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* Merge branch 'hdf5_1_14_0' of https://github.com/HDFGroup/hdf5 into hdf5_1_14_0Larry Knox2022-12-283-8/+42
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| * Adds RELEASE.txt notes and updates Doxygen (#2377)Dana Robinson2022-12-283-8/+42
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* | Set version to 1.14.0.Larry Knox2022-12-287-18/+18
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* Adds Doxygen markup to H5FDdriver_query() (#2373)Dana Robinson2022-12-282-4/+23
| | | | | | | * Adds Doxygen markup to H5FDdriver_query() * Fixes Doxygen warnings * Fixed missing *
* Commit files generated by autogen.sh with autotools versions on jelly. (#2372)Larry Knox2022-12-2890-16005/+11466
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* Update Platforms Tested. (#2369)Larry Knox2022-12-281-73/+85
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* Add note to known problems about MPI implementations derived from buggy ↵Neil Fortner2022-12-271-1/+11
| | | | | | | | MPICH or OpenMPI versions (#2368) * Add note to known problems about MPI implementations derived from buggy MPICH or OpenMPI versions. Fix typo. * Add note about increasing thread limit with OpenMPI and subfiling
* Brings Doxygen changes from develop (#2367)Dana Robinson2022-12-2710-51/+104
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* Brings the HL GIF tools configure changes from develop (#2362)Dana Robinson2022-12-2498-11589/+16071
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* Updated RELEASE.txt with known MPI problems (#2359)Dana Robinson2022-12-231-0/+19
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* Added additional 'known problems' notes to RELEASE.txt (#2358)Dana Robinson2022-12-231-0/+6
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* 1.14.0: Clean up release_docs directory (#2353)Dana Robinson2022-12-239-24844/+3554
| | | | | | | | | | | | | | | | | | | | | | | * Added a README to release_docs * Removed maintenance branch HISTORY documents * Consolidated HDF5 1.13 history into RELEASE.txt * Removed 1.12.0 entries that were not properly cleaned out * Fix unescaped brackets * Okay, let's try square brackets * Make the version notation uniform * Added some helpful text about introduction boilerplate * Added 1.X.0 release info to HISTORY files * Update the README.md file * Fixed text in HISTORY intros
* iFix sha256sum commands in release script. (#2348)Larry Knox2022-12-221-8/+8
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* Fixed version info. (#2345)Gerd Heber2022-12-221-1/+2
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* Update configure 1 14 0 (#2346)Larry Knox2022-12-2276-12/+118
| | | | | * Update configure and Makefile.ins. * disable CMake Installation.
* Adds Doxygen VOL flag markup (#2340) (#2342)Dana Robinson2022-12-211-55/+63
| | | | | | | | | | | | | * Initial doxygen markup * Committing clang-format changes * Adds Doxygen comments to VOL flags * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Onion VFD header cleanup (#2337) (#2339)Dana Robinson2022-12-213-112/+85
| | | | | | | | | | | * Partial work towards cleaning up the onion VFD code * Committing clang-format changes * A few minor tweaks to the onion VFD public header Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix up the H5Pencode2 test for virtual layout. (#2325) (#2336)Dana Robinson2022-12-211-91/+87
| | | | | | | | | | | | | * Fix up the H5Pencode2 test for virtual layout. * Committing clang-format changes * Remove VERIFY and use TEST_ERROR. Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1.14.0: Brings the following changesets over from develop: (#2330)Dana Robinson2022-12-2134-135/+229
| | | | | | | | | | | | | | | | | | | * Brings the following changesets over from develop: b9244a85d9f1cc5e9bbec61ca73c0cbd9c4cf249 Align arg types of H5D_chunk_iter_op_t with H5Dget_chunk_info (#2074) 70cf2c390bc2eef8e57f8fa023341011e2d02d9d Removed idioms and misc. text clean-up (#2320) 8102fa8c972bdc0d8fd8f3dae604e070893150d6 Only document Fortran functions (#2319) 784061b15e176b9919c19a220ce278a9f4cddf0e moved onion VFD to FAPL group (#2321) 6b6bcdead66f0456ac0528683faac6a8e48b6565 Hdffv 11052 (#2315) 10c693a04ff0c4a5219879d7f8900157dcbece66 Update hdf5_header.html 0cb58080875070db09b5ecae92482519d58872bc Hdffv 11052 (#2303) a1c81eda203addced514ef655f7a9079f3f0bb04 added doc. warning for H5Literate_async return value (#2295) 502b32b0f22a4bcf6333c85c256db34162c2764a Updated H5ES documenation (#2293) a9036005c3916e6fda0296026323f00d043300f8 Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC)… (#2291) * Brings the following changes over from develop: c1e44d32e616518e0626bdfe042bed0052846fef Fix doxygen warnings and remove javadocs (#2324) 149b8e9769887c5b23400b526dc10463f88f2c3e Disable hl tools by default (#2313)
* Fixes duplicated build mode in -Werror GitHub action names (#2317)Dana Robinson2022-12-161-2/+2
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* Converts the YAML build mode arrays to objects in special runs (#2308) (#2310)Dana Robinson2022-12-161-37/+41
| | | | | | | | | | | | | * Converts the YAML build mode arrays to objects in special runs * Adds a dump of the matrix context for each test This would have made it a LOT easier to debug the build_mode issues... * Disable the mirror VFD in the -Werror checks We can re-enable this after we fix the warnings, but I don't want to conflate code and GitHub changes, so this is a better way to get the CI to pass for now.
* Brings io_info warning fixes from develop (#2305)Dana Robinson2022-12-163-18/+17
| | | CI fails due to a problem with the GitHub actions, not this PR
* Fixed mis-indented autogen comments in main.ymlDana Robinson2022-12-151-2/+2
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* Replaced .dat exclusion in codespell CI actionDana Robinson2022-12-151-1/+1
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* Fixed matrix production mode in main.ymlDana Robinson2022-12-141-7/+7
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* Update hdf5 1 14 0 (#2299)Larry Knox2022-12-141-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Initial updates for HDF5 1.14.0 release December 2022 Update so numbers for release Set version to 1.14.0 Switch default build mode to production for release in configure.ac lines435 and 442 Switch AM_MAINTAINER_MODE to disabled with bin/switch_maint_mode Set HDF5_GENERATE_HEADERS to OFF in src/CMakeLists.txt Commit Makefile.ins and other generated files for release except 2 ...~ files and autom4te.cache. * Add autotools generated files with misspelled word to list for codespell to skip. * Add autom4te.cache to codespell list of files to skip * Update windows worker compilers (#2286) * Update windows worker compilers * Update bin and test issues * Update script and revert java test * Update release script, version in java files and so numbers in Makefile.ins. * Add hdf5-1_14_0 branch to main.yml. * Don't run autogen.sh for release branche hdf5_1_10_0. * Fix syntax in main.yml Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
* Update hdf5 1 14 0 (#2298)Larry Knox2022-12-1414-84/+87
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * Initial updates for HDF5 1.14.0 release December 2022 Update so numbers for release Set version to 1.14.0 Switch default build mode to production for release in configure.ac lines435 and 442 Switch AM_MAINTAINER_MODE to disabled with bin/switch_maint_mode Set HDF5_GENERATE_HEADERS to OFF in src/CMakeLists.txt Commit Makefile.ins and other generated files for release except 2 ...~ files and autom4te.cache. * Add autotools generated files with misspelled word to list for codespell to skip. * Add autom4te.cache to codespell list of files to skip * Update windows worker compilers (#2247) * Update release script, version in java files and so numbers in Makefile.ins. * Add hdf5-1_14_0 branch to main.yml. * Don't run autogen.sh for release branche hdf5_1_10_0. Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
* Initial updates for HDF5 1.14.0 release December 2022 (#2292)Larry Knox2022-12-13108-30/+193805
| | | | | | | | | | | | | * Initial updates for HDF5 1.14.0 release December 2022 Update so numbers for release Set version to 1.14.0 Switch default build mode to production for release in configure.ac lines435 and 442 Switch AM_MAINTAINER_MODE to disabled with bin/switch_maint_mode Set HDF5_GENERATE_HEADERS to OFF in src/CMakeLists.txt Commit Makefile.ins and other generated files for release except 2 ...~ files and autom4te.cache.
* added doc. warning for H5Oflush in parallel (#2289)Scot Breitenfeld2022-12-101-0/+3
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* fixed unclosed objects in test (#2290)Scot Breitenfeld2022-12-101-6/+10
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* Check for size==0 for all datatypes read from disk, not just compound (#2287)Neil Fortner2022-12-081-9/+5
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* Compound datatypes may not have members of size 0 (#2243)Egbert Eich2022-12-072-69/+125
| | | | | | | | | | | | | | | | | | | | | | * Compound datatypes may not have members of size 0 A member size of 0 may lead to an FPE later on as reported in CVE-2021-46244. To avoid this, check for this as soon as the member is decoded. This should probably be done in H5O_dtype_decode_helper() already, however it is not clear whether all sizes are expected to be != 0. This fixes CVE-2021-46244 / Bug #2242. Signed-off-by: Egbert Eich <eich@suse.com> * Rework error recovery code in H5O__dtype_decode_helper() and H5O__dtype_decode(). * Format changes for src/H5Odtype.c. Signed-off-by: Egbert Eich <eich@suse.com> Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Correct requires setting for pkgconfig files (#2280)Allen Byrne2022-12-076-10/+18
| | | | | * Correct requires setting for pkgconfig files * Add issue number
* Fixes warnings in H5Opline.c error messages (#2281)Dana Robinson2022-12-061-3/+5
| | | | | | | * Fixes warnings in H5Opline.c error messages * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Add text about release notes (#2246)Allen Byrne2022-12-061-10/+67
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* Develop jni trans (#2266)Allen Byrne2022-12-0611-421/+1407
| | | | | | | | | * Add compound and refactor out atomic types * Add Array String tests back * Convert Attribute version of compound example * Update transfer atom8ic read to return object
* H5E_ERR_CLS_g symbol missing when compiling C++ plugins (#2269)V. Armando Solé2022-12-061-0/+7
| | | | C++ HDF5 filter plugin SZ3 fails to build under windows with failure at linking time unless that extern "C" block is added.
* return error message related to calling API (#2276)Scot Breitenfeld2022-12-021-2/+2
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* CVE 2021 46242 develop (#2255)Egbert Eich2022-12-022-2/+18
| | | | | | | | | | | | | | | | | | | | | | * When evicting driver info block, NULL the corresponding entry Since H5C_expunge_entry() called (from H5AC_expunge_entry()) sets the flag H5C__FLUSH_INVALIDATE_FLAG, the driver info block will be freed. NULLing the pointer in f->shared->drvinfo will prevent use-after-free when it is used in other functions (like H5F__dest()) - as other places will check whether the pointer is initialized before using its value. This fixes CVE-2021-46242 / Bug #2254 Signed-off-by: Egbert Eich <eich@suse.com> * When evicting the superblock, NULL the corresponding entry The call to H5AC_expunge_entry() will free the corresonding structure, to avoid a use-after-free, the corrsponding pointer entry will be NULLed. Signed-off-by: Egbert Eich <eich@suse.com> Signed-off-by: Egbert Eich <eich@suse.com>
* Output should only be printed if verbose. (#2273)Allen Byrne2022-12-022-27/+42
| | | | | * Output should only be printed if verbose. * Add note
* Report error if dimensions of chunked storage in data layout < 2 (#2241)Egbert Eich2022-12-022-1/+18
| | | | | | | | | | | | | | | | For Data Layout Messages version 1 & 2 the specification state that the value stored in the data field is 1 greater than the number of dimensions in the dataspace. For version 3 this is not explicitly stated but the implementation suggests it to be the case. Thus the set value needs to be at least 2. For dimensionality < 2 an out-of-bounds access occurs as in CVE-2021-45833. This fixes CVE-2021-45833 / Bug #2240. Signed-off-by: Egbert Eich <eich@suse.com> Signed-off-by: Egbert Eich <eich@suse.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Add aarch64 toolchain and change dump test to long opt (#2271)Allen Byrne2022-12-012-1/+18
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* Develop fix ubuntu 22.04 openmpi install on github (#2268)Larry Knox2022-11-281-1/+1
| | | | | * Update install openmpi-bin to also install mpi-default-dev instead of libopenmpi-dev. This according to https://bugs.launchpad.net/ubuntu/+source/openmpi/+bug/1870780.
* Make sure testsuite can handle multiple dependent scripts (#2256)Egbert Eich2022-11-281-1/+8
| | | | | | | | | | | | | | | Commit afc54d75a19 to the test suite to eliminate a separate shell script did not take into account that there may be multiple dependent test scripts which resulted in the message: `/bin/sh: line 7: [: too many arguments`. when running the test suite. Beware that this new version still makes use of non-posix GNU extensions to `test`. Signed-off-by: Egbert Eich <eich@suse.com> Signed-off-by: Egbert Eich <eich@suse.com>
* Develop ubuntu 20.04 (#2267)Larry Knox2022-11-231-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | * Use ubuntu-20.04 for github autotools parallel tests until parallel configure is fixed on ubuntu 22.04. * Remove inactive developers from CODEOWNERS. * Temporarily cat config.log for autotools build in github actions. * Try ubuntu-latest. * Attempt to cat config.log even when configure fails. * Fix syntax. * Try again * Try again * Try again. * Back to original temporary fix. * Install libopenmpi-dev with openmpi-bin, which was installed as a dependency prior to ubuntu-22.04.
* Use ubuntu-20.04 for github autotools parallel tests until parallel (#2264)Larry Knox2022-11-182-2/+2
| | | | | | * Use ubuntu-20.04 for github autotools parallel tests until parallel configure is fixed on ubuntu 22.04.
* Bug Fix: Segfault in H5CX_get_vol_wrap_ctx when H5VLwrap_register is called ↵raylu-hdf2022-11-173-2/+111
| | | | | | | | | | | | | | | | from an application (#2248) * Jira HDFFV-10881: Segfault in H5CX_get_vol_wrap_ctx when H5VLwrap_register is called from an application. A quick and simple fix to make it fail with a relevant error message. * Format changes. * Committing clang-format changes * Minor change: split one condition check into two for clarity. * Adding doxygen comment for H5VLwrap_register. * Minor change: adding a little more detail to the Doxygen comment for H5VLwrap_register.
* 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
* Remove hard-coded version text (#2260)Allen Byrne2022-11-162-3/+3
| | | | | * Remove hard-coded version text * Use macOS 11 until accum test is fixed see #2261
* Refactor JNI translate functions to a recursive switch on datatype (#2232)Allen Byrne2022-11-167-488/+914
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