Merge branch 'master' of ssh://git.sv.gnu.org/srv/git/parallel

Conflicts:
	doc/release_new_version

doc/release_new_version

@@ -219,7 +219,7 @@ cc:Tim Cuthbertson <tim3d.junk@gmail.com>,
    Ryoichiro Suzuki <ryoichiro.suzuki@gmail.com>,
    Jesse Alama <jesse.alama@gmail.com>
 
-Subject: GNU Parallel 20160622 ('Orlando') released <<[stable]>>
+Subject: GNU Parallel 20160722 ('Brexit') released <<[stable]>>
 
 GNU Parallel 20160722 ('Brexit') <<[stable]>> has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
 
@@ -227,11 +227,18 @@ GNU Parallel 20160722 ('Brexit') <<[stable]>> has been released. It is available
 
 Haiku of the month:
 
+  <<>>
     -- Ole Tange
 
 
 New in this release:
 
+* env_parallel is now ready for wider testing. It is still beta quality.
+
+* env_parallel is heavily modified for all shells and testing has been increased.
+
+* Selectively choosing what to export using --env now works for env_parallel (bash, csh, fish, ksh, pdksh, tcsh, zsh).
+
 * <<Possibly http://link.springer.com/chapter/10.1007%2F978-3-319-22053-6_46>>
 
 * <<Possibly http://link.springer.com/article/10.1007/s12021-015-9290-5>>
@@ -258,6 +265,32 @@ for Big Data Applications https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumb
 
 * <<link No citation: Next-generation TCP for ns-3 simulator http://www.sciencedirect.com/science/article/pii/S1569190X15300939>>
 
+* <<No citation: Argumentation Models for Cyber Attribution http://arxiv.org/pdf/1607.02171.pdf>>
+
+* <<Possible: http://link.springer.com/article/10.1007/s12021-015-9290-5 http://link.springer.com/protocol/10.1007/978-1-4939-3578-9_14>>
+
+* GNU Parallel was cited in: HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment http://www.bioone.org/doi/full/10.3732/apps.1600016
+
+* GNU Parallel was cited in: StrAuto - Automation and Parallelization of STRUCTURE Analysis http://www.crypticlineage.net/download/strauto/strauto_doc.pdf
+
+* GNU Parallel was cited in: Tools and techniques for computational reproducibility http://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0135-4
+
+* GNU Parallel was cited in: FlashPCA: fast sparse canonical correlation analysis of genomic data http://biorxiv.org/content/biorxiv/suppl/2016/04/06/047217.DC1/047217-1.pdf
+
+* GNU Parallel was cited in: Computational Design of DNA-Binding Proteins http://link.springer.com/protocol/10.1007/978-1-4939-3569-7_16
+
+* GNU Parallel was cited in: Math Indexer and Searcher under the Hood: Fine-tuning Query Expansion and Unification Strategies http://research.nii.ac.jp/ntcir/workshop/OnlineProceedings12/pdf/ntcir/MathIR/05-NTCIR12-MathIR-RuzickaM.pdf
+
+* GNU Parallel was cited in: The Evolution and Fate of Super-Chandrasekhar Mass White Dwarf Merger Remnants http://arxiv.org/pdf/1606.02300.pdf
+
+* GNU Parallel was cited in: Evaluation of Coastal Scatterometer Products https://mdc.coaps.fsu.edu/scatterometry/meeting/docs/2016/Thu_AM/coastal-poster.pdf
+
+* GNU Parallel was used in: https://github.com/splitice/bulkdnsblcheck
+
+* The iconv slurp misfeature http://www.openfusion.net/linux/iconv_slurp_misfeature
+
+* แบบว่า CPU เหลือ https://veer66.wordpress.com/2016/06/15/gnu-parallel/
+
 * Bug fixes and man page updates.
 
 GNU Parallel - For people who live life in the parallel lane.

src/env_parallel.bash

@@ -52,12 +52,12 @@ env_parallel() {
             }
             if(grep { /^_$/ } @envvar) {
                 if(not open(IN, "<", "$ENV{HOME}/.parallel/ignored_vars")) {
-            	print STDERR "parallel: Error: ",
+             	    print STDERR "parallel: Error: ",
-            	"Run \"parallel --record-env\" in a clean environment first.\n";
+            	    "Run \"parallel --record-env\" in a clean environment first.\n";
                 } else {
-            	chomp(@ignored_vars = <IN>);
+            	    chomp(@ignored_vars = <IN>);
-            	$vars = join "|",map { quotemeta $_ } @ignored_vars;
+            	    $vars = join "|",map { quotemeta $_ } "env_parallel", @ignored_vars;
-            	print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
+		    print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
                 }
             }
             ' -- "$@"
@@ -87,7 +87,7 @@ env_parallel() {
     local _variable_NAMES="$(compgen -A variable |
         grep -E "^$_grep_REGEXP"\$ | grep -vE "^$_ignore_UNDERSCORE"\$ |
         grep -vFf <(readonly) |
-        egrep -v '^(BASHOPTS|BASHPID|EUID|GROUPS|FUNCNAME|DIRSTACK|_|PIPESTATUS|PPID|SHELLOPTS|UID|USERNAME|BASH_[A-Z_]+)$')"
+        grep -Ev '^(BASHOPTS|BASHPID|EUID|GROUPS|FUNCNAME|DIRSTACK|_|PIPESTATUS|PPID|SHELLOPTS|UID|USERNAME|BASH_[A-Z_]+)$')"
     local _list_variable_VALUES="typeset -p $_variable_NAMES"
     if [[ "$_variable_NAMES" = "" ]] ; then
 	# no variables selected

src/env_parallel.csh

@@ -57,12 +57,12 @@ else
             }
             if(grep { /^_$/ } @envvar) {
                 if(not open(IN, "<", "$ENV{HOME}/.parallel/ignored_vars")) {
-            	print STDERR "parallel: Error: ",
+             	    print STDERR "parallel: Error: ",
-            	"Run 'parallel --record-env' in a clean environment first.\n";
+            	    "Run \"parallel --record-env\" in a clean environment first.\n";
                 } else {
-            	chomp(@ignored_vars = <IN>);
+            	    chomp(@ignored_vars = <IN>);
-            	$vars = join "|",map { quotemeta $_ } @ignored_vars;
+            	    $vars = join "|",map { quotemeta $_ } "env_parallel", @ignored_vars;
-            	print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
+		    print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
                 }
             }
 'EOF'

src/env_parallel.fish

@@ -46,7 +46,8 @@ function env_parallel
     begin;
       set _grep_REGEXP (
         begin;
-          perl -e 'for(@ARGV){
+          perl -e '
+	    for(@ARGV){
                 /^_$/ and $next_is_env = 0;
                 $next_is_env and push @envvar, split/,/, $_;
                 $next_is_env = /^--env$/;
@@ -66,12 +67,12 @@ function env_parallel
             }
             if(grep { /^_$/ } @envvar) {
                 if(not open(IN, "<", "$ENV{HOME}/.parallel/ignored_vars")) {
-            	    print STDERR "parallel: Error: ",
+             	    print STDERR "parallel: Error: ",
             	    "Run \"parallel --record-env\" in a clean environment first.\n";
                 } else {
             	    chomp(@ignored_vars = <IN>);
-            	    $vars = join "|",map { quotemeta $_ } @ignored_vars;
+            	    $vars = join "|",map { quotemeta $_ } "env_parallel", @ignored_vars;
-            	    print $vars ? "($vars)" : "(nO,VaRs)";
+		    print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
                 }
             }
             ' -- $argv;

src/env_parallel.ksh

@@ -52,12 +52,12 @@ env_parallel() {
             }
             if(grep { /^_$/ } @envvar) {
                 if(not open(IN, "<", "$ENV{HOME}/.parallel/ignored_vars")) {
-            	print STDERR "parallel: Error: ",
+             	    print STDERR "parallel: Error: ",
-            	"Run \"parallel --record-env\" in a clean environment first.\n";
+            	    "Run \"parallel --record-env\" in a clean environment first.\n";
                 } else {
-            	chomp(@ignored_vars = <IN>);
+            	    chomp(@ignored_vars = <IN>);
-            	$vars = join "|",map { quotemeta $_ } @ignored_vars;
+            	    $vars = join "|",map { quotemeta $_ } "env_parallel", @ignored_vars;
-            	print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
+		    print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
                 }
             }
             ' -- "$@"
@@ -86,7 +86,7 @@ env_parallel() {
     # Grep variable names
     _variable_NAMES="$(typeset +p | perl -pe 's/^typeset .. //' |
         grep -E "^$_grep_REGEXP"\$ | grep -vE "^$_ignore_UNDERSCORE"\$ |
-        egrep -v '^(PIPESTATUS)$')"
+        grep -Ev '^(PIPESTATUS)$')"
     _list_variable_VALUES="typeset -p $_variable_NAMES"
     if [[ "$_variable_NAMES" = "" ]] ; then
 	# no variables selected

src/env_parallel.pdksh

@@ -52,12 +52,12 @@ env_parallel() {
             }
             if(grep { /^_$/ } @envvar) {
                 if(not open(IN, "<", "$ENV{HOME}/.parallel/ignored_vars")) {
-            	print STDERR "parallel: Error: ",
+             	    print STDERR "parallel: Error: ",
-            	"Run \"parallel --record-env\" in a clean environment first.\n";
+            	    "Run \"parallel --record-env\" in a clean environment first.\n";
                 } else {
-            	chomp(@ignored_vars = <IN>);
+            	    chomp(@ignored_vars = <IN>);
-            	$vars = join "|",map { quotemeta $_ } @ignored_vars;
+            	    $vars = join "|",map { quotemeta $_ } "env_parallel", @ignored_vars;
-            	print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
+		    print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
                 }
             }
             ' -- "$@"

src/env_parallel.pod

@@ -15,25 +15,36 @@ B<env_parallel> [options for GNU Parallel]
 =head1 DESCRIPTION
 
 B<env_parallel> is a shell function that exports the current
-environment to GNU Parallel.
+environment to GNU B<parallel>.
 
 If the shell function is not loaded, a dummy script will be run
 instead that explains how to install the function.
 
-B<env_parallel> is alpha quality and not production ready.
+B<env_parallel> is beta quality and not production ready.
+
+B<env_parallel> is 0.1 sec slower at startup than pure GNU
+B<parallel>, and takes up to 15 ms to start a job.
 
 =head2 Environment space
 
-B<env_parallel> only works if the size of the current environment is
+By default B<env_parallel> will export all environment variables,
-smaller than the maximal length of a command and smaller than half of
+arrays, aliases, functions and shell options (see details for the
-the max if running remotely. E.g. The max size of Bash's command is
+individual shells below).
-128 KB, so B<env_parallel> will fail if B<set | wc -c> is bigger than
+
-128 KB. Technically the limit is in execve(1) which IPC::open3 uses.
+But this only works if the size of the current environment is smaller
+than the maximal length of a command and smaller than half of the max
+if running remotely. E.g. The max size of Bash's command is 128 KB, so
+B<env_parallel> will fail if B<set | wc -c> is bigger than 128
+KB. Technically the limit is in execve(1) which IPC::open3 uses.
 
 Bash completion functions are well-known for taking up well over 128
 KB of environment space and the primary reason for causing
 B<env_parallel> to fail.
 
+Instead you can use B<--env> to specify which variables, arrays,
+aliases and functions to export as this will only export those with
+the given name.
+
 
 =head1 OPTIONS
 
@@ -93,6 +104,268 @@ E.g. by doing:
 
 =back
 
+
+=head2 csh
+
+B<--env> is supported to export only the variable, alias, function, or
+array with the given name. Multiple B<--env>s can be given.
+
+B<env_parallel> for B<csh> breaks B<$PARALLEL>, so do not use
+B<$PARALLEL>.
+
+Installation
+
+Put this in $HOME/.cshrc:
+
+  source `which env_parallel.csh`
+
+E.g. by doing:
+
+  echo 'source `which env_parallel.csh`' >> $HOME/.cshrc
+
+=over 8
+
+=item aliases
+
+  alias myecho echo
+  env_parallel myecho ::: test
+  env_parallel -S server myecho ::: test
+  env_parallel --env myecho myecho ::: work
+  env_parallel --env myecho -S server myecho ::: work
+
+=item functions
+
+Not supported by B<csh>.
+
+=item variables
+
+  set myvar=test
+  env_parallel echo "\$myvar" ::: test
+  env_parallel -S csh@server echo "\$myvar" ::: test
+  env_parallel --env myvar echo '$myvar' ::: work
+  env_parallel --env myvar -S server echo '$myvar' ::: work
+
+
+=item arrays with no special chars
+
+  set myarray=(foo bar baz)
+  env_parallel echo "\${myarray\[\{\}\]}" ::: 1 2 3
+  env_parallel -S csh@server echo "\${myarray\[\{\}\]}" ::: 1 2 3
+  env_parallel -k --env myarray echo \$'{myarray[{}]}' ::: 1 2 3
+  env_parallel -k --env myarray -S server echo \$'{myarray[{}]}' ::: 1 2 3
+
+=back
+
+
+=head2 fish
+
+B<--env> is supported to export only the variable, alias, function, or
+array with the given name. Multiple B<--env>s can be given.
+
+Installation
+
+Put this in $HOME/.config/fish/config.fish:
+
+  source (which env_parallel.fish)
+
+E.g. by doing:
+
+  echo 'source (which env_parallel.fish)' >> $HOME/.config/fish/config.fish
+
+=over 8
+
+=item aliases
+
+  alias myecho 'echo aliases'
+  env_parallel myecho ::: work
+  env_parallel -S server myecho ::: work
+  env_parallel --env myecho myecho ::: work
+  env_parallel --env myecho -S server myecho ::: work
+
+=item functions
+
+  function myfunc
+    echo functions $argv
+  end
+  env_parallel myfunc ::: work
+  env_parallel -S server myfunc ::: work
+  env_parallel --env myfunc myfunc ::: work
+  env_parallel --env myfunc -S server myfunc ::: work
+
+=item variables
+
+  set myvar variables
+  env_parallel echo '$myvar' ::: work
+  env_parallel -S server echo '$myvar' ::: work
+  env_parallel --env myvar echo '$myvar' ::: work
+  env_parallel --env myvar -S server echo '$myvar' ::: work
+
+=item arrays
+
+  set myarray arrays work, too
+  env_parallel -k echo '$myarray[{}]' ::: 1 2 3
+  env_parallel -k -S server echo '$myarray[{}]' ::: 1 2 3
+  env_parallel -k --env myarray echo '$myarray[{}]' ::: 1 2 3
+  env_parallel -k --env myarray -S server echo '$myarray[{}]' ::: 1 2 3
+
+=back
+
+
+=head2 ksh
+
+B<--env> is supported to export only the variable, alias, function, or
+array with the given name. Multiple B<--env>s can be given.
+
+Installation
+
+Put this in $HOME/.kshrc:
+
+  source `which env_parallel.ksh`
+
+E.g. by doing:
+
+  echo 'source `which env_parallel.ksh`' >> $HOME/.kshrc
+
+=over 8
+
+=item aliases
+
+  alias myecho='echo aliases'
+  env_parallel myecho ::: work
+  env_parallel -S server myecho ::: work
+  env_parallel --env myecho myecho ::: work
+  env_parallel --env myecho -S server myecho ::: work
+
+=item functions
+
+  myfunc() { echo functions $*; }
+  env_parallel myfunc ::: work
+  env_parallel -S server myfunc ::: work
+  env_parallel --env myfunc myfunc ::: work
+  env_parallel --env myfunc -S server myfunc ::: work
+
+=item variables
+
+  myvar=variables
+  env_parallel echo '$myvar' ::: work
+  env_parallel -S server echo '$myvar' ::: work
+  env_parallel --env myvar echo '$myvar' ::: work
+  env_parallel --env myvar -S server echo '$myvar' ::: work
+
+=item arrays
+
+  myarray=(arrays work, too)
+  env_parallel -k echo '${myarray[{}]}' ::: 0 1 2
+  env_parallel -k -S server echo '${myarray[{}]}' ::: 0 1 2
+  env_parallel -k --env myarray echo '${myarray[{}]}' ::: 0 1 2
+  env_parallel -k --env myarray -S server echo '${myarray[{}]}' ::: 0 1 2
+
+=back
+
+
+=head2 pdksh
+
+B<--env> is supported to export only the variable, alias, function, or
+array with the given name. Multiple B<--env>s can be given.
+
+Installation
+
+Put this in $HOME/.profile:
+
+  source `which env_parallel.pdksh`
+
+E.g. by doing:
+
+  echo 'source `which env_parallel.pdksh`' >> $HOME/.profile
+
+=over 8
+
+=item aliases
+
+  alias myecho="echo aliases";
+  env_parallel myecho ::: work;
+  env_parallel -S server myecho ::: work;
+  env_parallel --env myecho myecho ::: work;
+  env_parallel --env myecho -S server myecho ::: work
+
+=item functions
+
+  myfunc() { echo functions $*; };
+  env_parallel myfunc ::: work;
+  env_parallel -S server myfunc ::: work;
+  env_parallel --env myfunc myfunc ::: work;
+  env_parallel --env myfunc -S server myfunc ::: work
+
+=item variables
+
+  myvar=variables;
+  env_parallel echo "\$myvar" ::: work;
+  env_parallel -S server echo "\$myvar" ::: work;
+  env_parallel --env myvar echo "\$myvar" ::: work;
+  env_parallel --env myvar -S server echo "\$myvar" ::: work
+
+=item arrays
+
+  myarray=(arrays work, too);
+  env_parallel -k echo "\${myarray[{}]}" ::: 0 1 2;
+  env_parallel -k -S server echo "\${myarray[{}]}" ::: 0 1 2;
+  env_parallel -k --env myarray echo "\${myarray[{}]}" ::: 0 1 2;
+  env_parallel -k --env myarray -S server echo "\${myarray[{}]}" ::: 0 1 2
+
+=back
+
+
+=head2 tcsh
+
+B<--env> is supported to export only the variable, alias, function, or
+array with the given name. Multiple B<--env>s can be given.
+
+B<env_parallel> for B<tcsh> breaks B<$PARALLEL>, so do not use
+B<$PARALLEL>.
+
+Installation
+
+Put this in $HOME/.tcshrc:
+
+  source `which env_parallel.tcsh`
+
+E.g. by doing:
+
+  echo 'source `which env_parallel.tcsh`' >> $HOME/.tcshrc
+
+=over 8
+
+=item aliases
+
+  alias myecho 'echo aliases'
+  env_parallel myecho ::: work
+  env_parallel -S server myecho ::: work
+  env_parallel --env myecho myecho ::: work
+  env_parallel --env myecho -S server myecho ::: work
+
+=item functions
+
+Not supported by B<tcsh>.
+
+=item variables
+
+  set myvar=variables
+  env_parallel echo '$myvar' ::: work
+  env_parallel -S server echo '$myvar' ::: work
+  env_parallel --env myvar echo '$myvar' ::: work
+  env_parallel --env myvar -S server echo '$myvar' ::: work
+
+=item arrays with no special chars
+
+  set myarray=(arrays work, too)
+  env_parallel -k echo \$'{myarray[{}]}' ::: 1 2 3
+  env_parallel -k -S server echo \$'{myarray[{}]}' ::: 1 2 3
+  env_parallel -k --env myarray echo \$'{myarray[{}]}' ::: 1 2 3
+  env_parallel -k --env myarray -S server echo \$'{myarray[{}]}' ::: 1 2 3
+
+=back
+
+
 =head2 Zsh
 
 B<--env> is supported to export only the variable, alias, function, or
@@ -144,248 +417,6 @@ E.g. by doing:
 
 =back
 
-=head2 fish
-
-Installation
-
-Put this in $HOME/.config/fish/config.fish:
-
-  source (which env_parallel.fish)
-
-E.g. by doing:
-
-  echo 'source (which env_parallel.fish)' >> $HOME/.config/fish/config.fish
-
-=over 8
-
-=item aliases
-
-  alias myecho 'echo aliases'
-  env_parallel myecho ::: work
-  env_parallel -S server myecho ::: work
-  env_parallel --env myecho myecho ::: work
-  env_parallel --env myecho -S server myecho ::: work
-
-=item functions
-
-  function myfunc
-    echo functions $argv
-  end
-  env_parallel myfunc ::: work
-  env_parallel -S server myfunc ::: work
-  env_parallel --env myfunc myfunc ::: work
-  env_parallel --env myfunc -S server myfunc ::: work
-
-=item variables
-
-  set myvar variables
-  env_parallel echo '$myvar' ::: work
-  env_parallel -S server echo '$myvar' ::: work
-  env_parallel --env myvar echo '$myvar' ::: work
-  env_parallel --env myvar -S server echo '$myvar' ::: work
-
-=item arrays
-
-  set myarray arrays work, too
-  env_parallel -k echo '$myarray[{}]' ::: 1 2 3
-  env_parallel -k -S server echo '$myarray[{}]' ::: 1 2 3
-  env_parallel -k --env myarray echo '$myarray[{}]' ::: 1 2 3
-  env_parallel -k --env myarray -S server echo '$myarray[{}]' ::: 1 2 3
-
-=back
-
-=head2 ksh
-
-Installation
-
-Put this in $HOME/.kshrc:
-
-  source `which env_parallel.ksh`
-
-E.g. by doing:
-
-  echo 'source `which env_parallel.ksh`' >> $HOME/.kshrc
-
-=over 8
-
-=item aliases
-
-  alias myecho='echo aliases'
-  env_parallel myecho ::: work
-  env_parallel -S server myecho ::: work
-  env_parallel --env myecho myecho ::: work
-  env_parallel --env myecho -S server myecho ::: work
-
-=item functions
-
-  myfunc() { echo functions $*; }
-  env_parallel myfunc ::: work
-  env_parallel -S server myfunc ::: work
-  env_parallel --env myfunc myfunc ::: work
-  env_parallel --env myfunc -S server myfunc ::: work
-
-=item variables
-
-  myvar=variables
-  env_parallel echo '$myvar' ::: work
-  env_parallel -S server echo '$myvar' ::: work
-  env_parallel --env myvar echo '$myvar' ::: work
-  env_parallel --env myvar -S server echo '$myvar' ::: work
-
-=item arrays
-
-  myarray=(arrays work, too)
-  env_parallel -k echo '${myarray[{}]}' ::: 0 1 2
-  env_parallel -k -S server echo '${myarray[{}]}' ::: 0 1 2
-  env_parallel -k --env myarray echo '${myarray[{}]}' ::: 0 1 2
-  env_parallel -k --env myarray -S server echo '${myarray[{}]}' ::: 0 1 2
-
-=back
-
-=head2 pdksh
-
-Installation
-
-Put this in $HOME/.profile:
-
-  source `which env_parallel.pdksh`
-
-E.g. by doing:
-
-  echo 'source `which env_parallel.pdksh`' >> $HOME/.profile
-
-=over 8
-
-=item aliases
-
-  alias myecho="echo aliases";
-  env_parallel myecho ::: work;
-  env_parallel -S server myecho ::: work;
-  env_parallel --env myecho myecho ::: work;
-  env_parallel --env myecho -S server myecho ::: work
-
-=item functions
-
-  myfunc() { echo functions $*; };
-  env_parallel myfunc ::: work;
-  env_parallel -S server myfunc ::: work;
-  env_parallel --env myfunc myfunc ::: work;
-  env_parallel --env myfunc -S server myfunc ::: work
-
-=item variables
-
-  myvar=variables;
-  env_parallel echo "\$myvar" ::: work;
-  env_parallel -S server echo "\$myvar" ::: work;
-  env_parallel --env myvar echo "\$myvar" ::: work;
-  env_parallel --env myvar -S server echo "\$myvar" ::: work
-
-=item arrays
-
-  myarray=(arrays work, too);
-  env_parallel -k echo "\${myarray[{}]}" ::: 0 1 2;
-  env_parallel -k -S server echo "\${myarray[{}]}" ::: 0 1 2;
-  env_parallel -k --env myarray echo "\${myarray[{}]}" ::: 0 1 2;
-  env_parallel -k --env myarray -S server echo "\${myarray[{}]}" ::: 0 1 2
-
-=back
-
-=head2 csh
-
-B<env_parallel> for B<csh> breaks B<$PARALLEL>, so do not use
-B<$PARALLEL>.
-
-Installation
-
-Put this in $HOME/.cshrc:
-
-  source `which env_parallel.csh`
-
-E.g. by doing:
-
-  echo 'source `which env_parallel.csh`' >> $HOME/.cshrc
-
-=over 8
-
-=item aliases
-
-  alias myecho echo
-  env_parallel myecho ::: test
-  env_parallel -S server myecho ::: test
-  env_parallel --env myecho myecho ::: work
-  env_parallel --env myecho -S server myecho ::: work
-
-=item functions
-
-Not supported by B<csh>.
-
-=item variables
-
-  set myvar=test
-  env_parallel echo "\$myvar" ::: test
-  env_parallel -S csh@server echo "\$myvar" ::: test
-  env_parallel --env myvar echo '$myvar' ::: work
-  env_parallel --env myvar -S server echo '$myvar' ::: work
-
-
-=item arrays with no special chars
-
-  set myarray=(foo bar baz)
-  env_parallel echo "\${myarray\[\{\}\]}" ::: 1 2 3
-  env_parallel -S csh@server echo "\${myarray\[\{\}\]}" ::: 1 2 3
-  env_parallel -k --env myarray echo \$'{myarray[{}]}' ::: 1 2 3
-  env_parallel -k --env myarray -S server echo \$'{myarray[{}]}' ::: 1 2 3
-
-=back
-
-=head2 tcsh
-
-B<env_parallel> for B<tcsh> breaks B<$PARALLEL>, so do not use
-B<$PARALLEL>.
-
-Installation
-
-Put this in $HOME/.tcshrc:
-
-  source `which env_parallel.tcsh`
-
-E.g. by doing:
-
-  echo 'source `which env_parallel.tcsh`' >> $HOME/.tcshrc
-
-=over 8
-
-=item aliases
-
-  alias myecho 'echo aliases'
-  env_parallel myecho ::: work
-  env_parallel -S server myecho ::: work
-  env_parallel --env myecho myecho ::: work
-  env_parallel --env myecho -S server myecho ::: work
-
-=item functions
-
-Not supported by B<tcsh>.
-
-=item variables
-
-  set myvar=variables
-  env_parallel echo '$myvar' ::: work
-  env_parallel -S server echo '$myvar' ::: work
-  env_parallel --env myvar echo '$myvar' ::: work
-  env_parallel --env myvar -S server echo '$myvar' ::: work
-
-=item arrays with no special chars
-
-  set myarray=(arrays work, too)
-  env_parallel -k echo \$'{myarray[{}]}' ::: 1 2 3
-  env_parallel -k -S server echo \$'{myarray[{}]}' ::: 1 2 3
-  env_parallel -k --env myarray echo \$'{myarray[{}]}' ::: 1 2 3
-  env_parallel -k --env myarray -S server echo \$'{myarray[{}]}' ::: 1 2 3
-
-=back
-
-
 
 =head1 EXIT STATUS
 
@@ -530,7 +561,10 @@ B<env_parallel> uses GNU B<parallel>.
 
 =head1 SEE ALSO
 
-B<parallel>(1), B<bash>(1), B<ksh>(1), B<zsh>(1), B<ksh>(1),
+B<parallel>(1), 
-B<pdksh>(1)
+
+B<bash>(1), B<csh>(1), B<fish>(1), B<ksh>(1), B<pdksh>(1) B<tcsh>(1),
+B<zsh>(1).
+
 
 =cut

src/env_parallel.tcsh

@@ -57,12 +57,12 @@ else
             }
             if(grep { /^_$/ } @envvar) {
                 if(not open(IN, "<", "$ENV{HOME}/.parallel/ignored_vars")) {
-            	print STDERR "parallel: Error: ",
+             	    print STDERR "parallel: Error: ",
-            	"Run 'parallel --record-env' in a clean environment first.\n";
+            	    "Run \"parallel --record-env\" in a clean environment first.\n";
                 } else {
-            	chomp(@ignored_vars = <IN>);
+            	    chomp(@ignored_vars = <IN>);
-            	$vars = join "|",map { quotemeta $_ } @ignored_vars;
+            	    $vars = join "|",map { quotemeta $_ } "env_parallel", @ignored_vars;
-            	print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
+		    print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
                 }
             }
 'EOF'

src/env_parallel.zsh

@@ -52,12 +52,12 @@ env_parallel() {
             }
             if(grep { /^_$/ } @envvar) {
                 if(not open(IN, "<", "$ENV{HOME}/.parallel/ignored_vars")) {
-            	print STDERR "parallel: Error: ",
+             	    print STDERR "parallel: Error: ",
-            	"Run \"parallel --record-env\" in a clean environment first.\n";
+            	    "Run \"parallel --record-env\" in a clean environment first.\n";
                 } else {
-            	chomp(@ignored_vars = <IN>);
+            	    chomp(@ignored_vars = <IN>);
-            	$vars = join "|",map { quotemeta $_ } @ignored_vars;
+            	    $vars = join "|",map { quotemeta $_ } "env_parallel", @ignored_vars;
-            	print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
+		    print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
                 }
             }
             ' -- "$@"
@@ -86,11 +86,11 @@ env_parallel() {
     unset _function_NAMES
 
     # Grep variable names
-    # The egrep -v is crap and should be better
+    # The grep -Ev is crap and should be better
     _variable_NAMES="$(print -l ${(k)parameters} |
         grep -E "^$_grep_REGEXP"\$ | grep -vE "^$_ignore_UNDERSCORE"\$ |
-        egrep -v '^([-?#!$*@_0]|zsh_eval_context|ZSH_EVAL_CONTEXT|LINENO|IFS|commands|functions|options|aliases|EUID|EGID|UID|GID)$' |
+        grep -Ev '^([-?#!$*@_0]|zsh_eval_context|ZSH_EVAL_CONTEXT|LINENO|IFS|commands|functions|options|aliases|EUID|EGID|UID|GID)$' |
-        egrep -v 'terminfo|funcstack|galiases|keymaps|parameters|jobdirs|dirstack|functrace|funcsourcetrace|zsh_scheduled_events|dis_aliases|dis_reswords|dis_saliases|modules|reswords|saliases|widgets|userdirs|historywords|nameddirs|termcap|dis_builtins|dis_functions|jobtexts|funcfiletrace|dis_galiases|builtins|history|jobstates'
+        grep -Ev 'terminfo|funcstack|galiases|keymaps|parameters|jobdirs|dirstack|functrace|funcsourcetrace|zsh_scheduled_events|dis_aliases|dis_reswords|dis_saliases|modules|reswords|saliases|widgets|userdirs|historywords|nameddirs|termcap|dis_builtins|dis_functions|jobtexts|funcfiletrace|dis_galiases|builtins|history|jobstates'
         )"
     _list_variable_VALUES="typeset -p "$(echo $_variable_NAMES|xargs)" |
         grep -aFvf <(typeset -pr)

src/parallel

@@ -3734,7 +3734,7 @@ sub citation {
 	  "  url = {http://www.gnu.org/s/parallel},",
 	  "  year = {2011},",
 	  "  pages = {42-47},",
-	  "  doi = {10.5281/zenodo.16303}",
+	  "  doi = {http://dx.doi.org/10.5281/zenodo.16303}",
 	  "}",
 	  "",
 	  "(Feel free to use \\nocite{Tange2011a})",

src/parallel.pod

@@ -266,6 +266,14 @@ shell quote a string
 
 number of jobs in total
 
+=item Z<> B<$job->slot()>
+
+slot number of job
+
+=item Z<> B<$job->seq()>
+
+sequence number of job
+
 =back
 
 Example:
@@ -1476,7 +1484,7 @@ sequence numbers in B<--joblog> then the input, the command, and
 B<--joblog> all have to remain unchanged; otherwise GNU B<parallel>
 may run wrong commands.
 
-See also B<--joblog>, B<--results>, B<--resume-failed>.
+See also B<--joblog>, B<--results>, B<--resume-failed>, B<--retries>.
 
 
 =item B<--resume-failed>
@@ -1489,7 +1497,7 @@ numbers in B<--joblog> then the input, the command, and B<--joblog>
 all have to remain unchanged; otherwise GNU B<parallel> may run wrong
 commands.
 
-See also B<--joblog>, B<--resume>.
+See also B<--joblog>, B<--resume>, B<--retry-failed>, B<--retries>.
 
 
 =item B<--retry-failed>
@@ -1497,10 +1505,66 @@ See also B<--joblog>, B<--resume>.
 Retry all failed jobs in joblog. By reading B<--joblog> GNU
 B<parallel> will figure out the failed jobs and run those again.
 
-B<--retry-failed> ignore the command and arguments: It only looks at
+B<--retry-failed> ignores the command and arguments on the command
-the joblog.
+line: It only looks at the joblog.
 
-See also B<--joblog>, B<--resume>, B<--resume-failed>.
+    B<Differences between --resume, --resume-failed, --retry-failed>
+
+In this example B<exit {= $_%=2 =}> will cause every other job to fail.
+
+  timeout -k 1 4 parallel --joblog log -j10 'sleep {}; exit {= $_%=2 =}' ::: {10..1}
+
+4 jobs completed. 2 failed:
+
+  Seq	[...]	Exitval	Signal	Command
+  10	[...]	1	0	sleep 1; exit 1
+  9	[...]	0	0	sleep 2; exit 0
+  8	[...]	1	0	sleep 3; exit 1
+  7	[...]	0	0	sleep 4; exit 0
+
+B<--resume> does not care about the Exitval, but only looks at Seq. If
+the Seq is run, it will not be run again. So if needed, you can change
+the command for the seqs not run yet:
+
+  parallel --resume --joblog log -j10 'sleep .{}; exit {= $_%=2 =}' ::: {10..1}
+
+  Seq	[...]	Exitval	Signal	Command
+  [... as above ...]
+  1	[...]	0	0	sleep .10; exit 0
+  6	[...]	1	0	sleep .5; exit 1
+  5	[...]	0	0	sleep .6; exit 0
+  4	[...]	1	0	sleep .7; exit 1
+  3	[...]	0	0	sleep .8; exit 0
+  2	[...]	1	0	sleep .9; exit 1
+
+B<--resume-failed> cares about the Exitval, but also only looks at Seq
+to figure out which commands to run. Again this means you can change
+the command, but not the arguments. It will run the failed seqs and
+the seqs not yet run:
+
+  parallel --resume-failed --joblog log -j10 'echo {};sleep .{}; exit {= $_%=3 =}' ::: {10..1}
+
+  Seq	[...]	Exitval	Signal	Command
+  [... as above ...]
+  10	[...]	1	0	echo 1;sleep .1; exit 1
+  8	[...]	0	0	echo 3;sleep .3; exit 0
+  6	[...]	2	0	echo 5;sleep .5; exit 2
+  4	[...]	1	0	echo 7;sleep .7; exit 1
+  2	[...]	0	0	echo 9;sleep .9; exit 0
+
+B<--retry-failed> cares about the Exitval, but takes the command from
+the joblog. It ignores any arguments or commands given on the command
+line:
+
+  parallel --retry-failed --joblog log -j10 this part is ignored
+
+  Seq	[...]	Exitval	Signal	Command
+  [... as above ...]
+  10	[...]	1	0	echo 1;sleep .1; exit 1
+  6	[...]	2	0	echo 5;sleep .5; exit 2
+  4	[...]	1	0	echo 7;sleep .7; exit 1
+
+See also B<--joblog>, B<--resume>, B<--resume-failed>, B<--retries>.
 
 
 =item B<--retries> I<n>
@@ -1609,6 +1673,8 @@ Here are a few examples:
   --rpl '{0#} $f = "%0".int(1+log(total_jobs())/log(10))."d"; $_=sprintf($f,$job->seq())'
   Job sequence counting from 0
   --rpl '{#0} $_ = $job->seq() - 1'
+  Job slot counting from 2
+  --rpl '{%1} $_ = $job->slot() + 1'
 
 See also: B<{= perl expression =}> B<--parens>
 

testsuite/tests-to-run/parallel-local-30s.sh

@@ -15,7 +15,7 @@ par_tmp_full() {
     # Assume /tmp/shm is easy to fill up
     export SHM=/tmp/shm/parallel
     mkdir -p $SHM
-    sudo umount -l $SHM
+    sudo umount -l $SHM 2>/dev/null
     sudo mount -t tmpfs -o size=10% none $SHM
 
     echo "### Test --tmpdir running full. bug #40733 was caused by this"

testsuite/wanted-results/parallel-local-ssh7

@@ -62,13 +62,13 @@ par_bash_underscore	aliases in and arrays in functions work
 par_bash_underscore	aliases in and arrays in functions work
 par_bash_underscore	aliases in functions work
 par_bash_underscore	aliases in functions work
-par_bash_underscore	/bin/bash: line 139: myecho: command not found
+par_bash_underscore	/bin/bash: line 70: myecho: command not found
 par_bash_underscore	OK if no myecho      ^^^^^^^^^^^^^^^^^^^^^^^^^
-par_bash_underscore	/bin/bash: line 139: myecho: command not found
+par_bash_underscore	/bin/bash: line 70: myecho: command not found
 par_bash_underscore	OK if no myecho      ^^^^^^^^^^^^^^^^^^^^^^^^^
-par_bash_underscore	/bin/bash: line 136: myfunc: command not found
+par_bash_underscore	/bin/bash: line 68: myfunc: command not found
 par_bash_underscore	OK if no myfunc      ^^^^^^^^^^^^^^^^^^^^^^^^^
-par_bash_underscore	/bin/bash: line 136: myfunc: command not found
+par_bash_underscore	/bin/bash: line 68: myfunc: command not found
 par_bash_underscore	OK if no myfunc      ^^^^^^^^^^^^^^^^^^^^^^^^^
 par_csh_funky	3 arg alias_works
 par_csh_funky	myvar  works
@@ -274,13 +274,13 @@ par_ksh_underscore	aliases in and arrays in functions work
 par_ksh_underscore	aliases in and arrays in functions work
 par_ksh_underscore	aliases in functions work
 par_ksh_underscore	aliases in functions work
-par_ksh_underscore	/usr/bin/ksh[193]: myecho: not found [No such file or directory]
+par_ksh_underscore	/usr/bin/ksh[113]: myecho: not found [No such file or directory]
 par_ksh_underscore	OK if no myecho    ^^^^^^^^^^^^^^^^^
-par_ksh_underscore	/usr/bin/ksh[193]: myecho: not found [No such file or directory]
+par_ksh_underscore	/usr/bin/ksh[113]: myecho: not found [No such file or directory]
 par_ksh_underscore	OK if no myecho    ^^^^^^^^^^^^^^^^^
-par_ksh_underscore	/usr/bin/ksh: line 193: myfunc: not found
+par_ksh_underscore	/usr/bin/ksh: line 113: myfunc: not found
 par_ksh_underscore	OK if no myfunc         ^^^^^^^^^^^^^^^^^
-par_ksh_underscore	/usr/bin/ksh: line 193: myfunc: not found
+par_ksh_underscore	/usr/bin/ksh: line 113: myfunc: not found
 par_ksh_underscore	OK if no myfunc         ^^^^^^^^^^^^^^^^^
 par_pdksh_funky	3 arg alias_works
 par_pdksh_funky	function_works