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* fortran module folder from GH#1411 #1922 (#1943)Allen Byrne2022-07-2910-21/+78
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* Merge changes between branches (#1930)Allen Byrne2022-07-267-16/+19
| | | | | * Merge changes between branches * More merge synchs
* Port UG chapter 1 and some cleanup (#1924)Allen Byrne2022-07-2225-4/+560
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* Port UG chapter 2 and fix LD bad ref warning (#1921)Allen Byrne2022-07-2110-3/+806
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* Add doxygen chapter for files, fix autotools images (#1908)Allen Byrne2022-07-198-1/+1405
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* 1.10 eliminate unnecessary errors in the error stack (#1881)Allen Byrne2022-07-182-16/+19
| | | | | | | * Eliminate unnecessary error output * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1 10 Add utility JNI function for 1.10 style references (#1890)Allen Byrne2022-07-184-0/+98
| | | | | | | | | | | * Add utility JNI function for 1.10 style references * Clarify text * Correct signature * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Add doxygen for high level modules to hdf51.10 (#1899)vchoi-hdfgroup2022-07-1628-24/+4421
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* Cherry-pick of Autotools updates from develop (#1885) (#1893)Dana Robinson2022-07-152-2/+6
| | | | * Suppress Autoconf "obsolete" warnings in Java checks (#1853) * Use AC_CHECK_LIB instead of AC_HAVE_LIBRARY for Winsock (#1837)
* Create CODE_OF_CONDUCT.md (#1895)Dana Robinson2022-07-141-0/+128
| | | Taken directly from GitHub's suggested CoC document. We may modify this in the future.
* 1 10 HDFFV-11310 implement JNI VL support for primitive types (#1858)Allen Byrne2022-07-1215-502/+2415
| | | | | | | | | | | | | | | | | | | | | | | | | * HDFFV-11310 - implement vlen read/write for atomic types. * HDFFV-11310 - VL read/write function for primitive types * Add read/write VL option * fix function name typo * remove debugging prints * Remove more debugging code * Correct note to match change in code. * HDFFV-11318 add VL references as byte arrays * Fix unreleased allocations, fix debug * Fix format * Fix formatting * Correct typo
* Port UG groups chapter to doxygen (#1850)Allen Byrne2022-07-0623-6/+903
| | | | | | | * Port UG groups chapter to doxygen. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Add datasets UG chapter, plus fix doxygen refs (#1841)Allen Byrne2022-07-0524-37/+2984
| | | | | * Add datasets UG chapter, plus fix doxygen refs * Remove duplicates
* Port of datatypes UG. (#1829)Allen Byrne2022-06-2958-229/+3824
| | | | | * Port of datatypes UG. * Formatting fix
* Hdf5 1 10 sync (#1795)Allen Byrne2022-06-0978-276/+309
| | | | | * Branch sync updates and spelling * Revert format of getenv
* Update version to 1.10.10-1 (#1783)Larry Knox2022-05-1910-356/+137
| | | | Update so numbers to match 1.10.9 release. Clear 1.10.9 entries from RELEASE.txt.
* Change TestExpress #1722 (#1777)hdf5_1_10_9-baseAllen Byrne2022-05-199-30/+80
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* Add H5S UG chapter, adjust details (#1775)Allen Byrne2022-05-1730-30/+1524
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* Replace obsolete docver arg with arg to supply branch name #1771 (#1774)Allen Byrne2022-05-141-31/+11
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* Add H5P doxygen chapter (#1762)Allen Byrne2022-05-1434-143/+1506
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* Use windows ENV var for default install dir setting #1763 (#1768)Allen Byrne2022-05-132-2/+2
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* INITIAL attempt at User Guide in doxygen (#1678)Allen Byrne2022-05-139-43/+1021
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path * Update missing release note info. * Update code owners * Add known problem * Use only core library for testing dynamic plugins. CMake uses H5_HAVE_DIRECT instead of DIRECT_VFD * INITIAL attempt at User Guide in doxygen * Add quick H5E to show actual UG header sections * Add Error Handling chapter * Cleanup format changes * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes for various warnings/alignment with develop branch (#1755)jhendersonHDF2022-05-0838-353/+265
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* [1.10 Merge] Hdf5 1 10 warnings merge (#1754)jhendersonHDF2022-05-0868-4762/+3775
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Warnings fixes (#1680) * Clean stack size warnings in sio_engine (#1687) * Fixes stack size warnings in tcoords.c (#1688) * Address some warnings from casting away of const (#1684) * Fixes stack size warnings in dtransform (#1696) * Fixes stack size warnings in set_extent test (#1698) * Be a bit safer with signed arithmetic, thus quieting some signed-overflow warnings from GCC (#1706) * Avoid a signed overflow: check the range of `entry_ptr->age` before increasing it instead of increasing it and then checking the range. This quiets a GCC warning. * Avoid the potential for signed overflow by rewriting expressions `MAX(0, fwidth - n)` as `MAX(n, fwidth) - n` for various `n`. This change quiets some GCC warnings. * Change some local variables that cannot take sensible negative values from signed to unsigned. This quiets GCC warnings about potential signed overflow. * In a handful of instances, check the range of a signed integer before increasing/decreasing it, just in case the increase/decrease overflows. This quiets a handful of GCC signed-overflow warnings. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix object size warnings in cache.c test (#1701) * Fix some const cast and stack/static object size warnings (#1700) * Fix various warnings * Move HDfree_const to H5private.h for wider use * Print output from all ranks in parallel tests on allocation failure * Move const pointer freeing macro to h5test.h for now * Fixes a bug where t_cache fails due to a string size being too small (#1720) * Fixes a bug where t_cache fails due to a string size being too small Recent warning reductions led to an incorrect string size being passed to h5_fileaccess, causing the test to silently fail. In addition to fixing the bug, the test will now fail noisily on setup failures. * Updates the t_cache test to fail noisily on setup errors * Fix a few Clang sanitizer warnings (#1727) * Stop lying about H5S_t const-ness (#1209) Hyperslabs can be reworked inside several H5S callbacks, making H5S_t non-const in some places where it is marked const. This change switches these incorrectly const H5S_t pointer parameters and variables to non-const where appropriate. * Fix a few warnings after recent H5S const-related changes (#1225) * Adjustments for HDF5 1.10 * Hdf5 1 12 Miscellaneous warnings fixes (#1718) * Fixes const issues in the version 2 B-trees (#1172) The operations that were changed are fundamentally not const since the shadow operation can modify the node structure when SWMR is in use. * Quiets const warning in H5RS code (#1181) * Avoid calling H5Ropen_object with a misaligned H5R_ref_t: copy the (#1171) * Avoid calling H5Ropen_object with a misaligned H5R_ref_t: copy the raw H5R_ref_t bytes to a heap buffer that's known to have the right alignment. * Committing clang-format changes * Use an automatic H5R_ref_t instead of malloc'ing one. Go ahead and initialize the H5R_ref_t to all-0s so that arbitrary stack content doesn't foul things up. Bail out with an error if `size` exceeds `sizeof(H5R_ref_t)`. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Miscellaneous warnings fixes Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix several warnings (#747) Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Use git command to get branch name (#1750)Allen Byrne2022-05-071-1/+1
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* Update package scripts (#1745)Allen Byrne2022-05-062-4/+5
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* Brings random stuff over from develop (#1738)Dana Robinson2022-05-0648-584/+734
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* Align H5T code with develop to quiet warnings (#1717)jhendersonHDF2022-05-033-167/+176
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* Reinstate java API removed in 1.10.8 (#1697)Allen Byrne2022-04-294-5/+111
| | | | | | | * Revert java API removal with JNI private function * Fix name typo * Correct format
* Brings over minor changes in root, bin/, and release_docs (#1699)Dana Robinson2022-04-2817-114/+125
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* Add java to format source (#1690)Allen Byrne2022-04-26155-9202/+12118
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* Updates README.txt to README.md like the other branches (#1675)Dana Robinson2022-04-256-30/+38
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* HDF5 1.10: Removes HDF Group paths, adds shellcheck fixes (#1660)Dana Robinson2022-04-191-95/+41
| | | | | | For more information: https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ... https://www.shellcheck.net/wiki/SC2230 -- which is non-standard. Use builti... https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...
* Hdf5 1 10 parallel comp (#1644)jhendersonHDF2022-04-1427-3073/+9544
| | | | | * Hdf5 1 10 parallel compression merge
* 1.10 Add option for h5repack timing #1142 (#1576)Allen Byrne2022-04-149-82/+203
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* Fix these Doxygen warnings #1581 (#1591)Allen Byrne2022-04-142-7/+10
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* Hdf5 1 10 merges (#1633)jhendersonHDF2022-04-1449-358/+679
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* 1.10 Move error-stack text to top of usage display #1564 (#1567)Allen Byrne2022-04-1428-81/+135
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* Brings release timeline and github action changes from develop (#1597)Dana Robinson2022-04-064-0/+68
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* Brings MANIFEST removal from develop (#1596)Dana Robinson2022-04-0611-6319/+110
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* Update command format, avoid policy warning (#1552)Allen Byrne2022-03-301-3/+3
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* 1.10 Merge doxygen changes from develop (#1543)Allen Byrne2022-03-3067-963/+3758
| | | | | | | * Merge doxygen changes from develop * Remove 1.12 section * Minor comment cleanup
* Windows and *nix use different forms for warnings #1515 (#1525)Allen Byrne2022-03-264-5/+7
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* Change ENV to CMake var #1520 (#1522)Allen Byrne2022-03-261-2/+1
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* Merge free an MPI communicator #1503 (#1510)Allen Byrne2022-03-221-7/+8
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* 1.10 Update HDF5_ROOT usage (#1487)Allen Byrne2022-03-123-4/+13
| | | | | * Update HDF5_ROOT usage * Fix typo
* 1.10 Fix release check version logic #1438 (#1494)Allen Byrne2022-03-124-11/+26
| | | | | * Fix release check version logic #1438 * Correct list comment
* Implemented suggestion in #1381 for dtransform test (#1491)Allen Byrne2022-03-122-18/+22
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* 1 10 Add -showconfig to h5cc scripts to dump libhdf5.settings file (#1483)Allen Byrne2022-03-122-1/+29
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* Merge Mingw build fixes from develop (#1475)Baljak2022-03-096-32/+34
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