrich)
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
|
|
|
|
|
|
|
|
|
|
|
| |
- Added another overload for char* argument:
ssize_t getComment(const char* name, const size_t buf_size, char* comment)
- Changed default value to 0 for the other two getComment methods
- Added HDmemset to after every char string allocation to clear the buffer
Platforms tested:
Linux/ppc64 (ostrich)
Linux/32 2.6 (jam)
Linux/64 2.6 (platypus)/PGI compilers
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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)
|
|
|
|
|
|
|
| |
Fixed comments, documentation, and mis-matched DOXYGEN_SHOULD_SKIP_THIS pairs.
Platforms tested:
Linux/32 2.6 (jam)
Regenerated and verified generated documentation.
|
|
|
|
|
|
|
|
|
|
| |
Description:
Fixed miscellaneous inconsistencies and typos, which also took
care of the failure in Packet Table test on daily test today.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 2.6 (koala)
Mac Lion (duck)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Description:
In this bug, H5File doesn't have the ability to create attribute. The
following changes will provide that functionality and several others that
were also missing:
- Added an abstract class H5Location in between IdComponent and H5Object.
- New class structure of IdComponent, H5Location, H5Object, H5File
IdComponent
|
H5Location
/ \
H5Object H5File
- Wrappers in H5Object were moved to H5Location because the related C
functions take either file, group, dataset, or named datatype ID.
- Added wrapper for H5Rget_obj_type2
- Added tests for file attributes and H5Rget_obj_type2 wrapper
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 2.6 (koala)
SunOS 5.10 (linew)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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:
Closed various HDF5 objects in DataSet::getInMemDataSize and
Attribute::getInMemDataSize to remove some memory leaks.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 2.6 (amani)
SunOS 5.10 (linew)
|