Fixed --header bug for multiline headers. +testsuite.

Allow for --timeout 200.5% (float).
--workdir . --transfer fixed.

README

@@ -30,7 +30,11 @@ The 10 seconds installation will try do to a full installation; if
 that fails, a personal installation; if that fails, a minimal
 installation.
 
-  wget -O - pi.dk/3 | sh
+  wget -O - pi.dk/3 | bash
+
+or:
+
+  curl pi.dk/3/ | bash  
 
 This will literally install faster than reading the rest of this
 document.

doc/release_new_version

@@ -209,6 +209,9 @@ New in this release:
   http://www.keylength.com/en/4/ the signing key was changed from
   1024D/ID:FFFFFFF1 to 9888R/ID:88888888.
 
+* Job ad asking for GNU Parallel expertise
+  http://seattle.craigslist.org/est/sof/4006079352.html
+
 * Agalma: an automated phylogenomics workflow
   http://arxiv.org/pdf/1307.6432
 

src/parallel

@@ -305,12 +305,13 @@ sub spreadstdin {
     my $buf = "";
     my $header = "";
     if($opt::header) {
-	my $non_greedy_regexp = $opt::header;
+	if($opt::header eq ":") { $opt::header = "(.*\n)"; }
-	# ? , * , + , {} => ?? , *? , +? , {}?
+	# Number = number of lines
-	$non_greedy_regexp =~ s/(\?|\*|\+|\})/$1\?/g;
+	$opt::header =~ s/^(\d+)$/"(.*\n)"x$1/e;
 	while(read(STDIN,substr($buf,length $buf,0),$opt::blocksize)) {
-	    if($buf=~s/^(.*?$non_greedy_regexp)//) {
+	    if($buf=~s/^($opt::header)//) {
-		$header = $1; last;
+		$header = $1; 
+		last;
 	    }
 	}
     }
@@ -424,9 +425,8 @@ sub spreadstdin {
 		$blocksize = ceil($blocksize * 1.3 + 1);
 		::warning("A full record was not matched in a block. Increasing to --blocksize ".$blocksize."\n");
 	    }
-	}
+	} 
     }
-
     # If there is anything left in the buffer write it
     substr($buf,0,0) = "";
     write_record_to_pipe($chunk_number++,\$header,\$buf,$recstart,$recend,length $buf);
@@ -482,7 +482,7 @@ sub round_robin_write {
 	    if($job->stdin_buffer_length() > 0) {
 		$something_written += $job->non_block_write();
 	    } else {
-		$job->set_stdin_buffer($block_ref,$endpos,$recstart,$recend);
+		$job->set_stdin_buffer($header_ref,$block_ref,$endpos,$recstart,$recend);
 		$block_passed = 1;
 		$job->set_virgin(0);
 		$something_written += $job->non_block_write();
@@ -626,7 +626,7 @@ sub options_hash {
 	 "B=s" => \$opt::retired,
 	 "ctrlc|ctrl-c" => \$opt::ctrlc,
 	 "noctrlc|no-ctrlc|no-ctrl-c" => \$opt::noctrlc,
-	 "workdir|wd=s" => \$opt::workdir,
+	 "workdir|work-dir|wd=s" => \$opt::workdir,
 	 "W=s" => \$opt::retired,
 	 "tmpdir=s" => \$opt::tmpdir,
 	 "tempdir=s" => \$opt::tmpdir,
@@ -820,8 +820,9 @@ sub parse_options {
     if(defined $opt::fg) { $Global::semaphore = 1; }
     if(defined $opt::bg) { $Global::semaphore = 1; }
     if(defined $opt::wait) { $Global::semaphore = 1; }
-    if(defined $opt::timeout and $opt::timeout !~ /^\d+%?$/) {
+    if(defined $opt::timeout and $opt::timeout !~ /^\d+(\.\d+)?%?$/) {
 	::error("--timeout must be seconds or percentage\n");
+	wait_and_exit(255);
     }
     if(defined $opt::minversion) {
 	print $Global::version,"\n";
@@ -3739,8 +3740,8 @@ sub write {
 
 sub set_stdin_buffer {
     my $self = shift;
-    my ($block_ref,$endpos,$recstart,$recend) = @_;
+    my ($header_ref,$block_ref,$endpos,$recstart,$recend) = @_;
-    $self->{'stdin_buffer'} = substr($$block_ref,0,$endpos);
+    $self->{'stdin_buffer'} = ($self->virgin() ? $$header_ref : "").substr($$block_ref,0,$endpos);
     if($opt::remove_rec_sep) {
 	remove_rec_sep(\$self->{'stdin_buffer'},$recstart,$recend);
     }
@@ -3786,10 +3787,11 @@ sub non_block_write {
 	} else {
 	    # successfully wrote everything
 	    my $a="";
-	    $self->set_stdin_buffer(\$a,0,"","");
+	    $self->set_stdin_buffer(\$a,\$a,"","");
 	    $something_written = $rv;
 	}
     }
+
     ::debug("Non-block: $something_written");
     return $something_written;
 }
@@ -4231,7 +4233,7 @@ sub workdir {
 		my $home = $ENV{'HOME'};
 		eval 'use Cwd';
 		my $cwd = cwd();
-		$opt::workdir = $cwd;
+		$workdir = $cwd;
 		if($home) {
 		    # If homedir exists: remove the homedir from
 		    # workdir if cwd starts with homedir
@@ -4247,7 +4249,7 @@ sub workdir {
 			my ($parent_dev, $parent_ino) = (stat($parent))[0,1];
 			if($parent_dev == $home_dev and $parent_ino == $home_ino) {
 			    # dev and ino is the same: We found the homedir.
-			    $opt::workdir = join("/",@dir_parts);
+			    $workdir = join("/",@dir_parts);
 			    last;
 			}
 		    }
@@ -5842,12 +5844,11 @@ package TimeoutQueue;
 sub new {
     my $class = shift;
     my $delta_time = shift;
-    my ($pct,$avg_damper);
+    my ($pct);
-    if($delta_time =~ /(\d+)%/) {
+    if($delta_time =~ /(\d+(\.\d+)?)%/) {
 	# Timeout in percent
 	$pct = $1/100;
 	$delta_time = 1_000_000;
-	$avg_damper = (1-0.001)/0.9;
     }
     return bless {
 	'queue' => [],

src/parallel.pod

@@ -553,15 +553,18 @@ status will be the exit status from the failing job.
 =back
 
 
-=item B<--header> I<regexp>
+=item B<--header> I<regexp> (alpha testing)
 
-Use upto regexp as header. For normal usage the matched header
+Use regexp as header. For normal usage the matched header (typically
-(typically the first line: B<--header '\n'>) will be split using
+the first line: B<--header '.*\n'>) will be split using B<--colsep>
-B<--colsep> (which will default to '\t') and column names can be used
+(which will default to '\t') and column names can be used as
-as replacement variables: B<{column name}>. For B<--pipe> the matched
+replacement variables: B<{column name}>.
-header will be prepended to each output.
 
-B<--header :> is an alias for B<--header '\n'>.
+For B<--pipe> the matched header will be prepended to each output.
+
+B<--header :> is an alias for B<--header '.*\n'>.
+
+If I<regexp> is a number, it will match that many lines.
 
 
 =item B<-I> I<replace-str>

src/parallel.texi

@@ -584,16 +584,19 @@ status will be the exit status from the failing job.
 
 @end table
 
-@item @strong{--header} @emph{regexp}
+@item @strong{--header} @emph{regexp} (alpha testing)
-@anchor{@strong{--header} @emph{regexp}}
+@anchor{@strong{--header} @emph{regexp} (alpha testing)}
 
-Use upto regexp as header. For normal usage the matched header
+Use regexp as header. For normal usage the matched header (typically
-(typically the first line: @strong{--header '\n'}) will be split using
+the first line: @strong{--header '.*\n'}) will be split using @strong{--colsep}
-@strong{--colsep} (which will default to '\t') and column names can be used
+(which will default to '\t') and column names can be used as
-as replacement variables: @strong{@{column name@}}. For @strong{--pipe} the matched
+replacement variables: @strong{@{column name@}}.
-header will be prepended to each output.
 
-@strong{--header :} is an alias for @strong{--header '\n'}.
+For @strong{--pipe} the matched header will be prepended to each output.
+
+@strong{--header :} is an alias for @strong{--header '.*\n'}.
+
+If @emph{regexp} is a number, it will match that many lines.
 
 @item @strong{-I} @emph{replace-str}
 @anchor{@strong{-I} @emph{replace-str}}

testsuite/tests-to-run/parallel-local23.sh

@@ -33,6 +33,18 @@ stdout /usr/bin/time -f %e parallel --delay 2 true ::: 1 2 3 | perl -ne '$_ >= 4
 echo '### Exit value should not be affected if an earlier job times out'
   parallel -j2 --timeout 1 --joblog - -k  ::: "sleep 10" "exit 255" | field 7
 
+echo '### --header regexp'
+  (echo %head1; echo %head2; seq 5) | nice parallel -kj2 --pipe -N2 --header '(%.*\n)*' echo JOB{#}\;cat
+
+echo '### --header num'
+  (echo %head1; echo %head2; seq 5) | nice parallel -kj2 --pipe -N2 --header 2 echo JOB{#}\;cat
+
+echo '### --header regexp --round-robin'
+  (echo %head1; echo %head2; seq 5) | nice parallel -kj2 --pipe -N2 --round --header '(%.*\n)*' echo JOB{#}\;cat
+
+echo '### --header num --round-robin'
+  (echo %head1; echo %head2; seq 5) | nice parallel -kj2 --pipe -N2 --round --header 2  echo JOB{#}\;cat
+
 EOF
 
 rm -rf tmp

testsuite/tests-to-run/parallel-remote1.sh

@@ -14,3 +14,7 @@ seq 1 100 | parallel --sshlogin "/tmp/myssh1 $SSHLOGIN1, /tmp/myssh2 $SSHLOGIN2"
 
 echo '### --filter-hosts - OK, non-such-user, connection refused, wrong host'
   parallel --nonall --filter-hosts -S localhost,NoUser@localhost,154.54.72.206,"ssh 5.5.5.5" hostname
+
+echo '### test --workdir . in $HOME'
+  cd && mkdir parallel-test && cd parallel-test && 
+    echo OK > testfile && parallel --workdir . --transfer -S $SSHLOGIN1 cat {} ::: testfile

testsuite/wanted-results/parallel-local23

@@ -52,3 +52,57 @@ OK
 Exitval
 -1
 255
+### --header regexp
+JOB1
+%head1
+%head2
+1
+2
+JOB2
+%head1
+%head2
+3
+4
+JOB3
+%head1
+%head2
+5
+### --header num
+JOB1
+%head1
+%head2
+1
+2
+JOB2
+%head1
+%head2
+3
+4
+JOB3
+%head1
+%head2
+5
+### --header regexp --round-robin
+JOB1
+%head1
+%head2
+3
+4
+JOB2
+%head1
+%head2
+1
+2
+5
+### --header num --round-robin
+JOB1
+%head1
+%head2
+1
+2
+5
+JOB2
+%head1
+%head2
+3
+4