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* Fix path to libhdf5.settings in cmakehdf5 (#3140)H. Joe Lee2023-06-161-2/+2
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* Removed .lnt linter files (#3143)Dana Robinson2023-06-163-145/+0
| | | These were last usefully modified in 2004
* Add java options to build scripts (#3127)mattjala2023-06-152-1/+16
| | | | | | | | | | | | | | | | | | | * Add java options to build scripts Previously, cmakehdf5 turned on compiling of the java interface by default due to a value set in cacheinit.cmake. Now, consistent with how Fortran and CPP interfaces are handled, the script overwrites this default value to disable the libraries, fixing #2958. I also implemented the --enable-java/--disable java options for cmakehdf5, and -java for buildhdf5. Allen said these scripts should mention that compilers are to be specified in environment variables, but missing compilers causes errors at the CMake level, and CMake's error messages are already pretty informative (See the one in #2958 about JAVA_COMPILER).
* Revert long double checks (#3133)Dana Robinson2023-06-1510-25/+736
| | | | | | | * Revert "Remove long double conversion work-arounds (#3097)" This reverts commit 1e1dac1dac58fa18f6b7788346d1ba7d3315b0f9. * Update comments to reflect newer systems
* Fix function name in comment in ros3 VFD (#3131)H. Joe Lee2023-06-151-4/+1
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* Add Python for HDF-EOS zoo description (#3129)H. Joe Lee2023-06-151-2/+2
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* Make autogen.sh output message consistent (#3128)H. Joe Lee2023-06-151-1/+1
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* Fix spelling issues flagged by codespell (#3130)Dana Robinson2023-06-153-3/+3
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* Clean up mirror VFD code in utils dir (#3121)Dana Robinson2023-06-145-82/+24
| | | | | * Remove dead code * Replace mybzero with memset * Replace hbool_t/TRUE/FALSE with bool/true/false
* Adds an optional version arg to bin/format_source (#3119)Dana Robinson2023-06-141-1/+15
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* Remove unused HD macros (#3120)Dana Robinson2023-06-144-310/+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 the checkposix script (#3122)Dana Robinson2023-06-142-260/+0
| | | | | This script was used to ensure that all non-HDF5 calls were prefixed with 'HD'. We are removing this scheme so this script is no longer needed.
* Use 1.14 toolchain (#3116)Allen Byrne2023-06-131-4/+4
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* Add note for issue 3056 (#3117)Allen Byrne2023-06-131-1/+9
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* clang-tidy clang-analyzer-core issues addressed (#3113)Allen Byrne2023-06-132-5/+3
| | | | | | | | src/H5system.c:1293:13: warning: Dereference of null pointer [clang-analyzer-core.NullDereference] src/H5trace.c:4048:17: warning: Passed-by-value struct argument contains uninitialized data (e.g., via the field chain: 'initial.user') [clang-analyzer-core.CallAndMessage]
* Remove H5detect and H5make_libsettings (#3104)Dana Robinson2023-06-1323-1531/+911
| | | | | | | | 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
* Fix a misc warning in test/vol.c (#3112)Dana Robinson2023-06-131-5/+6
| | | | The compiler complains about using integers instead of size_t for some sizes.
* Fix gh pages so that the doxygen files are uploaded (#3102)Allen Byrne2023-06-131-20/+16
| | | | | | * Add workspace path * add debug * Make one job so workspace files are available * Put doxygen docs under docs folder in gh-pages
* Rework tools.cmake and add C flags (#3110)Allen Byrne2023-06-131-73/+62
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* Fix the default for API_VERSION to only allow one default (#3107)Allen Byrne2023-06-131-6/+0
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* Add Mark Kittisopikul to CODEOWNERS (#3111)Dana Robinson2023-06-131-1/+1
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* Remove long double conversion work-arounds (#3097)Dana Robinson2023-06-1210-733/+25
| | | | | | | | | | | | | | | | | | | | | 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
* Remove code paths where long long < 8 bytes (#3098)Dana Robinson2023-06-122-31/+4
| | | | | The C99 standard says that a long long is 8+ bytes. This change removes a few parts of the code where we assume that a long long could be less than that.
* Remove variable dereferences in CMake (#3080)Dana Robinson2023-06-121-3/+3
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* Address memory issues when copying empty enums (#3088)Dana Robinson2023-06-124-493/+545
| | | | | | | | | | When copying an empty enum type (including implicitly, as when an enum is contained in a compound type), the library would allocate 0-size blocks of memory and attempt to memcpy 0 bytes from NULL pointers, which are undefined behavior. In debug mode, the library would raise an assert in H5MM. The library now avoid undefined memory operations when copying empty enum types and a test that copies empty enums has been added.
* Make some changes to configure.ac to suppor MinGW (#3096)Dana Robinson2023-06-122-3/+8
| | | | | | | 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.
* Fixed typo: hdf5-examples should be hdf5_examples in a link (#3101)bmribler2023-06-111-1/+1
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* Fix misc warnings on Windows (#3094)Dana Robinson2023-06-113-21/+21
| | | | | * Debug functionality where pointers were munged into longs (which are only 32-bits on Windows) * Fix a missing cast in Wstrcasestr_wrap()
* 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.
* Build the ros3 VFD in GitHub actions (#3090)Dana Robinson2023-06-101-4/+20
| | | | | * Build the ros3 VFD in GitHub actions * Add curl to list of packages to install * Disable CMake while we figure out the curl path issues
* Remove template title text ([BUG], etc.) (#3093)Dana Robinson2023-06-102-4/+4
| | | We use labels for this now
* Minor cleanup of H5detect.c (#3081)Dana Robinson2023-06-091-152/+115
| | | | | | * Clean up H5detect.c * Whitespace cleanup * Align things a bit better * Comment changes
* Added new HDF5 logo and minor text and link changes to README.md (#3085)Lori Cooper2023-06-082-16/+8
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* ci: add h5py action (#2986) (#3028)H. Joe Lee2023-06-081-0/+36
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* Don't use -fstdarg-opt with clang-tidy (#3079)Dana Robinson2023-06-071-1/+3
| | | | | | | | | | | * HDFCompilerFlags: mask -fstdarg-opt with clang-tidy `clang-tidy` doesn't understand this `-f` flag and errors out. * Add helpful comment --------- Co-authored-by: Sean McBride <sean@rogue-research.com>
* Removes old header/library checks (#3078)Dana Robinson2023-06-073-22/+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 ref to format_source_patch (#3072)Dana Robinson2023-06-071-2/+0
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* Remove Win32 POSIX redefinitions (#3068)Dana Robinson2023-06-071-35/+15
| | | | | | Microsoft has redefined most POSIX API calls with a leading underscore in order to strictly comply with C99. Nobody else cares about this and we define _CRT_NONSTDC_NO_WARNINGS in CMake Windows builds to suppress their warnings.
* Fix MSVC 32/64 bit shift conversion warnings (#3067)Dana Robinson2023-06-071-5/+5
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* Fix paths for doxygen and add step to upload to gh-pages (#3061)Allen Byrne2023-06-072-5/+15
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* Update README.md (#3069)Dana Robinson2023-06-071-3/+2
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* Update the release schedule for 1.12.3 (#3066)Dana Robinson2023-06-072-2/+2
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* Add netCDF and HDF-EOS5 badges to README.md (#3065)Dana Robinson2023-06-072-1/+3
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* ci: add netcdf action (#2934) (#2981)H. Joe Lee2023-06-061-0/+53
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* Correct path for doxygen files (#3055)Allen Byrne2023-06-061-1/+1
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* Fix doxygen comments in structure and enable FAIL_ON_WARNINGS (#3059)Allen Byrne2023-06-062-1/+7
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* HDF5Array arrayify is missing break statement #3056 (#3060)Allen Byrne2023-06-061-0/+2
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* CMake build is missing H5FDsubfiling.h #3037 (#3053)Allen Byrne2023-06-061-2/+2
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* Move encode/decode macros to a new header (#3040)Dana Robinson2023-06-0634-456/+492
| | | | | | | | | | | Moves the file-independent encode and decode macros to a new H5encode.h header that is itself included in H5private.h. Removes UINT64ENCODE_VARLEN and UINT64DECODE_VARLEN, which were unused. Fixes include statements in files where H5VMprivate.h and H5MMprivate.h were included via H5Fprivate.h.
* Develop gh doxy (#3041)Allen Byrne2023-06-053-6/+36
| | | | | * Add doxygen generation to daily-build and main * Add doxygen option to matrix