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* Update version to 1.13.1-1 after creation of branch for 1.13.0 release. (#1236)Larry Knox2021-11-301-2/+2
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* Add support for parallel tools based on the 3rd party library mpiFileUtils ↵rawarren2021-11-293-0/+197
| | | | | | | | | | (libMFU) … (#1177) Adds tool h5dwalk and configure options to enable building it. Co-authored-by: Richard Warren <Richard.Warren@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Richard.Warren <richard.warren@jelly.ad.hdfgroup.org> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Fix Fortran REGEX and newlines (#1226)Allen Byrne2021-11-292-8/+8
| | | | | | | * Fix order of fortran define * fix typo * Fix REGEX and newlines
* Github #969 Use stdout instead of file for configure check (#1089)Allen Byrne2021-11-182-54/+26
| | | | | | | | | | | | | * Use stdout instead of file for configure check * Make change requested by #1157 * Change fortran to use stderr for configure * Correct typo * remove obsolete file check * Fortran statement fix
* Move -Werror=int-conversion from error-general to error-5 in (#1194)Larry Knox2021-11-142-1/+1
| | | gnu-warnings (unrecognized command line option for gcc 4.85/4.93.
* Make it an error if the library implicitly converts from integer to (#1165)David Young2021-11-131-0/+2
| | | | | pointer or from pointer to integer (-Werror=int-conversion). Also, make it an error if the library explicitly converts to pointer from an integer of a different size (-Werror=int-to-pointer-cast).
* Fix the function cast error in H5Dchunk.c and activate (#1170)David Young2021-11-081-4/+1
| | | `-Werror=cast-function-type`. Again.
* New references for Dimension Scale APIs (#1139)jhendersonHDF2021-11-052-25/+29
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Enable usage of new-style references with dimension scale APIs * Add API to check if an object ID represents a native connector object * Modified code to use new function H5DSwith_new_ref to determine if new references should be used with Dimension Scales. The new function return TRUE if non-native connector is used or if H5_DIMENSION_SCALES_WITH_NEW_REF varible is define at configure time (--enable-dimension-scales-with-new-ref). Tested on jelly. ToDo: generate testing file on BE system and enable the test; add flag to CMake; test netCDF-4 with the new references. * Adding new test files generated on BE system (hedgehog) created by 32 and 64-bit library. test_ds chokes on test_ds_le_new_ref.h5 on BE system; test passes for test_ds_be_new_ref-32bit.h5 for the 32-bit library and fails for the 64-bit library, and vice versa. I am checking the files for further investigation; but current implementation of the new references is not portable between LE and BE systems, and 32 and 64-bit systems. * Minor fixes for testing issues * Update test_ds.c Enabled broken test; tests pass now. * Update RELEASE.txt Documented new option to use new references with the HDF5 dimension scales APIs (H5DS*). * Update MANIFEST for new 32-bit new-style references test file for H5DS APIs * Update 'dimension scales w/ new-style refs' feature based on review Co-authored-by: Elena <epourmal@hdfgroup.org>
* Fix Java VOL tests (#1158)Allen Byrne2021-11-032-302/+6
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* Set the plugin path to the library default (#1144)Allen Byrne2021-10-291-0/+2
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* Split dir create into separate macro (#1141)Allen Byrne2021-10-282-1/+4
| | | | | * Split dir create into separate macro * Correct VFD settings
* Github #1019 - add Fortran developer flags (#1090)Allen Byrne2021-10-273-9/+9
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* Consolidate VFD create list macro (#1132)Allen Byrne2021-10-261-0/+1
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* Move test utilities to utils/test folder (#1109)Allen Byrne2021-10-205-4/+66
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Move test utilities to utils/test folder * Fix makefile assignment * Add new dir * add new folder * Correct copied makefile * Fix dir typo * Add missing include dir * Remove unnecessary lib link * Correct dependent dirs * Fix conditional checks * Disable test if not built * fix path to executable * Use fixture for swmr_vfd check * Add release note * Correct shell tests and c++ flag warning * Update autotools c++ warning * Fix typo
* To reduce maintenance effort, delete the `noerror-` variants of the compiler ↵David Young2021-10-0613-311/+26
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | flags files (#1033) * Avoid maintenance headaches: delete the `noerror-` variants of the compiler flags files, since they essentially duplicate the `error-` files modulo the replacement of `-Werror=` with `-W` and any changes in comments. (I verified the duplication with a script.) For autoconf, reinstate the use of the `demote_errors` shell function to derive the `noerror-` content from the `error-` content. `demote_errors` replaces `-Werror=` with `-W` when `WARNINGS_AS_ERRORS` is `no`. Slightly reorder `configure.ac` so that the setting of `WARNINGS_AS_ERRORS` takes effect before the `error-` files are sourced. * Take a stab at updating the CMake files to match the changes I made to the autoconf files to remove `noerror-` files. I'm not much of a CMake user so these changes are quite rough. Looks like the duplication can be reduced with the introduction of a new macro. * Delete `noerror-` files from the MANIFEST. * Reduce duplication in the CMake files: perform the HDF5_ENABLE_WARNINGS_AS_ERRORS test once in the ADD_H5_FLAGS macro. * Add a release note.
* VFD plugins (#602)jhendersonHDF2021-09-291-1/+18
| | | | | | | | | | | | | | | | | * Implement support for loading of Virtual File Drivers as plugins Fix plugin caching for VOL connector and VFD plugins Fix plugin iteration to skip paths that can't be opened * Enable dynamic loading of VFDs with HDF5_DRIVER environment variable * Temporarily disable error reporting during H5F_open double file open * Default to using HDstat in h5_get_file_size for unknown VFDs * Use macros for some environment variables that HDF5 interprets * Update "null" and "ctl testing" VFDs
* Update version to 1.13.0-7 after snapshot release 1.13.0-6. (#1048)Larry Knox2021-09-291-1/+1
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* Update Platforms Tested in RELEASE.txt. (#1045)hdf5-1_13_0-rc6Larry Knox2021-09-281-1/+1
| | | | | | * Update Platforms Tested in RELEASE.txt. Remove Tested Configuration Features Summary for updated replacement. * Set version to 1.13.0-6 for rc6 snapshot.
* Develop cmake install dir (#1041)Allen Byrne2021-09-282-4/+4
| | | | | | | * Corrected path searched by CMake find_package command * Correct path for depend libs * Adjust examples script for install path
* Develop libaec up (#1037)Allen Byrne2021-09-281-1/+7
| | | | | * Upgrade libaec to 1.0.6 * correct include file name
* MS clang needs EHsc flag (#1035)Allen Byrne2021-09-241-2/+2
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* Need to match clang and versions not just "Clang" (#1029)Allen Byrne2021-09-224-20/+12
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* HDFFV-11266 - add option to build HL tools (#1018)Allen Byrne2021-09-162-0/+2
| | | | | | | * HDFFV-11266 - add option to build HL tools * Correct if syntax * Correct name of conditional
* Disable fortran warning (#1014)Allen Byrne2021-09-162-7/+8
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* Update examples version because of HDFFV-11269 (#998)Allen Byrne2021-09-102-2/+2
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* Correction of pkg-config compile script. (#974)Allen Byrne2021-09-071-1/+1
| | | | | * Correction of pkg-config compile script. * Reword note.
* Sync CMake java macros with cmake repo (#982)Allen Byrne2021-09-074-369/+536
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* Small doxygen fixes plus simple doc fixes (#989)Allen Byrne2021-09-041-1/+1
| | | | Change doxygen generated file location Clang format override for flags
* cmake: simplify try_run result comparisons (#950)Ben Boeckel2021-08-231-5/+5
| | | | | | Instead of looking at `MATCHES 0` which runs a regex and returns a false positive for any result such as `10`, check if they are equal to `0`. Also quote `0` to avoid looking it up as a variable (which was left behind prior to the fix to use `${RETURN_VAR}` in the `c_run` macro).
* Remove incorrect compiler check for windows clang sanitizer (#942)Allen Byrne2021-08-201-1/+1
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* Develop windows compiler fixes (#912)Allen Byrne2021-08-193-32/+39
| | | | | | | | | | | | | | * Fix windows compiler issues Restore MS C++ Default exception handling behavior #885 Remove clang toolchain as it skips compiler checks * Add check and header gaurd for pwd.h * Revert change * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixed the CMake processing for C++ warnings and flags (#888)Allen Byrne2021-08-166-274/+337
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* Fix clang/sanitizer for windows (#883)Allen Byrne2021-08-162-7/+12
| | | | | * Fix clang/sanitizer for windows * Restrict MSVC version for sanitize
* Update examples version used by CMake (#882)Allen Byrne2021-08-123-3/+5
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* Issue #833 fix setting return result (#843)Allen Byrne2021-07-211-2/+2
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* Changes to docs for using plugins (#814)Allen Byrne2021-07-144-5/+8
| | | | | | | * Changes to docs for using plugins * VS2019 corrections * Fix typo
* Remove checks for winsock2.h (#813)Dana Robinson2021-07-062-9/+0
| | | | This is only needed on Windows and always available, so there's no need to check for it.
* Removes remaining H5_TIME_WITH_SYS_TIME cruft (#810)Dana Robinson2021-06-302-4/+0
| | | Mostly from CMake
* Cleans up POSIX/C bits in H5private.h (#804)Dana Robinson2021-06-292-5/+0
| | | | | | | | | | | | | | | | | | * Cleans up POSIX/C bits in H5private.h * Assume difftime exists (C89) * Reorg AC_CHECK_HEADERS so headers are in alphabetical order * Split off networking-related AC_CHECK_HEADERS * Remove unused UNAME_CYGWIN from configure.ac * Remove checks for unused sys/timeb.h * Tidying pass over H5private.h HD prefix macros * Tidy H5win32defs.h * Add HD prefix to various scanf calls * Committing clang-format changes * Fixes to the alarm(2) code used in the tests to make Windows happy Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes obsolete equivalents of C99's __func__ (#800)Dana Robinson2021-06-293-49/+0
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* Assume frexpl/f and fabsl/f, which are C99 (#799)Dana Robinson2021-06-252-8/+0
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* Removes checks for signal and set/longjmp, which are C89 (#798)Dana Robinson2021-06-252-26/+3
| | | Also removes checks for setjmp.h and stddef.h
* Normalization of CMake H5pubconf.h with Autotools (#791)Dana Robinson2021-06-231-11/+12
| | | | | | Mostly just moving things around and changing the comments to keep the delta small. The only symbol change is that for curl/curl.h which I changed to H5_HAVE_CURL_CURL_H to match the Autotools. This symbol is not used in the library and is just an artifact of the checks.
* Removes checks for system(), which is C89/90 (#782)Dana Robinson2021-06-232-5/+0
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* Removes outdated checks for ways inline might be defined (#781)Dana Robinson2021-06-233-34/+0
| | | These are obsolete now that we require C99.
* Removes checks for (v)snprintf, which are C99 (#772)Dana Robinson2021-06-213-39/+0
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* Removes checks and work-arounds for strtoll and strtoull (#769)Dana Robinson2021-06-182-8/+0
| | | | | * Removes checks and work-arounds for strtoll and strtoull * Removes CMake checks for strtoll and strtoull
* Fix cmake configure path (#760)Allen Byrne2021-06-171-1/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 * Some Javadoc warning fixes * Updated javadoc fixes * # WARNING: head commit changed in the meantime HDFFV-11229 Fix long double usage in tools and java Changed h5dump and h5ls to just print 128-bit for long double type. Added test and file for dataset and attributes with all three float types. * Committing clang-format changes * HDFFV-11229 Add release note * HDFFV-11229 windows testfile needed * fix typo * Remove non supported message text * HDFFV-11229 - change ldouble test to check both native and general * HDFFV-11229 add second file compare * HDFFV-11229 fix reference file * HDFFV-11229 autotools check two refs * HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output * Committing clang-format changes * Update release note * Update attribute type of ref file * Change source of ninja for macs * try port instead of brew * Recommended is to use brew. * Undo non long double changes * remove unneeded file * Fix perl and doxygen CMake code * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument * Add stamp files to BYPRODUCTS * Only one copy of file exists * Fix custom cmmand depends targets * Fix fortran custom command DEPENDS * Add LD_LIBRARY_PATH to tests * Add custom target for DEPENDS * Add h5detect conditionaly to generated target DEPENDS * Correct DEPENDS targets * Parallel builds need the mpi compiler for pkgconfig scripts. * install only if MPI build * Fortran target depends * Remove incorrect source attribute * doxygen adjustments * doxygen build updates * Correct version * Correct function version - function has been merged to 1.12 * Correct version string for map functions * Cleanup warnings for tools debug builds * TRILAB-227 - fix indexing for h5diff selections * Correct location of pos to index function call * TRILAB-227 Enable test * Quote subset args * Use MATCHES because of AppleClang * if blocks needed for build modes * Update list of DT platforms * VS2019 correctly displays float values * revert VS2019 change * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * Java reference functions updated enabled fortran in cmake gcc action yaml file java reference test changed to correctly test refs jni reference functions that create ids changed to use jni id logging * Correct BYPRODUCTS argument * Correct more genereated files BYPRODUCTS * BYPRODUCTS must have unique locations * Fix typo * Fix fortran configure checks * Rework H5_PAC_C_MAX_REAL_PRECISION setting logic * Add note about fortran configure change * Adds a quick for for some egregious chunk_info badness (#722) * Fixes issue with ccmake that prevents building Fortran (#723) ccmake runs iteratively, and the check_fortran_source_runs macros were clobbering a single output file that did not get updated on further configure iterations * Fix conflicts with merge * Move MAX_PRECISION back to HDF5UseFortran.cmake * Use STREQUAL to test macro argument * Move C language test to ConfigureChecks from HDF5UseFortran * MAX_PRECISION defines must be defined * Organize flags and align autotools and cmake * Fix comment in no-error-general warnings files. * Flag cleanup and fix typos * Add comment * Correct VAR used to find configure time file * Set the path correctly Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Fix warnings files (#753)Allen Byrne2021-06-159-49/+111
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 * Some Javadoc warning fixes * Updated javadoc fixes * # WARNING: head commit changed in the meantime HDFFV-11229 Fix long double usage in tools and java Changed h5dump and h5ls to just print 128-bit for long double type. Added test and file for dataset and attributes with all three float types. * Committing clang-format changes * HDFFV-11229 Add release note * HDFFV-11229 windows testfile needed * fix typo * Remove non supported message text * HDFFV-11229 - change ldouble test to check both native and general * HDFFV-11229 add second file compare * HDFFV-11229 fix reference file * HDFFV-11229 autotools check two refs * HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output * Committing clang-format changes * Update release note * Update attribute type of ref file * Change source of ninja for macs * try port instead of brew * Recommended is to use brew. * Undo non long double changes * remove unneeded file * Fix perl and doxygen CMake code * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument * Add stamp files to BYPRODUCTS * Only one copy of file exists * Fix custom cmmand depends targets * Fix fortran custom command DEPENDS * Add LD_LIBRARY_PATH to tests * Add custom target for DEPENDS * Add h5detect conditionaly to generated target DEPENDS * Correct DEPENDS targets * Parallel builds need the mpi compiler for pkgconfig scripts. * install only if MPI build * Fortran target depends * Remove incorrect source attribute * doxygen adjustments * doxygen build updates * Correct version * Correct function version - function has been merged to 1.12 * Correct version string for map functions * Cleanup warnings for tools debug builds * TRILAB-227 - fix indexing for h5diff selections * Correct location of pos to index function call * TRILAB-227 Enable test * Quote subset args * Use MATCHES because of AppleClang * if blocks needed for build modes * Update list of DT platforms * VS2019 correctly displays float values * revert VS2019 change * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * Java reference functions updated enabled fortran in cmake gcc action yaml file java reference test changed to correctly test refs jni reference functions that create ids changed to use jni id logging * Correct BYPRODUCTS argument * Correct more genereated files BYPRODUCTS * BYPRODUCTS must have unique locations * Fix typo * Fix fortran configure checks * Rework H5_PAC_C_MAX_REAL_PRECISION setting logic * Add note about fortran configure change * Adds a quick for for some egregious chunk_info badness (#722) * Fixes issue with ccmake that prevents building Fortran (#723) ccmake runs iteratively, and the check_fortran_source_runs macros were clobbering a single output file that did not get updated on further configure iterations * Fix conflicts with merge * Move MAX_PRECISION back to HDF5UseFortran.cmake * Use STREQUAL to test macro argument * Move C language test to ConfigureChecks from HDF5UseFortran * MAX_PRECISION defines must be defined * Organize flags and align autotools and cmake * Fix comment in no-error-general warnings files. * Flag cleanup and fix typos * Add comment Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Fix problem in gnu-cxxflags; remove empty if block that throws away all (#748)Larry Knox2021-06-121-4/+1
| | | C++ flags.
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