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* Fix Autotools -Werror cleanup (#4144)Dana Robinson2024-03-151-6/+19
| | | | | | | | | | | The Autotools temporarily scrub -Werror(=whatever) from CFLAGS, etc. so configure checks don't trip over warnings generated by configure check programs. The sed line originally only scrubbed -Werror but not -Werror=something, which would cause errors when the '=something' was left behind in CFLAGS. The sed line has been updated to handle -Werror=something lines. Fixes one issue raised in #3872
* Add cygwin CI and update yaml files for consistency and accuracy (#4131)Allen Byrne2024-03-141-0/+4
| | | | | | | | | | | | | | | | | | | | | | | | | * Add cygwin CI * add cygwin packages * Correct option names * Cleanup yaml file and synch look and feel * Synch CI look and feel and correct path issues * Upgrade oneapi version * pwsh needs env: for vars * No continuation char for pwsh * restore correct pwsh step * Run subset of tests for cygwin workflow * Remove space chars in regex * restore full tests
* Use AC_SYS_LARGEFILE on Autotools (#4119)Dana Robinson2024-03-121-20/+3
| | | | | We previously used a hack introduced in 1.8.5 to paper over differences in off_t and off64_t when determining the type sizes. We no longer explicitly support off64_t in the library and AC_SYS_LARGEFILE works fine.
* Remove printf debugging from H5Smpio.c (#4098)Dana Robinson2024-03-101-2/+2
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* Remove H5B debug checks (#4089)Dana Robinson2024-03-091-1/+1
| | | | | | | | | | | | | | | | | | The H5B (version 1 B-tree) package would add some computationally expensive integrity checks when H5B_DEBUG was defined. Due to their negative effects on performance, this option was rarely turned on, making the H5B__assert() check function stale, if not dead, code. This change: * Builds H5B__assert() when NDEBUG is not defined (the function relies on assert()) so it gets compiled more often. * Removes some printf debugging statements in the B-tree code * Removes all H5B "extra debug" checks that are leftover from past debugging sessions. Maintainers can add H5B__assert() selectively to perform integrity checks when debugging. * Removes the HDF5_ENABLE_DEBUG_H5B CMake option H5B_DEBUG now has no effect
* Remove printf debugging in H5I package (#4088)Dana Robinson2024-03-081-2/+2
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* Remove printf debugging in H5HL code (#4086)Dana Robinson2024-03-081-2/+2
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* Added new H5E with tests. (#4049)Scot Breitenfeld2024-03-071-0/+6
| | | | | | | | | | | Added Fortran H5E APIs: h5eregister_class_f, h5eunregister_class_f, h5ecreate_msg_f, h5eclose_msg_f h5eget_msg_f, h5epush_f, h5eget_num_f, h5ewalk_f, h5eget_class_name_f, h5eappend_stack_f, h5eget_current_stack_f, h5eset_current_stack_f, h5ecreate_stack_f, h5eclose_stack_f, h5epop_f, h5eprint_f (C h5eprint v2 signature) Addresses Issue #3987
* Fix the datatype passed to H5*exists_async APIs in tests. (#4033)Scot Breitenfeld2024-02-231-0/+11
| | | Add a new testing function to verify C_BOOL values.
* Add API support for Fortran MPI_F08 module definitions. (#3959)Scot Breitenfeld2024-01-291-0/+19
| | | | | * revert to using c-stub for _F08 MPI APIs * use mpi compiler wrappers for cmake and nvhpc
* Fix doxygen errors (#3962)Allen Byrne2024-01-291-2/+2
| | | | | | | | | | | * Switch warnings as errors to default OFF * Enable mac docs * Add doxygen action uses step * Use html div around snippet * Allow preset name to be an argument to cmake-ctest.yml
* renamed defined H5_VERS* to avoid conflicts (#3926)Scot Breitenfeld2024-01-051-12/+12
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* New Fortran Examples added (#3916)Scot Breitenfeld2024-01-031-4/+11
| | | | | * added subfiling example * Added filtered writes with no selection example
* Add 'warning density' computation to the warnhist script (#3910)Quincey Koziol2023-12-291-0/+39
| | | | | | | | | * Add 'warning density' computation to the warnhist script, along with several cleanups to it. Add "--enable-show-all-warnings" configure (and CMake) option to disable compiler diagnostic suppression (and therefore show all the otherwise suppressed compiler diagnostics), disabled by default. Clean up a buncn of misc. warnings. Signed-off-by: Quincey Koziol <qkoziol@amazon.com>
* Add variable option syncing for examples (#3885)Allen Byrne2023-12-141-16/+0
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* Remove Autotools sed hack (#3848)Dana Robinson2023-11-131-6/+0
| | | | | | | | | | configure.ac contains a sed line that cleans up incorrect library flags which was added to paper over some bugs in earlier versions of the Autotools. These issues are not a problem with the current versions of the Autootols. The sed line causes problems on MacOS, so it has been removed. Fixes #3843
* Renamed h5fuse.sh to h5fuse (#3834)Scot Breitenfeld2023-11-071-2/+2
| | | * provide an alternative to mapfile for older bash
* Add an option to disable doxygen warn as error (#3708)Allen Byrne2023-10-191-0/+25
| | | | | | | | | | | | Add for both CMake and the Autotools * HDF5_ENABLE_DOXY_WARNINGS: ON/OFF (Default: ON) * --enable-doxygen-errors: enable/disable (Default: enable) The default will fail compile if the doxygen parsing generates warnings. The option can be disabled if certain versions of doxygen have parsing issues. i.e. 1.9.5, 1.9.8. Fixes #3398
* Add support for AOCC & Flang w/ the Autotools (#3674)Dana Robinson2023-10-151-3/+6
| | | | | | | | | | | | | * Adds a config/clang-fflags options file to support Flang * Corrects missing "-Wl," from linker options in the libtool wrappers when using Flang, the MPI Fortran compiler wrappers, and building the shared library. This would often result in unrecognized options like -soname. * Enable -nomp w/ Flang to avoid linking to the OpenMPI library. CMake can build the parallel, shared library w/ Fortran using AOCC and Flang, so no changes were needed for that build system. Fixes GitHub issues #3439, #1588, #366, #280
* Drop MPI-2 support (#3643)Scot Breitenfeld2023-10-081-0/+14
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* Removed the use of -commons linking option on Darwin (#3581)Scot Breitenfeld2023-09-251-8/+0
| | | | Removed the use of -commons linking option on Darwin as COMMON and EQUIVALENCE is no long used
* Adds link to h5fuse.sh in testpar for autotools (#3557)Scot Breitenfeld2023-09-221-0/+5
| | | | * Make the h5fuse.sh utility available to parallel subfiling tests so h5fuse testing is not skipped.
* Convert some H5MM calls to standard C equivalents (#2382)Dana Robinson2023-08-251-2/+2
| | | | | | | | | * H5MM_calloc and malloc are now mapped to stdlib C calls * H5MM_memcpy now maps directly to memcpy in release builds * H5MM_memcpy is still implemented as a separate function that checks for buffer overlap when H5MM_DEBUG is defined (default w/ debug builds) * Switches many library memcpy calls to use H5MM_memcpy * Fixes a possible zero allocation in H5Olayout.c
* Enable szip by default in Autotools (#3412)Dana Robinson2023-08-231-3/+8
| | | | | Since libaec is so prevalent and BSD-licensed for both encode and decode, we build the szip filter by default when the szip or aec libraries are found.
* Subfiling VFD source cleanup (#3241)jhendersonHDF2023-07-131-0/+17
| | | | | | | | | | | | | | | | * Subfiling VFD source cleanup Modularize Subfiling CMake code into separate CMakeLists.txt file Update Mercury util code to latest version and update Copyright Generate mercury_util_config.h header file instead of using pre-generated file Remove unnecessary Mercury functionality Fix minor warning in Subfiling VFD code * Remove Mercury headers from Autotools publicly-distributed header list
* Remove checks for setsysinfo, which is unused (#3205)Dana Robinson2023-06-291-1/+1
| | | | * Autotools * CMake
* Revert long double checks (#3133)Dana Robinson2023-06-151-0/+173
| | | | | | | * Revert "Remove long double conversion work-arounds (#3097)" This reverts commit 1e1dac1dac58fa18f6b7788346d1ba7d3315b0f9. * Update comments to reflect newer systems
* Remove unused HD macros (#3120)Dana Robinson2023-06-141-2/+1
| | | | | | | | | * Remove unused HD macros The library prefixes most C and POSIX API calls with 'HD'. We are going to start removing these so the code looks like normal C. This PR removes most of the unused HD markup macros. * Replace ntohl/ntohs
* Remove H5detect and H5make_libsettings (#3104)Dana Robinson2023-06-131-5/+19
| | | | | | | | Removes H5detect and H5make_libsettings from the build and replaces their functionality with things that don't affect cross-compiling. H5detect --> floating-point types are now detected on library load H5make_libsettings --> Moved functionality to a new H5build_settings.c template file
* Remove long double conversion work-arounds (#3097)Dana Robinson2023-06-121-173/+0
| | | | | | | | | | | | | | | | | | | | | Several options and public symbols that were provided to paper over non-standard long double conversions between signed/unsigned long and long long values were removed from the Autotools and CMake. These were added twenty years ago, when C99 and 64-bit platforms were less common and are no longer needed. Autotools: --enable-dconv-accuracy CMake: HDF5_WANT_DATA_ACCURACY H5pubconf.h symbols: H5_WANT_DATA_ACCURACY H5_LDOUBLE_TO_LONG_SPECIAL H5_LONG_TO_LDOUBLE_SPECIAL H5_LDOUBLE_TO_LLONG_ACCURATE H5_LLONG_TO_LDOUBLE_CORRECT H5_DISABLE_SOME_LDOUBLE_CONV
* Make some changes to configure.ac to suppor MinGW (#3096)Dana Robinson2023-06-121-1/+6
| | | | | | | Adds some H5pubconf.h entries and cpp flags for building on MinGW using the Autotools. Also updates the Windows-related H5pubconf.h comments to be more accurate in CMake.
* Add cross-compile defaults to Autotools (#3095)Dana Robinson2023-06-101-8/+14
| | | | | Most instances of AC_RUN_IFELSE do not have an action set for cross-compiling, even though there is an obvious 'reasonable' value.
* Removes old header/library checks (#3078)Dana Robinson2023-06-071-2/+2
| | | | | | | | | | | | | In both CMake and the Autotools, remove checks for: * lstat * srandom In CMake, remove checks for: * string.h * strings.h * stdlib.h We assume these exist. Configure will always check for them (we don't add any special code to do this), but there's no reason to duplicate that nonsense in CMake.
* Remove most unused options which are defaulted #2998 (#3019)Allen Byrne2023-05-261-1/+1
| | | | | * Remove most unused options which are defaulted #2998 * Fix property list references
* Bump Autoconf version to 2.71 (#2944)Dana Robinson2023-05-121-1/+1
| | | Required for building with Intel's oneAPI
* chore(configure.ac): fix output message for enabling tools (#2684) (#2854)H. Joe Lee2023-04-291-1/+1
| | | Close #2684.
* Fix improper include of build directory (#2422, #2621) (#2667)jhendersonHDF2023-04-111-4/+2
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* Fix new codespell issues (#2521)Mark Kittisopikul2023-03-081-1/+1
| | | | | * Fix new codespell issues * Have codespell ignore ./config/sanitizer/sanitizers.cmake
* Fix for Autotools --disable-deprecated-symbols (#2363)Dana Robinson2022-12-241-4/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | * Fix for Autotools --disable-deprecated-symbols When we added v116 as a valid option, we left the default as v114 so using --disable-deprecated-symbols leads configure to complain that you can't set a default API that was deprecated. The GitHub action didn't catch this because it explicitly specifies v116 This only affects develop w/ the Autotools when --disable-deprecated-symbols is requested. * Added v116 & default to the --with-default-api-version help string The Autotools --with-default-api-version help string was missing v116. This has been added, as well as a "default" target so the CI can catch version problems when we forget to update the defaults upon creating a new major version. The GitHub CI also now uses "default" as the target for the deprecated symbols build. * Fixes the 1.14 API GitHub CI threadsafe/build_mode This action still had the bug we fixed where we set the build mode and threadsafety using an array of size one instead of an object.
* HL GIF tools changes (#2360)Dana Robinson2022-12-241-32/+21
| | | | * Fixes the broken Autotools option * Removes the "build HL tools" option
* H5F_LIBVER_LATEST changes for move to 1.15 (#2288)Allen Byrne2022-12-211-2/+7
| | | | | | | | | | | | | | | * H5F_LIBVER_LATEST changes for move to 1.15 * Add new default api check * Format fixes * Fix default configure * fix lib version tests * Fix another version variable * Add 1.14 doc link
* Disable hl tools by default (#2313)Allen Byrne2022-12-171-0/+17
| | | | | | | | | | | * Disable hl tools by default * identify the tools * Only GIF tools are depecated * Add new option * Update autotools
* Simplify & fix check for szlib encoder (#2263)Ryan Schmidt2022-11-171-4/+1
| | | | | | | | | | Return the result rather than setting the exit code. "return" is a language keyword whereas "exit" is a function for which the <stdlib.h> header has to be included which it wasn't in this test, therefore the test would previously fail to identify that the encoder was enabled if "-Werror=implicit-function-declaration" was used, which it is by default with clang from Xcode 12 and later. Fixes #2262
* moved quad precision checks (#2252)Scot Breitenfeld2022-11-121-25/+25
| | | | | * Only check quad sizes if fortran is enabled * fixed if struct
* removed uninterpretable line (#2249)Scot Breitenfeld2022-11-111-1/+1
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* Removes MPE instrumentation support. (#2245)Dana Robinson2022-11-091-64/+0
| | | | | | | | | | | * Removes MPE instrumentation support. The Autotools will no longer accept --with-mpe= and the logging commands have been removed from the FUNC_ENTER macros. CMake has never supported instrumenting for MPE. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes dmalloc support (#2239)Dana Robinson2022-11-091-77/+0
| | | | | | | | | | This has not been used to debug the library in a very long time. Most developers use valgrind, -fsanitize=address, or some other memory checker instead of this library. This removes: * dmalloc.h include from H5private.h * --with-dmalloc= Autotools configure option * HDF5_ENABLE_USING_DMALLOC CMake option
* Removes the memory allocation sanity checks feature (#2218)Dana Robinson2022-11-031-46/+0
| | | | | | | | | | | | | | | * Removes the memory allocation sanity checks feature * Committing clang-format changes * Removes zero size checks for H5MM_(c|m)alloc() * Explicitly return NULL when size == 0 in H5allocate_memory() * Committing clang-format changes * Format fix Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update copyright headers (#2184)Larry Knox2022-11-011-1/+0
| | | | | * Updated source file copyright headers to remove "Copyright by the Board of Trustees of the University of Illinois", which is kept in the top-level COPYING file.
* Update develop branch version to 1.13.4-1 (#2189)Larry Knox2022-10-261-1/+1
| | | | | | * Updated version to 1.13.4-1 after creating hdf5_1_13_3 branch for 1.13.3 release. Added new version to exceptions in lines 74-5 of src/H5.c
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