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* Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2019-12-111-10/+11
|\ | | | | | | | | | | | | * commit '6b670e353c1ea7f13ef72cc4297d9973102078bb': Correct assignment Fix java include, h5watch and remove clang tool. Add missing filenames
| * Correct assignmentAllen Byrne2019-12-101-1/+1
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| * Fix java include, h5watch and remove clang tool.Allen Byrne2019-12-101-10/+11
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* | HDFFV-10974 Change defines to eliminate Windows conflictAllen Byrne2019-12-108-180/+175
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* Fix windows 10 compile errorAllen Byrne2019-12-071-6/+18
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* Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2019-12-022-5/+1
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '0772b975d1d2bfa15aedeb4b6e2c2aac78c61a2f': Fix missing free in H5T__ref_mem_read() Fix bugs in H5VL file comparison code. Add short circuit success to H5VL_cmp_connector_cls(). Implement file comparison VOL callback. Other changes to allow references to work with non-native connectors. There is a bug somewhere. Add support for point selections to H5S_select_project_intersection. Remove H5VL_NATIVE_FILE_GET_FILE_ID and add H5VL_OBJECT_GET_FILE Revert "Make a squash commit of 'Quiet some warnings by adjusting warnings level and fixing some code.' (commit 5c911d8baf3)" Revert "Oops, remove more C99 designated initializers for VS 2010 compatibility." H5R: fix H5Tconv to check for null references Trivial parameter renaming in VOL API calls. Move checking for zero offset in selection adjust calls to the selection callbacks. This makes the procedure for checking it consistent across selection types and between _s and _u, ensures it is always is performed even when called within the H5S package, and removes the redundant check that would occur when callins H5S_select_adjust_s() from outside the H5S package. Replace H5Sselect_adjust_u() and H5Shyper_adjust_s() with H5Sselect_adjust. Implement "adjust_s" callback for all selection types. Add range checking to H5Sselect_adjust().
| * Revert "Make a squash commit of 'Quiet some warnings by adjusting warnings ↵David Young2019-11-272-2/+2
| | | | | | | | level and fixing some code.' (commit 5c911d8baf3)"
| * Revert "Oops, remove more C99 designated initializers for VS 2010 ↵David Young2019-11-271-5/+1
| | | | | | | | | | | | compatibility." This reverts commit f907b511d06612dafc7814a7c30f2f3d2b76d52b.
* | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2019-11-262-1/+5
|\ \ | |/ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit 'a8892bb42d6f6e4fbc30fae0eb2b957f81c938b9': (45 commits) Oops, remove more C99 designated initializers for VS 2010 compatibility. Add an #include to get a function declaration. Don't use C99 designated initializers, they're not compatible with Visual Studio 2010. Quiet some more maybe-uninitialized warnings---each is a false positive, *sigh*. This is more code that may not compile with VS2010, *sigh sigh*. Always warn on maybe-uninitialized. -Wincompatible-pointer-types was not available until GCC 5, so enable it only if that's the GCC version we're using. Only promote maybe-uninitialized warnings to errors on GCC 8. Even on GCC 8, there may be false positives at low optimization levels? I need to check. Only use -Werror=cast-function-type with GCC 8 and later. Put all of the -W options back into the order I found them in so that it's easier to compare old and new config/gnu-flags. Add new source files to CMakeLists.txt. Mention the -Werror= flags in libhdf5.settings.in. free -> HDfree Promote decleration-after-statement warnings to errors. Quiet decleration-after-statement warnings. Move a statement under some declarations since some vintages of Visual Studio don't like declarations after statements. Document H5D__chunk_mem_xfree_wrapper(). Undo accidental test deletion. Oops, delete a debug printf that snuck in here. Undo my changes to the HD macros, hadn't really intended those to be on this branch.... Make errors of some more warnings. Move disabled warnings to DEVELOPER_WARNING_CFLAGS. Put just one warning option on a line, and sort some of the options. Cast to the parameter type, H5VL_token_t *, instead of to unsigned char *. ...
| * Oops, remove more C99 designated initializers for VS 2010 compatibility.David Young2019-11-251-1/+5
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| * Avoid unused-variable warnings: change static const strings in a coupleDavid Young2019-11-131-1/+1
| | | | | | | | of header-file templates to #defines.
| * Initialize a variable before its first use.David Young2019-11-131-1/+1
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* | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2019-11-132-2/+2
|\ \ | |/ | | | | | | | | | | | | | | * commit 'e08b69d3d2e572de4707b1fbf908111d29f40a1b': Use HD prefix. Fix issue where H5R__reopen_file did not make the file "post open" callback. Apparently, + has no special meaning, and neither does \+, in so-called "obsolete" / POSIX "basic" regular expressions. Also, not every version of `sed` out there supports the `-E` option. So delete the -E flag and use the regex `[^/][^/]*` instead of `[^/]+`. Implement H5VLget_file_type() to return a copy of a datatype with the location set to be in a file. Only meant to be used by VOL connectors. Implement H5VLpeek_connector_id() to support connectors querying their own IDs. Fix app_ref with connector IDs in a couple places (external VOLs registered as default through ENV should be visible to the application). Modify vlen and reference interfaces to work with arbitrary VOL connectors. Implement file "post open" specific callback, to enable connectors to update their file structs after a wrap context has been set. Fix HDFFV-10937: use a more reliable (and probably faster) scheme for visiting all elements of a matrix in an arbitrary order.
| * Apparently, + has no special meaning, and neither does \+, in so-calledDavid Young2019-11-122-2/+2
| | | | | | | | | | | | | | | | "obsolete" / POSIX "basic" regular expressions. Also, not every version of `sed` out there supports the `-E` option. So delete the -E flag and use the regex `[^/][^/]*` instead of `[^/]+`. Add config/netbsd to the MANIFEST.
* | HDFFV-10876 Update h5dump and h5ls for new ref api.Allen Byrne2019-11-071-70/+70
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* Merge pull request #1984 in HDFFV/hdf5 from ~DYOUNG/netbsd:develop to developDavid Young2019-11-056-12/+59
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '0b721858e46a317c370a24115032d5be41688f67': Make these scripts relocatable again: derive a relative path for the original installation prefix from the examples prefix. Use that relative path to locate the current installation prefix, always. Fall back to an absolute installation prefix if the relative path cannot be derived. Get the path to prefix right: needs a ../ to back out of subdirectory c/. Make this script relocatable again: derive a relative path for the original installation prefix from the examples prefix. Use that relative path to locate the current installation prefix, always. Fall back to an absolute installation prefix if the relative path cannot be derived. Let us override the examples directory using --with-examplesdir=DIR. This is handy for NetBSD where HDF5 examples are installed by convention in $prefix/share/examples/hdf5/ rather than in ${prefix}/share/hdf5_examples/, which is the HDF5 default. Follow longstanding execv convention for compatibility with NetBSD. Under the examples directories, always find the installed HDF5 executables and scripts using @prefix@ instead of a relative path, because the number of ../ in the relative path will be different on NetBSD than on other systems. Make the HDF5 configure script grok NetBSD. For portability, insulate the HDF5 library from some system macros. Not every system has perl installed in /usr/bin/, so change the shebang (#!) line to `/usr/bin/env perl` to locate perl on the PATH. For portability, use the POSIX sh(1) string-comparison operator `=` instead of `==`.
| * Make these scripts relocatable again: derive a relative path for theDavid Young2019-11-052-2/+49
| | | | | | | | | | | | | | original installation prefix from the examples prefix. Use that relative path to locate the current installation prefix, always. Fall back to an absolute installation prefix if the relative path cannot be derived.
| * Let us override the examples directory using --with-examplesdir=DIR.David Young2019-10-036-9/+9
| | | | | | | | | | | | | | | | | | This is handy for NetBSD where HDF5 examples are installed by convention in $prefix/share/examples/hdf5/ rather than in ${prefix}/share/hdf5_examples/, which is the HDF5 default. Place hdf5_examples/ under ${datarootdir} which on most systems will be ${prefix}/share/, anyway.
| * Under the examples directories, always find the installed HDF5David Young2019-10-033-3/+3
| | | | | | | | | | | | | | | | | | | | executables and scripts using @prefix@ instead of a relative path, because the number of ../ in the relative path will be different on NetBSD than on other systems. Examples on NetBSD are installed at ${prefix}/share/examples/hdf5/ instead of at ${prefix}/share/hdf5_examples/, by convention. It may be the same on other BSDs, I'm not sure.
* | Make wrappers, tests and tools use H5Treclaim() instead of H5Dvlen_reclaim()Jerome Soumagne2019-10-082-9/+9
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* OESS-29 Update HD prefix mostlyAllen Byrne2019-08-245-83/+83
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* This test cannot use HD prefix macro with printf of fprintfAllen Byrne2019-08-171-2/+2
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* Update HD prefix and reconcile hl/cpp testAllen Byrne2019-08-1613-1215/+1223
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* Add HD prefix to testsAllen Byrne2019-08-154-120/+118
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* Merge pull request #1826 in HDFFV/hdf5 from ↵Dana Robinson2019-08-013-4/+3
|\ | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:develop_minor_pr to develop * commit '4227b8948d7091205b4f8dc1271d7dcae01bb0fb': Reverts the removal of config/conclude_fc.am while keeping the changes to config/gnu-fflags. Fixed a couple of typos.
| * Reverts the removal of config/conclude_fc.am while keepingDana Robinson2019-08-013-4/+3
| | | | | | | | the changes to config/gnu-fflags.
* | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2019-07-293-3/+4
|\ \ | |/ | | | | | | | | | | | | * commit 'd169391529f253a9903b8e6cacf38c59ceefab07': Parallel Fortran tests now use the MPI module instead of including mpif.h. First stab at gfortran versions. Tested on gfortran 7-9 so far. Moved the -std=f2008 option to gfortran 9 for now. Updated gfortran options. * Removed conclude_fc.am, which was causing verbose builds. Need to investigate more, though. * Added gfortran 9 warnings and flags. This will need to be separated into other version blocks based on when the options first appeared. * The standard is now explicitly set at 2008.
| * Merge pull request #1808 in HDFFV/hdf5 from ↵Dana Robinson2019-07-293-3/+4
| |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:gnu-flags-work to develop * commit '7d291d059da6287f769951c4854c566da0b93ce8': Parallel Fortran tests now use the MPI module instead of including mpif.h. First stab at gfortran versions. Tested on gfortran 7-9 so far. Moved the -std=f2008 option to gfortran 9 for now. Updated gfortran options. * Removed conclude_fc.am, which was causing verbose builds. Need to investigate more, though. * Added gfortran 9 warnings and flags. This will need to be separated into other version blocks based on when the options first appeared. * The standard is now explicitly set at 2008.
| | * Updated gfortran options.Dana Robinson2019-07-173-3/+4
| | | | | | | | | | | | | | | | | | | | | | | | * Removed conclude_fc.am, which was causing verbose builds. Need to investigate more, though. * Added gfortran 9 warnings and flags. This will need to be separated into other version blocks based on when the options first appeared. * The standard is now explicitly set at 2008.
* | | Correct generator and add HD prefixAllen Byrne2019-07-261-3/+3
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* | | HDFFV-10529 Update CMake tests to use test fixturesAllen Byrne2019-07-238-102/+134
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* | HDFFV-10845 use of TARGETFILE disables auto emulatorAllen Byrne2019-07-179-13/+22
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* | HDFFV-10845 add_custom_command requires emulatorAllen Byrne2019-07-171-2/+2
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* | HDFFV-10845 fix configure check and PATHsAllen Byrne2019-07-172-2/+2
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* Use H5DOpen2 in hl/test/test_dset_append.c.Larry Knox2019-07-111-2/+2
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* Cleaned up test_dset_append and enabled the bug1/2 tests.Dana Robinson2019-07-101-500/+496
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* Merge branch 'develop' into feature/update_gcc_flagsQuincey Koziol2019-07-103-4/+4
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| * HDFFV-10581 fix locations for static pdb filesAllen Byrne2019-07-083-4/+4
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* | Add support for GCC9, update warnhist script, and clean up warnings.Quincey Koziol2019-07-035-374/+382
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* Updated configure & CMake compiler flags for GCC 8.x, along with correspondingQuincey Koziol2019-06-281-2/+2
| | | | | changes to warnhist script (and some extra improvements for condensing C++ and Java warnings), and fixed a bunch of warnings.
* Add support for GCC 7.x warnings, update warnhist script to account for them,Quincey Koziol2019-06-215-14/+15
| | | | clean up warnings.
* Add H5_HLDLL prefix for windows linkAllen Byrne2019-06-201-5/+12
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* HDFFV-10805 cleanup examples and test codeAllen Byrne2019-06-202-8/+20
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* HDFFV-10805 Add option to only build shared targetsAllen Byrne2019-06-1813-298/+378
| | | | | HDFFV-10805 Add ONLY_SHARED_LIBS option and prefer shared over static HDFFV-10803 Update FindSZIP.cmake find module Remove unneeded modules and update java modules
* Modified Makefile.ams for h5repack, h5watch and gif2h5 to allowLarry Knox2019-06-122-17/+22
| | | | | | | disabling tests. Moved h5cc.in from tools/src/misc to src directory to always create h5cc whether or not tools are enabled. Added configuration status of tools and tests to libhdf5.settings.
* Add options to enable or disable building tools and tests. The defaultLarry Knox2019-06-063-3/+25
| | | | is enabled for each.
* HDFFV-10741 - remove SKIP_ERRSTK_TESTS optionAllen Byrne2019-04-151-20/+12
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* Merge remote-tracking branch 'origin/develop' into env_vol_loadQuincey Koziol2019-04-035-43/+51
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| * HDFFV-10741 - add option to skip tool error stack testsAllen Byrne2019-03-261-12/+20
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| * HDFFV-10738 Wrong INTENT for H5LTread_dataset_double_fM. Scot Breitenfeld2019-03-254-31/+31
| | | | | | | | | | | | Fixed. Also fixed INTENT issues for H5DS, H5IM and H5TB when reading or getting.
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