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1 12 merge java copyright header changes #391

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Mar 1, 2021
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6dc618c
OESS-98 fix tools test for plugins
byrnHDF Dec 15, 2020
1682bdf
sync fork
byrnHDF Jan 11, 2021
f856d77
Merge of changes from dev
byrnHDF Jan 15, 2021
317148f
Move problem option to bottom of the list until fixed
byrnHDF Jan 17, 2021
3cdb272
HDFFV-11106 - fix parsing optional args
byrnHDF Jan 19, 2021
2ccd184
HDFFV-11106 add note
byrnHDF Jan 19, 2021
0d0f7db
grammer fix
byrnHDF Jan 19, 2021
ffae47b
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Jan 20, 2021
0c86a42
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Jan 23, 2021
7839aa8
Whitespace after clang formatting
byrnHDF Jan 27, 2021
687da3b
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Jan 28, 2021
68407f1
Undo format version 11 changes
byrnHDF Jan 28, 2021
5ae710c
Update check to working version
byrnHDF Jan 28, 2021
9aa3dfb
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Feb 1, 2021
95a2b2e
Merge workflow and minor changes from develop
byrnHDF Feb 1, 2021
bac4c43
Update supported platforms
byrnHDF Feb 2, 2021
f0620df
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Feb 3, 2021
f2ce0fc
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Feb 4, 2021
f87bd33
PR#3 merge from develop
byrnHDF Feb 4, 2021
9c925ad
Merge gcc 10 diagnostics option from develop
byrnHDF Feb 8, 2021
c14d750
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Feb 8, 2021
ce8ce57
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Feb 9, 2021
7e5fa9d
Merge #318 OSX changes from develop
byrnHDF Feb 9, 2021
098f01d
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Feb 9, 2021
7c90450
Merge serval small changes from dev
byrnHDF Feb 16, 2021
c9734a2
fix typo
byrnHDF Feb 17, 2021
63cc7be
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Feb 17, 2021
be2c50a
Minor non-space formatting changes
byrnHDF Feb 18, 2021
3bceb92
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Feb 19, 2021
304fb27
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Feb 20, 2021
321404e
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Feb 24, 2021
c2e100b
GH #386 copyright corrections for java folder
byrnHDF Feb 26, 2021
8691d6c
revert because logic requires false return
byrnHDF Mar 1, 2021
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3 changes: 3 additions & 0 deletions MANIFEST
Original file line number Diff line number Diff line change
Expand Up @@ -2007,6 +2007,7 @@
./tools/testfiles/tintsnodata.h5
./tools/testfiles/tlarge_objname.ddl
./tools/testfiles/tlarge_objname.h5
./tools/testfiles/tldouble.ddl
./tools/testfiles/tldouble.h5
./tools/testfiles/tlonglinks.ddl
./tools/testfiles/tlonglinks.h5
Expand Down Expand Up @@ -3416,6 +3417,7 @@
./java/test/testfiles/JUnit-TestH5Pvirtual.txt
./java/test/testfiles/JUnit-TestH5PL.txt
./java/test/testfiles/JUnit-TestH5R.txt
./java/test/testfiles/JUnit-TestH5Rref.txt
./java/test/testfiles/JUnit-TestH5Sbasic.txt
./java/test/testfiles/JUnit-TestH5S.txt
./java/test/testfiles/JUnit-TestH5Tparams.txt
Expand Down Expand Up @@ -3456,6 +3458,7 @@
./java/test/TestH5Pvirtual.java
./java/test/TestH5PL.java
./java/test/TestH5R.java
./java/test/TestH5Rref.java
./java/test/TestH5Sbasic.java
./java/test/TestH5S.java
./java/test/TestH5Tparams.java
Expand Down
47 changes: 39 additions & 8 deletions configure.ac
Original file line number Diff line number Diff line change
Expand Up @@ -37,14 +37,42 @@ AC_CONFIG_MACRO_DIR([m4])
AM_INIT_AUTOMAKE([foreign subdir-objects])
m4_ifdef([AM_SILENT_RULES], [AM_SILENT_RULES([yes])]) # use silent rules where available - automake 1.11

## AM_MAINTAINER_MODE turns off "rebuild rules" that contain dependencies
## for Makefiles, configure, src/H5config.h, etc. If AM_MAINTAINER_MODE
## is enabled, these files will be rebuilt if out of date. This is a
## problem because if users try to build on a machine with
## the wrong versions of autoconf and automake, these files will be
## rebuilt with the wrong versions and bad things can happen.
## Also, CVS doesn't preserve dependencies between timestamps, so
## Makefiles will often think rebuilding needs to occur when it doesn't.
## AM_MAINTAINER_MODE determines the behavior of "rebuild rules" that contain
## dependencies for Makefile.in files, configure, src/H5config.h, etc. If
## AM_MAINTAINER_MODE is enabled, these files will be rebuilt if out of date.
## When disabled, the autotools build files can get out of sync and the build
## system will not complain or try to regenerate downstream files.
##
## The AM_MAINTAINER_MODE macro also determines whether the
## --(enable|disable)-maintainer-mode configure option is available. When the
## macro is present, with or without a parameter, the option will be added
## to the generated configure script.
##
## In summary:
##
## AM_MAINTAINER_MODE([enable])
## - Build dependencies ON by default
## - Configure option exists
##
## AM_MAINTAINER_MODE([disable])
## - Build dependencies OFF by default
## - Configure option exists
##
## AM_MAINTAINER_MODE
## - Build dependencies OFF by default
## - Configure option exists
##
## No AM_MAINTAINER_MODE macro
## - Build dependencies ON by default
## - No configure option to control build dependencies
##
## The biggest concern for us is that version control systems like git
## usually don't preserve dependencies between timestamps, so the build
## system will often think that upstream build files like Makefile.am are
## dirty and that rebuilding needs to occur when it doesn't. This is a problem
## in release branches where we provide the autotools-generated files. Users
## who don't have autoconf, automake, etc. will then have difficulty building
## release branches checked out from git.
##
## By default, it is enabled. Users can configure with
## --disable-maintainer-mode to prevent running the autotools.
Expand Down Expand Up @@ -3264,6 +3292,9 @@ if test "x$HAVE_LIBHDFS" = "xyes"; then
[Proceed to build with libhdfs])
fi

## Read-only HDFS files are not built if not required.
AM_CONDITIONAL([HDFS_VFD_CONDITIONAL], [test "X$HAVE_LIBHDFS" = "Xyes"])

## Checkpoint the cache
AC_CACHE_SAVE

Expand Down
1 change: 0 additions & 1 deletion java/Makefile.am
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
Expand Down
1 change: 0 additions & 1 deletion java/examples/Makefile.am
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
Expand Down
11 changes: 5 additions & 6 deletions java/examples/datasets/H5Ex_D_Alloc.java
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
Expand Down Expand Up @@ -65,11 +64,11 @@ public static H5D_space_status get(int code) {
}

private static void allocation() {
long file_id = -1;
long filespace_id = -1;
long dataset_id1 = -1;
long dataset_id2 = -1;
long dcpl_id = -1;
long file_id = HDF5Constants.H5I_INVALID_HID;
long filespace_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id1 = HDF5Constants.H5I_INVALID_HID;
long dataset_id2 = HDF5Constants.H5I_INVALID_HID;
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = { DIM_X, DIM_Y };
int[][] dset_data = new int[DIM_X][DIM_Y];
int space_status = 0;
Expand Down
15 changes: 7 additions & 8 deletions java/examples/datasets/H5Ex_D_Checksum.java
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
Expand Down Expand Up @@ -93,10 +92,10 @@ private static boolean checkFletcher32Filter() {
}

private static void writeChecksum() {
long file_id = -1;
long filespace_id = -1;
long dataset_id = -1;
long dcpl_id = -1;
long file_id = HDF5Constants.H5I_INVALID_HID;
long filespace_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = { DIM_X, DIM_Y };
long[] chunk_dims = { CHUNK_X, CHUNK_Y };
int[][] dset_data = new int[DIM_X][DIM_Y];
Expand Down Expand Up @@ -193,9 +192,9 @@ private static void writeChecksum() {
}

private static void readChecksum() {
long file_id = -1;
long dataset_id = -1;
long dcpl_id = -1;
long file_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
int[][] dset_data = new int[DIM_X][DIM_Y];

// Open an existing file.
Expand Down
17 changes: 8 additions & 9 deletions java/examples/datasets/H5Ex_D_Chunk.java
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
Expand Down Expand Up @@ -66,10 +65,10 @@ public static H5D_layout get(int code) {
}

private static void writeChunk() {
long file_id = -1;
long filespace_id = -1;
long dataset_id = -1;
long dcpl_id = -1;
long file_id = HDF5Constants.H5I_INVALID_HID;
long filespace_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = { DIM_X, DIM_Y };
long[] chunk_dims = { CHUNK_X, CHUNK_Y };
int[][] dset_data = new int[DIM_X][DIM_Y];
Expand Down Expand Up @@ -201,10 +200,10 @@ private static void writeChunk() {
}

private static void readChunk() {
long file_id = -1;
long filespace_id = -1;
long dataset_id = -1;
long dcpl_id = -1;
long file_id = HDF5Constants.H5I_INVALID_HID;
long filespace_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
int[][] dset_data = new int[DIM_X][DIM_Y];

// Open an existing file.
Expand Down
17 changes: 8 additions & 9 deletions java/examples/datasets/H5Ex_D_Compact.java
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
Expand Down Expand Up @@ -60,10 +59,10 @@ public static H5D_layout get(int code) {
}

private static void writeCompact() {
long file_id = -1;
long filespace_id = -1;
long dataset_id = -1;
long dcpl_id = -1;
long file_id = HDF5Constants.H5I_INVALID_HID;
long filespace_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = { DIM_X, DIM_Y };
int[][] dset_data = new int[DIM_X][DIM_Y];

Expand Down Expand Up @@ -163,10 +162,10 @@ private static void writeCompact() {
}

private static void readCompact() {
long file_id = -1;
long filespace_id = -1;
long dataset_id = -1;
long dcpl_id = -1;
long file_id = HDF5Constants.H5I_INVALID_HID;
long filespace_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
int[][] dset_data = new int[DIM_X][DIM_Y];

// Open file and dataset using the default properties.
Expand Down
15 changes: 7 additions & 8 deletions java/examples/datasets/H5Ex_D_External.java
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
Expand Down Expand Up @@ -34,10 +33,10 @@ public class H5Ex_D_External {
private static final int NAME_BUF_SIZE = 32;

private static void writeExternal() {
long file_id = -1;
long dcpl_id = -1;
long filespace_id = -1;
long dataset_id = -1;
long file_id = HDF5Constants.H5I_INVALID_HID;
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
long filespace_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = { DIM_X, DIM_Y };
int[][] dset_data = new int[DIM_X][DIM_Y];

Expand Down Expand Up @@ -138,9 +137,9 @@ private static void writeExternal() {
}

private static void readExternal() {
long file_id = -1;
long dcpl_id = -1;
long dataset_id = -1;
long file_id = HDF5Constants.H5I_INVALID_HID;
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
int[][] dset_data = new int[DIM_X][DIM_Y];
String[] Xname = new String[1];

Expand Down
9 changes: 4 additions & 5 deletions java/examples/datasets/H5Ex_D_FillValue.java
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
Expand Down Expand Up @@ -40,10 +39,10 @@ public class H5Ex_D_FillValue {
private static final int FILLVAL = 99;

private static void fillValue() {
long file_id = -1;
long dcpl_id = -1;
long dataspace_id = -1;
long dataset_id = -1;
long file_id = HDF5Constants.H5I_INVALID_HID;
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
long dataspace_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = { DIM_X, DIM_Y };
long[] extdims = { EDIM_X, EDIM_Y };
long[] chunk_dims = { CHUNK_X, CHUNK_Y };
Expand Down
15 changes: 7 additions & 8 deletions java/examples/datasets/H5Ex_D_Gzip.java
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
Expand Down Expand Up @@ -95,10 +94,10 @@ private static boolean checkGzipFilter() {
}

private static void writeGzip() {
long file_id = -1;
long filespace_id = -1;
long dataset_id = -1;
long dcpl_id = -1;
long file_id = HDF5Constants.H5I_INVALID_HID;
long filespace_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = { DIM_X, DIM_Y };
long[] chunk_dims = { CHUNK_X, CHUNK_Y };
int[][] dset_data = new int[DIM_X][DIM_Y];
Expand Down Expand Up @@ -196,9 +195,9 @@ private static void writeGzip() {
}

private static void readGzip() {
long file_id = -1;
long dataset_id = -1;
long dcpl_id = -1;
long file_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
int[][] dset_data = new int[DIM_X][DIM_Y];

// Open an existing file.
Expand Down
15 changes: 7 additions & 8 deletions java/examples/datasets/H5Ex_D_Hyperslab.java
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
Expand Down Expand Up @@ -34,9 +33,9 @@ public class H5Ex_D_Hyperslab {
private static final int RANK = 2;

private static void writeHyperslab() {
long file_id = -1;
long filespace_id = -1;
long dataset_id = -1;
long file_id = HDF5Constants.H5I_INVALID_HID;
long filespace_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = { DIM_X, DIM_Y };
int[][] dset_data = new int[DIM_X][DIM_Y];

Expand Down Expand Up @@ -142,10 +141,10 @@ private static void writeHyperslab() {
}

private static void readHyperslab() {
long file_id = -1;
long filespace_id = -1;
long dataset_id = -1;
long dcpl_id = -1;
long file_id = HDF5Constants.H5I_INVALID_HID;
long filespace_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
int[][] dset_data = new int[DIM_X][DIM_Y];

// Open an existing file.
Expand Down
17 changes: 8 additions & 9 deletions java/examples/datasets/H5Ex_D_Nbit.java
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
Expand Down Expand Up @@ -96,11 +95,11 @@ private static boolean checkNbitFilter() {
}

private static void writeData() throws Exception {
long file_id = -1;
long filespace_id = -1;
long dataset_id = -1;
long dtype_id = -1;
long dcpl_id = -1;
long file_id = HDF5Constants.H5I_INVALID_HID;
long filespace_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long dtype_id = HDF5Constants.H5I_INVALID_HID;
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = { DIM_X, DIM_Y };
long[] chunk_dims = { CHUNK_X, CHUNK_Y };
int[][] dset_data = new int[DIM_X][DIM_Y];
Expand Down Expand Up @@ -157,9 +156,9 @@ private static void writeData() throws Exception {
}

private static void readData() throws Exception {
long file_id = -1;
long dataset_id = -1;
long dcpl_id = -1;
long file_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
int[][] dset_data = new int[DIM_X][DIM_Y];

// Open an existing file.
Expand Down
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