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* Merge remote-tracking branch 'hdffv/develop' into rebased-fprintf-experimentDavid Young2020-07-303-66/+92
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| * Tools refactorAllen Byrne2020-07-152-65/+72
| | | | | | | | | | | | Move error_stack setup to tools library Add structure for h5dump properties Eliminate duplicated h5diff functions Use properties structure in place of argument lists.
| * HDFFV-11116 Add option for install location of Fortran MOD filesAllen Byrne2020-07-091-1/+20
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* | Squash my changes on branch `fprintf-experiment` into one commit forDavid Young2020-07-071-2/+2
|/ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | reapplication to my new warnings branch, `warnings-again`. These changes are included: commit 915551b7bf64e777dd2007386ec77b1d117770da Merge: 63858c2 a8892bb Author: David Young <dyoung@hdfgroup.org> Date: Mon Nov 25 17:39:49 2019 -0600 Merge remote-tracking branch 'hdf5/develop' into fprintf-experiment commit a8892bb42d6f6e4fbc30fae0eb2b957f81c938b9 Merge: 5c911d8 f907b51 Author: David Young <dyoung@hdfgroup.org> Date: Mon Nov 25 17:33:54 2019 -0600 Merge pull request #2055 in HDFFV/hdf5 from ~DYOUNG/vchoi_fork:add-werror-and-squash-some to develop * commit 'f907b511d06612dafc7814a7c30f2f3d2b76d52b': Oops, remove more C99 designated initializers for VS 2010 compatibility. commit 63858c22e168acaec0af8ced6641f26102cc6bb0 Merge: 20ae787 5c911d8 Author: David Young <dyoung@hdfgroup.org> Date: Mon Nov 25 17:04:42 2019 -0600 Merge remote-tracking branch 'hdf5/develop' into fprintf-experiment commit 5c911d8baf3ee7fe654269088eebdf07f59a8192 Merge: b8a5671 62208b0 Author: David Young <dyoung@hdfgroup.org> Date: Mon Nov 25 16:58:27 2019 -0600 Merge pull request #2030 in HDFFV/hdf5 from ~DYOUNG/vchoi_fork:add-werror-and-squash-some to develop * commit '62208b056a09c01855fbac7f75146be58ad6bfe5': (44 commits) 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 *. Change hdset_reg_ref_t and H5R_ref_t from arrays of unsigned char to structs containing those arrays. Encapsulating the arrays in this way makes it easier to write and think about pointers to these types, casts to/from these types, etc. ... commit 20ae7877e33931b95e8c3502b027d6c3fe94a11f Merge: 46f8c61 edd5297 Author: David Young <dyoung@hdfgroup.org> Date: Fri Nov 22 15:34:09 2019 -0600 Merge remote-tracking branch 'origin/add-werror-and-squash-some' into fprintf-experiment commit 46f8c613d5117a8be5bc8385a072daa0b4262f06 Author: David Young <dyoung@hdfgroup.org> Date: Fri Nov 22 15:29:00 2019 -0600 GCC really wants us to use `ll` to format `long long`, so try to make that work before any other format modifier. Seems like we're not compiling the autoconf test program with -Werror=format ? Probably should. commit eee35b8ef3759c391327cd48a9b3c56b6f8abc99 Author: David Young <dyoung@hdfgroup.org> Date: Fri Nov 22 15:28:05 2019 -0600 It's hard to know just how wide an HDoff_t will be, and I don't think POSIX or C standards provide a PRI macro for it, so cast to intmax_t and format using PRIdMAX. commit 86eab12df7a89b546a38e99f8178dd2adbcb3433 Author: David Young <dyoung@hdfgroup.org> Date: Fri Nov 22 15:26:25 2019 -0600 URemove some casts.se the right format string for the argument. Here and there stop casting a printf argument. commit f722f7cbecbaa99449941484b014426f62f1bed5 Merge: 58e3743 6d5ec83 Author: David Young <dyoung@hdfgroup.org> Date: Fri Nov 22 14:44:16 2019 -0600 Merge branch 'add-werror-and-squash-some' into fprintf-experiment commit 58e3743b7faa9836606ee91798fe80dfc0040da7 Author: David Young <dyoung@hdfgroup.org> Date: Wed Nov 20 21:07:21 2019 -0600 Remove custom HDfprintf implementation, using the standard library's, instead. Take a swipe at repairing fprintf format strings, mainly replacing "%Hu" with "%" PRIuHSIZE, "%a" with "%" PRIuHADDR, "%Zu" with "%zu". Here and there remove an awkward cast of a printf argument to `long long` and use PRI[doux]8, PRI[doux]32, or PRI[doux]64, instead. Change occurrences of "%t" to "%s" and perform a suitable change of argument, `cond` -> `cond ? "TRUE" : "FALSE"`. Some occurrences of %Hu, %a, and %t remain, they just weren't flagged by the compiler because of #ifdef'age. commit d4366909293fa970c23512ac80e5d865d76cddbf Author: David Young <dyoung@hdfgroup.org> Date: Wed Nov 20 20:54:32 2019 -0600 Promote format-string warnigns to errors.
* Fix HDFFV-10591Binh-Minh Ribler2020-06-192-12/+24
| | | | | | | | | | | | Description: h52gif produced a segfault when a buffer overflow occurred because the data size was corrupted and became very large. This commit added a check on the data size against the buffer size to prevent the segfault. It also added error reporting to h52gif to display an error message instead of silently exiting when the failure occurred. Platforms tested: Linux/64 (jelly) SunOS 5.11 (emu)
* Merge pull request #2610 in HDFFV/hdf5 from ↵David Young2020-06-163-6/+6
|\ | | | | | | | | | | | | ~DYOUNG/werror:hdffv-11060-examples-destdir to develop * commit '4cebd8aa6c965fe2e5dde6dbff36b2be3ca58bf1': Make examples installation respect DESTDIR. Fixes HDFFV-11060.
| * Make examples installation respect DESTDIR. FixesDavid Young2020-05-263-6/+6
| | | | | | | | HDFFV-11060.
* | Eliminate unneccesary creation of DXPLQuincey Koziol2020-06-021-14/+3
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* | Removed trailing space from Fortran files.Dana Robinson2020-05-268-252/+252
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* Fix NoFilter buildAllen Byrne2020-04-241-1/+1
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* Trim trailing whitespaceQuincey Koziol2020-04-2027-448/+448
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* Fix shadowed typeAllen Byrne2020-04-131-3/+3
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* TRILAB-192 update LTparse filesAllen Byrne2020-04-073-1206/+1129
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* Minor updates and fix settings for fortran flagsAllen Byrne2020-04-061-1/+1
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* Remove overzealous additionsAllen Byrne2020-04-052-3/+1
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* Flag construction must be after compiler detectionAllen Byrne2020-04-053-59/+27
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* TRILAB-192 add c++ and fortran warnings build systems one fileAllen Byrne2020-04-059-61/+44
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* Merge pull request #2469 in HDFFV/hdf5 from tools_vol_update to developJordan Henderson2020-03-271-1/+9
|\ | | | | | | | | | | | | * commit 'ea952b25ba0fd5c4b5f60a94e75a1b5b78e66172': A few small tweaks to the tools from review Replace usage of some standard library functions with HD- versions Update Tools library to be better compatible with VOL connectors
| * Update Tools library to be better compatible with VOL connectorsJordan Henderson2020-03-171-1/+9
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Modify h5repack to integrate with VOL connectors Update tools library to accomodate VOL connectors Update logic in h5tools_fopen for VOL connectors Add command-line options to h5repack for specifying in/out VOL connectors Implement h5tools_set_vol_fapl Fix library shutdown issue Integrate ROS3 and HDFS VFDs into new h5tools_get_fapl() scheme Avoid H5Ocopy in h5repack when using different VOL connectors Update h5tools_test_utils.c for ROS3 and HDFS integration
* | TRILAB-192 restrict extensive warnings to librariesAllen Byrne2020-03-242-0/+12
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* So that I can use PASSED(); anywhere a statement can go, #define PASSED() withDavid Young2020-02-281-1/+1
| | | | a do-while wrapper.
* TRILAB-142 Change minimum CMake version to 3.12Allen Byrne2020-02-2115-15/+15
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* HDFFV-11012 - add correct fortran include path propertiesAllen Byrne2020-02-041-2/+2
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* Merge pull request #2328 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor ↵Dana Robinson2020-01-307-718/+988
|\ | | | | | | | | | | | | to develop * commit 'a67c238feef1487814b02132bfd7961f22d9d6eb': Cleaned up remaining warnings in high-level library.
| * Cleaned up remaining warnings in high-level library.Dana Robinson2020-01-307-718/+988
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* | HDFFV-11011 correct issues with target file extensionAllen Byrne2020-01-282-20/+8
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* Squashed commit of the token_refactoring branch:Dana Robinson2020-01-162-64/+111
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* HDFFV-11001 fix if blockAllen Byrne2020-01-151-3/+2
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* HDFFV-11001 need to qualify all by parallel or serial typesAllen Byrne2020-01-157-9/+8
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* HDFFV-11001 Add fine control over testingAllen Byrne2020-01-1511-17/+27
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* Merge pull request #2071 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/intel_warnings ↵Kimmy Mu2020-01-061-1/+1
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | to develop * commit '0a2bb11b248df6841daabca3970df5d8504adfc7': address problems from comments fix and address comments change according to previous comments add missing piece remove unnecessary check macro fix intel compile warnings Revert "fix warnings from Intel compiler" Revert "fix warnings and some text alignment" Revert "let hdf5 pick up the right compiler in Intel environment" Revert "fix issues from previous PR comments" Revert "using a different MACRO" using a different MACRO fix issues from previous PR comments let hdf5 pick up the right compiler in Intel environment fix warnings and some text alignment fix warnings from Intel compiler
| * Merge branch 'develop' into bugfix/intel_warningskmu2019-12-092-5/+1
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| * | remove unnecessary check macrokmu2019-12-061-2/+1
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| * | fix intel compile warningskmu2019-12-041-1/+2
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* | | Small changes from the token_refactoring branch, to reduce the delta to developQuincey Koziol2020-01-041-18/+18
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* | | In portable shell scripts (using #!/bin/sh) we have to use single squareDavid Young2019-12-191-1/+1
| | | | | | | | | | | | brackets, [ ], instead of the bash-ism double square brackets, [[ ]].
* | | 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.
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