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* Squashed commit of the following:David Young2020-01-3122-201/+195
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | commit ff7a9a34de2fcd78f5d32a1532f3d0e224b20d94 Author: Kimmy Mu <kmu@hdfgroup.org> Date: Wed Jan 29 14:12:18 2020 -0600 Merge pull request #2324 in HDFFV/hdf5 from ~KMU/hdf5:hdf5_1_12 to hdf5_1_12 * commit '781fa57f6ee816e037dd12fff02d37ff7ec9c2b1': pick up missing piece from merge Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop remove redundent definition Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop Merge pull request #2315 in HDFFV/hdf5 from ~KMU/hdf5:develop to develop missing prototype warning prototype issue Merge pull request #2306 in HDFFV/hdf5 from ~KMU/hdf5:develop to develop Merge pull request #2300 in HDFFV/hdf5 from ~KMU/hdf5:squashed_cast to develop Merge pull request #2291 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/uninitialized to develop Merge pull request #2295 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/float to develop Merge pull request #2292 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/prototype to develop Merge pull request #2094 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/unused to develop commit 9f3d808c05d2a3b308f32c958c6671fcac0a432c Author: David Young <dyoung@hdfgroup.org> Date: Wed Jan 29 11:43:55 2020 -0600 testpar/t_2Gio.c: Fix a typo that I think was introduced by a previous warnings PR. An array element was assigned to itself---shape[2]Â =Â shape[2];---instead of being assigned to chunk[2]. fortran/src/H5Pf.c: move conditional compilation controlled by H5_NO_DEPRECATED_SYMBOLS outside of a function for readability. fortran/src/H5match_types.c: put a variable's declaration under the same conditional compilation (H5_FORTRAN_HAVE_C_LONG_DOUBLE) as its use. For now, skip compilation of some unused debug dump routines in the JNI. While I'm in the JNI, delete a set-but-unused variable. src/H5Z.c: condition a variable declaration on H5_NO_DEPRECATED_SYMBOLS so that it's not declared but unused or vice versa. test/cache_common.h: add an #include in to get some symbols we need to avoid implicit declaration warnings. test/dsets.c: use a more conventional conditional-compilation syntax. test/dt_arith.c, test/fillval.c: initialize a bunch of uninitialized variables before use. test/vfd.c: pass the expected type of `void **` to posix_memalign(3) instead of `int **`. testpar/t_bigio.c: explicitly compare with 0 instead of using ! when "equal to 0?" is the question not "is false?" Repair some indentation while I'm here. testpar/testpar.h: repair misaligned line-continuation backslashes in a macro that probably should be a function so that we don't have to fiddle with the line continuation to begin with. tools/src/h5repack/h5repack_main.c: fix some compiler fussing about enums. tools/test/perform/pio_engine.c: the compiler fusses if you cast a function call returning double directly to off_t. It's ok if you cast a variable that's a double to off_t, however. Write and use a new function, sqrto(), to avoid the cast warnings. commit 43a4b80b21c0329fbc1f9a0e2854795189f0bb50 Author: David Young <dyoung@hdfgroup.org> Date: Wed Jan 29 10:47:30 2020 -0600 Reduce casts of HDcalloc()/HDmalloc() that -Wc++-compat required. Reduce gratuitous casts---e.g., (size_t)1. Use the right format string for a pointer. In the H5C sanity checks, change a "size increase" variable from ssize_t (too narrow) to int64_t (wide enough). Parenthesize every appearance of `storage` in the macro `H5D_CHUNK_STORAGE_INDEX_CHK(storage)` so that you can pass in an expression like &sc and it works properly. Disallow re-assignment of the `dset` parameter to H5D__chunk_init() because it helped assure me that it's safe to replace the repeating expression `&dset->shared->layout.storage.u.chunk` with `sc` throughout. Replace lengthy expressions such as `&dset->shared->layout.storage.u.chunk` with `sc` throughout several functions in H5Dchunk.c ISTR that the compiler warned that `sc` was declared but unused in a couple of functions, and then I found that `sc` could be used in many places. Maybe the disused `sc` appeared because a bunch of code was copied and pasted, I don't know. Anyway, it's a lot tighter code now that I use `sc`. In H5D__chunk_update_old_edge_chunks() and H5D__chunk_delete() I actually expand `sc` and another temporary variable, `pline`, because they're used only in !defined(NDEBUG) code. This squashes unused-variable warnings in the defined(NDEBUG) configuration. Don't drop the `volatile` qualification with a cast in tools/src/h5import/h5import.c. commit 035bfa0769a4012881fc659b673bacf44d146537 Author: David Young <dyoung@hdfgroup.org> Date: Tue Jan 28 20:35:28 2020 -0600 Reduce differences between my -Werror branch and `develop`: Rename index -> idx, fileno -> fnumber, fileno -> fno to avoid GCC shadowed declaration warnings about index(3). Convert #pragma GCC diagnostic push/pop/ignored to the HDF5 library's H5_GCC_DIAG_OFF()/H5_GCC_DIAG_ON() macros.
* Merge pull request #2331 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Allen Byrne2020-01-312-0/+9
|\ | | | | | | | | | | | | | | | | | | | | hdf5_1_12 * commit 'a29f9e8451ffa391c8395db1142bd003f40f3aaa': Merge changes from develop to fix various issues Remove commented flags Revert accidental change Chnage tools debug macros to not use the error stack Create common warnings for build systems
| * Merge changes from develop to fix various issuesAllen Byrne2020-01-302-0/+9
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* | Introduce new H5VL _by_value routinesJordan Henderson2020-01-295-25/+227
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* Merge pull request #2324 in HDFFV/hdf5 from ~KMU/hdf5:hdf5_1_12 to hdf5_1_12Kimmy Mu2020-01-2954-241/+250
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '781fa57f6ee816e037dd12fff02d37ff7ec9c2b1': pick up missing piece from merge Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop remove redundent definition Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop Merge pull request #2315 in HDFFV/hdf5 from ~KMU/hdf5:develop to develop missing prototype warning prototype issue Merge pull request #2306 in HDFFV/hdf5 from ~KMU/hdf5:develop to develop Merge pull request #2300 in HDFFV/hdf5 from ~KMU/hdf5:squashed_cast to develop Merge pull request #2291 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/uninitialized to develop Merge pull request #2295 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/float to develop Merge pull request #2292 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/prototype to develop Merge pull request #2094 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/unused to develop
| * Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to developKimmy Mu2020-01-281-1/+1
| | | | | | | | | | | | | | | | | | * commit '406330addf45529ecdd088f4d22e9aab9a03661d': rename macro change condition pick up from Dave's fix leave Wswitch-default for later fix fix Wredundant-decls, Wswitch-default, Wdeclaration-after-statement, Wsign-compare, Wmisleading-indentation, Wshadow
| * prototype issuekmu2020-01-281-1/+1
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| * Merge pull request #2300 in HDFFV/hdf5 from ~KMU/hdf5:squashed_cast to developKimmy Mu2020-01-2811-91/+93
| | | | | | | | | | | | * commit 'af5c33afabdae2e39bb45eb1b3e9c8366da01145': remove unnecessary stuff squash cast warning fix
| * Merge pull request #2291 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/uninitialized ↵Kimmy Mu2020-01-281-2/+2
| | | | | | | | | | | | | | to develop * commit '2de0ce0d8ba2fb58fadefc5d718a3c0fedab25c8': fix uninitizlized warning
| * Merge pull request #2292 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/prototype to ↵Kimmy Mu2020-01-281-1/+2
| | | | | | | | | | | | | | develop * commit '9f80ffa1f1908975b3100814b2529bf779521e13': fix missing prototype warning
| * Merge pull request #2094 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/unused to developKimmy Mu2020-01-2843-145/+151
| | | | | | | | | | | | | | | | | | | | | | * commit '145ef3ceee20c28a443bd11507c58858bea3f889': more cleanup change it back pick up missing piece fix unused related warnings removed unused parameter more fix and address comments remove unsed var,function,macro, etc
* | Update version to 1.12.1-snap0 for hdf5_1_12 branch.Larry Knox2020-01-281-3/+3
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* Merge pull request #2238 in HDFFV/hdf5 from ~KMU/hdf5:hdf5_1_12 to hdf5_1_12Kimmy Mu2020-01-2428-55/+63
|\ | | | | | | | | | | | | * commit '48cc850199901c5b67a40183262f4ead975b884f': fix test assert fail error Merge pull request #2071 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/intel_warnings to develop Merge pull request #2234 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/intel_warnings to develop
| * Merge pull request #2071 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/intel_warnings ↵Kimmy Mu2020-01-0827-55/+62
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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 pull request #2234 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/intel_warnings ↵Kimmy Mu2020-01-081-0/+1
| | | | | | | | | | | | | | to develop * commit '30ac64d83aff5e022d51a17fd6c1d72903ae4f02': add new type support
* | Merge pull request #2289 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-01-221-5/+14
| | | | | | | | | | | | | | * commit 'a92cfed71e0da0ff61af2550640e38bf6d415fee': Remove irrelevant sentence from comment. Remove duplicate lines noted on forum by Eric Bavier Add v111 version for H5O functions to enable version1 default for HDF5 1.8-1.10 and version 3 default for HDF5 1.12. Version 2 functions are available (deprecated) but will not be the default for any version.
* | Squashed commit of the token_refactoring branch:Dana Robinson2020-01-1966-998/+4065
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* | H5R: set app ref when incrementing ref_count on location held by referenceJerome Soumagne2020-01-175-18/+39
|/ | | | (fix HDFFV-10992)
* Cherry pick of 0225e6d5969Quincey Koziol2020-01-0422-148/+190
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* Cleanups from PR reviewsQuincey Koziol2020-01-044-102/+101
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* Remove unnecessary H5CX callQuincey Koziol2020-01-041-4/+0
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* Refactor H5Dvlen_get_buf_size to use optional dataset operation, with ↵Quincey Koziol2020-01-047-54/+255
| | | | generic fallback for VOL connectors that don't implement operation
* Refactor all the 'H5VL_*_optional' callbacks to move the type of operation outQuincey Koziol2020-01-0445-1571/+2860
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | of the va_list, so it's at least possible for another connector to know what the operation is and decide whether to implement it or not. Added a new VOL sub-class called "introspect" where callbacks that report information about the connector or container can be placed. Added an 'opt_query' callback to this sub-class, for a connector to report back to the library whether a particular optional callback operation is supported. Also added a 'get_conn_cls' introspection callback, to retrieve the H5VL_class_t of a connector (either the "current" connector, H5VL_GET_CONN_LVL_CURR, or the terminal connector, H5VL_GET_CONN_LVL_TERM). Moved the "post open" operation from a file 'specific' operation to a file 'optional' operation, now that it's possible to detect (with the 'opt_query' introspection callback) whether a VOL connector implements an optional operation, without just returning an error. Added new internal VOL helper routines: H5VL_object_is_native, to determine if an object is in (or is a) native file, and H5VL_file_is_same, to determine if two objects are in (or are) the same terminal VOL connector's container. (And moved the special handling for FILE_IS_EQUAL operation out of internal VOL callback routine into H5VL_file_is_same) Made new dataset 'get' operation for H5Dvlen_get_buf_size, aligning it better with other 'get' operations in API. Fixed several issues with pass-through connectors, which are now passing the 'make check-passthrough-vol' tests again. A bunch of warning and style cleanups as well.
* For portability, insulate the HDF5 library from some system macros.David Young2019-12-191-1/+18
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* Minor tweaks noticed while going over VOL documentation.Dana Robinson2019-12-163-6/+6
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* Yanked -Wc++-compat from the flags used to build the C library in bothDana Robinson2019-12-168-51/+36
| | | | the Autotools and CMake.
* Trivial parameter renaming in VOL API calls.Dana Robinson2019-12-164-23/+23
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* Modify H5VL initialization routines to initialize all VOL-managed objectNeil Fortner2019-12-1311-2/+153
| | | | | types. Modify H5VLwrap_register() to reject non-VOL-managed object types. Also fix overisights in h5trace.c from previous changes.
* Update version to 1.12.0-alpha1.Larry Knox2019-12-121-2/+2
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* Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_12)Allen Byrne2019-12-112-2/+2
|\ | | | | | | | | * commit '9b38aef978299a76b6b19586396bf626a1e58df6': Fix 2010 compile issue
| * Fix 2010 compile issueAllen Byrne2019-12-112-2/+2
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* | HDFFV-10876 Merge from developAllen Byrne2019-12-091-21/+17
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* Merge pull request #2116 in HDFFV/hdf5 from ↵Jerome Soumagne2019-12-0919-180/+429
|\ | | | | | | | | | | | | | | | | | | ~JSOUMAGNE/hdf5:hdf5-1_12-ref_token to hdf5_1_12 * commit '1aea46ce671daf2828ac65d0b8551b369f497922': Fix H5VL_token_t type and fix H5VL_loc_by_token to use H5VL_token_t * 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. H5R: fix H5Tconv to check for null references Remove H5VL_NATIVE_FILE_GET_FILE_ID and add H5VL_OBJECT_GET_FILE
| * Fix H5VL_token_t type and fix H5VL_loc_by_token to use H5VL_token_t *Jerome Soumagne2019-12-097-33/+35
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| * Change hdset_reg_ref_t and H5R_ref_t from arrays of unsigned char toDavid Young2019-12-091-2/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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. An interesting side-effect that we probably should *not* rely on is that the struct-encapsulation changes the alignment so that some GCC warnings about casts that increase the alignment requirement of the operand go away. Warnings like that have to be taken seriously: I will add -Werror=cast-align to the default compiler flags so that they stop the build quickly. GCC warnings led me to some surprising casts in test/trefer.c. I found that it was possible to make many simplifications after introducing the struct-encapsulation that I described, above. In test objcopy_ref `same_file` is assigned but never used. Delete it.
| * H5R: fix H5Tconv to check for null referencesJerome Soumagne2019-12-094-42/+300
| | | | | | | | | | | | Valid for both deprecated and non-deprecated references Update test
| * Remove H5VL_NATIVE_FILE_GET_FILE_ID and add H5VL_OBJECT_GET_FILEJerome Soumagne2019-12-0916-103/+88
| | | | | | | | Remove H5F__get_file_id() and use only private routine instead
* | Modify H5Ssel_iter_get_seq_list() to accept iterators that have reachedNeil Fortner2019-12-091-1/+1
|/ | | | | the end of iteration (returning zero sequences). Previously it could cause an assertion failure.
* Merge pull request #2114 in HDFFV/hdf5 from ~JSOUMAGNE/hdf5:hdf5-1_12-revert ↵Jerome Soumagne2019-12-0935-142/+68
|\ | | | | | | | | | | | | to hdf5_1_12 * commit '49fe497201bcefcd9beb01fe8fc2175974b73799': Revert "Merge branch 'hdf5_1_12' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into hdf5_1_12"
| * Revert "Merge branch 'hdf5_1_12' of ↵Jerome Soumagne2019-12-0935-142/+68
| | | | | | | | | | | | | | https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into hdf5_1_12" This reverts commit 9f9336a5bd541752f472bab4c93da8de89f862cd, reversing changes made to 437a1919e7ba60fe75a33a466d264183a0255319.
* | Merge pull request #2104 in HDFFV/hdf5 from ~NFORTNE2/hdf5_naf:tmp_112_3 to ↵Neil Fortner2019-12-061-1/+2
|\ \ | | | | | | | | | | | | | | | | | | hdf5_1_12 * commit 'afb6ae776b3c60b37898dae4ee93f8976da90d42': Add H5VL_MAP_OPTIONAL operation id (unused currently).
| * | Add H5VL_MAP_OPTIONAL operation id (unused currently).Neil Fortner2019-12-061-1/+2
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* | Merge pull request #2103 in HDFFV/hdf5 from ~NFORTNE2/hdf5_naf:tmp_112_2 to ↵Neil Fortner2019-12-063-8/+26
|\ \ | | | | | | | | | | | | | | | | | | hdf5_1_12 * commit 'aefd0cbc60eeed3319776f76f0cde889072cc31b': Implement support for using H5Dvlen_get_buf_size with non-native VOL connectors.
| * | Implement support for using H5Dvlen_get_buf_size withNeil Fortner2019-12-063-8/+26
| |/ | | | | | | non-native VOL connectors.
* | Add support for scalar dataspaces to H5Sproject_intersection. AddNeil Fortner2019-12-062-87/+130
|/ | | | checking for ank validity.
* Merge pull request #2101 in HDFFV/hdf5 from ~NFORTNE2/hdf5_naf:tmp_112_5 to ↵Neil Fortner2019-12-061-4/+4
|\ | | | | | | | | | | | | hdf5_1_12 * commit '47f6c293a78aaa92c80b327795b1f1a242ea30a5': Fix issues with using H5Pget_fill_value() with file datatypes retrieved from H5VLget_file_type().
| * Fix issues with using H5Pget_fill_value() with file datatypes retrievedNeil Fortner2019-12-061-4/+4
| | | | | | | | from H5VLget_file_type().
* | Merge pull request #2096 in HDFFV/hdf5 from ~NFORTNE2/hdf5_naf:tmp_112 to ↵Neil Fortner2019-12-061-0/+9
|\ \ | | | | | | | | | | | | | | | | | | hdf5_1_12 * commit '681d227e9ee7876922fb05e609db18425cb1630d': Fix issue where H5R__reopen_file did not make the file "post open" callback.
| * | Fix issue where H5R__reopen_file did not make the file "post open"Neil Fortner2019-12-062-1/+10
| | | | | | | | | | | | callback.
* | | Merge pull request #2100 in HDFFV/hdf5 from ~NFORTNE2/hdf5_naf:tmp_112_4 to ↵Neil Fortner2019-12-065-34/+163
|\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | hdf5_1_12 * commit '209a86de37497b160ff49b9956f58558194eee25': 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.
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