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* Bring async branch to develop (#166)Quincey Koziol2020-12-141-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Add H5Fwait, H5Dwait, and other changes for async vol connector * Revert temporary testing changes * Add H5Fwait to header file * Add H5VLreset_lib_state() routine. * Correct VOL wrap context when retrieving library state for file open & create. * Manage the API context's VOL connector state as part of the library state. * Set the 'VOL connector property valid' flag when restoring the library state. * Don't push new API context on stack when retrieving "current" one. * Check for NULL VOL wrap context before decrementing refcount on it, when freeing the API context state. * Manage recount of underlying connector for VOL wrap context. * Add H5TSmutex_acquire() and H5TSmutex_release() routines to acquire and release the global lock on the HDF5 library. * Update library with new functions related to library global lock * Add asynchronous token API * Add new lightweight FUNC_ENTER / LEAVE macros for helping to structure the threadsafety (H5TS*) routines. * Sync w/develop * Initial event set code framework. * Elaborate on the H5ES routines, starting to add API routines. Update the "close ID" callbacks to allow asynchronous request tokens to be passed in from an asynchronous close API call. Refactor current asynchronous API routines (H5Fopen/H5Fclose and H5Dread/H5Dread) to use event sets instead of directly working with request tokens from the application. Clean up a few other minor warnings & code style issues. * Implement H5EScreate, H5ESget_count, and H5ESclose. It should be possible to write a simple application that creates an event set and uses it with H5Fopen_async, H5Dread_async, H5Dwrite_async, and H5Fclose_async, then calls H5ESclose (which waits for all async events to complete). * Add source file for event set test. * Refactor sync & async API routines to call common routine. Move dataset API read / write routines to src/H5D.c, along with all the other API routines. Progress on "fake" async VOL connector, for testing. * Modify async implementation to wrap async requests in a H5VL_object_t struct so the VOL layer can find the connector when accessing the request at a later point. * Free the requests is H5ESclose. Remove comments implying that request wait, notify, and cancel callbacks should free the request. * Fix bug in error handling in H5Fclose. * Fix bugs in async file routines. Rename H5VL_create_object_generic to H5VL_create_object. * Add explicit async version of H5Fcreate. * Add more _async routines * Correct typo for return value from H5Awrite changes * Add H5EStest and H5ESwait routines * Updated with API tracing info * Fix NULL pointer dereference in H5ES__wait * Add H5is_library_terminating() routine, so that VOL connectors can detect when the library is shutting down. * Fix typo * Remove event from event set's linked list * Move block of code so that vol_obj is valid * Avoid setting properties in the DXPL when reseting the library state (and in the test code). * Refactor argument tracing to implement new capability for tracing arguments of non-API routines, with the H5ARG_TRACE macro. This macro is updated automatically with the bin/trace script that runs as part of the autogen.sh process. Major changes were in src/H5trace.c and bin/trace, with the other changes being cleanups to the argument lists, to improve their presentation in the tracing output. Also - added the "managed string" routines, which can dynamically allocate strings, appending printf-formatted output to the string efficiently. * Release memory for managed strings * Fix printf() formats. * More printf() format fixes. * Add H5Eappend_stack routine and regression tests * Clean up a few missed merge conflicts and update the error stacks. * Remove unnecessary fork() operations and ten second sleep(). * Restore commented out attribute out, to better enable tracking down the previous failure * Allow multiple H5ARG_TRACE macros within a routine to be updated * Switch to using "new" H5ES_insert (which takes the arguments for the caller routine) for all event set operations. Renames H5ES_insert_new to H5ES_insert and removes the previous H5ES_insert. * Merge "managed" string routines into "ref-counted" strings, and refactor code to use them. * Add missing file. * Add caller's name and arguments to event, for error reporting * Refactor event set setup for "API common" internal routines * Checkin async API routines for H5A* and H5G* modules as listed in ID-283. Fix couple h5dump expected output files due to the changes. * Add some of the error query routines needed for event sets. * Refactor to make async setup / teardown and "common" routines cleaner * (1) Add async APIs to H5L, H5F, and H5D modules (2) Fix errors in previous checkins of async APIs in H5A and H5G modules (3) h5dump expected output changes * Enhance event info, for better error handling * Change name of temporary vol_obj variable, to help reduce coding errors * Fix oversight with vol_obj pointer * Minor code cleanup * Add missing \'valid\' flag for VOL wrapper context, when restoring the library\'s state * Run source formatter * Change H5TSmutex lock and release to include a lock count * Update error reporting ideas * Minor updates to improve sanity checking for retrieving / restoring library state * Updated with feedback from h5py team members * Refactor internal event set list and event handling, add implementation for H5ESget_err_info * Change the VOL request subclass callbacks that switch from using "H5ES_status_t" to "H5VL_request_status_t", and also add a H5VL_request_status_t* parameter to the 'cancel' callback in the request subclass. Also more code quality cleanups to add iterator callbacks to internal event set routines. * Update API tracing for new H5VL_request_status_t typedef * Finish converting internal event set operations to use list iterator callbacks, instead of directly accessing the list structure * Add H5VL_REQUEST_GET_ERR_STACK operation to request subclass, for retrieving a copy of the error stack for a failed asynchronous operation * Remove 'canceled' event status from Java constants * Be safer about releasing resources when inserting a newly opened/created object or file into an event set * Remove H5EStest, add H5ES_WAIT_NONE for 0 timeout, and revise parameters to H5ESwait, to make it more "aggregate". * Remove H5ES_STATUS_CANCELED from Java wrappers also * (a) Add async APIs for H5O module as listed in jira issue ID-283. (b) Remove verification of name parameter in async related routines for H55A and H5L modules because it is checked in H5VL_setup* routine. (c) Modify h5dump expected output due to the async changes. * Corrections based on PR feedback. * Further changes to make based on PR feedback. * Fix missed merge marker, and reformatted line * Clean up some warnings * Correct level of indirection * Relocate prototype (and doxygen info) for H5Aclose * Change non-static function declarations to be static * Ensure that H5TSpublic.h header gets installed (#129) * Add 'wrapper' versions of async calls, to allow language wrappers and layers on top of HDF5 to pass in their application information. * Switch H5Aexists\*_async and H5Lexists\*_async to use flag to return status, instead of return value. Make the corresponding changes through most of the v1 and v2 B-tree code. Clean up warnings in H5public.h and cmpd_dtransform.c. * Add H5Iregister_future routine and tests. * Correct return value for H5Lexists_async * Add H5_DLL macro to public H5ES API routines * Update supported -> flags parameter for introspect_query callback * Remove my email address. Update passthrough VOL connector ID. * Fix comment for post_open_api_common * Remove unused non-blocking VOL connector * Minor cleanup in async branch in preparation for merge to develop * Update CMake and the Autotools to use the new pass-through VOL ID * Fix for SWMR daily test failures (#160) The H5I_register_using_existing_id() call did not initialize the future ID callbacks, causing the library to segfault when it tried to resolve those function pointers. * Added selective async APIs (#150) * Added selective async APIs Description: Added the following APIs: H5Ropen_attr_async H5Ropen_object_async H5Ropen_region_async H5Mcreate_async H5Mopen_async H5Mput_async H5Mget_async H5Mclose_async H5Tcommit_async H5Topen_async H5Tcopy_async H5Tclose_async - Updated an expected output file to include a new internal function in the error stack for the failure case. * Updated async APIs per reviews, including removing async version of H5Tcopy. * Removed statements that were added by mistake in the previous commit. * Fix compile issues in H5M and warnings elsewhere * Reformat code * Brings VOL_LIST changes from develop. (#163) Co-authored-by: Houjun Tang <htang4@lbl.gov> Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org> Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: vchoi-hdfgroup <55293060+vchoi-hdfgroup@users.noreply.github.com> Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Dana Robinson <derobins@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* Basic alignment with async branch (#115)Quincey Koziol2020-11-231-1/+1
| | | | | | | * Basic alignment with async branch - trivial changes to reduce clutter in overall diff. * Update minor error code to reflect change within library * Update the error output to match library
* CMake: Add an option to opt-out static libgccMichel Zou2020-10-311-1/+1
| | | | | With sjlj exception model, statically link to libgcc/libstdc++ prevents exceptions to be caught from other dynamic libraries.
* Clang-format of source filesAllen Byrne2020-09-3017-2689/+2592
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* OESS-98 merge with clang-format changesAllen Byrne2020-09-251-1/+1
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* CMake and script changes for clang-formatAllen Byrne2020-09-041-1/+8
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* TRILAB-244 separate CXX warnings and errors from CAllen Byrne2020-04-233-6/+5
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* Trim trailing whitespaceQuincey Koziol2020-04-208-22/+22
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* TRILAB-192 add c++ and fortran warnings build systems one fileAllen Byrne2020-04-051-0/+1
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* TRILAB-142 Change minimum CMake version to 3.12Allen Byrne2020-02-211-1/+1
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* Squashed commit of the token_refactoring branch:Dana Robinson2020-01-167-32/+32
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* HDFFV-11001 need to qualify all by parallel or serial typesAllen Byrne2020-01-151-1/+1
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* HDFFV-11001 Add fine control over testingAllen Byrne2020-01-151-1/+3
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* Fix VFD tests and repackAllen Byrne2019-08-031-37/+44
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* HDFFV-10529 Update CMake tests to use test fixturesAllen Byrne2019-07-231-1/+2
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* HDFFV-10845 make flags privateAllen Byrne2019-07-181-0/+5
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* HDFFV-10845 use of TARGETFILE disables auto emulatorAllen Byrne2019-07-172-1/+3
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* HDFFV-10805 Add option to only build shared targetsAllen Byrne2019-06-181-7/+8
| | | | | HDFFV-10805 Add ONLY_SHARED_LIBS option and prefer shared over static HDFFV-10803 Update FindSZIP.cmake find module Remove unneeded modules and update java modules
* Added new C++ wrappers - HDFFV-10622Binh-Minh Ribler2019-04-221-6/+118
| | | | | | | | | | | | | | | | Description: Added wrappers for H5Pset/get_create_intermediate_group: // Specifies in property list whether to create missing // intermediate groups void setCreateIntermediateGroup(bool crt_intmd_group) const; // Determines whether property is set to enable creating missing // intermediate groups bool getCreateIntermediateGroup() const; Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1011test)
* Add C++, Java, and FORTRAN wrappers and tests for H5Fget_filenoQuincey Koziol2019-04-141-0/+59
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* Merge branch 'develop' of ↵Binh-Minh Ribler2019-03-203-279/+142
|\ | | | | | | https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5_bmr_fixbug into develop
| * Code improvementBinh-Minh Ribler2019-02-162-279/+10
| | | | | | | | | | | | | | Description: Removed dead code and accidentally leftover code Platforms tested: Linux/64 (jelly) - very minor
| * Adding a C++ wrapperBinh-Minh Ribler2019-02-141-12/+144
| | | | | | | | | | | | | | | | | | | | | | | | | | Description: - Added a wrapper for H5Ovisit2 to class H5Object // Recursively visit elements reachable from this object. void visit(H5_index_t idx_type, H5_iter_order_t order, visit_operator_t user_op, void *op_data, unsigned int fields); - Fixed various typos in documentation Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1011test)
| * Refactor out timeout valuesAllen Byrne2019-02-061-1/+1
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* | Fixed HDFFV-10210 and HDFFV-10587Binh-Minh Ribler2019-03-201-2/+2
|/ | | | | | | | | | | Description: - Added parameter validation (HDFFV-10210) - Added detection of division by zero (HDFFV-10587 - CVE-2018-17438) - Fixed typos in various tests Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1011test)
* Remove unused CMake filesAllen Byrne2018-12-212-29/+0
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* HDFFV-10656 Add CHECK_VOL support to CMakeAllen Byrne2018-12-203-48/+99
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* Add support for "make check-vol", along with a few minor cleanups, etc.Quincey Koziol2018-11-291-5/+0
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* Develop normalization with vol_integration.Dana Robinson2018-09-191-4/+4
| | | | | Mostly peripheral things like the tools and wrappers, with just enough core library code to support that.
* Added class DSetAccPropListBinh-Minh Ribler2018-07-221-2/+113
| | | | | | | | | | | | | | | | | | | | | | | | | | | | 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)
* Code improvementBinh-Minh Ribler2018-07-216-35/+34
| | | | | | | | | | | Description: Moved the new H5Object::getInfo member functions to H5Location and made them overloaded with the existing H5Location::getObjinfo. This way is cleaner than the previous approach. Platforms tested: Linux/64 (jelly) Linux/32 (jam) Darwin (osx1010test)
* Fixed EED-319Binh-Minh Ribler2018-07-181-3/+12
| | | | | | | | | Description: - Fixed doc issue Added an html version for the C++ function mapping table and removed the single web page version. Updated cpp_doc_config to use the html file. - Added a couple more minor tests
* Fixed HDFFV-10472Binh-Minh Ribler2018-07-171-0/+81
| | | | | | | | | | Description: Added operator!= to DataType bool operator!=(const DataType& compared_type) Platforms tested: Linux/64 (jelly) Linux/32 (jam) Darwin (osx1010test)
* Fixed HDFFV-10458 partiallyBinh-Minh Ribler2018-07-172-0/+77
| | | | | | | | | | | | | | | | | | | Description: Added wrappers for H5Oget_info_by_idx2. // Returns information about an HDF5 object, given its index. void getInfo(const char* grp_name, H5_index_t idx_type, H5_iter_order_t order, hsize_t idx, H5O_info_t& objinfo, unsigned fields = H5O_INFO_BASIC, const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) void getInfo(const H5std_string& grp_name, H5_index_t idx_type, H5_iter_order_t order, hsize_t idx, H5O_info_t& objinfo, unsigned fields = H5O_INFO_BASIC, const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) Platforms tested: Linux/64 (jelly) Linux/32 (jam) Darwin (osx1010test)
* Fixed HDFFV-10458 partiallyBinh-Minh Ribler2018-07-174-10/+128
| | | | | | | | | | | | | | | | | | | | Description: Added wrappers for H5Oget_info2 and H5Oget_info_by_name2. // Returns information about an HDF5 object. void getInfo(H5O_info_t& objinfo, unsigned fields = H5O_INFO_BASIC) // Returns information about an HDF5 object, given its name. void getInfo(const char* name, H5O_info_t& objinfo, unsigned fields = H5O_INFO_BASIC, const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) void getInfo(const H5std_string& name, H5O_info_t& objinfo, unsigned fields = H5O_INFO_BASIC, const LinkAccPropList& lapl = LinkAccPropList::DEFAULT) Platforms tested: Linux/64 (jelly) Linux/32 (jam) Darwin (osx1010test)
* Fixed HDFFV-10404Binh-Minh Ribler2018-07-132-8/+8
| | | | | | | | | Description: Applied the typo fixes from user's report. The previous pull request couldn't be merged because it was too old, and it was too complicated for me to resolve conflicts. Platform tested: Linux/64 (jelly) - very minor
* Fix MPI on Windows by adding MPI include folderAllen Byrne2018-05-091-1/+1
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* Correct COMPILE defs usageAllen Byrne2018-05-091-1/+1
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* TRILABS-19 remove add_defintions and use generator expressionsAllen Byrne2018-04-261-20/+7
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* TRILABS-20 set a compiler name on all project commandsAllen Byrne2018-04-201-1/+15
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* TRILABS-19 Initial conversion of include_directories to targetsAllen Byrne2018-04-171-0/+1
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* Merge pull request #936 in HDFFV/hdf5 from ~BMRIBLER/hdf5_bmr_cpp3:develop ↵Binh-Minh Ribler2018-03-121-9/+119
|\ | | | | | | | | | | | | | | | | | | | | | | | | to develop Modified 43158f3bb352f374c31556a5d0dc463a09e0b32e and additional wrappers. * commit 'b638bbd74b79f935a43aa6a804492e035ec315f6': Code improvement Description: - Removed memory leaks caused by accidentally invoking p_get_member_type - Added the call to test_lcpl, missed previously Platforms tested: Linux/64 (jelly) Linux/ppc64 (ostrich) Darwin (osx1010test) Updated RELEASE.txt Description: - Wrappers for H5Lcreate_soft, H5Lcreate_hard, H5Lcopy, H5Lmove, H5Ldelete, and H5Lget_info - Class LinkCreatPropList - Fixed typo in source file Platforms tested: Linux/64 (jelly) Updated for H5LcreatProp.[h,cpp] Updated MANIFEST for H5LcreatProp.[h,cpp] HDFFV-10149 continued 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.
| * Code improvementBinh-Minh Ribler2018-03-121-6/+7
| | | | | | | | | | | | | | | | | | | | Description: - Removed memory leaks caused by accidentally invoking p_get_member_type - Added the call to test_lcpl, missed previously Platforms tested: Linux/64 (jelly) Linux/ppc64 (ostrich) Darwin (osx1010test)
| * HDFFV-10149 continuedBinh-Minh Ribler2018-03-121-9/+118
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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)
* | Merge pull request #932 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2018-03-121-1/+1
|\ \ | |/ |/| | | | | | | | | * commit '75db73efc514aff2af63618cc7be357fc4e77cb6': Add release note Remove obsolete comments Change CMake min to 3.10
| * Change CMake min to 3.10Allen Byrne2018-03-091-1/+1
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* | Merge pull request #833 in HDFFV/hdf5 from ~BMRIBLER/hdf5_bmr_cpp3:develop ↵Binh-Minh Ribler2018-03-101-126/+265
|\ \ | |/ |/| | | | | | | | | | | | | | | | | to develop Update for new support website. * commit '801191b4c374adc462345f2c068f1cfc6f4adf97': Upated cpp doc. Added C++ wrappers - HDFFV-10149 Description: Added the following wrappers to class H5::Group: + H5Lcreate_soft: // Creates a soft link from link_name to target_name. void newLink(const char *target_name, const char *link_name,...) void newLink(const H5std_string& target_name,...) Update for new support website 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
| * Added C++ wrappers - HDFFV-10149Binh-Minh Ribler2018-03-101-126/+265
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description: Added the following wrappers to class H5::Group: + H5Lcreate_soft: // Creates a soft link from link_name to target_name. void newLink(const char *target_name, const char *link_name,...) void newLink(const H5std_string& target_name,...) + H5Lcreate_hard: // Creates a hard link from new_name to curr_name. void newLink(const char *curr_name, const Group& new_loc,...) void newLink(const H5std_string& curr_name, const Group& new_loc,...) // Creates a hard link from new_name to curr_name in same location. void newLink(const char *curr_name, const hid_t same_loc,...) void newLink(const H5std_string& curr_name, const hid_t same_loc,...) + H5Lcopy: // Copy an object from a group of file to another. void copyLink(const char *src_name, const Group& dst,...) void copyLink(const H5std_string& src_name, const Group& dst,...) // Copy an object from a group of file to the same location. void copyLink(const char *src_name, const char *dst_name,...) void copyLink(const H5std_string& src_name,...) + H5Lmove: // Rename an object in a group or file to a new location. void moveLink(const char* src_name, const Group& dst,...) void moveLink(const H5std_string& src_name, const Group& dst,...) // Rename an object in a group or file to the same location. void moveLink(const char* src_name, const char* dst_name,...) void moveLink(const H5std_string& src_name,...) Platforms tested: Linux/64 (jelly) Linux/ppc64 (ostrich) Darwin (osx1010test)
* | Inc CMake min, Add new tests, rework test CMake filesAllen Byrne2018-02-271-1/+1
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* | HDFFV-10385 rework java namesAllen Byrne2018-01-171-1/+0
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