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Hdf5 merge issue 537 v112 #538

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merged 42 commits into from
Apr 2, 2021
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Hdf5 merge issue 537 v112 #538

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bcaf211
Snapshot version 1.12 release 1-3. Update version to 1.12.1-4.
lrknox Nov 23, 2020
9b9ef60
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5 into hdf…
lrknox Nov 26, 2020
7a78fd1
First cut of the H5 public API documentation. (#80)
gheber Nov 18, 2020
ba77da0
Full set of current H5F documentation. (#105)
gheber Nov 21, 2020
3c0394b
Doxygen - added (mostly) beginner functions (#112)
bljhdf Nov 23, 2020
3360ebd
Add src/H5module.h to MANIFEST.
lrknox Nov 26, 2020
5be0fe8
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5 into hdf…
lrknox Dec 11, 2020
a1ec23d
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5 into hdf…
lrknox Dec 14, 2020
0937643
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5 into hdf…
lrknox Dec 17, 2020
93f4ce1
close #195. (#196)
hyoklee Dec 17, 2020
d9fcbec
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5 into hdf…
lrknox Dec 26, 2020
16ca6d1
Avoid aligned access for references by decoding into temporary buffer…
qkoziol Dec 19, 2020
acfe570
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5 into hdf…
lrknox Jan 6, 2021
edf801c
Modify temporary rpath for testing in java example scripts. (#230)
lrknox Dec 29, 2020
3736bd1
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5 into hdf…
lrknox Jan 9, 2021
dbc345b
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5 into hdf…
lrknox Feb 23, 2021
3af66dd
Fix undefined left shifting of negative numbers (#338)
seanm Feb 19, 2021
67d2ada
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5 into hdf…
lrknox Mar 10, 2021
febde7c
Fixes various warnings noticed on Windows (#425)
derobins Mar 5, 2021
ac550e1
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5 into hdf…
lrknox Mar 10, 2021
9840892
Applied clang-tidy readability-non-const-parameter warning fixes auto…
seanm Mar 9, 2021
e391ca0
Added C++11 override keyword where appropriate (#433)
seanm Mar 10, 2021
aaa4929
Various clang tidy warning fixes (#448)
seanm Mar 10, 2021
c7ae947
Removed checks/workarounds for pre-C++89 compatibility (#449)
seanm Mar 10, 2021
eb95b11
Fixed all clang-tidy bugprone-suspicious-string-compare warnings (#451)
seanm Mar 10, 2021
80d2a1d
Remove 2 functions incorrectly merged from develop in a cherry-pick m…
lrknox Mar 11, 2021
fb6f838
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5 into hdf…
lrknox Mar 21, 2021
afccbcd
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5 into hdf…
lrknox Apr 1, 2021
0ae7773
Merge branch 'hdf5_1_12' of https://github.com/HDFGroup/hdf5 into hdf…
lrknox Apr 2, 2021
5ec73a5
More warning fixes (#400)
seanm Mar 4, 2021
674ec98
Changes found during merge to 1.12 (#414)
byrnHDF Mar 4, 2021
0400e61
Align with "parallel fence" changes (#479)
qkoziol Mar 24, 2021
6afe966
File locks now work on Windows (#480)
derobins Mar 22, 2021
3cbe31f
small edits (#481)
brtnfld Mar 22, 2021
51d6a79
Adds an implementation for nanosleep on Windows (#483)
derobins Mar 22, 2021
131b532
Updates HSYS_GOTO_ERROR to emit GetLastError() values on Win32 (#492)
derobins Mar 23, 2021
f5ffa1c
Updates that allow accum SWMR tests to work on Windows (#493)
derobins Mar 27, 2021
2d482bf
Disable long double tests and remove CMake flag groups (#494)
byrnHDF Mar 22, 2021
4ac9e9e
Misc warning fixes (#495)
derobins Mar 24, 2021
c1b0cf1
Removes support for pre-2015 Visual Studio (#496)
derobins Mar 24, 2021
263f112
Remove extra parameter from merge.
lrknox Apr 2, 2021
e6df490
Resolve missed merge conflict.
lrknox Apr 2, 2021
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6 changes: 3 additions & 3 deletions c++/src/H5AbstractDs.h
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Original file line number Diff line number Diff line change
Expand Up @@ -12,8 +12,8 @@
* [email protected]. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

#ifndef AbstractDs_H
#define AbstractDs_H
#ifndef H5AbstractDs_H
#define H5AbstractDs_H

namespace H5 {

Expand Down Expand Up @@ -81,4 +81,4 @@ class H5_DLLCPP AbstractDs {
}; // end of AbstractDs
} // namespace H5

#endif // AbstractDs_H
#endif // H5AbstractDs_H
6 changes: 3 additions & 3 deletions c++/src/H5CommonFG.h
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Expand Up @@ -12,8 +12,8 @@
* [email protected]. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

#ifndef CommonFG_H
#define CommonFG_H
#ifndef H5CommonFG_H
#define H5CommonFG_H

namespace H5 {

Expand Down Expand Up @@ -83,7 +83,7 @@ class H5_DLLCPP CommonFG {
}; // end of CommonFG
} // namespace H5

#endif // CommonFG_H
#endif // H5CommonFG_H

/***************************************************************************
Design Note
Expand Down
6 changes: 3 additions & 3 deletions c++/src/H5Group.h
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Original file line number Diff line number Diff line change
Expand Up @@ -12,8 +12,8 @@
* [email protected]. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

#ifndef Group_H
#define Group_H
#ifndef H5Group_H
#define H5Group_H

namespace H5 {

Expand Down Expand Up @@ -83,4 +83,4 @@ class H5_DLLCPP Group : public H5Object, public CommonFG {
}; // end of Group
} // namespace H5

#endif // Group_H
#endif // H5Group_H
6 changes: 3 additions & 3 deletions c++/src/H5IdComponent.h
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Original file line number Diff line number Diff line change
Expand Up @@ -12,8 +12,8 @@
* [email protected]. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

#ifndef IdComponent_H
#define IdComponent_H
#ifndef H5IdComponent_H
#define H5IdComponent_H

namespace H5 {

Expand Down Expand Up @@ -113,4 +113,4 @@ class H5_DLLCPP IdComponent {
}; // end class IdComponent
} // namespace H5

#endif // IdComponent_H
#endif // H5IdComponent_H
27 changes: 15 additions & 12 deletions c++/test/tarray.cpp
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Expand Up @@ -81,7 +81,7 @@ test_array_compound_array()
// Initialize array data to write
for (idxi = 0; idxi < SPACE1_DIM1; idxi++)
for (idxj = 0; idxj < ARRAY1_DIM1; idxj++) {
wdata[idxi][idxj].i = idxi * 10 + idxj;
wdata[idxi][idxj].i = static_cast<int>(idxi * 10 + idxj);
for (idxk = 0; idxk < ARRAY1_DIM1; idxk++) {
float temp = idxi * 10.0 + idxj * 2.5 + idxk;
wdata[idxi][idxj].f[idxk] = temp;
Expand Down Expand Up @@ -178,8 +178,9 @@ test_array_compound_array()
// Check the array dimensions
for (ii = 0; ii < ndims; ii++)
if (rdims1[ii] != tdims1[ii]) {
TestErrPrintf("Array dimension information doesn't match!, rdims1[%d]=%zd, tdims1[%d]=z%d\n",
ii, rdims1[ii], ii, tdims1[ii]);
TestErrPrintf(
"Array dimension information doesn't match!, rdims1[%d]=%lld, tdims1[%d]=%lld\n", ii,
rdims1[ii], ii, tdims1[ii]);
continue;
} // end if

Expand All @@ -196,8 +197,9 @@ test_array_compound_array()
// Check the array dimensions
for (ii = 0; ii < ndims; ii++)
if (rdims1[ii] != tdims1[ii]) {
TestErrPrintf("Array dimension information doesn't match!, rdims1[%d]=%zd, tdims1[%d]=%zd\n",
ii, rdims1[ii], ii, tdims1[ii]);
TestErrPrintf(
"Array dimension information doesn't match!, rdims1[%d]=%lld, tdims1[%d]=%lld\n", ii,
rdims1[ii], ii, tdims1[ii]);
continue;
} // end if

Expand Down Expand Up @@ -246,8 +248,9 @@ test_array_compound_array()
// Check the array dimensions
for (ii = 0; ii < ndims; ii++)
if (rdims1[ii] != tdims1[ii]) {
TestErrPrintf("Array dimension information doesn't match!, rdims1[%d]=%zd, tdims1[%d]=%zd\n",
ii, rdims1[ii], ii, tdims1[ii]);
TestErrPrintf(
"Array dimension information doesn't match!, rdims1[%d]=%lld, tdims1[%d]=%lld\n", ii,
rdims1[ii], ii, tdims1[ii]);
continue;
} // end if

Expand All @@ -262,9 +265,9 @@ test_array_compound_array()
for (idxi = 0; idxi < SPACE1_DIM1; idxi++) {
for (idxj = 0; idxj < ARRAY1_DIM1; idxj++) {
if (wdata[idxi][idxj].i != rdata[idxi][idxj].i) {
TestErrPrintf(
"Array data information doesn't match!, wdata[%d][%d].i=%d, rdata[%d][%d].i=%d\n",
idxi, idxj, wdata[idxi][idxj].i, idxi, idxj, rdata[idxi][idxj].i);
TestErrPrintf("Array data information doesn't match!, wdata[%lld][%lld].i=%d, "
"rdata[%lld][%lld].i=%d\n",
idxi, idxj, wdata[idxi][idxj].i, idxi, idxj, rdata[idxi][idxj].i);
continue;
} // end if
} // end for
Expand Down Expand Up @@ -383,7 +386,7 @@ test_array_info()
// Initialize array data to write
for (idxi = 0; idxi < SPACE1_DIM1; idxi++)
for (idxj = 0; idxj < ARRAY1_DIM1; idxj++) {
wdata[idxi][idxj].i = idxi * 10 + idxj;
wdata[idxi][idxj].i = static_cast<int>(idxi * 10 + idxj);
for (idxk = 0; idxk < ARRAY1_DIM1; idxk++) {
float temp = idxi * 10.0 + idxj * 2.5 + idxk;
wdata[idxi][idxj].f[idxk] = temp;
Expand Down Expand Up @@ -455,7 +458,7 @@ test_array_info()
for (ii = 0; ii < ndims; ii++)
if (rdims1[ii] != tdims1[ii]) {
TestErrPrintf(
"Array dimension information doesn't match!, rdims1[%d]=%zd, tdims1[%d]=z%d\n", ii,
"Array dimension information doesn't match!, rdims1[%d]=%llu, tdims1[%d]=z%llu\n", ii,
rdims1[ii], ii, tdims1[ii]);
continue;
} // end if
Expand Down
36 changes: 18 additions & 18 deletions c++/test/tattr.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -169,8 +169,8 @@ test_attr_basic_write()
// Verify values read in
for (i = 0; i < ATTR1_DIM1; i++)
if (attr_data1[i] != read_data1[i])
TestErrPrintf("%d: attribute data different: attr_data1[%d]=%d,read_data1[%d]=%d\n", __LINE__,
i, attr_data1[i], i, read_data1[i]);
TestErrPrintf("%d: attribute data different: attr_data1[%llu]=%d,read_data1[%llu]=%d\n",
__LINE__, i, attr_data1[i], i, read_data1[i]);

// Create two more attributes for this dataset, but only write to one.
Attribute ds_attr2 = dataset.createAttribute(ATTR2_NAME, PredType::NATIVE_INT, att_space);
Expand All @@ -185,7 +185,7 @@ test_attr_basic_write()
// Verify values read in
for (i = 0; i < ATTR1_DIM1; i++)
if (attr_data1a[i] != read_data1[i])
TestErrPrintf("%d: attribute data different: attr_data1a[%d]=%d,read_data1[%d]=%d\n",
TestErrPrintf("%d: attribute data different: attr_data1a[%llu]=%d,read_data1[%llu]=%d\n",
__LINE__, i, attr_data1a[i], i, read_data1[i]);

// Close both attributes
Expand Down Expand Up @@ -448,8 +448,8 @@ test_attr_rename()
// Verify values read in
for (i = 0; i < ATTR1_DIM1; i++)
if (attr_data1[i] != read_data1[i])
TestErrPrintf("%d: attribute data different: attr_data1[%d]=%d,read_data1[%d]=%d\n", __LINE__,
i, attr_data1[i], i, read_data1[i]);
TestErrPrintf("%d: attribute data different: attr_data1[%llu]=%d,read_data1[%llu%d\n",
__LINE__, i, attr_data1[i], i, read_data1[i]);

// Close attribute
attr1.close();
Expand All @@ -472,7 +472,7 @@ test_attr_rename()
// Verify values read in
for (i = 0; i < ATTR1_DIM1; i++)
if (attr_data1a[i] != read_data1[i])
TestErrPrintf("%d: attribute data different: attr_data1a[%d]=%d,read_data1[%d]=%d\n",
TestErrPrintf("%d: attribute data different: attr_data1a[%llu]=%d,read_data1[%llu]=%d\n",
__LINE__, i, attr_data1a[i], i, read_data1[i]);

// Close attribute
Expand Down Expand Up @@ -537,7 +537,7 @@ test_attr_basic_read()
// Verify values read in
for (i = 0; i < ATTR1_DIM1; i++)
if (attr_data1[i] != read_data1[i])
TestErrPrintf("%d: attribute data different: attr_data1[%d]=%d, read_data1[%d]=%d\n",
TestErrPrintf("%d: attribute data different: attr_data1[%llu]=%d, read_data1[%llu]=%d\n",
__LINE__, i, attr_data1[i], i, read_data1[i]);

/*
Expand Down Expand Up @@ -568,9 +568,9 @@ test_attr_basic_read()
for (i = 0; i < ATTR2_DIM1; i++)
for (j = 0; j < ATTR2_DIM2; j++)
if (attr_data2[i][j] != read_data2[i][j]) {
TestErrPrintf(
"%d: attribute data different: attr_data2[%d][%d]=%d, read_data2[%d][%d]=%d\n",
__LINE__, i, j, attr_data2[i][j], i, j, read_data2[i][j]);
TestErrPrintf("%d: attribute data different: attr_data2[%llu][%llu]=%d, "
"read_data2[%llu][%llu]=%d\n",
__LINE__, i, j, attr_data2[i][j], i, j, read_data2[i][j]);
}
PASSED();
} // end try block
Expand Down Expand Up @@ -1044,7 +1044,7 @@ test_attr_mult_read()
hsize_t dims[ATTR_MAX_DIMS]; // Attribute dimensions
int ndims = space.getSimpleExtentDims(dims);
if ((long)dims[0] != (long)ATTR1_DIM1)
TestErrPrintf("%d:attribute dimensions different: dims[0]=%d, should be %d\n", __LINE__,
TestErrPrintf("%d:attribute dimensions different: dims[0]=%d, should be %llu\n", __LINE__,
(int)dims[0], ATTR1_DIM1);

/* Verify Datatype */
Expand Down Expand Up @@ -1072,8 +1072,8 @@ test_attr_mult_read()
// Verify values read in
for (i = 0; i < ATTR1_DIM1; i++)
if (attr_data1[i] != read_data1[i])
TestErrPrintf("%d: attribute data different: attr_data1[%d]=%d,read_data1[%d]=%d\n", __LINE__,
i, attr_data1[i], i, read_data1[i]);
TestErrPrintf("%d: attribute data different: attr_data1[%llu]=%d,read_data1[%llu]=%d\n",
__LINE__, i, attr_data1[i], i, read_data1[i]);

// Verify Name
H5std_string attr_name = attr.getName();
Expand Down Expand Up @@ -1127,9 +1127,9 @@ test_attr_mult_read()
for (i = 0; i < ATTR2_DIM1; i++)
for (j = 0; j < ATTR2_DIM2; j++)
if (attr_data2[i][j] != read_data2[i][j])
TestErrPrintf(
"%d: attribute data different: attr_data2[%d][%d]=%d, read_data2[%d][%d]=%d\n",
__LINE__, i, j, attr_data2[i][j], i, j, read_data2[i][j]);
TestErrPrintf("%d: attribute data different: attr_data2[%llu][%llu]=%d, "
"read_data2[%llu][%llu]=%d\n",
__LINE__, i, j, attr_data2[i][j], i, j, read_data2[i][j]);

// Verify Name
attr_name = attr.getName();
Expand Down Expand Up @@ -1182,8 +1182,8 @@ test_attr_mult_read()
for (j = 0; j < ATTR3_DIM2; j++)
for (k = 0; k < ATTR3_DIM3; k++)
if (attr_data3[i][j][k] != read_data3[i][j][k])
TestErrPrintf("%d: attribute data different: attr_data3[%d][%d][%d]=%f, "
"read_data3[%d][%d][%d]=%f\n",
TestErrPrintf("%d: attribute data different: attr_data3[%llu][%llu][%llu]=%f, "
"read_data3[%llu][%llu][%llu]=%f\n",
__LINE__, i, j, k, attr_data3[i][j][k], i, j, k, read_data3[i][j][k]);

// Verify Name
Expand Down
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