| Commit message (Collapse) | Author | Age | Files | Lines |
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Purpose:
minor bugs fixed
Description:
Typos in H5Fpkg.h and H5TB.c
Solution:
Platforms tested:
linux 2.2.18
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Code cleanup
Description:
Cleanup compiler warnings found by the SGI compiler and gcc 3.0
Platforms tested:
FreeBSD 4.5 w/gcc 3.0 (hack) && IRIX64 (modi4)
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Code cleanup
Description:
Windows is generating hundreds of warnings from some of the practices in
the library. Mostly, they are because size_t is 32-bit and hsize_t is
64-bit on Windows and we were carelessly casting the larger values down to
the smaller ones without checking for overflow.
Also, some other small code cleanups,etc.
Solution:
Re-worked some algorithms to eliminate the casts and also added more
overflow checking for assignments and function parameters which needed
casts.
Kent did most of the work, I just went over his changes and fit them into
the the library code a bit better.
Platforms tested:
FreeBSD 4.4 (hawkwind)
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Code cleanup (sorta)
Description:
When the first versions of the HDF5 library were designed, I remembered
vividly the difficulties of porting code from a 32-bit platform to a 16-bit
platform and asked that people use intn & uintn instead of int & unsigned
int, respectively. However, in hindsight, this was overkill and
unnecessary since we weren't going to be porting the HDF5 library to
16-bit architectures.
Currently, the extra uintn & intn typedefs are causing problems for users
who'd like to include both the HDF5 and HDF4 header files in one source
module (like Kent's h4toh5 library).
Solution:
Changed the uintn & intn's to unsigned and int's respectively.
Platforms tested:
FreeBSD 4.4 (hawkwind)
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Update
Description:
Changed
#include <hdf_file.h>
construct to
#include "hdf_file.h"
so that the GNU compiler can more easily pick up the dependencies
which it places in the .depend and Dependencies files. Also
regenerated the Dependencies to go along with this.
Platforms tested:
Linux
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Bug fix (sort of)
Description:
The RCSID string in H5public.h was causing the C++ code problem as it
was included multiple times and C++ did not like multiple definitions
of the same static variable.
Solution:
Since we don't really make use of the RCSID strings as we have not
installed it in all source files, we decided to remove it.
Platforms tested:
eirene (linux), modi4 (IRIX64-64) both serial and parallel modes.
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Code cleanup.
Description:
Fixed _lots_ (I mean _tons_) of warnings spit out by the gcc with the
extra warnings. Including a few show-stoppers for compression on IRIX
machines.
Solution:
Changed lots of variables' types to more sensible and consistent types,
more range-checking, more variable typecasts, etc.
Platforms tested:
FreeBSD 4.2 (hawkwind), IRIX64-64 (modi4)
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scheme.
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** src/H5Tconv.c
** src/H5Tpkg.h
** src/H5Tpublic.h
The H5T_conv_struct_opt() function had a design flaw -- it
didn't keep information about the stride to use to step
through the temporary/background-value buffer and thus nested
invocations would clobber each other's temp buffers. This was
fixed by splitting the `stride' argument into `buf_stride' and
`bkg_stride' arguments for all the conversion functions. THIS
IS AN API CHANGE, but users will get a compiler warning when
they pass their conversion function pointer to H5Tregister().
** src/H5T.c
** src/H5Tprivate.h
Added a bkg_stride argument to the H5T_convert() definition in
order to fix a bug related to the optimized compound datatype
conversion function.
** src/H5T.c
** src/H5A.c
** src/H5D.c
** src/H5Ofill.c
** src/H5P.c
Added bkg_stride=0 argument to the H5T_convert() calls.
** test/dtypes.c
Added a test for the H5T_conv_struct_opt() bug fixed above.
** src/H5FL.c
The H5FL_term() function should return non-zero even when it
couldn't free all the free lists do to their being used by
some other package. When that other package terminates it
will return non-zero, causing H5FL_term() to be called
again. This fixes some of the `infinite loop closing library'
messages.
** tools/pdb2hdf
Uses print_version() instead of doing that itself.
** src/H5Ppublic.h
Renamed H5Pget_gc_reference() declaration to make it match the
definition.
** src/H5FDlog.c
Added API tracing macros.
Removed `const' qualifier from a `char*' member of a struct
which was allocated on the heap.
** src/H5TB.c
Added curly braces to a couple deeply-nested `if' statements
to make them clearer and to shut up the increadibly stupid and
just plain incorrect gcc warning about ambiguous `else'.
** test/titerate.c
Removed incomplete initialization in favor of memset() for one
auto variable to stop compiler warnings.
** tools/Depencencies
Regenerated to remove references to h5dumputil.c
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library and
updated it for integrating with the H5 library. I'm thinking about using them
for the data-structures in some caching improvements I'm working on.
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"temporary buffer"
code, since the functionality was superceded. See the followup document for
details on the free-list code.
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Changes since 19990614
----------------------
./src/H5D.c
Changed the way the plist_id argument of H5Dvlen_reclaim() is
checked so that it's more specific and works when debugging is
turned off.
./src/H5TB.c
Removed an unused local variable.
./test/fillval.c
./test/h5test.c
./test/h5test.h
Changed `basename' variables to `base_name' to prevent a
warning about a global with the same name.
./tools/h5ls.c
Changed `indent' variables to `ind' to prevent a warning about
a global with the same name.
./tools/h5toh4.c
Commented out declarations for things that normally appear in
system header files since our definitions might be
incompatible with the system and prevent h5toh4 from
compiling. If all looks good on other systems then we can
permanently remove these declarations...
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currently working
is H5Tvlen_create().
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functionality is here,
accessed with H5Tvlen_create, but I need to start writing tests now. Also the
more esoteric API calls (such as H5Tget_vlen_buf_size and the memory management
calls) aren't implemented yet.
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----------------------
./tools/h5tools.c
./tools/h5tools.h
Finally fixed a long-standing bug that caused core dumps if
a compound datum rendered to more than some number of
characters (we kept bumping up the limit at the risk of
violating stack size limits on some machines). The fix works
only on systems that have the vsnprintf() function (otherwise
a 4kB limit is imposed, which if violated probably dumps
core). If vsnprintf() is present then the library dynamically
allocates space for the output string.
Also made it possible to control how compound data is rendered
across multiple lines of output by allowing the caller to
specify where optional line-breaks get inserted. The output
functions split up the value at one or more optional
line-breaks to prevent it from wrapping around the screen.
If a datum doesn't fit on the current line but would fit on
the next line then it is printed on the next line regardless
of whether optional line-breaks would have prevent wrapping
around the screen. This makes it easier to find the beginnings
of compound data values. This feature is disabled by default
but can be enabled by the application.
If a datum doesn't fit on the current line and the previous
datum also occupied more than one line then we move to the
next line before printing. This makes it easier to find the
beginnings of compound data values but prevents the output
from looking fragmented if there are only a few long values
among mostly short values. This feature is disabled by
default but can be enabled by the application.
The application can control the printf() formats used for all
the native data types. The defaults are what the library used
to use: %g, %ld, %lu, %d, and %u
./tools/h5ls.c
Compound datatype values can now be split across multiple
lines of output instead of just wrapping. Also, when lots of
compound values are too long they all start at the beginning
of a line. This only required about 10 lines of changes in the
setup for tools library calls (I didn't modify the h5dump
program because it uses its own version of the tools library
that forked off long ago).
Added code for Win32 which is unable to cast `unsigned long
long' to `double'. If the dataset size exceeds (2^63)-1 then
the percent utilization is not displayed (this is easily
possible with chunked datasets). This is untested yet.
./configure.in
./src/H5config.h.in
./src/H5.c
./src/H5private.h
Check for vsnprintf() and provide a simple, stupid definition
if it isn't available. The stupid definition just calls
vsprintf() and ignores the second argument. This can result in
buffer overflows in h5ls and h5dump since vsprintf() is an
unsafe function (and anyone can create an hdf5 file that runs
an arbitrary command from h5ls and h5dump in that case)!
./config/conclude.in
Remove more *.o files for `make clean'
./src/H5A.c
./src/H5D.c
./src/H5F.c
./src/H5I.c
./src/H5Iprivate.h
./src/H5P.c
./src/H5R.c
./src/H5RA.c
./src/H5S.c
./src/H5T.c
./src/H5TB.c
Cleaned up a memory leak during H5_term_library() by allowing
H5I_clear_group() to skip items that couldn't be freed. This
allows the item to remain in the group until we can free it
later.
./src/H5F.c
The H5F_close_all() function fails if a file cannot be closed.
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./configure [REGENERATED]
./src/H5D.c
./src/H5O.c
Removed H5AC, H5B, and H5T from the default list of packages
to debug (because they're pretty expensive debugging), and
added H5O. Also fixed a bug for undefined variable in H5D when
H5S debugging is turned on but H5T debugging is turned off.
./config/conclude.in
Fixed installation of header files for building in a directory
other than the source directory. This fixes a bug where
H5config.h wasn't being installed.
./src/H5.c
./src/H5A.c
./src/H5D.c
./src/H5F.c
./src/H5G.c
./src/H5I.c
./src/H5Iprivate.h
./src/H5P.c
./src/H5R.c
./src/H5RA.c
./src/H5S.c
./src/H5T.c
./src/H5TB.c
./src/H5Tprivate.h
./src/H5Z.c
./src/H5detect.c
./src/H5private.h
Changed the way the library shuts down again. Now it handles
cycles between packages and isn't so sensitive to dependencies
between packages. A package might shut down only to be
restarted to process a request from some other package being
shut down. Loops are detected after 100 iteractions and the
shutdown is aborted with a message on standard error. This
also makes it a lot easier to debug.
./src/H5A.c
Fixed H5A_write() and H5A_read() so they pass a non-null
background buffer to the conversion functions. This is
necessary when an attribute has a compound data type.
./src/H5Flow.c
./src/H5Fprivate.h
./src/H5Fsec2.c
Reindented new Win32 stuff.
./src/H5Odtype.c
Fixed a bug when enumeration types are used in a compound data
type. The byte pointer wasn't incremented after the type
information was written.
./tools/h5ls.c
Compound data types display their total size because it's not
always obvious from looking at the members.
Scalar attributes show their space as `scalar' instead of
`{}'.
The index value is not printed for attributes that have only a
few values. Instead the word `Data:' is printed on the first
line of attribute data.
Named types display their data type only if verbose output was
requested.
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----------------------
./src/H5.c
./src/H5A.c
./src/H5AC.c
./src/H5B.c
./src/H5D.c
./src/H5E.c
./src/H5F.c
./src/H5Farray.c
./src/H5Fcore.c
./src/H5Ffamily.c
./src/H5Fistore.c
./src/H5Flow.c
./src/H5Fmpio.c
./src/H5Fsec2.c
./src/H5Fsplit.c
./src/H5Fstdio.c
./src/H5G.c
./src/H5Gent.c
./src/H5Gnode.c
./src/H5Gstab.c
./src/H5HG.c
./src/H5HL.c
./src/H5I.c
./src/H5Iprivate.h
./src/H5MF.c
./src/H5MM.c
./src/H5O.c
./src/H5Oattr.c
./src/H5Ocomp.c
./src/H5Ocont.c
./src/H5Odtype.c
./src/H5Oefl.c
./src/H5Ofill.c
./src/H5Olayout.c
./src/H5Omtime.c
./src/H5Oname.c
./src/H5Osdspace.c
./src/H5Oshared.c
./src/H5Ostab.c
./src/H5P.c
./src/H5R.c
./src/H5RA.c
./src/H5S.c
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Smpio.c
./src/H5Snone.c
./src/H5Spoint.c
./src/H5Sselect.c
./src/H5T.c
./src/H5TB.c
./src/H5Tbit.c
./src/H5Tconv.c
./src/H5V.c
./src/H5Z.c
./src/H5detect.c
./src/H5private.h
Most of these changes are because the `interface_initialize_g'
variable change from hbool_t to int. It's a one line change.
Changed the way the library is closed so we have more control
over the order the interfaces are shut down. Instead of
registering an atexit() function for every interface in some
haphazard order we just register one: H5_term_library() which
then calls the H5*_term_interface() functions in a
well-defined order.
If the library is closed and then reopened repeatedly by
calling H5close() and H5open() in a loop we only add one copy
of the library termination functions with atexit().
Termination is a two-step process in order to help detect
programming errors that would cause an infinite loop caused by
the termination of one interface waking up some other
previously terminated interface. The first step terminates
the interface and *marks it as unusable*. After all
interfaces are terminated then we mark them all as usable
again. The FUNC_ENTER() macro has been modified to return
failure or to dump core (depending on whether NDEBUG is
defined) if we try to call an interface while it's shutting
down.
./src/H5.c
The H5dont_atexit() function returns failure if it's called
more than once or if it's called too late. However, the error
stack is not automatically printed on failure because the
library might not be initialized yet
./test/chunk.c
./test/flush1.c
./test/flush2.c
./test/iopipe.c
./test/overhead.c
./test/ragged.c
Changed the extra cast for Win32 so we do floating point
division again -- it was just confusion about precedence and
associativity of casting and the C coercion rules. Removed
extra carriage returns inserted by broken operating system.
./src/H5Ffamily.c
Fixed an bug where H5F_fam_write() lowered the EOF marker for
one of the family members causing H5F_fam_read() to read
zeros.
./test/h5test.h [NEW]
./test/h5test.c [NEW]
./test/Makefile.in
./test/bittests.c
./test/cmpd_dset.c
./test/dsets.c
./test/dtypes.c
./test/extend.c
./test/external.c
Support library for test files. This isn't done yet but
Katie's contractions are ~10 minutes apart so I figured I
better back this stuff up just in case I'm not here next
week...
Eventually all test files will understand HDF5_DRIVER to name
the low level file driver and parameters so we can easily test
various drivers. They will also understand HDF5_PREFIX to
prepend to the beginning of file names which is necessary for
testing ROMIO with various drivers. Also, the cleanup function
will know how to use the file name prefix and will understand
different file driver naming schemes like file families. I'm
not sure they'll understand the `gsf:' type prefixes yet.
Note, the external test is completely commented out because
I'm in the middle of modifying it. It will still compile and
run but it doesn't test anything at the moment.
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----------------------
./INSTALL.parallel [NEW]
We're beginning to unify some of the parallel installation
steps. This file will contain general information for
installing the parallel library. It's not complete yet.
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
Check for xdr_int() in libnsl required on Solaris when linking
with hdf4. It's found on the Irix system I tested which
complains that `-lnsl' didn't resolve any symbols. Oh well.
Fixed the order of searching for libdf and libmfhdf for hdf4
linking.
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
./src/H5Z.c
Check for compress() in libz in order to find older versions
of the library that will still work for hdf4. Added a
separate check for compress2() that hdf5 will use.
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
./src/H5.c
./src/H5private.h
./src/H5A.c
./src/H5B.c
./src/H5Bprivate.h
./src/H5D.c
./src/H5F.c
./src/H5Farray.c
./src/H5Fcore.c
./src/H5Ffamily.c
./src/H5Fistore.c
./src/H5Flow.c
./src/H5Fmpio.c
./src/H5Fprivate.h
./src/H5Fsec2.c
./src/H5Fsplit.c
./src/H5Fstdio.c
./src/H5Gent.c
./src/H5Gnode.c
./src/H5Gpkg.h
./src/H5Gprivate.h
./src/H5HG.c
./src/H5HL.c
./src/H5O.c
./src/H5Oattr.c
./src/H5Ocomp.c
./src/H5Ocont.c
./src/H5Odtype.c
./src/H5Oefl.c
./src/H5Ofill.c
./src/H5Olayout.c
./src/H5Omtime.c
./src/H5Oname.c
./src/H5Oprivate.h
./src/H5Osdspace.c
./src/H5Oshared.c
./src/H5Ostab.c
./src/H5R.c
./src/H5RA.c
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Snone.c
./src/H5Spoint.c
./src/H5Sprivate.h
./src/H5Sselect.c
./src/H5T.c
./src/H5Tbit.c
./src/H5Tconv.c
./src/H5Tpkg.h
./src/H5V.c
./test/bittests.c
./test/gheap.c
./test/hyperslab.c
./test/istore.c
./test/tmeta.c
./test/trefer.c
./test/tselect.c
./tools/h5debug.c
./tools/h5tols.c
Added checks for Posix.1g types like `int8_t'. If not defined
then H5private.h defines them. Changed all `int8' etc. to
`int8_t'.
./src/H5A.c
./src/H5D.c
./src/H5F.c
./src/H5G.c
./src/H5I.c
./src/H5P.c
./src/H5R.c
./src/H5RA.c
./src/H5S.c
./src/H5T.c
./src/H5TB.c
./src/H5Z.c
Calling H5*_term_interface() resets interface_initialize_g to
FALSE so a subsequent call to H5open() (implied or explicit)
reinitializes global variables properly.
./src/H5private.h
./src/H5Oefl.c
./src/H5S.c
Changed MAX_SIZET, MAX_SSIZET, MAX_HSIZET, and MAX_HSSIZET to
SIZET_MAX, SSIZET_MAX, HSIZET_MAX, and HSSIZE_MAX to they
match the Posix.1 constants in <limits.h>.
./src/H5T.c
./src/H5Tconv.c
./src/H5Tpkg.h
./src/H5Tprivate.h
./src/H5detect.c
Added 36 more integer hardware conversion functions to the
type conversion table for conversions to/from `long long' and
`unsigned long long'. The `long long' names will be changed
shortly to make them portable to Win32.
Changed H5T_init() to H5T_native_open() and added an
H5T_native_close() to open and close the predefined native
data types.
Increased the initial size of the type conversion table from
64 to 128 entries.
Reordered the 90 new integer conversion functions so the names
that are printed favor `int' over `short' or `long' when two
of them are the same.
./test/dtypes.c
Added hardware and software integer conversion tests for the
56 functions I added recently but not the additional 36
checked in this time. That will come next.
Call H5close() after each test so type conversion statistics
are easier to follow. Try this: $ HDF5_DEBUG=t ./dtypes
Added more debugging output for when things go wrong.
./src/H5private.h
Removed trailing carriage-returns inserted by broken operating
system ;-)
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"non-negative/negative"
and also fixed a few more explicit checks against FAIL.
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----------------------
./MANIFEST
./test/Makefile.in
./test/flush1.c [NEW]
./test/flush2.c [NEW]
Test to see if calling H5Fflush() results in a consistent
file.
./src/H5.c
./src/H5A.c
./src/H5D.c
./src/H5Fistore.c
./src/H5I.c
./src/H5S.c
./src/H5Shyper.c
./src/H5Sselect.c
./src/H5TB.c
Changed comparisons against SUCCEED and FAIL to >=0 and <0 in
about 15 places.
./src/H5.c
./src/H5V.c
./src/H5detect.c
./src/H5private.h
./src/H5public.h
./test/big.c
./test/chunk.c
./test/cmpd_dset.c
./test/dsets.c
./test/dtypes.c
./test/external.c
./test/fillval.c
./test/iopipe.c
./test/links.c
./test/mount.c
./test/mtime.c
./test/ragged.c
./test/shtype.c
./test/unlink.c
Removed ^M from the end of lines inserted on broken OS's ;-)
./src/H5private.h
Changed c++ comments to c comments.
./src/H5R.c
Added tracing macros.
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align with the
library.
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which were
calling malloc too often. Also, added caching of hyperslab blocks, which
improves performance _significantly_ for hyperslab I/O.
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----------------------
./MANIFEST
./src/H5R.c [NEW]
./src/H5Rprivate.h [NEW]
./src/H5Rpublic.h [NEW]
./src/Makefile.in
./src/hdf5.h
./test/ragged.c [NEW]
Preliminary support for 2d ragged arrays for Mark Miller and
Jim Reus. Not fully implemented yet. The test is not actually
part of `make test' because we still have some memory problems.
./src/H5E.c
./src/H5Epublic.h
Added H5E_RAGGED as a major error number.
./bin/release
Checks the MANIFEST file against `svf ls' on systems that have
it.
./bin/trace
Fixed a bug that caused arguments of type `void *x[]' to not
be handled.
./src/H5.c
Removed unused variables and changed a couple types to
fix compiler warnings.
Added tracing support for ragged array object ID's and arrays
of pointers.
./src/H5D.c
H5Dcreate() will complain if either of the property lists are
invalid (instead of using the default).
./src/H5D.c
./src/H5Dprivate.h
Split H5Dget_space() into an API and internal function so it
can be called from the new ragged array layer.
./src/H5Fistore.c
Fixed warnings about unsigned vs. signed comparisons.
./src/H5Flow.c
Fixed a warning about a variable being shadowed in the MPI-IO
stuff.
./src/H5Iprivate.h
./src/H5Ipublic.h
Added the H5_RAGGED atom group.
./src/H5Shyper.c
Fixed some freeing-free-memory errors that resulted when
certain arrays were freed but the pointers were left in the
data structures. I simply set the pointers to null after they
were freed.
./src/H5Sprivate.h
./src/H5Sselect.c
Split the H5Sselect_hyperslab() function into an API and a
private function so it could be called from the ragged array
layer.
Added H5S_SEL_ERROR and H5S_SEL_N to the switch statements to
get rid or compiler warnings.
./src/H5Tconv.c
Removed a misleading comment.
./test/bittests.c
Fixed a warning about a printf().
./test/cmpd_dset.c
Fixed warnings about unused variables because of test #11
being commented out.
./bin/trace
Shortened the right margin for the output to allow room for
the `);' at the end of the TRACE() macros.
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----------------------
./src/H5.c
Handle hid_t of type H5_TEMPBUF, arguments usually called tbuf_id.
Added array tracing where the array rank is stored in a simple
data space. Just use the name of the data space argument when
declaring the array argument:
herr_t
H5Sselect_hyperslab (hid_t space_id, H5S_seloper_t op,
const hssize_t start[/*space_id*/],
const hsize_t _stride[/*space_id*/],
const hsize_t count[/*space_id*/],
const hsize_t _block[/*space_id*/])
and when the program runs you'll see array values printed:
H5Sselect_hyperslab(space=218103813, op=H5S_SELECT_SET,
start=0xbfffef4c {0}, _stride=NULL,
count=0xbfffef44 {64},
_block=NULL) = SUCCEED;
Added more symbolic data types to the tracing output.
./src/H5A.c
./src/H5Apublic.h
./src/H5D.c
./src/H5Dpublic.h
./src/H5F.c
./src/H5Fpublic.h
./src/H5G.c
./src/H5Gpublic.h
./src/H5P.c
./src/H5Ppublic.h
./src/H5S.c
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Spoint.c
./src/H5Spublic.h
./src/H5Sselect.c
./src/H5Ssimp.c
./src/H5TB.c
./src/H5V.c
Changed some API argument names to be more consistent with
other API functions and to produce better tracing output.
Reformatted some long lines. Indented printf statements.
./tools/h5ls.c
Fixed warnings about unsigned vs. signed comparisons.
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----------------------
./src/H5Fistore.c
./src/H5S.c
Fixed places where `herr_t' functions returned NULL for
failure: H5F_istore_get_addr() and printf(?!?) (probably
because a printf() was in the first column :-/ so I don't know
what function it really was that I fixed), and H5S_extent_copy().
./src/H5Fprivate.h
Added declarations for H5F_istore_get_addr() and
H5F_istore_allocate().
./src/H5S.c
./src/H5Sprivate.h
Split H5Sset_extent_simple() into H5S_set_extent_simple() and
replaced calls to the API function with calls to the internal
function.
Changed calls to H5Screate() to H5S_create() and H5Sclose() to
H5S_close().
./src/H5Shyper.c
./src/H5Spoint.c
Removed unused labels and variable.
./src/H5T.c
./src/H5Tconv.c
Changed calls to H5Tfind() to H5T_find().
./src/H5TB.c
Split function return type onto a separate line for five
functions and added API tracing calls.
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one incorrect
type. Should compile much cleaner now.
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to match
API defined in the html/Dataspaces.html document. This code does not include
support for strides, merging selections, or permutations of coordinates yet,
but it's a drop-in replacement for the existing API with the same features.
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