parallel: --header with {colnames} for multiple :::'s

configure.ac

@@ -1,4 +1,4 @@
-AC_INIT([parallel], [20111222], [bug-parallel@gnu.org])
+AC_INIT([parallel], [20120122], [bug-parallel@gnu.org])
 AM_INIT_AUTOMAKE([-Wall -Werror foreign])
 AC_CONFIG_HEADERS([config.h])
 AC_CONFIG_FILES([

doc/promo

@@ -25,7 +25,7 @@ http://nd.gd/0s http://www.youtube.com/watch?v=OpaiGYxkSuQ
 http://nd.gd/0t http://en.wikipedia.org/wiki/Xargs#The_separator_problem
 http://nd.gd/3k http://www.gnu.org/software/parallel/man.html#differences_between_xargs_and_gnu_parallel
 http://nd.gd/po http://www.gnu.org/software/parallel/man.html#example__distributing_work_to_local_and_remote_computers
-http://nd.gd/039 http://www.youtube.com/playlist?list=PL284C9FF2488BC6D1
+http://ur1.ca/7h7yx http://www.youtube.com/playlist?list=PL284C9FF2488BC6D1
 
 If you like xargs you may love GNU Parallel: http://nd.gd/0s
 
@@ -64,7 +64,8 @@ You can install GNU Parallel simply by:
     chmod 755 parallel
     cp parallel sem
 
-Watch the intro videos for GNU Parallel to learn more: http://nd.gd/039
+Watch the intro videos for GNU Parallel to learn more:
+https://www.youtube.com/playlist?list=PL284C9FF2488BC6D1
 
 
 GNU Parallel also makes it possible to run small scripts. Try this:

doc/release_new_version

@@ -185,27 +185,42 @@ cc:Sandro Cazzaniga <kharec@mandriva.org>,
    Ryoichiro Suzuki <ryoichiro.suzuki@gmail.com>,
    Jesse Alama <jesse.alama@gmail.com>
 
-Subject: GNU Parallel 20120122 ('Fhqwhgads') released
+Subject: GNU Parallel 20120122 ('Dead SOPA') released
 
-GNU Parallel 20120122 ('Fhqwhgads') has been released. It is
+GNU Parallel 20120122 ('Dead SOPA') has been released. It is
 available for download at: http://ftp.gnu.org/gnu/parallel/
 
 New in this release:
 
-* niceload now propagates exit status correctly. Passes testsuite.
+* --header : uses the first input line as column names and you can
+  then use {colname} as a replacement string in the command. This also
+  works with multiple :::'s.
 
-* Show your support for GNU Parallel. For 20 EUR incl world wide
+* --header <regexp> matches a header as a regular expression and
-  shipping get a GNU Parallel T-shirt+mug+pen+100 postcards. Email
+  repeats the header for each block with --pipe.
-  your shirt size and address for details to
-  parallel-support@tange.dk.
 
-* --header uses the first input line as column names and you can then
+* --resume resumes from the last unfinished job. Useful if you stop
-  use {colname} as a replacement string in the command.
+  GNU Parallel and restart it later with the same arguments.
 
-* --resume resumes from the last unfinished job.
+* niceload now propagates exit status correctly.
+
+* Show your support for GNU Parallel. For a limited time you can get a
+  GNU Parallel T-shirt+mug+pen+100 postcards at 20 EUR. See
+  https://www.gnu.org/software/parallel/merchandise.html
 
 * Options -g -B -T -U -W -Y are retired as warned 6 months ago.
 
+* GNU Parallel referenced in article on Holographic Grid Cloud. Thanks
+  to Stefano Gallozzi. http://arxiv.org/pdf/1112.6128
+
+* Article in IEEE Software on GNU Parallel. Thanks to Diomidis
+  Spinellis.  http://www.spinellis.gr/blog/20110911/
+
+* An article on Narwhal which uses GNU Parallel. They forgot to add
+  the reference. Please remember --bibtex if you use GNU Parallel in
+  an article. 
+  http://bioinformatics.oxfordjournals.org/content/early/2011/11/08/bioinformatics.btr613.full.pdf
+
 * Blog post on using GNU Parallel to speed up BLAST queries:
   http://blog.mckuhn.de/2012/01/embarrassingly-parallel-blast-search.html
 

src/niceload

@@ -24,7 +24,7 @@
 use strict;
 use Getopt::Long;
 $Global::progname="niceload";
-$Global::version = 20111222;
+$Global::version = 20120122;
 Getopt::Long::Configure("bundling","require_order");
 get_options_from_array(\@ARGV) || die_usage();
 if($::opt_version) {

src/parallel

@@ -74,18 +74,20 @@ if($::opt_skip_first_line) {
 }
 if($::opt_header and not $::opt_pipe) {
     my $fh = $fhlist[0];
-    my $line = <$fh>;
-    chomp($line);
     # split with colsep or \t
     # TODO should $header force $colsep = \t if undef?
     my $delimiter = $::opt_colsep;
     my $id = 1;
+    for my $fh (@fhlist) {
+	my $line = <$fh>;
+	chomp($line);
 	::debug("Delimiter: '$delimiter'");
 	for my $s (split /$delimiter/o, $line) {
 	    ::debug("Colname: '$s'");
 	    $command =~ s:\{$s(|/|//|\.|/\.)\}:\{$id$1\}:g;
 	    $id++;
 	}
+    }
 }
 
 if($::opt_nonall or $::opt_onall) {
@@ -541,7 +543,7 @@ sub get_options_from_array {
 sub parse_options {
     # Returns: N/A
     # Defaults:
-    $Global::version = 20120113;
+    $Global::version = 20120122;
     $Global::progname = 'parallel';
     $Global::infinity = 2**31;
     $Global::debug = 0;

src/parallel.pod

@@ -1382,6 +1382,8 @@ Compare these two:
   parallel echo {1} {2} ::: 1 2 3 ::: a b c
   parallel --xapply echo {1} {2} ::: 1 2 3 ::: a b c
 
+See also B<--header>.
+
 
 =item B<--shebang>
 
@@ -1688,30 +1690,6 @@ can be written like this:
 B<cat list | parallel "do_something {} scale {.}.jpg ; do_step2 <{} {.}" | process_output>
 
 
-=head1 EXAMPLE: Using shell variables
-
-When using shell variables you need to quote them correctly as they
-may otherwise be split on spaces.
-
-Notice the difference between:
-
- V=("My brother's 12\" records are worth <\$\$\$>"'!' Foo Bar)
- parallel echo ::: ${V[@]} # This is probably not what you want
-
-and:
-
- V=("My brother's 12\" records are worth <\$\$\$>"'!' Foo Bar)
- parallel echo ::: "${V[@]}"
-
-When using variables in the actual command that contains special
-characters (e.g. space) you can quote them using B<'"$VAR"'> or using
-"'s and B<-q>:
-
- V="Here  are  two "
- parallel echo "'$V'" ::: spaces
- parallel -q echo "$V" ::: spaces
-
-
 =head1 EXAMPLE: Rewriting nested for-loops
 
 Nested for-loops like this:
@@ -1739,6 +1717,44 @@ can be written like this:
 B<parallel echo {1} {2} ::: M F ::: S M L XL XXL | sort>
 
 
+=head1 EXAMPLE: for-loops with column names
+
+When doing multiple nested for-loops it can be easier to keep track of
+the loop variable if is is named instead of just having a number. Use
+B<--header :> to let the first argument be an named alias for the
+positional replacement string:
+
+  parallel --header : echo {gender} {size} ::: gender M F ::: size S M L XL XXL
+
+This also works if the input file is a file with columns:
+
+  cat addressbook.tsv | parallel --colsep '\t' --header : echo {Name} {E-mail address}
+
+
+=head1 EXAMPLE: Using shell variables
+
+When using shell variables you need to quote them correctly as they
+may otherwise be split on spaces.
+
+Notice the difference between:
+
+ V=("My brother's 12\" records are worth <\$\$\$>"'!' Foo Bar)
+ parallel echo ::: ${V[@]} # This is probably not what you want
+
+and:
+
+ V=("My brother's 12\" records are worth <\$\$\$>"'!' Foo Bar)
+ parallel echo ::: "${V[@]}"
+
+When using variables in the actual command that contains special
+characters (e.g. space) you can quote them using B<'"$VAR"'> or using
+"'s and B<-q>:
+
+ V="Here  are  two "
+ parallel echo "'$V'" ::: spaces
+ parallel -q echo "$V" ::: spaces
+
+
 =head1 EXAMPLE: Group output lines
 
 When running jobs that output data, you often do not want the output

src/sql

@@ -556,7 +556,7 @@ $Global::Initfile && unlink $Global::Initfile;
 exit ($err);
 
 sub parse_options {
-    $Global::version = 20111222;
+    $Global::version = 20120122;
     $Global::progname = 'sql';
 
     # This must be done first as this may exec myself

testsuite/tests-to-run/test65.sh

@@ -18,6 +18,9 @@ echo "### Test --header with -N";
 echo "### Test --header with --block 1k";
 (echo h1; echo h2; perl -e '$a="x"x110;for(1..22){print $_,$a,"\n"'})| parallel -j1 --pipe -k --block 1k --header '\n.*\n' echo Start\;cat \; echo Stop
 
+echo "### Test --header with multiple :::"
+parallel --header : echo {a} {b} {1} {2} ::: b b1 ::: a a2
+
 echo '### Test --shellquote'
 cat <<'_EOF' | parallel --shellquote  
 awk -v FS="\",\"" '{print $1, $3, $4, $5, $9, $14}' | grep -v "#" | sed -e '1d' -e 's/\"//g' -e 's/\/\/\//\t/g' | cut -f1-6,11 | sed -e 's/\/\//\t/g' -e 's/ /\t/g

testsuite/wanted-results/test45

@@ -16,9 +16,9 @@ OK
 ### Test --timeout
 1.1
 1.1
-5.5
 6.6
 7.7
+8.8
 ### Test retired
 parallel: -g has been retired. Use --group.
 parallel: -B has been retired. Use --bf.

testsuite/wanted-results/test65

@@ -58,5 +58,7 @@ Start
 h1
 h2
 Stop
+### Test --header with multiple :::
+a2 b1 b1 a2
 ### Test --shellquote
 awk\ -v\ FS=\"\\\",\\\"\"\ \'\{print\ \$1,\ \$3,\ \$4,\ \$5,\ \$9,\ \$14\}\'\ \|\ grep\ -v\ \"\#\"\ \|\ sed\ -e\ \'1d\'\ -e\ \'s/\\\"//g\'\ -e\ \'s/\\/\\/\\//\\t/g\'\ \|\ cut\ -f1-6,11\ \|\ sed\ -e\ \'s/\\/\\//\\t/g\'\ -e\ \'s/\ /\\t/g