parallel: --no-keep-order will reverse --keep-order. --no-notice => --will-cite.

doc/release_new_version

@@ -57,6 +57,8 @@ pushd
 
 == Upload ==
 
+eval `gpg-agent --daemon`
+
 YYYYMMDD=`yyyymmdd`
 cp parallel-$YYYYMMDD.tar.bz2 parallel-latest.tar.bz2
 cp doc/parallel.directive parallel-$YYYYMMDD.tar.bz2.directive
@@ -158,7 +160,7 @@ git diff
 
 git commit -a
 
-Released as 20140x22 ('').
+Released as 20150x22 ('').
 
 TAG=MyTag
 YYYYMMDD=`yyyymmdd`
@@ -226,7 +228,7 @@ cc:Tim Cuthbertson <tim3d.junk@gmail.com>,
    Ryoichiro Suzuki <ryoichiro.suzuki@gmail.com>,
    Jesse Alama <jesse.alama@gmail.com>
 
-Subject: GNU Parallel 20150122 ('Manila QZ8501') released
+Subject: GNU Parallel 20150122 (' (((:~{> Hebdo Manila QZ8501') released
 
 GNU Parallel 20150122 ('Hebdo Manila QZ8501') has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
 
@@ -236,20 +238,46 @@ Haiku of the month:
 
 New in this release:
 
-* Remote jobs now sends stderr (standard error) to stderr (standard error) instead of stdout (standard output)
+* Remote jobs now send stderr (standard error) to stderr (standard error) instead of stdout (standard output).
 
-* Remote execution is now packed using hex encoded bzip2. That means that big environments (app. 250 KB) can be transferred. This change makes remote execution alpha quality.
+* Remote execution command is now packed using hex encoded bzip2. This means that big environments (app. 250 KB) can be transferred. This change makes remote execution alpha quality.
 
 * --semaphoretimeout now takes a negative value. This means give up if the semaphore is not gotten within the timeout.
 
+* --halt -1 and -2 now means halt if a job succeeds (so the opposite of 1 and 2).
+
+* Bash's second fix of shellshock caused --env to break again when exporting functions. This has been fixed again.
+
 * A semibig refactoring of big functions. All non-trivial functions are now less than 100 lines. The refactoring makes this release beta quality.
 
+* GNU Parallel was cited in: SlideToolkit: An Assistive Toolset for the Histological Quantification of Whole Slide Images http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0110289
+
+* GNU Parallel was cited in: Improving Energy and Performance with Spintronics Caches in Multicore Systems http://link.springer.com/chapter/10.1007/978-3-319-14313-2_24
+
 * GNU Parallel was cited in: Parallel post-processing with MPI-Bash http://dl.acm.org/citation.cfm?id=2691137
 
 * GNU Parallel was cited in: Distinguishing cause from effect using observational data: methods and benchmarks http://arxiv-web3.library.cornell.edu/pdf/1412.3773.pdf
 
 * GNU Parallel was cited in: Bayesian Inference of Protein Structure from Chemical Shift Data https://peerj.com/preprints/692.pdf
 
+* GNU Parallel was cited in: Data Science at the Command Line http://cdn.oreillystatic.com/oreilly/booksamplers/9781491947852_sampler.pdf
+
+* GNU Parallel was cited in: Speaker environment classification using rhythm metrics in Levantine Arabic dialect http://ieeexplore.ieee.org/xpl/abstractReferences.jsp?tp=&arnumber=6923918
+
+* GNU Parallel was cited in: Resolution of Genetic Map Expansion Caused by Excess Heterozygosity in Plant Recombinant Inbred Populations http://www.g3journal.org/content/4/10/1963.full.pdf
+
+* GNU Parallel was cited in: Bayesian Inference of Protein Structure from Chemical Shift Data https://peerj.com/preprints/692v1.pdf
+
+* GNU Parallel was cited in: Clonal interference and Mullerʼs ratchet in spatial habitats http://iopscience.iop.org/1478-3975/11/5/056003
+
+* GNU Parallel was cited in: Web-scale content reuse detection ftp://info.isi.edu/isi-pubs/tr-692.pdf
+
+* GNU Parallel was cited in: Computação Verde na Camada de Aplicação https://linux.ime.usp.br/~tpaiva/mac0499/files/monografia.pdf
+
+* GNU Parallel was cited in: Frameshift alignment: statistics and post-genomic applications http://bioinformatics.oxfordjournals.org/content/30/24/3575.full.pdf+html
+
+* GNU Parallel was cited in: Towards Recommender Engineering Tools and Experiments for Identifying Recommender Differences http://elehack.net/research/thesis/mde-thesis.pdf
+
 * GNU Parallel: Open Source For You (OSFY) magazine, October 2013 edition http://www.shakthimaan.com/posts/2014/11/27/gnu-parallel/news.html
 
 * Multithreaded Encryption and Compression http://www.krazyworks.com/multithreaded-encryption-and-compression/
@@ -258,6 +286,8 @@ New in this release:
 
 * How to build gnu parallel from source on Ubuntu PC? http://blog.ovidiuparvu.com/build-gnu-parallel-source-ubuntu-pc/
 
+* GNU parallel for openaddr-process-one https://nelsonslog.wordpress.com/2015/01/09/gnu-parallel-for-openaddr-process-one/
+
 * From SRA Project to FastQ http://danielecook.com/sra-project-fastq/
 
 * コマンドを並列に実行するGNU parallelがとても便利 http://bicycle1885.hatenablog.com/entry/2014/08/10/143612

src/parallel

@@ -600,8 +600,8 @@ sub options_hash {
 	 "resume" => \$opt::resume,
 	 "resume-failed|resumefailed" => \$opt::resume_failed,
 	 "silent" => \$opt::silent,
-	 #"silent-error|silenterror" => \$opt::silent_error,
 	 "keep-order|keeporder|k" => \$opt::keeporder,
+	 "no-keep-order|nokeeporder|nok|no-k" => \$opt::nokeeporder,
 	 "group" => \$opt::group,
 	 "g" => \$opt::retired,
 	 "ungroup|u" => \$opt::ungroup,
@@ -681,10 +681,10 @@ sub options_hash {
 	 "files|output-as-files|outputasfiles" => \$opt::files,
 	 "block|block-size|blocksize=s" => \$opt::blocksize,
 	 "tollef" => \$opt::retired,
-	 "gnu" => \$opt::gnu,
+	 "gnu" => \$opt::ignored_option,
 	 "xapply" => \$opt::xapply,
 	 "bibtex" => \$opt::bibtex,
-	 "nn|nonotice|no-notice" => \$opt::no_notice,
+	 "wc|willcite|will-cite|nn|nonotice|no-notice" => \$opt::willcite,
 	 "memfree=s" => \$opt::memfree,
 	 # xargs-compatibility - implemented, man, testsuite
 	 "max-procs|P=s" => \$opt::jobs,
@@ -774,6 +774,10 @@ sub parse_options {
     init_globals();
     @ARGV=read_options();
 
+    # no-* overrides *
+    if($opt::nokeeporder) { $opt::keeporder = undef; }
+    if($opt::noctrlc) { $opt::ctrlc = undef; }
+
     if(@opt::v) { $Global::verbose = $#opt::v+1; } # Convert -v -v to v=2
     $Global::debug = $opt::D;
     $Global::shell = $ENV{'PARALLEL_SHELL'} || parent_shell($$) || $ENV{'SHELL'} || "/bin/sh";
@@ -2699,7 +2703,7 @@ sub onall {
 	     (@opt::env ? map { "--env ".::shell_quote_scalar($_) } @opt::env : ""),
 	);
     ::debug("init", "| $0 $options\n");
-    open(my $parallel_fh, "|-", "$0 --no-notice -j0 $options") ||
+    open(my $parallel_fh, "|-", "$0 --will-cite -j0 $options") ||
 	::die_bug("This does not run GNU Parallel: $0 $options");
     my @joblogs;
     for my $host (sort keys %Global::host) {
@@ -2914,11 +2918,11 @@ sub usage {
 
 
 sub citation_notice {
-    # if --no-notice or --plain: do nothing
+    # if --will-cite or --plain: do nothing
     # if stderr redirected: do nothing
     # if ~/.parallel/will-cite: do nothing
     # else: print citation notice to stderr
-    if($opt::no_notice
+    if($opt::willcite
        or
        $opt::plain
        or
@@ -2937,7 +2941,7 @@ sub citation_notice {
 	     "This helps funding further development; and it won't cost you a cent.\n",
 	     "If you pay 10000 EUR you should feel free to use GNU Parallel without citing.\n",
 	     "\n",
-	     "To silence this citation notice run 'parallel --bibtex' once or use '--no-notice'.\n\n",
+	     "To silence this citation notice run 'parallel --bibtex' once or use '--will-cite'.\n\n",
 	    );
     }
 }
@@ -2979,9 +2983,6 @@ sub die_bug {
 
 sub version {
     # Returns: N/A
-    if($opt::tollef and not $opt::gnu) {
-	print "WARNING: YOU ARE USING --tollef. IF THINGS ARE ACTING WEIRD USE --gnu.\n";
-    }
     print join("\n",
                "GNU $Global::progname $Global::version",
                "Copyright (C) 2007,2008,2009,2010,2011,2012,2013,2014,2015 Ole Tange",
@@ -2998,9 +2999,6 @@ sub version {
 
 sub bibtex {
     # Returns: N/A
-    if($opt::tollef and not $opt::gnu) {
-	print "WARNING: YOU ARE USING --tollef. IF THINGS ARE ACTING WEIRD USE --gnu.\n";
-    }
     print join("\n",
 	       "Academic tradition requires you to cite works you base your article on.",
 	       "When using programs that use GNU Parallel to process data for publication please cite:",
@@ -3022,8 +3020,10 @@ sub bibtex {
 	       "",
 	       "This helps funding further development.",
 	       "",
-	       "If you pay 10000 EUR you should feel free to use GNU Parallel without citing.\n",
+	       "If you pay 10000 EUR you should feel free to use GNU Parallel without citing.",
-	       ""
+	       "",
+	       "If you send a copy of your published article to tange\@gnu.org, it will be",
+	       "mentioned in the release notes of next version of GNU Parallel.\n\n",
         );
     while(not -e $ENV{'HOME'}."/.parallel/will-cite") {
 	print "\nType: 'will cite' and press enter.\n> ";

src/parallel.pod

@@ -4263,6 +4263,9 @@ change your alias to a script.
 Report bugs to <bug-parallel@gnu.org> or
 https://savannah.gnu.org/bugs/?func=additem&group=parallel
 
+See a perfect bug report on
+https://lists.gnu.org/archive/html/bug-parallel/2015-01/msg00000.html
+
 Your bug report should always include:
 
 =over 2