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ChangeLog
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2011-03-21 Andrew L Janke <a.janke@gmail.com
* Shifted from cvs to git
* Clean up off documentation
* Removed Batch.pm as it was causing more problems than it's worth
and with the shift to neuro.debian.net it's something that we
just dont want
* Removing anything to do with batch processing from Spawn.pm
2007-09-14 Claude Lepage <claude@bic.mni.mcgill.ca>
* fixed get_dimension_order to report proper dimension order with minc2
2001-07-11 Chris COCOSCO <crisco@luciana.bic.mni.mcgill.ca>
* MNI/TagPoint.pm (new) : weight, structure_id, structure_id
now initialized by default to 'undef' (makes more sense this
way...)
2001-07-04 Chris COCOSCO <crisco@feeble.bic.mni.mcgill.ca>
* MNI/TagSet.pm (load) : fixed input parsing to match the tag
file format as defined by the volume_io documentation
* MNI/TagPoint.pm (to_string) : fixed output to match what
volume_io is doing
* MNI/TagSet.pm (find_tag): new function
* MNI/TagSet.pm (fast_find_tag): new function
2001-06-11 Steve M. Robbins <steve@nyongwa.montreal.qc.ca>
* MNI/Batch.pm (JobStatus): Set verbose and execute options for
the spawner. Cache "baq" output for 60 seconds to avoid invoking
this command too often (it is slow).
2001-06-11 Steve M. Robbins <steve@nyongwa.montreal.qc.ca>
* MNI/Batch.pm (_emit_syncfile_shellcode): Use "touch" and "mv"
to create syncfile; avoids problems if "touch" wants to examine
the file after creating it (SGI does this). Thanks to Chris
for uncovering this.
2001-06-09 Chris Cocosco <crisco@bic.mni.mcgill.ca>
* MNI/Spawn.pm (set_undefined_option): also try main::$varname if
the calling package doesn't define/export $varname (bugfix for
MNI/Batch.pm::JobStatus)
2001-02-26 Steve M. Robbins <steve@nyongwa.montreal.qc.ca>
* MNI/Batch.pm (GetJobid): New. Returns ID of currently-open job.
* MNI.pm: Set VERSION to 0.07.
* MNI/Batch.pm (JobStatus): New. Return status of job, as
determined by "baq".
2000-09-22 Steve ROBBINS <stever@bic.mni.mcgill.ca>
* MNI/TagSet.pm (new): option name is `comment' not `comments'.
(get_point): bugfix; used `grep' where should have used `map'.
Localize all usages of `$_'.
2000-09-19 Steve ROBBINS <stever@bic.mni.mcgill.ca>
* MNI/TagSet.pm:
* MNI/TagPoint.pm: new. Future replacement of MNI::Tag.
A TagSet corresponds to a `.tag' file; it holds a list of
TagPoint objects. The TagPoint objects allow read access to
all fields in the tag.
* t/tag.t: new. Exercise the MNI::TagSet.
2000-09-14 Steve Robbins <steve@nyongwa.montreal.qc.ca>
* MNI/Tag.pm: add POD documentation of all user-level functions.
2000-04-11 Steve ROBBINS <stever@bic.mni.mcgill.ca>
* MNI/Tag.pm (_volume): change diagnostics.
2000-03-13 Steve ROBBINS <stever@bic.mni.mcgill.ca>
* MNI/Batch.pm (StartJob): don't clear entire set of SyncFiles,
only the ones corresponding to the PID of the starting job.
(Synchronize): fix bug that prevented counting number of outstanding
jobs; reported by Jason Lerch.
* t/batch-2.t: new. Test Synchronize() function.
2000-02-21 Steve Robbins <steve@nyongwa.montreal.qc.ca>
* MNI/Startup.pm (startup): if TMPDIR is not defined, check for /usr/tmp,
/var/tmp, and /tmp; use the first directory found for TmpDir.
Sun Jan 16 15:37:54 2000 Steve Robbins <steve@nyongwa.montreal.qc.ca>
* MNI.pm: bump VERSION to 0.06.
Sun Jan 16 15:16:02 2000 Steve Robbins <steve@nyongwa.montreal.qc.ca>
* MNI/Tag.pm (load, save): qualify `open' and `close' calls with CORE:: to
distinguish them from Tag::open and Tag::close.
Sun Jan 16 14:58:54 2000 Steve Robbins <steve@nyongwa.montreal.qc.ca>
* NEWS: new file. Summary of USER-visible changes between
releases.
* MNI/Batch.pm (StartJob): clear %SyncFiles before assigning to it
when starting new job; otherwise old values for same JobPID will
be returned.
* t/batch-0.t: new file. Test basic features of MNI::Batch.pm,
mostly the return values.
* t/batch-1.t: renamed from 'batch.t' in order that it be executed
_after_ batch-0.t.
* MNI/Batch.pm (QueueCommands): return startfile (if StartJob
called), along with finish and fail files.
Sat Dec 18 08:55:23 1999 Steve Robbins <steve@nyongwa.montreal.qc.ca>
* MNI/Batch.pm (_queue_one_command): bugfix. If passed an array
ref, take program name from first element of array to avoid
becoming confused by shellquote's quoting of metacharacters.
Fri Dec 17 17:59:20 1999 Steve Robbins <steve@nyongwa.montreal.qc.ca>
* MNI/Batch.pm (_queue_one_command): code reorganization; there is
now no useful return value.
* MNI/Batch.pm (QueueCommands): code reorganization; clean up pod
documentation.
* MNI/Batch.pm (Synchronize): code reorganization and bugfix. The
old computation for $numjobs overcounted in the case that some
jobs synchronize on 'start' and some synchronize on 'finish'. We
now count just the jobs that synchronize for the desired
condition.
* MNI/Batch.pm (FinishJob): code reorganization; now returns
array of filenames (finishfile, failfile). For backwards
compatibility, returns scalar finishfile in scalar context.
* MNI/Batch.pm (StartJob): code reorganization, no semantic
changes.
* MNI/Batch.pm (_emit_rmtmpdir_shellcode):
* MNI/Batch.pm (_emit_mktmpdir_shellcode):
* MNI/Batch.pm (_emit_syncfile_shellcode): new. Write shell
code to BATCH filehandle.
* MNI/Batch.pm (_set_syncfile_name): new. Generate syncfile
name for given condition and store in %SyncFiles.
* MNI/Batch.pm (create_sync_file): split into two subroutines:
_set_syncfile_name and _emit_syncfile_shellcode.
* MNI/Batch.pm (_syncfile_name): renamed to _get_syncfile_name;
$pid defaults to $JobPID if not specified.
* t/batch.t (wait_for_files): test that StartJob() returns a
defined start file and that FinishJob() returns (in scalar
context) a defined finish file.
Thu Dec 9 16:52:04 1999 Steve ROBBINS <stever@bic.mni.mcgill.ca>
* MNI/Tag.pm (copy): croak if copy is not invoked on a valid
reference.
1999-12-02 Chris Cocosco <crisco@bic.mni.mcgill.ca>
* MNI/Batch.pm: functionality changes!
= 'fail' sync files are now _not_ created unless the "synchronize"
option is set to 'finish' or 'both'.
= "syncdir" now defaults to './.sync' if 'HOME' is not defined in
the environment (which is the case for CGI scripts for example)
1999-12-02 Chris Cocosco <crisco@bic.mni.mcgill.ca>
* MNI/Batch.pm: new option: 'batch_reports'
("should the underlying batch process run in verbose mode?")
Unless the user explicitly sets it, this option defaults to
whatever value 'verbose' has.
[*Caveat*] the text produced by the underlying process goes to
STDOUT even if the 'verbose' text (which is produced by Batch.pm)
is redirected somewhere else by means of the 'loghandle' option
1999-11-30 Chris COCOSCO <crisco@thaisa.bic.mni.mcgill.ca>
* MNI/FileUtilities.pm (check_files): documentation fixes.
* MNI/Batch.pm: documentation fixes.
(set_undefined_option): made it more robust (now it
can properly handle the case when the calling package is
MNI::Spawn and not main:: )
(StartJob): fixed a bug related to set_undefined_option
* MNI/Spawn.pod: added a clarification about redirection clobber
when using batch.
1999-11-17 Chris COCOSCO <crisco@thaisa.bic.mni.mcgill.ca>
* MNI/Spawn.pm: added a carp warning about the redirection
clobber/append when running through batch.
Wed Oct 27 18:38:15 1999 Steve ROBBINS <stever@bic.mni.mcgill.ca>
* MNI/Batch.pm (create_sync_file): use underscore rather than
period to sanitize names; files with leading periods are a
nuisance to find using 'ls'.
Tue Oct 26 13:24:13 1999 Steve ROBBINS <stever@bic.mni.mcgill.ca>
* MNI/Tag.pm (save): don't use self->{_comments} if it
isn't defined.
* MNI/Batch.pm (create_sync_file): sanitize sync file names by
replacing any non-safe character with a period.
Fri Oct 22 17:47:24 1999 Steve ROBBINS <stever@bic.mni.mcgill.ca>
* t/batch.t (test): register programs spawned during the tests.
* MNI/Batch.pm (QueueCommands): now returns *both* the fail file
and the finish file names. For backwards compatibilty, only the
finish file is returned in scalar context.
Thu Oct 14 18:34:16 1999 Steve ROBBINS <stever@bic.mni.mcgill.ca>
* MNI/Tag.pm: add code to update tag coordinates and write tags to
file. The tag code still ignores comments and "auxiliary" data.
* MNI/Tag.pm(new): for creating a new tag file; this is a change
in constructor semantics!
* MNI/Tag.pm(open): for opening existing tag file; this is what
the old "new" constructor did.
* t/example1.tag:
* t/tag.t: new files. Regression testing for MNI::Tag.
* preptest:
* preptest.sh:
* rlog.out: removed junk files.
Tue Oct 12 12:40:48 1999 Steve ROBBINS <stever@bic.mni.mcgill.ca>
* MNI/Batch.pm: typos in documentation.
Fri Aug 13 20:12:12 1999 Steve ROBBINS <stever@bic.mni.mcgill.ca>
* MNI/Tag.pm: new file. Manipulate tag files as perl objects.
Thu Aug 12 14:17:14 1999 Steve Robbins <steve@nyongwa.montreal.qc.ca>
* MNI/Batch.pm (_batch_optstring): fixed 'shell' option; forgot to
lowercase it when making the previous changes.
Wed Aug 11 19:46:41 1999 Steve ROBBINS <stever@bic.mni.mcgill.ca>
* MNI/Batch.pm: don't lexically scope ProgramName.
Sun Aug 8 17:11:58 1999 Steve Robbins <steve@nyongwa.montreal.qc.ca>
* MNI/Batch.pm (create_sync_file): take care when job_name is not
defined.
Sat Aug 7 16:58:16 1999 Steve Robbins <steve@nyongwa.montreal.qc.ca>
* MNI/Batch.pm: all package variables, other than @ISA,
@EXPORT_OK, and %EXPORT_TAGS localised with `my'. Option
identifiers changed to "lower_case_underscore_separated", the
style used in MNI::Spawn.
* MNI/Batch.pm (StartJob): all parameters are optional, passed in
"key => value" style. Return value changed to be the name of the
`start' sync file, if any; return value was previously the JobPID
(undocumented).
* MNI/Batch.pm (FinishJob): new option `close_delay' used if delay
not given as parameter. Return value is name of `finish' sync
file, if any.
* MNI/Batch.pm (QueueCommand): QueueCommand() will call StartJob
and FinishJob if no job open; no longer carps about this usage.
If QueueCommand calls FinishJob, the name of the `finish' sync
file, if any, is returned.
* MNI/Batch.pm (QueueCommands): if QueueCommands calls FinishJob,
the name of the `finish' sync file, if any, is returned.
* t/batch.t: updated to account for changes to Batch.pm; no new
test coverage.
Fri Aug 6 18:09:11 1999 Steve Robbins <steve@nyongwa.montreal.qc.ca>
* MNI/Spawn.pm (spawn): batch's QueueCommand option MergeErrors
became merge_stderr.
Tue Jul 27 19:00:42 1999 Steve ROBBINS <stever@bic.mni.mcgill.ca>
* MNI/Batch.pm (Synchronize): fix documentation of return value.
Return ref to empty array if not executing.
* MNI/Batch.pm: Allow `JobName', `StartAfter', `MergeErrors',
`stdout', and `stderr' as global options.
* MNI/Spawn.pm (spawn): change parameters for Batch::QueueCommand
call.
Thu Jul 22 19:52:36 1999 Steve ROBBINS <stever@bic.mni.mcgill.ca>
* MNI/Batch.pm (gen_batch_options, StartJob, QueueCommand): allow
overriding any option on a per-job basis. Implement `StartAfter'
option, passed on to batch as `-a'.
(StartJobAfter): removed function.
* t/batch.t: bugfix (start_batchtest) and changes related to above.
* MNI/Batch.pm (QueueCommands): compacted the code. No semantic
changes made.
Tue May 18 18:36:39 1999 Steve ROBBINS <stever@bic.mni.mcgill.ca>
* MNI/Batch.pm (StartJobAfter): experimental batch interface using
'-a' option to delay a job. This really ought to be specified
via Batch( job, After => whatever, ... ), like the Spawn interface.
Mon May 17 16:41:18 1999 Steve ROBBINS <stever@bic.mni.mcgill.ca>
* t/batch.t: added simple testing of StartJob, QueueCommand,
QueueCommands, and FinishJob. No testing of synchronization, yet.
* MNI/Batch.pm (QueueCommands): StartBatchJob --> StartJob typo
fixed. Expand documentation; all options documented.
Thu May 13 19:33:40 1999 Steve ROBBINS <stever@bic.mni.mcgill.ca>
* t/batch.t: new file. Start of MNI::Batch regression tests.
* MNI/Batch.pm (Synchronize): rearrange the code slightly. Returns
true if -noexecute.
* MNI/Batch.pm (QueueCommands): fix bug that prevented method
from working.
* MNI/Batch.pm: add pod documentation. Remove $fakeJobPID.
* MNI/Batch.pm (sync_file_name): folded into create_sync_file().
Wed May 12 18:52:39 1999 Steve ROBBINS <stever@bic.mni.mcgill.ca>
* MANIFEST: add MNI/Batch.pm.
Wed May 12 18:44:49 1999 Steve ROBBINS <stever@bic.mni.mcgill.ca>
* doc/.cvsignore: new file.
* doc/Makefile (SOURCE,TMPDIRS): remove Getopt stuff.
Wed May 12 18:23:10 1999 Steve ROBBINS <stever@bic.mni.mcgill.ca>
* .cvsignore:
* MNI/.cvsignore:
* t/.cvsignore: new files.
* MANIFEST: removed getopt-related files.
* Makefile.PL (PMLIBDIRS): removed Getopt.
Wed May 12 16:56:06 1999 Steve ROBBINS <stever@bic.mni.mcgill.ca>
* MNI/Batch.pm: new file.
* MNI/Spawn.pm: Chris Cocosco's batch enhancements, a port from
older batch code of Greg.
Wed May 12 16:51:54 1999 Steve ROBBINS <stever@bic.mni.mcgill.ca>
* ChangeLog: new file.
* Initial import of Greg Ward's MNI perl library. This is based
on the version 0.05 sources found in ~greg/src/libperl/mnilib/
with the following removals:
Getopt: released in own package ``Getopt::Tabular''.
Makefile.old: built file (from Makefile.PL)
junk: directory full of assorted test code
log2: contains the message `junk/shred: this goes to log2'
mni_perllib-0.05.tar.gz: tar package of code
t/getopt.pl: symlink to Getopt::Tabular test code