Commit Graph

175 Commits

Author SHA1 Message Date
Dana Robinson
5d0be1b196 Manual sync with develop (#95)
Brings all features from develop. Note that RELEASE.txt has not been
updated (will be done in a future PR).
2020-11-17 07:47:52 -06:00
Allen Byrne
1971106e2a HDFFV-10868 Corrections from review 2020-10-29 13:15:09 -05:00
Allen Byrne
7416cd2598 HDFFV-10868 merge from develop 2020-10-28 09:25:26 -05:00
Allen Byrne
72f5f74b67 OESS-98 add CMake option to build plugins project within hdf5 2020-10-16 11:09:02 -05:00
Allen Byrne
f1ba03cea5 Source formatted 2020-10-01 09:04:36 -05:00
Allen Byrne
ff9f228949 warning format fixes and define name from develop 2020-09-30 07:22:30 -05:00
Allen Byrne
7c742a8518 Add clang-format changes from develop. 2020-09-28 13:57:41 -05:00
Allen Byrne
2a3d394f7c Whitespace cleanup 2020-05-12 15:59:59 -05:00
Allen Byrne
e0183056d5 Add github actions and cleanup java whitespace 2020-05-06 11:19:50 -05:00
Allen Byrne
6108186feb TRILAB-192 - merge changes from develop
Single source, config files, for warnings for both autotools and CMake.
Update CMake libraries, tools, tests to use correct flags.
2020-04-07 09:47:29 -05:00
Allen Byrne
ac32ce96a3 TRILAB-192 merging warnings changes from develop 2020-03-30 09:28:05 -05:00
Allen Byrne
2ec2361b9f Update examples and fix version references 2020-02-26 14:03:39 -06:00
Allen Byrne
6b1e2d835f Fix Fortran macro use and jni comment 2020-02-25 09:21:14 -06:00
Allen Byrne
9ed096fb39 Merge changes from develop mostly cmake 3.12 minimum version 2020-02-23 11:55:47 -06:00
Allen Byrne
a6706e3a78 Merge changes from develop for CMake and Java 2020-02-21 15:41:05 -06:00
David Young
d42bee3688 Squashed commit of the following:
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.
2020-01-31 13:53:26 -06:00
Jordan Henderson
edec1f017d Introduce new H5VL _by_value routines 2020-01-29 16:59:41 -06:00
Larry Knox
3ecbb767c3 Update version to 1.12.1-snap0 for hdf5_1_12 branch. 2020-01-28 15:55:05 -06:00
Dana Robinson
2b1709f6ff Squashed commit of the token_refactoring branch: 2020-01-18 20:02:16 -08:00
Allen Byrne
37529db25c HDFFV-10976,-10980 h5dump, h5ls, h5diff use new ref APIs 2019-12-20 13:40:08 -06:00
Allen Byrne
df20cd8864 Add missing include folder 2019-12-10 12:07:01 -06:00
Allen Byrne
310b42e35a HDFFV-10876 Merge from develop 2019-12-09 15:44:38 -06:00
Jerome Soumagne
49fe497201 Revert "Merge branch 'hdf5_1_12' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into hdf5_1_12"
This reverts commit 9f9336a5bd, reversing
changes made to 437a1919e7.
2019-12-09 12:16:52 -06:00
Richard Warren
0c06cfc6ef Merged HDFFV-10929_2GB_testing to hdf5_1_12 2019-12-06 16:42:36 -05:00
Jordan Henderson
f3f67a5645 Fix various Java issues when deprecated symbols are disabled 2019-10-10 16:03:34 -05:00
Larry Knox
e7dbf81191 Set versions in initial hdf5_1_12 revision. 2019-09-25 15:57:22 -05:00
Allen Byrne
adce9e7f4e HDFFV-10903 - fix VFD constants in JNI 2019-09-17 10:30:04 -05:00
Allen Byrne
e20331651e revert as CHECK will first check for exception 2019-09-10 14:19:29 -05:00
Allen Byrne
afb07f9b39 Clear exception for getting JNI string to clear the exception 2019-09-10 13:47:24 -05:00
Allen Byrne
3e816bd089 Add statement for label if code unimplemented 2019-09-05 15:49:57 -05:00
Allen Byrne
60cc470a35 Fix unused var 2019-09-05 15:21:02 -05:00
Allen Byrne
3467de59f8 Correct label and var names 2019-09-05 14:57:35 -05:00
Allen Byrne
dcab85c83b Add back missing java implementation 2019-09-05 14:35:33 -05:00
Allen Byrne
09d13b3c13 OESS-29 Fix HD prefix in perform and enable test compile 2019-08-27 16:49:10 -05:00
Dana Robinson
8c40dab59e Untangle #ifdef mess in ROS3 code. 2019-08-19 18:02:47 -07:00
Allen Byrne
935f27c1b8 HDFFV-10887 Implement requested functions 2019-08-19 11:58:52 -05:00
Larry Knox
8008294578 Squashed commit of the following:
Merge changes from update_merged_S3_HDFS branch into develop.

commit d5034315aea88629929ac0c9c59ebfafd5f21a31
Merge: 9c48823 d3fdcd8
Author: Larry Knox <lrknox@hdfgroup.org>
Date:   Thu Jul 25 08:24:53 2019 -0500

    Merge branch 'develop' into update_merged_S3_HDFS
2019-07-25 11:47:12 -05:00
Allen Byrne
1878e68558 Move before null check 2019-07-08 13:52:05 -05:00
Allen Byrne
e7f16c6f2c HDFFV-10805 Add option to only build shared targets
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
2019-06-18 07:46:25 -05:00
Dana Robinson
2bd041f878 Added H5Fdelete call and VOL support (but no VFD/native implementation). 2019-06-11 09:04:23 -07:00
Allen Byrne
d3a6a9ed8f Merge pull request #1715 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit '1ecce0e9bbc07cb3eb6f6bc1fca9d42c9e9c8176':
  Fix minor issues
  Update macro
  Java formatting of args
2019-06-05 15:06:53 -05:00
Dana Robinson
a18727bc77 Added a VOL initialization property list type. 2019-06-05 04:34:36 -07:00
Allen Byrne
1ecce0e9bb Fix minor issues 2019-06-03 10:45:20 -05:00
Allen Byrne
748da4d3e2 Java formatting of args 2019-05-30 15:56:02 -05:00
hdftest
1cec61a775 Snapshot version 1.11 release 5.
Update version to 1.11.6.
2019-05-02 10:42:53 -05:00
Jordan Henderson
0a73ce19a4 Fix Java JUnit-TestH5P failure on 32-bit arch 2019-04-30 15:32:37 -05:00
Allen Byrne
6bf109d1ae Fix java for new H5Fget_info function 2019-04-15 11:19:29 -05:00
Quincey Koziol
d7e1464058 Add C++, Java, and FORTRAN wrappers and tests for H5Fget_fileno 2019-04-13 22:58:16 -05:00
Vailin Choi
2886cd9e45 HDFFV-10365: Changes as described in the RFC: H5Sencode/H5Sdecode Format Change.
This also addresses HDFFV-10255: H5Sencode/decode performance issue.
2019-04-06 16:55:14 -05:00
Vailin Choi
0073f19897 Set V112 as the latest format and extend the arrays of version bounds. 2019-04-04 16:29:37 -05:00