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* Various warning fixes (#1812)Sean McBride2022-06-221-8/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fixed -Wreserved-id-macro warnings from header include guards * Removed all __int64 and LL suffix stuff now that C99 is minimum requirement * Rename `H5FD_CTL__` to `H5FD_CTL_` to fix -Wreserved-id-macro warnings Double underscore is reserved in C++ and this public header should be C++ compatible. * Never define __STDC_FORMAT_MACROS anymore Defining it causes a -Wreserved-id-macro. Happily, according to the C++11 standard: "The macros defined by <stdint> are provided unconditionally. In particular, the symbols __STDC_LIMIT_MACROS and __STDC_CONSTANT_MACROS (mentioned in C99 footnotes 219, 220, and 222) play no role in C++." https://cplusplus.github.io/LWG/issue984 So looks like it's not necessary to define it with reasonably new toolchains. * Fixed some -Wunused-macros warnings, removed dead code * Fixed all -Wdouble-promotion warnings in C++ files * Fixed remaining -Wsuggest-destructor-override warnings * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Develop sync (#1793)Allen Byrne2022-06-092-2/+2
| | | | | * Synch update * Branch sync changes
* Update windows VS2019 and fix comments (#1781)Allen Byrne2022-05-201-2/+2
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* Use windows ENV var for default install dir setting (#1763)Allen Byrne2022-05-122-2/+2
| | | | | * Use windows ENV var for default install dir setting * Change variable name
* Re-promote some GNU warnings to errors (#1508)David Young2022-05-061-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Promote some GCC warnings back to errors and deal with build breakage. I tested configuring and building with GCC 8.3.0 with `.../configure --prefix=$HOME/wrk/install/manydsets --enable-build-mode=production --enable-symbols=-gdwarf-4 --enable-warnings-as-errors --enable-java --enable-hl --enable-fortran --enable-cxx --enable-mirror-vfd --enable-ros3-vfd --enable-direct-vfd` and with the same options but `--enable-build-mode=debug`. * Promote -Wrestrict to -Werror=restrict to help catch overlapping arguments to strcpy, memcpy, et cetera, at compile time. * NFCI: sort lines. * Committing clang-format changes * NFCI: remove whitespace at EOL. * Re-use temporary variable `shared`. * Remove merge oopsie. * Mention that no op codes are understood per review comment. * Change this back to the develop branch's way, since this change isn't integral to the PR. * Committing clang-format changes * NFCI: reduce differences with `develop` branch in the hope that that also kicks off CI. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Minor things noticed while merging to 1.10 (#1739)Dana Robinson2022-05-061-1/+1
| | | | | * Minor things noticed while merging to 1.10 * Set HDF5_DRIVER back in string
* Remove H5_NO_ALIGNMENT_RESTRICTIONS (#1426)David Young2022-04-163-60/+0
| | | | | | | | | | | | | | | | | * Do not conditionally compile code that uses a pointer dereference and assignment to copy a potentially unaligned variable to aligned automatic storage, or vice versa. Instead, always use naked `memcpy(3)`s. Disassembling the generated code reveals that the `memcpy(3)`s optimize (`-O3`) to a single `mov` instruction for x86_64, which is not strict about alignment. This change reduces the size of code and scripts by 143 lines, eases our way to cross-compilation, and avoids invoking undefined behavior. * Committing clang-format changes * Per discussion, use HD and add comments. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Change ENV to CMake var (#1520)Allen Byrne2022-03-241-2/+1
| | | | | | | * Change ENV to CMake var * Fix typo deletion * Fix typo
* Windows and *nix use different forms for warnings (#1515)Allen Byrne2022-03-241-3/+3
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* Update version to 1.13.2-1 after 1.13.1 release; add new Makefile.in files ↵Larry Knox2022-03-011-1/+1
| | | | | | to MANIFEST (#1460)
* Add release note for #1438 (#1457)Allen Byrne2022-02-251-1/+1
| | | | | * Add release note for #1438 * fix typos.
* Parallel Compression improvements (#1302)jhendersonHDF2022-02-241-0/+3
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* Add SZ filter and adjust compression file names to avoid conflicts (#1434)Allen Byrne2022-02-174-14/+16
| | | | | | | | | * Updated plugins project required adjustments * Updated plugins need to distinguish external libs * Fix missed rename * Use same name for windows as linux - avoid name clash
* Add -showconfig to h5cc scripts to dump libhdf5.settings file (#1391)Allen Byrne2022-02-111-1/+22
| | | | | * Add -showconfig to h5cc scripts to dump libhdf5.settings file * Added note
* Update doc with HDF5_ROOT usage. (#1414)Allen Byrne2022-02-021-2/+2
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* Update the java slf4j logging jars to latest 1.7.33 (#1369)Allen Byrne2022-01-181-2/+2
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* Updated README.txt to README.md (#1375)Scot Breitenfeld2022-01-141-1/+1
| | | | | | | | | | | * H5Lexists docs: Removed reference to 1.8.16 since the change is the 1.8.x releases, HDFFV-11289 * H5Oget_info_by_name, name can be any object, not just a group * Converted README.txt to README.md and updated files referring to README.txt to README.md. * removed references to README.txt * updated MANIFEST
* Fixed Spelling Errors (#1166)Scot Breitenfeld2021-12-074-5/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * fixed missed closing of a dataset * fixed missed closing of a dataset * fixed typo in error return * Committing clang-format changes * minor edits * code format * Committing clang-format changes * code format * minor edit * switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging * Committing clang-format changes * changed size_i in printf to reflect the I/O. * Committing clang-format changes * Fixed seg fault with xlf on BE with -qintsize=8 * fixed error function string * spelling corrections via codespell, added new spell check github actions * Committing clang-format changes * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * work around for https://github.com/codespell-project/codespell/issues/2137 * misc * added missing file * misc * misc. * misc * switch to using Codespell with GitHub Actions * misc. * misc. * fixed more sp errors * Fix new typos found by codespell. * fixed proceed with precede * fixed variable in fortran test * fixed minnum * updated spelling list Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* 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
* 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 Byrne2021-10-271-5/+5
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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 Byrne2021-10-202-2/+39
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Young2021-10-062-33/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
* 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
* 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 Byrne2021-09-222-7/+5
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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 Byrne2021-09-161-3/+4
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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).
* Develop windows compiler fixes (#912)Allen Byrne2021-08-192-31/+38
| | | | | | | | | | | | | | * 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 Byrne2021-08-162-266/+335
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* 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 Robinson2021-07-061-3/+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 Robinson2021-06-301-3/+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>
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