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* CMake updates:Allen Byrne2020-07-152-8/+44
| | | | | | Add build folder as Include for generated files Add install option for copying Fortran mod files to include folder Add PRI defines to win32defs file Exclude mingw from extra flags
* Squashed commit of the following:Larry Knox2020-06-211-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | commit 45b0cbc71929930a874e1c09e0770aa64d0ae697 Author: Larry Knox <lrknox@hdfgroup.org> Date: Thu Apr 23 13:14:56 2020 -0500 Add C++ warnings treated as error for autotools builds. commit 6debcddcc766601799d5bd661bd60946f951a07e Author: Larry Knox <lrknox@hdfgroup.org> Date: Fri Jun 19 16:50:03 2020 -0500 Remove tests for develop branch from testh5cc.sh.in. Add @H5_ECXXFLAGS@ to AM_CXXFLAGS. commit fed497e7f207313b2a133d3b68c942b7d7104b90 Author: Larry Knox <lrknox@hdfgroup.org> Date: Fri Jun 12 15:06:39 2020 -0500 Merge pull request #2646 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop * commit '998c6470d78e14228695419c3b514c35ecf3d69e': Remove unnecessary version conditions for Clang compilers. commit 92e52ce5c211bd1d3991a3b8bb67287ac7b652aa Author: Larry Knox <lrknox@hdfgroup.org> Date: Wed Jun 10 18:53:45 2020 -0500 Merge pull request #2639 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop * commit 'a33667faf226f5d8c9633bf537893e8fce1bf1f6': Add c++ to --enable-sanitize-checks option. commit 2e802534fb997b81fa98fdd1c7d97d4310898e0d Author: Larry Knox <lrknox@hdfgroup.org> Date: Wed Jun 10 15:18:36 2020 -0500 Merge pull request #2633 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop * commit '20eab963899841c9a003baebead8e3bc07d9e127': Remove duplicate entries in MANIFEST. Make changes to CMake CompilerFlags.cmake files so extra flags are loaded for non-GNU compilers. Update new clang files to not pick up clang as vendor for pgCC. Add new files to MANIFEST Temporary demotion of 2 -Werror warning flags that fail on macos 10.12 Remove Production flag unknown to Apple clang. commit 96ef60a58a23847a7da89a891f2415055ec2ab60 Author: Larry Knox <lrknox@hdfgroup.org> Date: Mon Jun 8 16:24:49 2020 -0500 Merge pull request #2631 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop * commit 'b942a4d8a3e27317cac50ce37ff5302d477664d8': Clean up code to get clang version in config/linux-gnulibc1 commit 8a7c687da568e8b50b38fa53da1ca63759be6ec4 Author: Larry Knox <lrknox@hdfgroup.org> Date: Mon Jun 8 11:42:37 2020 -0500 Merge pull request #2623 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop * commit 'c7626f79fdee4eee13925e240ef41e61f3367eab': Add flags from config/clang-warnings/*general files to H5 C and CXX flags for all versions of Clang and Clang++ compilers. Switched from cut to awk in testcheck_version.sh.in to avoid dependence on tab vs. " " in version definitions in H5public.h. Add files for adding warning flags for clang compilers in autotools configure. commit db3ef7ff3c1ed79167cecef831501411cff8291f Merge: 5a0f8d7 f9f1310 Author: Larry Knox <lrknox@hdfgroup.org> Date: Fri Jun 19 14:46:22 2020 -0500 Merge branch 'hdf5_1_12' of https://bitbucket.hdfgroup.org/scm/~lrknox/hdf5_lrk into hdf5_1_12 commit 5a0f8d7940ae57b445f545a0abd7e303ce6924ee Author: Larry Knox <lrknox@hdfgroup.org> Date: Wed Jun 10 20:15:41 2020 -0500 Merge pull request #2636 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:HDFFV-11000-update-testh5cc.sh.in-for-version to develop * commit '5c0bd670d6e9919c463fbc05de99e2ba55b0761e': Add tests for all version to H5_NO_DEPRECATED_SYMBOLS section and to section for current version, with and without default API version flags. HDFFV-11000: update-testh5cc.sh.in to test sample versioned functions in HDF5 1.10, 1.12 and develop.
* Reduce overhead for H5open, which is involved in the public symbols like ↵Quincey Koziol2020-06-182-5/+32
| | | | H5T_NATIVE_INT, etc.
* Merge remote-tracking branch 'origin/hdf5_1_12' into ↵Quincey Koziol2020-06-111-27/+32
|\ | | | | | | hdf5_1_12_cache_last_id_info
| * Merge remote-tracking branch 'origin/hdf5_1_12' into ↵Quincey Koziol2020-06-111-4/+4
| |\ | | | | | | | | | hdf5_1_12_opt_single_selection_io
| * | Eliminate allocating file & memory offset & length arrays when performing ↵Quincey Koziol2020-06-101-27/+32
| | | | | | | | | | | | I/O on a single element.
* | | Remember the info for the last ID looked up for a given ID type.Quincey Koziol2020-06-111-2/+22
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* | Remove redundant metadata cache tagging from some low-level internal chunk ↵Quincey Koziol2020-06-101-4/+4
|/ | | | functions. The metadata cache tagging has already been done by routines further up the call stack.
* Detect when there's the same-shaped selection of a single block of elements onQuincey Koziol2020-06-071-0/+9
| | | | | | both selections, but with different selection types (i.e. one selection defined as an 'all' type and the other as a hyperslab or point type), without falling into the generic selection iteration case.
* Whitespace cleanupAllen Byrne2020-05-13104-1240/+1242
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* Whitespace cleanupAllen Byrne2020-05-1348-2020/+2022
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* src/H5Eint.c: #include H5TSprivate.h for H5TS_thread_id() definitions.David Young2020-05-111-0/+1
| | | | test/thread_id.c: move threads_failure() inside #ifdefs.
* Remove tongue-in-cheek credit for Rusty Shackleford and Dale Alvin Gribble.David Young2020-05-111-21/+0
| | | | | | | | | | | | Delete the comment questioning whether pthread_mutex_lock is allowed in a key destructor, since pthread_key_create(3) provides the answer: There is no notion of a destructor-safe function. If an application does not call pthread_exit() from a signal handler, or if it blocks any signal whose handler may call pthread_exit() while calling async-unsafe functions, all functions may be safely called from destructors. Delete redundant comment.
* Follow HDF5 conventions.David Young2020-05-111-30/+89
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* Make sure that H5TS_thread_id() is available as either a function or a macro inDavid Young2020-05-112-12/+5
| | | | | | | | | all configurations. Previously it was neither declared nor defined in --disable-threadsafety builds. The compiler's warning got lost in the noise---I first saw the issue because my -Werror branch stopped compiling cold---and the tests still linked and ran.
* Use a naked pthread_self() call in the HDF5 thread wrappers.David Young2020-05-112-6/+2
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* If H5_HAVE_THREADSAFE is not #defined, define nothing but a stub implementationDavid Young2020-05-111-0/+7
| | | | of H5TS_thread_id().
* Change thread IDs to uint64_t from unsigned long, per Quincey's suggestion.David Young2020-05-064-13/+13
| | | | | Fix a typo in the H5TS_thread_init() comment and reword some ID properties.
* Replace pthread_self_ulong() with H5TS_thread_id(). The POSIX ThreadsDavid Young2020-05-066-21/+124
| | | | | implementation ought to be portable to any system that has POSIX Threads. On Windows, I use the same API call as before.
* Avoid allocating a chunk index for datasets with 0-sized dimensions, untilQuincey Koziol2020-05-042-3/+5
| | | | the dataset is extended.
* Merge pull request #2528 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_12 to ↵hdftest2020-04-271-4/+1
|\ | | | | | | | | | | | | | | | | | | | | hdf5_1_12 * commit '8a4905b9d329b582b04d1cc2705d9e367f4dd20b': Restrict errors to gcc 4.8 and above. Merge pull request #2537 in HDFFV/hdf5 from ~DYOUNG/werror:fix-werrors to develop Fix NoFilter build TRILAB-244 separate CXX warnings and errors from C Don't add general warnings flags for unsupported old versions of gcc and g++ (older than gcc/g++ 4.2). Correct gnu-cxxflags to determine warnings flags to be added based on C++ compiler version instead of C compiler version.
| * Merge pull request #2537 in HDFFV/hdf5 from ~DYOUNG/werror:fix-werrors to ↵David Young2020-04-261-4/+1
| | | | | | | | | | | | | | | | | | develop * commit 'd16eb45d536bd13ca3cf1b0bdc76c58d95d13f17': For compatibility with non-C99 Visual Studio versions, use "%" PRIuMAX instead of "%ju". Fix `test/swmr_sparse_reader.c:118:77: error: cast from pointer to integer of different size [-Werror=pointer-to-int-cast]` and `test/snapshots-hdf5/current/test/swmr_sparse_reader.c:129:100: error: cast from pointer to integer of different size [-Werror=pointer-to-int-cast]`. Fix `src/H5FDdirect.c:1346:5: error: ISO C90 forbids mixed declarations and code [-Werror=declaration-after-statement]`.
* | Snapshot version 1.12 release 1 (snap0)hdftest2020-04-271-2/+2
|/ | | | Update version to 1.12.1-1
* Merge pull request #2497 in HDFFV/hdf5 from ↵Vailin Choi2020-04-141-5/+3
|\ | | | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/112_dtype_close_on_error to hdf5_1_12 * commit '365f08e555e7e92f04b095ccfb3dae09b27fd0ad': Fix according to PR feedback. Fix error in previous merge: should use NULL instead of FAIL.
| * Fix according to PR feedback.vchoi2020-04-071-1/+1
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| * Fix error in previous merge: should use NULL instead of FAIL.vchoi2020-04-071-4/+2
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* | TRILAB-192 - merge changes from developAllen Byrne2020-04-072-7/+3
| | | | | | | | Single source, config files, for warnings for both autotools and CMake. Update CMake libraries, tools, tests to use correct flags.
* | Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_12)Allen Byrne2020-04-051-2/+12
|\ \ | |/ | | | | | | * commit 'db3f89ce9dc7eae17cb15d39e402112c3fbd2955': Merge pull request #2461 in HDFFV/hdf5 from ~VCHOI/my_third_fork:bugfix/dtype_close_on_error to develop
| * Merge pull request #2461 in HDFFV/hdf5 from ↵Vailin Choi2020-04-021-2/+12
| | | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/dtype_close_on_error to develop * commit 'afdcac28b85d690eebc80ab568fa5266081baaaa': A fix in the cleaning up code for datatype when datatype initialization via H5D__init_type() fails. This is triggered by the tests for revised references when the libver bounds setting does not allow version 4 datatype message to be created. The test failure is abort core dumped. This is due to the datatype initialization fails before the datatype ID is registered. The datatype cleanup code should provide for the above situation. The code to fix the problem is the same as what is done in H5D__open_oid().
* | TRILAB-192 merging warnings changes from developAllen Byrne2020-03-301-0/+6
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* Remove VCS merge conflictQuincey Koziol2020-03-241-6/+0
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* Revise API for H5get_alloc_stats() to take a struct instead of separate values.Quincey Koziol2020-03-234-61/+33
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* Add routines to query the library's free list sizes and allocation stats.Quincey Koziol2020-03-238-211/+472
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* Merge pull request #2451 in HDFFV/hdf5 from ↵Vailin Choi2020-03-165-5/+23
| | | | | | | ~VCHOI/my_third_fork:bugfix/develop_seg_fault_sel_compat to develop * commit '81b1ed4e1724b8a6a731ab2b8fb03234a8b49d15': Fix issues when deserializing point/all/none selection with version beyond the library's supported version: (1) Verify the decoded version before proceeding further with deserialization (2) Close the dataspace if errors occurred after opening the dataspace
* Merge pull request #2425 in HDFFV/hdf5 from ~JAKE.SMITH/hdf5:hdf5_1_12 to ↵Jake Smith2020-03-011-2/+2
|\ | | | | | | | | | | | | | | hdf5_1_12 * commit '46f0de82c7674a28b08e4da3b0149c793b762203': Fix improper signing key null check. (HDFFV-11015) Add updates from develop, PR 1958.
| * Fix improper signing key null check. (HDFFV-11015)Jacob Smith2020-02-281-2/+2
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* | Switch the 'get offset' operation from a dataset 'get' callback to a [native]Quincey Koziol2020-02-285-37/+21
| | | | | | | | dataset 'optional' operation.
* | Merge pull request #2325 in HDFFV/hdf5 from ~DYOUNG/werror:h5t_copy to developDavid Young2020-02-2515-194/+480
| | | | | | | | | | | | | | | | | | | | | | Merged per discussion with Elena. * commit '3f903a441ad84001ea66589728bd8b036b6fdfca': Take out the temporary performance tests. Make calls through a function pointer. Use the same number of arguments, always. Increase iterations, provide a baseline for no-op, simplify the overhead case a bit. Temporarily add some code that measures the time to run the simplest possible H5T__copy_all()-like routine 10 million times and then measures the version with FUNC_ENTER_STATIC/_LEAVE_NOAPI and a HGOTO_ERROR() statement. H5T_copy() constification plus Quincey's contributions.
* | Merge pull request #2391 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Allen Byrne2020-02-241-1/+1
|\ \ | | | | | | | | | | | | | | | | | | | | | | | | hdf5_1_12 * commit '5b5ff6ee094033f2ecd974b8e0bdaac2b0c7e617': Correct usage of add_compile_definitions Merge changes from develop mostly cmake 3.12 minimum version Merge changes from develop for CMake and Java
| * | Merge changes from develop mostly cmake 3.12 minimum versionAllen Byrne2020-02-231-1/+1
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* | | Partial fix for HDFFV-10792Jordan Henderson2020-02-211-4/+45
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* | Merge pull request #2338 in HDFFV/hdf5 from ~JHENDERSON/hdf5:hdf5_1_12 to ↵Jordan Henderson2020-02-1715-117/+102
|\ \ | | | | | | | | | | | | | | | | | | hdf5_1_12 * commit '2dbcd87fcddfb519369a368a00acbe8826d5a0eb': Fix some places where H5P_DEFAULT gets passed down to a VOL connector
| * | Fix some places where H5P_DEFAULT gets passed down to a VOL connectorJordan Henderson2020-02-0115-117/+102
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* | | Squashed commit of the following:David Young2020-01-3122-201/+195
|/ / | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | commit ff7a9a34de2fcd78f5d32a1532f3d0e224b20d94 Author: Kimmy Mu <kmu@hdfgroup.org> Date: Wed Jan 29 14:12:18 2020 -0600 Merge pull request #2324 in HDFFV/hdf5 from ~KMU/hdf5:hdf5_1_12 to hdf5_1_12 * commit '781fa57f6ee816e037dd12fff02d37ff7ec9c2b1': pick up missing piece from merge Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop remove redundent definition Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop Merge pull request #2315 in HDFFV/hdf5 from ~KMU/hdf5:develop to develop missing prototype warning prototype issue Merge pull request #2306 in HDFFV/hdf5 from ~KMU/hdf5:develop to develop Merge pull request #2300 in HDFFV/hdf5 from ~KMU/hdf5:squashed_cast to develop Merge pull request #2291 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/uninitialized to develop Merge pull request #2295 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/float to develop Merge pull request #2292 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/prototype to develop Merge pull request #2094 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/unused to develop commit 9f3d808c05d2a3b308f32c958c6671fcac0a432c Author: David Young <dyoung@hdfgroup.org> Date: Wed Jan 29 11:43:55 2020 -0600 testpar/t_2Gio.c: Fix a typo that I think was introduced by a previous warnings PR. An array element was assigned to itself---shape[2]Â =Â shape[2];---instead of being assigned to chunk[2]. fortran/src/H5Pf.c: move conditional compilation controlled by H5_NO_DEPRECATED_SYMBOLS outside of a function for readability. fortran/src/H5match_types.c: put a variable's declaration under the same conditional compilation (H5_FORTRAN_HAVE_C_LONG_DOUBLE) as its use. For now, skip compilation of some unused debug dump routines in the JNI. While I'm in the JNI, delete a set-but-unused variable. src/H5Z.c: condition a variable declaration on H5_NO_DEPRECATED_SYMBOLS so that it's not declared but unused or vice versa. test/cache_common.h: add an #include in to get some symbols we need to avoid implicit declaration warnings. test/dsets.c: use a more conventional conditional-compilation syntax. test/dt_arith.c, test/fillval.c: initialize a bunch of uninitialized variables before use. test/vfd.c: pass the expected type of `void **` to posix_memalign(3) instead of `int **`. testpar/t_bigio.c: explicitly compare with 0 instead of using ! when "equal to 0?" is the question not "is false?" Repair some indentation while I'm here. testpar/testpar.h: repair misaligned line-continuation backslashes in a macro that probably should be a function so that we don't have to fiddle with the line continuation to begin with. tools/src/h5repack/h5repack_main.c: fix some compiler fussing about enums. tools/test/perform/pio_engine.c: the compiler fusses if you cast a function call returning double directly to off_t. It's ok if you cast a variable that's a double to off_t, however. Write and use a new function, sqrto(), to avoid the cast warnings. commit 43a4b80b21c0329fbc1f9a0e2854795189f0bb50 Author: David Young <dyoung@hdfgroup.org> Date: Wed Jan 29 10:47:30 2020 -0600 Reduce casts of HDcalloc()/HDmalloc() that -Wc++-compat required. Reduce gratuitous casts---e.g., (size_t)1. Use the right format string for a pointer. In the H5C sanity checks, change a "size increase" variable from ssize_t (too narrow) to int64_t (wide enough). Parenthesize every appearance of `storage` in the macro `H5D_CHUNK_STORAGE_INDEX_CHK(storage)` so that you can pass in an expression like &sc and it works properly. Disallow re-assignment of the `dset` parameter to H5D__chunk_init() because it helped assure me that it's safe to replace the repeating expression `&dset->shared->layout.storage.u.chunk` with `sc` throughout. Replace lengthy expressions such as `&dset->shared->layout.storage.u.chunk` with `sc` throughout several functions in H5Dchunk.c ISTR that the compiler warned that `sc` was declared but unused in a couple of functions, and then I found that `sc` could be used in many places. Maybe the disused `sc` appeared because a bunch of code was copied and pasted, I don't know. Anyway, it's a lot tighter code now that I use `sc`. In H5D__chunk_update_old_edge_chunks() and H5D__chunk_delete() I actually expand `sc` and another temporary variable, `pline`, because they're used only in !defined(NDEBUG) code. This squashes unused-variable warnings in the defined(NDEBUG) configuration. Don't drop the `volatile` qualification with a cast in tools/src/h5import/h5import.c. commit 035bfa0769a4012881fc659b673bacf44d146537 Author: David Young <dyoung@hdfgroup.org> Date: Tue Jan 28 20:35:28 2020 -0600 Reduce differences between my -Werror branch and `develop`: Rename index -> idx, fileno -> fnumber, fileno -> fno to avoid GCC shadowed declaration warnings about index(3). Convert #pragma GCC diagnostic push/pop/ignored to the HDF5 library's H5_GCC_DIAG_OFF()/H5_GCC_DIAG_ON() macros.
* | Merge pull request #2331 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Allen Byrne2020-01-312-0/+9
|\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | hdf5_1_12 * commit 'a29f9e8451ffa391c8395db1142bd003f40f3aaa': Merge changes from develop to fix various issues Remove commented flags Revert accidental change Chnage tools debug macros to not use the error stack Create common warnings for build systems
| * | Merge changes from develop to fix various issuesAllen Byrne2020-01-302-0/+9
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* | | Introduce new H5VL _by_value routinesJordan Henderson2020-01-295-25/+227
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* | Merge pull request #2324 in HDFFV/hdf5 from ~KMU/hdf5:hdf5_1_12 to hdf5_1_12Kimmy Mu2020-01-2954-241/+250
|\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '781fa57f6ee816e037dd12fff02d37ff7ec9c2b1': pick up missing piece from merge Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop remove redundent definition Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop Merge pull request #2315 in HDFFV/hdf5 from ~KMU/hdf5:develop to develop missing prototype warning prototype issue Merge pull request #2306 in HDFFV/hdf5 from ~KMU/hdf5:develop to develop Merge pull request #2300 in HDFFV/hdf5 from ~KMU/hdf5:squashed_cast to develop Merge pull request #2291 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/uninitialized to develop Merge pull request #2295 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/float to develop Merge pull request #2292 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/prototype to develop Merge pull request #2094 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/unused to develop
| * | Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to developKimmy Mu2020-01-281-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '406330addf45529ecdd088f4d22e9aab9a03661d': rename macro change condition pick up from Dave's fix leave Wswitch-default for later fix fix Wredundant-decls, Wswitch-default, Wdeclaration-after-statement, Wsign-compare, Wmisleading-indentation, Wshadow
| * | prototype issuekmu2020-01-281-1/+1
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