| Commit message (Collapse) | Author | Age | Files | Lines |
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Switch from using H5L_index_t/H5L_INDEX_<foo> to H5_index_t/H5_INDEX_<foo>
in order to accommodate indices on aspects of attributes as well as links.
Add basic support for deleting attributes in dense storage (needs more
support/tests for shared attributes in dense storage still).
Misc. cleanups, etc.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Added H5Gget_info[_by_idx] routines and deprecated H5Gget_num_objs routine.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Finish removing library's internal code that uses H5G_get_objinfo() and
retarget it at either getting the link information or the object information,
as appropriate. (Still need to add user-level tests for H5Oget_info(), but
since several internal components of the library depend on the internal version,
it appears to be working correctly).
Tested on:
FreeBSD/32 4.11 (sleipnir)
Linux/322.4 (heping)
Linux/64 2.4 (mir)
AIX/32 5.? (copper)
Mac OS X/32 10.4.8 (amazon)
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Finish implementation of H5Literate() [still needs real tests]
Clean up datatype macro warnings a bit more.
Unify iterator callback macros and put up in public header file, with the
iterator directions.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
Linux/64 2.4 (mir)
AIX/32 5.? (copper)
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Add H5Lget_name_by_idx routine & tests
Move more H5G routines to deprecated API file
Tested on:
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/32 2.4 (heping) C++ & FORTRAN
Linux/64 2.4 (mir) w/build-all & enable_compat1.6
AIX/32 5.? (copper) w/parallel & FORTRAN
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Implement basic framework for H5Lget_info_by_idx and get it working for
creation order indices on compact groups.
Clean up code a bit.
Close resource link in user-defined link traversal.
Tested on:
Linux/32 2.6 (chicago)
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Rename new H5Gcopy() routine to H5Ocopy() as discussed in last Friday's
design discussion.
Tested on:
Linux/32 2.6 (chicago)
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Changed H5Lget_linkval() to H5Lget_val(), per our design discussion last
Friday afternoon.
Tested on:
Linux/32 2.6 (chicago)
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Clean up formatting and re-organize a bit...
Tested on:
Max OS X/32 10.4.8 (amazon)
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
Linux/64 2.4 (mir)
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File format is not stable, don't keep files produced!
Description:
First stage of checkins modifying the format of groups to support creation
order. Implement "dense" storage for links in groups.
Try to clarify some of the symbols for the H5L API.
Add the H5Pset_latest_format() flag for FAPLs, to choose to use the newest
file format options (including "dense" link storage in groups)
Add the H5Pset_track_creation_order() flag for GCPLs, to enable creation
order tracking in groups (although no index on creation order yet).
Remove --enable-group-revision configure flag, as file format issues are
now handled in a backwardly/forwardly compatible way.
Clean up lots of compiler warnings and other minor formatting issues.
Tested on:
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/32 2.4 (heping) w/FORTRAN & C++
Linux/64 2.4 (mir) w/enable-v1.6 compa
Mac OSX/32 10.4.8 (amazon)
AIX 5.3 (copper) w/parallel & FORTRAN
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Review, revise & checkin in Peter's latest round of object copy changes,
which add basic support for datasets & attributes with reference datatypes.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Users can create external links using H5L_create_external(). These links
point to an object in another HDF5 file. Users can alter the behavior of
external links or create new kinds of links by registering callbacks
using the H5L interface.
Added tests, tools support, etc.
Also a number of other, minor changes have been made (some restructuring of
the H5L interface, for instance).
Additional documentation and examples are forthcoming.
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Feature
Description:
Revised Link APIs.
Solution:
New link APIs use H5L*
H5*create_expand do not create links to the objects created; this must
be done manually with H5Llink.
Added APIs to link an object given its ID (H5Llink), to copy links (H5Lcopy),
and changed creation APIs (H5Lcreate_hard and H5Lcreate_soft) and query
API (H5Lget_linkinfo instead of H5Gget_objinfo).
All old APIs are still supported in H5Gdeprec.c .
Platforms tested:
sol, mir, copper
Misc. update:
Forgot to update MANIFEST and release docs. Will do after checkin.
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Code cleanup
Description:
Trim trailing whitespace in Makefile.am and C/C++ source files to make
diffing changes easier.
Platforms tested:
None necessary, whitespace only change
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New feature
Description:
Check in Peter's code to add support for "shallow copy", "create
intermediate groups", "no attributes" and "expand soft links" support.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4 (chicago) w/ & w/o group-revision enabled
h5committest
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Anti-feature
Description:
Revert changes to H5G_stat_t struct, to make it compatible with the 1.6.x
branch again. The information that was added to the H5G_stat_t struct will
be reported through other API routines.
Platforms tested:
FreeBSD 4.11 (sleipnir) w/C++
Linux 2.4/64 (mir) w/C++ & Fortran
Solaris 2.9 (shanti)
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"Hide" file format changes (for now)
Description:
Add ifdef's (controlled by the --enable-group-revision configure flag)
to disable group revision changes to the file format, in order to allow alpha
release to go ahead without releasing an unsupported version into the wild.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4 32-bit (heping)
Linux 2.4 64-bit (mir)
Solaris 2.9 (shanti)
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New/expanded features
Description:
Check in Peter's changed for the object copy code:
- Allow/fix copying datasets using named variable-length datatypes
- Start adding framework for property list to control how object
copying occurs.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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New feature
Description:
Add in a combination of Peter's & my code to support copying
variable-length data from one file to another, although currently only
supported with contiguous data storage.
Platforms tested:
FreeBSD 4.11 (sleipnir)
h5committest
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New feature
Description:
Check in baseline for compact group revisions, which radically revises the
source code for managing groups and object headers.
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
This initiates the "unstable" phase of the 1.7.x branch, leading up
to the 1.8.0 release. Please test this code, but do _NOT_ keep files created
with it - the format will change again before the release and you will not
be able to read your old files!!!
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
Solution:
There's too many changes to really describe them all, but some of them
include:
- Stop abusing the H5G_entry_t structure and split it into two separate
structures for non-symbol table node use within the library: H5O_loc_t
for object locations in a file and H5G_name_t to store the path to
an opened object. H5G_entry_t is now only used for storing symbol
table entries on disk.
- Retire H5G_namei() in favor of a more general mechanism for traversing
group paths and issuing callbacks on objects located. This gets us out
of the business of hacking H5G_namei() for new features, generally.
- Revised H5O* routines to take a H5O_loc_t instead of H5G_entry_t
- Lots more...
Platforms tested:
h5committested and maybe another dozen configurations.... :-)
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New feature
Description:
Add in baseline "object copy" code from Peter [in the form of a new API
routine: H5Gcopy()]. There's still some work to do (like handling variable-
length datatypes and possibly support for references) and it hasn't been tested
on mounted files yet, but the core functionality is there and working
correctly.
I've also got a set of patches to update the 1.6 branch with tweaks to
keep the branches mostly in sync, but Elena will kill me if I import them
before the 1.6.5 release is out... :-)
Platforms tested:
FreeBSD 4.11 (sleipnir)
h5committested
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Code cleanup/reorganization
Description:
Merge back some more changes extracted from the "compact group" set.
This bunch cleans up and prepares the H5G_* routines for eventual import of
new features.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4
Mac OS X.4
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Code cleanup (sorta)
Description:
Adjust H5G_stat_t to prepare for eventual "external link" information.
This also puts the information for regular objects and soft links into more
obviously separate places.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4
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Code cleanup
Description:
Trim trailing whitespace, which is making 'diff'ing the two branches
difficult.
Solution:
Ran this script in each directory:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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New feature
Description:
Add group creation & access property lists, dataset access property lists
and named datatype creation & access property lists. Currently have
<foo>_extend() API names, which will need to be changed for the final release.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4 (heping)
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Feature add
Description:
Add a few new fields to the H5G_stat_t structure, to allow more information
about the object header to be retrieved.
Platforms tested:
FreeBSD 4.9 (sleipnir)
h5committest
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Bug fix
Description:
H5Gget_num_objs, H5Gget_objname_by_idx and H5Gget_objtype_by_idx were
only accepting a group ID, instead of a location ID, as our documentation for
them stated.
Solution:
Allow them to accept a location ID.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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Feature change
Description:
Change the fileno field in H5G_stat_t from 'unsigned long[2]' to just
'unsigned long'.
Change the objno field in H5G_stat_t from 'unsigned long[2]' to 'haddr_t'
Platforms tested:
h5committested
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Version update
Description:
Removed 1.4 compatibility code in the library.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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Description: 1.4 compatibility for H5G_obj_t type and H5Zregister test.
Solution: use macro H5_WANT_H5_V1_4_COMPAT
Platforms tested: h5committest
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Code cleanup
Description:
Remove some cruft left over from the switch from int->H5G_obj_t
Platforms tested:
FreeBSD 4.8 (sleipnir), triple check not necessary.
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Purpose: A little code rewriting
Description: object types were defined as macros in H5Gpublic.h
Solution: changed them to enumerate type
Platforms tested: h5committtest
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Update
Description:
Updated copyright statement in files which hadn't been updated yet.
Platforms tested:
Linux (Only comment change)
Misc. update:
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Purpose:
new functions
Description:
H5Gget_num_objs, H5Gget_objname_by_idx and H5Gget_objtype_by_idx.
Platforms tested:
modi4, arabica, eirene
Misc. update:
RELEASE.txt updated.
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Purpose:
__DLL__ is a keyword in some platforms and __DLL__ is also defined as a macro for windows DLL applications.
That causes problems.
Description:
Solution:
Use H5_DLL*** to replace __DLL***__ at all header files.
Change the macro defination at H5api_adpt.h.
Platforms tested:
linux2.2.18smp, irix64, solaris 2.7 and windows 2000
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Purpose:
New feature
Description:
Allow H5Glink and H5Gmove to handle links across different locations.
Solution:
Added H5Glink2 and H5Gmove2 functions with new parameter of destination
location.
Platforms tested:
Linux 2.2(eirene)
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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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Code update
Description:
Remove ragged array code & tests from library before release.
Platforms tested:
FreeBSD 4.2 (hawkwind)
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----------------------
./src/H5.c
Fixed more dependency problems in H5_term_library(). There was
a bug in the previous version that could cause the wrong EOF
marker to be written to the boot block under certain
circumstances. Hopefully this fixes it although I don't ready
access to a test case (Mark Miller will test it).
./src/H5F.c
./src/H5Fprivate.h
Added an H5F_close_all() that is similar to
H5F_term_interface() but which doesn't close the
interface. Files that don't have open object headers are
closed, others are delayed until all object headers close. All
files are flushed.
./src/H5ACprivate.h
./src/H5Bprivate.h
./src/H5Dprivate.h
./src/H5Eprivate.h
./src/H5Fprivate.h
./src/H5Gpkg.h
./src/H5Gprivate.h
./src/H5Gpublic.h
./src/H5HGprivate.h
./src/H5HLprivate.h
./src/H5Iprivate.h
./src/H5MFprivate.h
./src/H5MMprivate.h
./src/H5Oprivate.h
./src/H5Pprivate.h
./src/H5Ppublic.h
./src/H5RAprivate.h
./src/H5Sprivate.h
./src/H5Spublic.h
./src/H5Tpkg.h
./src/H5Tprivate.h
./src/H5Tpublic.h
./src/H5Vprivate.h
./src/H5Zprivate.h
./src/H5private.h
./src/H5public.h
Reindented after __DLL__ was added.
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----------------------
./configure.in
./acconfig.h
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
./src/H5public.h
./src/H5Omtime.c
Check for <stddef.h>
Checks for `__tm_gmtoff' in `struct tm' because old versions
of GNU libc are different than recent versions. This fixes the
failing mtime test.
./bin/config.guess
./config/freebsd2.2.7 [REMOVED]
./config/freebsd [ADDED]
Changed the name so it works with all versions of FreeBSD.
./src/H5.c
Moved H5F after H5T and H5G in H5_term_library() to satisfy
dependencies.
./src/H5G.c
Fixed a bug that caused H5Gcreate() to fail if the group name
had trailing slashes.
./src/H5Gpublic.h
Changed `group_name' to `name' in a prototype.
./src/Makefile.in
Dynamic library on Linux, but needs for work to be generally
useful.
./src/H5HG.c
./src/H5HGprivate.h
Fixed alignment problems when using old GCC compilers (like
the one shipped with RedHad Linux).
./tools/h5ls.c
Fixed a bug where the contents of the root group could be
listed twice if there was a link back to the root
group. Similarly for groups that are mentioned on the command
line.
Fixed a bug where unknown types were printed with a random
type class number.
./src/H5T.c
./src/H5Tconv.c
./src/H5Tprivate.h
Fixed O(log N) conversion bugs.
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changed the HDF5DLL and HDF5GLOBAL to __DLL__ and __DLLVAR__
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----------------------
./bin/snapshot
Made same fix as for the release script yesterday.
./src/H5D.c
./src/H5Dprivate.h
./src/H5G.c
./src/H5Gprivate.h
./src/H5Gpublic.h
./src/H5O.c
./src/H5Oprivate.h
./src/H5RA.c
./src/H5RAprivate.h
./src/H5T.c
./src/H5Tprivate.h
Improved object type checking. Instead of determining the
object type by trying to open each of the possible types, we
keep a table of associations between object type number (like
H5G_GROUP, H5G_DATASET, H5D_TYPE, and H5D_RAGGED) and an `isa'
function that returns true if the object header has the right
messages to make the object a particular type. This mechanism
also allows specialization of object types by permitting an
object to satisfy more than one `isa' function.
Added `isa' functions for groups, datasets, ragged arrays, and
committed data types.
./src/H5config.h.in
Added HAVE_STAT_ST_BLOCKS. I thought this had already been
added, but apparently not.
./tools/h5ls.c
Removed system include files since they're already included by
H5private.h and since I wasn't including them portably anyway.
By default, 1-byte integer types are printed as integer values
instead of ASCII characters. However, the `-s' or `--string'
command-line switch causes the data to be interpretted as
ASCII. String data types are always printed as character
data.
Ragged arrays are now identified as ragged arrays and h5ls
doesn't descend into the group automatically. This uses the
new object type specialization stuff.
./tools/h5tools.c
./tools/h5tools.h
Added the ability to print 1-byte integer types as either
ASCII or numeric data instead of always ASCII. The default is
to print as numeric data.
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----------------------
./src/H5F.c
./src/H5Fprivate.h
./src/H5G.c
./src/H5Gpkg.h
./src/H5Gprivate.h
./src/H5Gpublic.h
./test/istore.c
./test/tstab.c
Removed CWG functionality.
./tools/Makefile.in
Added `_test' where I added `test' last week. Maybe now the
snapshots will start up again...
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H5Gget_objinfo
and renamed internal functions to match up with the renamed API functions.
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----------------------
./src/H5G.c
Fixed a link count on groups. Groups were always created with
a link count of zero instead of one.
./src/H5Gpublic.h
Added H5G_NTYPES so applications can easily declare arrays
which are indexed by object type.
./src/H5O.c
Calling `H5O_link(&ent,0)' will succeed when the file is open
for read only because it's the only way to get the object's
current link count.
./tools/h5ls.c
Can take non-group object names on the command line (and
multiple objects). Reorganized to be more extendible. The
link count is displayed for `-v'.
./src/H5F.c
Dumping of cache statistics is controlled by only the
HDF5_DEBUG environment variable and not the H5F_ACC_DEBUG flag
for H5Fopen() and H5Fcreate() since this makes it similar to
the other debugging options.
./src/H5R.c
./test/ragged.c
./test/Makefile.in
Tests pass but still a little work left to be done.
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----------------------
./src/H5G.c
./src/H5Gpublic.h
./test/links.c
Fixed a bug in H5Gstat() that caused the wrong information to
be returned sometimes. Added check for named data types.
./test/extend.c
./test/links.c
./test/mtime.c
Added `all tests passed' messages.
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----------------------
./MANIFEST
./doc/html/H5.format.html
./src/H5O.c
./src/H5Oprivate.h
./src/H5Omtime.c [NEW]
./src/H5private.h
./src/Makefile.in
Added the modification time message. If an object header has
this message then it's value is updated with the current time
whenever anything changes in the object header.
./acconfig.h
./configure.in
Alas, there seems to be no standard way to convert a string
time like 19980727122800 in UTC to a time_t since mktime()
only converts local times to time_t. So I've modified the
configuration to check for various ways of getting the time
zone information:
* Added checks for the `tm_gmtoff' field of `struct tm'.
* Added a check for the `timezone' global variable.
* Added a check for `struct timezone'.
* Added a check for BSDgettimeofday().
* Added a check for gettimeofday() although it doesn't
actually set the timezone argument on some systems.
* Added a check to see if `tm_zone' is a member of `struct tm'.
* Added a check to see if `tzname' is a global variable.
* Added a check to see if `struct tm' is defined in time.h
or sys/time.h.
It's not difficult to get the right UTC modification message
into the object header, but some systems might have problems
getting the right time back out (Irix64 is one) and those
systems will report zero for the H5G_stat_t.mtime from an
H5Gstat() call as if the mtime message isn't even present. It
will, however, continue to be updated as normal.
./src/H5G.c
./src/H5Gpublic.h
The H5G_stat_t struct now contains an `mtime' field which will
hold the object modification time. If the object has no
object modification time then the `mtime' will be initialized
to zero.
Fixed a bug in H5G_stat() that caused the `objno' field of the
H5G_stat_t to be set incorrectly on some machines.
./src/H5D.c
Writing to external datasets fail if the hdf5 file is not open
for writing.
A modification time message is added to the dataset object
header when it's created and H5O_touch() is called from
H5D_write() to update that message.
./src/H5T.c
Fixed a bug in H5Tget_member_dims() that caused a segmentation
fault if one of the output array arguments was the null
pointer.
Relaxed the member dimension checking in H5Tinsert_array() so
it can also be used for scalar members.
./test/Makefile.in
Added additional file names to the `mostlyclean' target.
./tools/h5dump.c
./tools/h5tools.h
Increased the temporary buffer size to 1MB.
Added support for printing compound data types with array
members.
When printing H5T_NATIVE_CHAR and H5T_NATIVE_UCHAR we escape
double quote characters.
./tools/h5ls.c
Changed the output format a little because we were starting to
get too much info to fit on a line. Without `--verbose' each
object occupies one line of output. Otherwise, additional
information is printed below the object name: object file
address, comment, and modification time. If `--dump' is given
then the data is printed after the other information.
./test/cmpd_dset.c
Changed the way the dataset is initialized to be more uniform.
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----------------------
./src/H5A.c
./src/H5Apublic.h
./test/tattr.c
Switched the order of the second and third argument of
H5Aget_name() to make it consistent with other functions that
take buffers and buffer sizes.
./src/H5G.c
./src/H5Gpublic.h
./src/H5Gprivate.h
The H5Gget_comment() function returns the size of the comment
including the null terminator. If the object has no comment
then zero is returned. If an error occurs then a negative
value is returned.
./MANIFEST
./tools/Makefile.in
./tools/h5tools.h [NEW]
./tools/h5dump.c [NEW]
Created a library for printing values of datasets in a way
that looks nice. It's not done yet, but I needed it for
debugging the contents of files from Jim Reus.
./tools/h5ls.c
Added the `-d' and `--dump' options which cause the contents
of a dataset to be printed. Added `-w N' and `--width=N'
options to control how wide the raw data output should be. If
you want single-column output then say `-w1'.
Printing dataset values can now handle datasets of any integer
or floating point atomic type. As a special case, integers
which are one byte wide are treated a character strings for
now.
Sample output:
$ h5ls --dump --width=60 banana.hdf
ARCHIVE 0:0:0:744 Dataset {52/Inf}
Data:
(0) "U struct complex { double R; double I; };\012V"
(43) " double;\012"
U 0:0:0:2500 Dataset {256/512}
Data: printing of compound data types is not implemented yet
V 0:0:0:3928 Dataset {256/512}
Data:
(0) 0, 0.015625, 0.03125, 0.046875, 0.0625,
(5) 0.078125, 0.09375, 0.109375, 0.125, 0.140625,
(10) 0.15625, 0.171875, 0.1875, 0.203125, 0.21875,
(15) 0.234375, 0.25, 0.265625, 0.28125, 0.296875,
...
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