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* Hdf5 merge issue 537 v112 (#538)Larry Knox2021-04-021-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Snapshot version 1.12 release 1-3. Update version to 1.12.1-4. * First cut of the H5 public API documentation. (#80) * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Full set of current H5F documentation. (#105) * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Migrated documentation for SWMR functions. * Catching up on MDC functions. * Integrated the H5F MDC function documentation. * Added MDC and parallel H5F functions. * Slightly updated main page. * Added doxygen/dox/H5AC_cache_config_t.dox to MANIFEST. * Doxygen - added (mostly) beginner functions (#112) * Doxygen - added (mostly) beginner functions * Removed duplicate H5Pset_szip function * Add src/H5module.h to MANIFEST. * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Avoid aligned access for references by decoding into temporary buffer and then copying the result into the actual buffer. Update test to be more thorough with using compound datatype fields everywhere. (#206) * Modify temporary rpath for testing in java example scripts. (#230) * Fix undefined left shifting of negative numbers (#338) Undefined Bahavior Sanitizer errored here about left shifting negative numbers. * Fixes various warnings noticed on Windows (#425) * Fixes various warnings noticed on Windows - Adds a prototype for our implementation of vasprintf - Return type of H5_get_utf16_str() is now non-const - Fixes possible uninitialized return type in Wremove_utf8 - Better isolation of fork() code in accum.c:test_swmr_write_big() - Better isolation of non-zlib code in dsets.c:test_filter_delete() - Removed unused variable in trefer.c:test_reference_cmpnd_obj() * Fixes clang-format issues * Applied clang-tidy readability-non-const-parameter warning fixes auto… (#429) * Automatically applied clang-tidy readability-avoid-const-params-in-decls fixes Removes useless const declarations. * Fixed most readability-non-const-parameter warnings These changes were made automatically by clang-tidy, but I manually reverted the changes related to the H5Z_func_t signature. * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Added C++11 override keyword where appropriate (#433) Added H5_OVERRIDE macro for compatibility with both C++11 and older. * Various clang tidy warning fixes (#448) * Fixed clang-tidy bugprone-reserved-identifier warnings * Fixed clang-tidy bugprone-assert-side-effect warnings * Fixed clang-tidy bugprone-copy-constructor-init warning * Fixed clang-tidy readability-redundant-preprocessor warning For error_test.c the removed code was already dead, because it was in the else of an `#if H5_USE_16_API` block. Based on H5Location.h, I think p_get_ref_obj_type was meant to be in `#ifndef DOXYGEN_SHOULD_SKIP_THIS` and an `#endif` was missing. Similarly, in the header, getObjTypeByIdx is only in H5_NO_DEPRECATED_SYMBOLS, not DOXYGEN_SHOULD_SKIP_THIS. * Fixed clang-tidy readability-redundant-string-init warnings * Fixed some clang-tidy performance-type-promotion-in-math-fn warnings * Fixed clang-tidy performance-unnecessary-value-param warnings * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Removed checks/workarounds for pre-C++89 compatibility (#449) After 30+ years, just assume that the following exist: - extension-less includes - namespaces - std:: - static_cast - bool * Fixed all clang-tidy bugprone-suspicious-string-compare warnings (#451) * Fixed all clang-tidy bugprone-suspicious-string-compare warnings This change was generated entirely by clang-tidy itself. * Reformat code with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Remove 2 functions incorrectly merged from develop in a cherry-pick merge of PR #451. * More warning fixes (#400) * Fixed -Wunused-local-typedef warning * Fixed -Wformat warnings In one case also removed a `z` character. There was a `z%d` that I think was supposed to be `%zd` * Fixed -Wshorten-64-to-32 warnings * Fixed -Wself-assign warnings * Fixed -Wreserved-id-macro warnings * Commit format changes from clang-format, clang version 10.0.1. * Fixed -Wself-assign warnings * Fixed -Wunused-local-typedef warning * Fixed -Wformat warnings In two cases also removed a `z` character. There was a `z%d` that was supposed to be `%zd`. * Fixed -Wshorten-64-to-32 warnings * Fixed -Wreserved-id-macro warnings * Fixed -Wself-assign warnings * Format source. * Remove blank lines to pass format check. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Changes found during merge to 1.12 (#414) * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit * Note LLVM 10 to 11 format default changes * Update format plugin * Undo clang-format version 11 changes * One more correction * Update supported platforms * Revert whitespace changes * Correct whitespace * Changes from PR#3 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments * GH #386 java folder copyright corrections * Whitespace * GH #359 implement and fix tools 1.6 API usage * remove excessive comments * Flip inits to correct ifdef section * rework ifdef to be simpler * format issue * Reformat ifdef inits * remove static attribute * format compliance * Update names * Revert because logic relies on float not being int * Changes noticed from creating merge of #412 * Double underscore change * Correct compiler version variable used * Remove header guard underscores * Whitespace cleanup * Align with "parallel fence" changes (#479) * Small code updates and simplifications * Committing clang-format changes * Fix 'make installcheck' for parallel builds Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * File locks now work on Windows (#480) * File locks now work on Windows Uses LockFileEx() and UnlockFileEx(). Fixes HDFFV-10191 (partial). * Committing clang-format changes * Committing clang-format changes * Fixes commenting in h5repack * Reworks H5Fis_accessible() H5Fis_accessible() created a new file handle and attempted to read through it, which will fail when a file has been opened with an exclusive lock on operating systems that have mandatory locks. This change uses the same scheme we use in H5Fopen() to check if the file is already open and only tries to read the file signature if the file has not already been opened. Also adds a test for this behavior. * Committing clang-format changes * Trivial change to force github to run actions Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * small edits (#481) * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Adds an implementation for nanosleep on Windows (#483) * Adds an implementation for nanosleep on Windows * Committing clang-format changes * Fix insane formatter issue Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Updates HSYS_GOTO_ERROR to emit GetLastError() values on Win32 (#492) * Committing clang-format changes * Updates H5SYS_GOTO_ERROR to emit Win32's GetLastError() * Committing clang-format changes * Format source changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Updates that allow accum SWMR tests to work on Windows (#493) * Committing clang-format changes * Updates the accum test to work on Windows Uses CreateProcess() on Windows * Source formatting * Fix for Unix child result * Fixes process return code bug on Windows Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Disable long double tests and remove CMake flag groups (#494) * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit * Note LLVM 10 to 11 format default changes * Update format plugin * Undo clang-format version 11 changes * One more correction * Update supported platforms * Revert whitespace changes * Correct whitespace * Changes from PR#3 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments * GH #386 java folder copyright corrections * Whitespace * GH #359 implement and fix tools 1.6 API usage * remove excessive comments * Flip inits to correct ifdef section * rework ifdef to be simpler * format issue * Reformat ifdef inits * remove static attribute * format compliance * Update names * Revert because logic relies on float not being int * Changes noticed from creating merge of #412 * Double underscore change * Correct compiler version variable used * Remove header guard underscores * Whitespace cleanup * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * correct window os name * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes * HDFFV-11113 long double in tools * HDFFV-11113 add note * Disable long double tests for now * HDFFV-11228 remove arbitrary CMake warning groups. * Make each flag a string Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Misc warning fixes (#495) * Committing clang-format changes * Misc warning fixes from Visual Studio * Committing clang-format changes * Fixes warnings in swmr.c test * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes support for pre-2015 Visual Studio (#496) * Committing clang-format changes * Removes work-around code for pre-2015 Visual Studio HDF5 no longer provides an implementation for: * <inttypes.h> * snprintf and vsnprintf * llround(f), lround(f), round(f) * strtoll and strtoull * va_copy * struct timespec Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Remove extra parameter from merge. * Resolve missed merge conflict. Co-authored-by: Gerd Heber <gheber@hdfgroup.org> Co-authored-by: bljhdf <58825073+bljhdf@users.noreply.github.com> Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Quincey Koziol <quincey@koziol.cc> Co-authored-by: Sean McBride <sean@rogue-research.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Co-authored-by: Quincey Koziol <koziol@lbl.gov> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
* 1 12 Merges from develop (#421)Allen Byrne2021-03-041-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 fix tools test for plugins * sync fork * Merge of changes from dev * Move problem option to bottom of the list until fixed * HDFFV-11106 - fix parsing optional args * HDFFV-11106 add note * grammer fix * Whitespace after clang formatting * Undo format version 11 changes * Update check to working version * Merge workflow and minor changes from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge serval small changes from dev * fix typo * Minor non-space formatting changes * GH #386 copyright corrections for java folder * revert because logic requires false return * Merges from develop #358 patches from vtk #361 fix header guard spelling * Remove case statement for H5I_EVENTSET * Correct call with versioning * Remove tabs * Double underscore change * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings Remove more underscores from header guards
* Update URL in source file Copyright headers for web copy of COPYINGLarry Knox2021-02-201-1/+1
| | | | file - files not in src or test.
* Source formattedAllen Byrne2020-10-011-53/+56
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* Fixed documentationBinh-Minh Ribler2018-03-131-13/+0
| | | | | | | | Description: - Updated the description of copy constructor for clarification. - Removed unnecessary comments. Platforms tested: Linux/64 (jelly)
* Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-251-6/+4
| | | | | | | | | | 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.
* Description:Binh-Minh Ribler2017-03-171-1/+1
| | | | | | | Miscellaneous clean-up: format and comments Platforms tested: Linux/64 (jelly) Darwin (osx1010test)
* Purpose: Add new C++ wrappersBinh-Minh Ribler2017-03-141-1/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description: Added wrappers for H5Iis_valid, H5Ps/get_nlinks, H5Tget_create_plist, H5Oopen, H5Oclose and H5Pset_virtual // Checks if the given ID is valid. static bool isValid(hid_t an_id); // Sets the number of soft or user-defined links that can be // traversed before a failure occurs. void setNumLinks(size_t nlinks) const; // Gets the number of soft or user-defined link traversals allowed size_t getNumLinks() const; // Returns a copy of the creation property list of a datatype. PropList getCreatePlist() const; // Opens an object within a group or a file, i.e., root group. hid_t getObjId(const char* name,...); hid_t getObjId(const H5std_string& name,...); // Closes an object opened by getObjId(). void closeObjId(hid_t obj_id) const; // Maps elements of a virtual dataset to elements of the source dataset. void setVirtual(const DataSpace& vspace, const char *src_fname,...); void setVirtual(const DataSpace& vspace, const H5std_string src_fname,...); Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
* Description:Binh-Minh Ribler2017-03-031-56/+56
| | | | | | Only format changes: mostly tabs vs. spaces Platforms tested: Linux/64 (jelly) - very minor
* Purpose: Add new C++ wrappersBinh-Minh Ribler2017-02-231-0/+6
| | | | | | | | | | | | | | | | | | | Description: Added wrappers for H5Fget_info2, H5Inmembers, and H5Itype_exists // Gets general information about this file. void getFileInfo(H5F_info2_t& file_info) const; // Returns the number of members in a type. static hsize_t getNumMembers(H5I_type_t type); // Determines if an element type exists. static bool typeExists(H5I_type_t type); Platforms tested: Linux/32 2.6 (jam) Linux/64 (jelly) Darwin (osx1010test)
* Description:Binh-Minh Ribler2016-10-191-4/+0
| | | | | | | | | | | | 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
* Purpose: Updated documentationBinh-Minh Ribler2016-09-271-2/+0
| | | | | | | | | Description: Revised class brief description and other comments for up-to-date info. Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
* [svn-r28027] Purpose: Fix memory leaksBinh-Minh Ribler2015-10-111-16/+20
| | | | | | | | | | | | | Description: - Removed H5Library::instance because it is unnecessary. All H5Library's methods are static. This, in turn, removed the memory leaks by H5Library::instance not being deleted. - Added ObjCreatPropList::deleteConstants to atexist() list - Cleaned up comments and format inconsistencies with 1.8 Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
* [svn-r27945] Purpose: Fix HDFFV-9529Binh-Minh Ribler2015-10-041-0/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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)
* [svn-r26655] Purpose: Fixed HDFFV-7947Binh-Minh Ribler2015-03-301-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | 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)
* [svn-r26457] Purpose: Fix warnings HDFFV-8658Binh-Minh Ribler2015-03-151-1/+8
| | | | | | | | | | | | | | | | | | | | | | | | 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)
* [svn-r24969] Description:Binh-Minh Ribler2014-04-061-0/+3
| | | | | | | | | | | | | | - Added wrappers to H5Object for H5Iget_name() to get object's name ssize_t getObjName(char *obj_name, size_t buf_size = 0) const; ssize_t getObjName(H5std_string& obj_name, size_t len = 0) const; H5std_string getObjName() const; - Added tests tobject.cpp - Added to various cleanup_* functions in tests to remove generated files - Added an overload H5I_type_t getHDFObjType() to get object's type Platforms tested: Linux/ppc64 (ostrich) Linux/32 2.6 (jam) SunOS 5.11 (emu) with gmake
* [svn-r24291] Description:Binh-Minh Ribler2013-10-151-4/+8
| | | | | | | | | - Added a lot of documentation to classes for Reference Manual. - Fixed some format inconsistencies Platforms tested: Linux/ppc64 (ostrich) Linux/32 2.6 (jam) Linux/64 2.6 (koala)/PGI compilers
* [svn-r24189] Purpose: Fixed bug HDFFV-1060Binh-Minh Ribler2013-09-231-3/+3
| | | | | | | | Description: Changed header guards from single underscore to double underscore. Platforms tested: Linux/32 2.6 (jam) - very minor Linux/64 2.6 (koala)/PGI compilers
* [svn-r24143] Description:Binh-Minh Ribler2013-09-161-0/+2
| | | | | | | Fixed comments, documentation, and mis-matched DOXYGEN_SHOULD_SKIP_THIS pairs. Platforms tested: Linux/32 2.6 (jam) Regenerated and verified generated documentation.
* [svn-r22845] Purpose: Misc fixesBinh-Minh Ribler2012-09-281-1/+1
| | | | | | | | | | 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)
* [svn-r15959] Description:Binh-Minh Ribler2008-10-271-3/+0
| | | | | | | | | | | | Added missing wrappers for H5Rdereference. Also, for these wrappers, improved exception handlings to report specific overloaded functions, where failure occurs. Will do the same for more functions later... Platforms tested: Linux 2.6 (kagiso) SunOS 5.10 (linew) FreeBSD (duty)
* [svn-r15407] Purpose: Fix bugBinh-Minh Ribler2008-07-251-1/+5
| | | | | | | | | | | | | | | | | 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)
* [svn-r15308] Purpose: Fixed bugsBinh-Minh Ribler2008-07-021-27/+6
| | | | | | | | | | | | | | | | 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)
* [svn-r14148] Description:Quincey Koziol2007-09-141-0/+2
| | | | | | | | | | | | | | | | Add H5Rget_obj_type() to the API versioning and switch internal routines to use H5Rget_obj_type2() Misc. other code cleanups, etc. Tested on: FreeBSD/32 6.2 (duty) FreeBSD/64 6.2 (liberty) Linux/32 2.6 (kagiso) Linux/64 2.6 (smirom) AIX/32 5.3 (copper) Solaris/32 2.10 (linew) Mac OS X/32 10.4.10 (amazon)
* [svn-r13253] Updated all C and C++ style source code files with the THG ↵Albert Cheng2007-02-071-2/+3
| | | | | | | | | copyright notice. 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.
* [svn-r12795] Purpose: Fixing bugBinh-Minh Ribler2006-10-221-3/+13
| | | | | | | | | | | | | | | | | | | | | | | | | Description: Wrappers of H5Rcreate had incorrect prototypes. Solution: Added these overloaded functions for H5Rcreate wrapper to IdComponent: void reference(void* ref, const char* name, DataSpace& dataspace, H5R_type_t ref_type = H5R_DATASET_REGION) const; void reference(void* ref, const char* name) const; void reference(void* ref, const H5std_string& name) const; Added these overloaded functions for H5Rdereference: void dereference(IdComponent& obj, void* ref); DataSet(IdComponent& obj, void* ref); Group(IdComponent& obj, void* ref); DataType(IdComponent& obj, void* ref); The incorrect wrappers will be removed after announcing. Platform tested: Linux 2.4 (heping) AIX 5.1 (copper) SunOS 5.8 64-bit (sol)
* [svn-r12404] Purpose: Fix typos/formatsBinh-Minh Ribler2006-06-051-10/+10
| | | | | | | | | | 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)
* [svn-r12200] Purpose: MaintenanceBinh-Minh Ribler2006-04-051-3/+3
| | | | | | | | | | | | Description: Changed to alias string instead of std, i.e. H5std_string instead of H5std, because the old way wasn't working when std didn't exist. Platforms tested: Linux 2.4 (heping) SunOS 5.8 64-bit (sol) HPUX 11.00 (kelgia) - this was the problematic platform but I wasn't able to test before.
* [svn-r12180] Purpose: MaintenanceBinh-Minh Ribler2006-03-301-6/+3
| | | | | | | | | | | 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)
* [svn-r11755] Purpose: Code improvementBinh-Minh Ribler2005-12-031-1/+1
| | | | | | | | | | | | | | | | | 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)
* [svn-r11555] Purpose: Code cleanupBinh-Minh Ribler2005-10-121-12/+3
| | | | | | | | | | Description: Removed obsolete function CompType::getMemberDims. Fixed some typos. Platforms tested: Linux 2.4 (heping) SunOS 5.8 64-bit (sol)
* [svn-r11487] Purpose:Quincey Koziol2005-10-011-12/+12
| | | | | | | | | | | Code cleanup Description: Tweak copyright on C++ source files to reduce whining by copyright checking script. Platforms tested: FreeBSD 4.11 (sleipnir) w/C++
* [svn-r11264] Purpose: Additional code improvementBinh-Minh Ribler2005-08-181-0/+8
| | | | | | | | | | Description: Used "using" declaration and directive better to reduce namespace pollution. Platforms tested: Linux 2.4 (heping) SunOS 5.8 64-bit (sol)
* [svn-r11206] Purpose: Additional wrapper/Code improvementBinh-Minh Ribler2005-08-081-7/+16
| | | | | | | | | | | | | | | | Description: Added wrapper for H5Iget_type. Added try/catch to many APIs that call private functions so that more specific information can be provided at failure. Added IdComponent::inMemFunc to help providing specific info. Added const to parameters of several functions that missed that. Platforms tested: Linux 2.4 (heping) SunOS 5.8 64-bit (sol) AIX 5.1 (copper) IRIX64 with -n32 (modi4) HPUX 11.00 (kelgia)
* [svn-r11060] Purpose: Fix bug (reported by user)Binh-Minh Ribler2005-07-101-4/+17
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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)
* [svn-r9127] Purpose: Adding wrapper for new C API and other updatesBinh-Minh Ribler2004-08-201-30/+36
| | | | | | | | | | | | | Description: Added wrappers for H5Fget_name: H5File::getFileName H5Object::getFileName Moved some functions from Group into the base class CommonFG for H5File too. Platforms tested: SunOS 5.7 (arabica) Linux 2.4 (eirene)
* [svn-r8602] Purpose:Quincey Koziol2004-06-011-10/+0
| | | | | | | | | | | 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
* [svn-r8595] Purpose:Binh-Minh Ribler2004-05-281-0/+3
| | | | | | | | | | | | | | 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:
* [svn-r8588] Purpose:Binh-Minh Ribler2004-05-271-30/+9
| | | | | | | | | | | | | | | | | | | Add C++ wrappers - incrementally check-in Description Added wrapper for these C APIs: H5Rcreate H5Rget_obj_type H5Rget_region This is an incremental check-in to preserve the code, corresponding tests will follow in a few weeks. Platforms: Linux 2.4 (eirene) I'm checking the code out and test on arabica too. Misc. update:
* [svn-r6236] Purpose: CopyrightBinh-Minh Ribler2003-01-071-0/+14
| | | | | | | | | Description: Added copyright notice to C++ API files, including *.h, *.cpp, and Makefile.in Platforms: Linux 6.2 (eirene)
* [svn-r5932] MuQun Yang2002-09-201-1/+1
| | | | | | | | | Purpose: use H5_DLLCPP to replacer __DLLCPP__ for c++ interfaces. Description: Solution: Platforms tested: linux 2.2.18smp, IRIX64, solaris 2.7, windows 2000
* [svn-r4977] Binh-Minh Ribler2002-02-161-1/+1
| | | | | | | | | | | | | | | | | | | | | | | Purpose: Adding support for dll Description: Added __DLLCPP__ to all public classes and templates. Added #include "H5Include.h" to H5RefCounter.cpp because of the use of DLLCPP in .h file and it needs the following chain: H5Include.h/hdf5.h/H5public.h/H5api_adpt.h Added #pragma warning(disable: 4251) to H5Exception.h to eliminate this warning on private data members of type 'string.' This occurs because 'string' is not yet instantiated at compilation time; however, since the class is exported, the warning is harmless. Changed this member function's parameter to be passed as reference. from: void CompType::insertMember( const string name,... to: void CompType::insertMember( const string& name,... Platforms tested: Linux 6.2 (eirene) Windows 2000
* [svn-r4707] Binh-Minh Ribler2001-12-121-1/+1
| | | | | | | | | | | | Purpose: Bug fixing Description: H5IdComponent::operator= shouldn't be virtual because the subclass' operator= have different type for the rhs argument. Removed virtual Platforms tested: SunOS 5.7 (arabica) IRIX64 (modi4) - only tested that the warnings went away, still working on other configuration problems.
* [svn-r3707] Purpose: Bug fixes and code clean upBinh-Minh Ribler2001-03-251-4/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description and Solution: - Predefined type objects become outdated when the application calls H5close and then H5open to use the library again. Solution: + Reimplemented PredType using enum type to obtain up-to-date values for predefined types, i.e. H5T_xxx_yyy's, when they are used. + Added to PredType its own version of getId() to return the appropriate predefined type id according to the enum value. + Made IdComponent::getId() a virtual function - Since Albert already fixed the "multiply defined RcsId" problem, removed the now become unnessary "#undef RCSID" from H5Include.h - Added a check for func_name != NULL in one of the Exception constructors because seg. fault. might occur in some situations. - It is more convenient to make a copy of a datatype, dataspace, or property list by using assignment operator Solution: + Added assignment operator to DataType, DataSpace, and PropList so that they will invoke H5Tcopy, H5Scopy, and H5Pcopy, respectively, instead of just simply copying the data members as for other classes. So, now a type, space, or property list can be copied by either : mytype = original_type, or mytype.copy(original_type) Note that copy constructors are still just copying the data members. + Added an assignment operator to DataType that takes a predefined type. + Made IdComponent::operator= a virtual function Platforms tested: arabica (sparc-sun-solaris 2.7)
* [svn-r3540] Purpose:Binh-Minh Ribler2001-03-021-1/+1
| | | | | | | | | | | | | | | | | | | | Feasibility improvement Description: - Some member functions in class Exception can be called without an Exception instance exits, but because they are not static, they cannot. - Many exception throwings don't provide any information to callers. Solution: - Add 'static' to several member functions in class Exception. - Added <class name::function name> to some exceptions thrown in H5File.cpp and H5FcreatProp.cpp. I'm trying this for users' comments. More information may be added later and to all exceptions. - Changed the comment line for emacs editor to: // C++ informative line for the emacs editor: -*- C++ -*- because... I'd rather not say that the code "may look like C" :-) Platforms tested: Linux (gcc version egcs-2.91.66)
* [svn-r3534] Purpose:Bill Wendling2001-03-021-0/+1
| | | | | | | | | Bug Fix Description: Added comments to the top of C++ files to indicate that it's a C++ file and not a C source code file. Also added a macro which makes emacs automagically enter c++-mode. (Recommended by Frank Schimmel fschimme@monsoon.CAPS.ou.edu)
* [svn-r3122] Purpose:Binh-Minh Ribler2000-12-131-1/+1
| | | | | | | | | | | | | | | | Fix and improve Description: - Put functions that are common to H5File and Group into a prototype class, CommonFG. I didn't do that before because of the fear of the consequences of multiple inheritance, since H5File and Group already inherit from different super classes. I recently read a C++ book and learned to use MI more safely. This change reduced some more of code redundancy. - Added missing const to some function parameters Platforms tested: Solaris/CC 5.0 (arabica)
* [svn-r3114] Purpose: FixBinh-Minh Ribler2000-12-121-2/+2
| | | | | | | | | | | | | | | | | | | | Description: Dec CC compiler doesn't support some new c++ features. Some typos caused compilation erros on Dec Alpha. Solution: - Added macro BOOL_NOTDEFINED to define bool type on Dec Alpha (gondolin) since its compiler doesn't support bool. - Added macro NO_STATIC_CAST to prevent the use of the new c++ feature static_cast since Dec CC compiler doesn't support. - Added const to parameters of some functions to match the functions' declaration and definition. Typos errors and Dec CC complained. Platform: Solaris (arabica). Also tried to build on Dec Alpha but still not linked due to some missing compiler flags; its compilation went fine though.
* [svn-r2897] Purpose:Binh-Minh Ribler2000-11-141-0/+95
C++ API for 1.3.x branch Description: The *.C and *.h files named different than those in 1.2.x. They are in the form: 'H5' + classname, or just classname if the classname is already prefixed with 'H5' to avoid ambiguity in documentation context. This version has several hidden bugs fixed and an improvement on the reference counting approach. The classes and their inheritance structure are listed below: --------------------------------------- H5Library Exception RefCounter IdComponent H5File DataSpace H5Object Group AbstractDs DataSet Attribute DataType PredType EnumType CompType AtomType StrType IntType FloatType PropList FileCreatPropList FileAccPropList DSetCreatPropList DSetMemXferPropList --------------------------------------- IdComponent uses RefCounter to keep track of opened objects so proper termination of HDF5 objects can be maintained. Each class has a .h file containing the class declaration and a .C file containing its definition. In addition to the classes files, the following files do not have class information: - H5Cpp.h: header file to be included in user's application - H5Idtemplates.h: contains a template function used by several classes - H5Classes.h: contains forward class declarations - H5CommonFG.*: contains common code used by classes H5File and Group - H5Include.h: contains the hdf5.h header file and the #undef RCSID to work around the problem: multiple defined RcsId - H5Alltypes.h: simply serves as a container to hold the header files of all datatypes to simplify the header file inclusion Platforms: Solaris (arabica) and Linux
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