gentooboontoo-gphys 0.6.1.3 → 1.3.1.1

data/LICENSE.txt

@@ -0,0 +1,34 @@
+GPhys is copyrighted free software by Takeshi Horinouchi and
+GFD Dennou Club (http://www.gfd-dennou.org/).
+
+Copyright 2003-2013 (C) Takeshi Horinouchi and GFD Dennou Club
+(http://www.gfd-dennou.org/) All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+   1. Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright
+      notice, this list of conditions and the following disclaimer in
+      the documentation and/or other materials provided with the
+      distribution.
+
+THIS SOFTWARE IS PROVIDED BY GFD DENNOU CLUB AND CONTRIBUTORS ``AS IS'' 
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GFD DENNOU CLUB OR
+CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+The views and conclusions contained in the software and documentation
+are those of the authors and should not be interpreted as representing
+official policies, either expressed or implied, of Takeshi Horinouchi
+and GFD Dennou Club.

data/README

@@ -1,32 +1,30 @@
+= GPhys -- a class of multi-dimensional Gridded Physical quantities
 
-GPhys -- a class of multi-dimensional Gridded Physical quantities
+== Description and general information
+See http://ruby.gfd-dennou.org/products/gphys/
 
-by T Horinouchi
-2003/05/14
+== Licence
+See LICENSE.txt
 
-* DESCRIPTION
+== Dependent libraries 
 
-To be written. 
-See http://ruby.gfd-dennou.org/workshop200303/horinout/ (in Japanese).
+As of GPhys 1.2.0. 
 
-* INSTALL
+Dependent libraries and their versions (required or recommended):
+* Ruby 1.8 or 1.9
+* NArray: 0.5.7 or later
+* NumRu::Misc : 0.1.0 or later
+* NumRu::Units : 1.7 or later
+* NArrayMiss : 1.2.4 or later
+* RubyNetCDF : 0.6.6 or later
+* RubyDCL : 1.6.1 or later
+* Ruby-FFTW3 : 0.3 or later
+* RubyGSL : 1.14 or later
 
-# ruby ./install.rb
+Recommended libraries:
+* Ruby-LAPACK : 1.5 or later (used for efficiency if installed)
 
-* SAMPLE PROGRAMS
-
-Each library file has a sample program part, which is invoked by
-directly feeding the file to Ruby. For example
-
-% cd lib
-% ruby ggraph.rb
-
-% cd lib/gphys
-% ruby gphys.rb
-% ruby gphys_netcdf_io.rb
-
-Sample programs are also found in the
-
-   ./sample
-
-diredtory.
+Optional dependent libraries:
+* rb-GRIB : 0.2.0 or later (used if installed and explicitly specified.
+  Needed to read GRIB2 data. But rb-GRIB 0.2.0 is experimental, so it
+  is not recommended. Wait for a future version.)

data/bin/gdir_client

@@ -1,9 +1,27 @@
+#!/usr/bin/env ruby
 irb -r numru/gdir_connect_ftp-like
 
-# =begin
-# =gdir_client
-# A client of gdir_server using irb.
-# 
-# This command is just equal to
-#    irb -r numru/gdir_connect_ftp-like
-# =end
+=begin
+= NAME
+
+gdir_client - A client of gdir_server using irb.
+
+= SYNOPSIS
+
+  % gdir_client top_dir [[host:]port] [-a allowed_address] ...
+
+= DESCRIPTION
+
+((*gdir_client*)) command is just equal to
+
+   irb -r numru/gdir_connect_ftp-like
+
+= OPTIONS
+
+same as gdir_server
+
+= SEE ALSO
+
+((*gdir_server(1)*))
+
+=end

data/bin/gdir_server

@@ -1,31 +1,37 @@
 #!/usr/bin/env ruby
-
 =begin
-=Command gdir_server 
-
-A stand-alone server program to provide a directory service of GPHys
-objects by using GDir.
+= NAME
 
-==Usage
+gdir_server - A stand-alone server program to provide a directory service of GPhys
 
-At the  command line,
+= SYNOPSIS
 
    % gdir_server top_dir [[host:]port] [-a allowed_address]..
 
-where 
-* top_dir: can be ".", "/", or whatever directory in your files system.
-* host: host address (name or ip) -- use it if you want to specify
+= DESCRIPTION
+
+A stand-alone server program to provide a directory service of GPhys
+objects by using GDir.
+
+= OPTION
+
+:top_dir: 
+  can be ".", "/", or whatever directory in your files system.
+:host: 
+  host address (name or ip) -- use it if you want to specify
   explicitly, such as "localhost", which is useful for ssh port forwarding.
-* port: the port number you want to assign (internally determined
+:port: 
+  the port number you want to assign (internally determined
   if not specified). A complete URI is printed if the server is started.
-* -a: limits accesses from remote hosts only to the ones specified.
+:-a: 
+  limits accesses from remote hosts only to the ones specified.
   Can be repeated multiple times. (Need the space between '-a' and the rest)
 
-==Examples
     % gdir_server . 12345
     % gdir_server . localhost:12345 -a all
     % gdir_server . -a hoge.hero.org -a localhost
     % gdir_server . 12345 -a '192.168.1.*' -a localhost
+
 =end
 
 require "drb/drb"

data/bin/gpaop

@@ -1,48 +1,61 @@
 #!/usr/bin/env ruby
 =begin
-=gpaop
+= NAME
 
-   Carrying out an arithmetric operation (addition, subtraction, 
-   multiplication and division) multiple GPhys variables. 
+gpaop - Carrying out an arithmetric operation multiple GPhys variables.
 
-==USAGE 
-
-   Operation, gphys1 (+-*/) gphys2 (+-*/) gphys3 (+-*/) ... is performed 
-   by the following  command formats. 
+= USAGE
 
    % gpaop -f func [options] gturl1 gturl2 ...
 
-     Format of 'gturl*' is 'path@varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]'
+= DESCRIPTION
+
+Carrying out an arithmetric operation (addition, subtraction, 
+multiplication and division) multiple GPhys variables. 
+
+= SYNOPSYS 
+
+Operation, gphys1 (+-*/) gphys2 (+-*/) gphys3 (+-*/) ... is performed 
+by the following  command formats. 
+
+  % gpaop -f func [options] gturl1 gturl2 ...
+
+Format of 'gturl*' is 'path[@|/]varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]'
 
-   % gpaop -f func --var varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]] \
-        [options] gtfile1 gtfile2 ...
+  % gpaop -f func --var varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]] [options] gtfile1 gtfile2 ...
 
-  * Commands which compute arithmetric operation on gphys variables are 
-    successively installed by linking this sciript as a 
-    "gp+(add|sub|multi|div)". You can omit '--func' option by using 
-    these commands.  
+Commands which compute arithmetric operation on gphys variables are 
+successively installed by linking this sciript as a 
+"gp+(add|sub|multi|div)". You can omit '--func' option by using 
+these commands.  
 
-==OPTIONS
+= OPTIONS
 
-   -f func  --func func    : kind of operation (add|sub|multi|div|)
-   -v url   --var url      : set the variable name and slicing parameters.
-   -h,      --help         : print this message. 
-   -o file, --output file  : output filename (optional). 
-                           : Default output filename is 'gphys.nc'.
+:-f func, --func func
+  kind of operation (add|sub|multi|div|)
+:-v url, --var url
+  set the variable name and slicing parameters.
+:-h, --help
+  print this message. 
+:-o file, --output file
+  output filename (optional). 
+  Default output filename is 'gphys.nc'.
 
-==EXAMPLE
+Usage Examples
 
-   % gpaop -f add gtool.nc@temp gtool.nc@temp
-   % gpaop -f sub gtool.nc@temp,t=1 gtool.nc@temp,t=2
+ % gpaop -f add gtool.nc@temp gtool.nc@temp
+ % gpaop -f sub gtool.nc@temp,t=1 gtool.nc@temp,t=2
 
-   % gpaop -f multi --var temp gtool*.nc
-   % gpaop -f div --var temp,t=1 gtool*.nc
-   % gpaop -o temp.nc --var temp,t=1 gtool*.nc
+ % gpaop -f multi --var temp gtool*.nc
+ % gpaop -f div --var temp,t=1 gtool*.nc
+ % gpaop -o temp.nc --var temp,t=1 gtool*.nc
 
-==HISTORY
+= HISTORY
 
   2005/08/21  S Takehiro (created)
-  2005/08/23  S Takehiro (common methods to gp* command moved to gpcommon.rb)
+  2005/08/23  S Takehiro (common methods to gp* commandmoved to gpcommon.rb)
+  2010/03/10  Y SASAKI (change help block into RD format)
+  2012/02/19  S Takehiro (description for gturl format updated)
 
 =end
 

data/bin/gpcat

@@ -1,29 +1,37 @@
 #!/usr/bin/env ruby
 =begin
+= NAME
 
-=gpcat
+gpcat - Read a variable in multiple NetCDF files, concatenate and write them to a single netcdf file. 
 
-Read a variable in multiple NetCDF files, concatenate and write them to a single netcdf file. 
+= DESCRIPTION
 
-==USAGE
+((*gpcat*)) is command line tools for read a variable in multiple
+  NetCDF files, concatenate and write them to a single netcdf file.
 
-  % gpcat -v VAR [options] FILE1 FILE2...
+= USAGE
 
+  % gpcat -v VAR [options] FILE1 FILE2...
 
-==OPTIONS
+= OPTIONS
 
-      -h,      --help         : print this message. 
-      -v var,  --variable var : variable name (required).
-      -s sfmt, --slice  sfmt  : slice,thinnng  (optional).
-      -o file, --output file  : output filename (optional).
-                              : Default output filename is 'gphys.nc'.
+:-h, --help
+   print this message. 
+:-v var, --variable var
+   variable name (required).
+:-s sfmt, --slice sfmt
+   slice,thinnng  (optional).
+:-o file, --output file
+   output filename (optional). Default output filename is 'gphys.nc'.
+                                 
 
-==HISTORY
+= HISTORY
 
   2005/05/17  S Takehiro (created)
   2005/08/10  S Takehiro (utilize internal function for printing help message)
   2005/08/21  S Takehiro (global attributes copied to the output file)
   2005/08/23  S Takehiro (common methods to gp* command moved to gpcommon.rb)
+  2010/03/10  Y SASAKI (change help block into RD format)
 
 =end
 

data/bin/gpcut

@@ -1,27 +1,36 @@
 #!/usr/bin/env ruby
 =begin
-=gpcut
+= NAME
 
-Extract, slicing and thinning a GPhys variable.
+gpcut - Extract, slicing and thinning a GPhys variable.
 
-==USAGE 
+= DESCRIPTION
 
-   % gpcut [options] path@varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]
+((*gpcut*)) is command line tools for extract, slicing and thinning a GPhys variables.
 
-==OPTIONS
+= USAGE 
 
-   -h,      --help         : print this message. 
-   -m dim,  --mean dim     : average along dim axis (optional).
-   -o file, --output file  : output filename (optional). 
-                           : Default output filename is 'gphys.nc'.
+   % gpcut [options] path[@|/]varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]
 
-==HISTORY
+= OPTIONS
+
+:-h, --help
+  print this message. 
+:-m dim, --mean dim
+   average along dim axis (optional).
+:-o file, --output file
+   output filename (optional). 
+   Default output filename is 'gphys.nc'.
+
+= HISTORY
 
   2005/05/17  S Takehiro (created)
   2005/07/15  S Takehiro (open_gturl method is used for opening gphys variable)
   2005/08/10  S Takehiro (utilize internal function for printing help message)
   2005/08/21  S Takehiro (global attributes copied to the output file)
   2005/08/23  S Takehiro (common methods to gp* command moved to gpcommon.rb)
+  2010/03/10  Y SASAKI (change help block into RD format)
+  2012/02/19  S Takehiro (description for gturl format updated)
 
 =end
 
@@ -33,7 +42,7 @@ require "getoptlong"
 
 #------------------------ Default Settings ------------------------
 Output_default = 'gphys.nc'
-URLfmt = "path@varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]"
+URLfmt = "path[@|/]varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]"
 
 #---------------------- Option Configuration ----------------------
 parser = GetoptLong.new(

data/bin/gpedit

@@ -1,5 +1,37 @@
 #!/usr/bin/env ruby
+=begin
+= NAME
 
+:gpedit:
+   Create or overwrite the attributes of a variable specified by
+   a gtool4-type URL (Only netCDF files are supported).
+  
+= USAGE
+
+  % gpedit [options] path[@|/][varname:var_attr=...][varname|+global_attr]
+
+= EXAMPLES
+
+* Add
+        % gpedit data.nc@temp:units=W/m
+        % gpedit -a data.nc@temp:missing_value=-2.0e20
+        % gpedit --add data.nc@temp+title=\"surface temperature\"
+
+* Delete
+        % gpedit -d data.nc@lon:topology
+        % gpedit --delete data.nc@lon+Conventions
+"
+=  HISTORY
+
+   2012/02/19  S Takehiro (gturl format updated)
+   2010/03/10  Y SASAKI (change help block into RD format)
+   2007/07/18  Y. Morikawa  'gpattr' is renamed to 'gpedit'
+   2006/09/29  Y. Morikawa  A value looks like numeric is treated as a numerical value
+   2005/01/09  Y. Morikawa
+   2005/01/07  D. Tsukahara
+
+
+=end
 ##################################################
 #= gpedit
 #== SYNOPSIS
@@ -10,6 +42,7 @@ SYNOP
 
 #== HISTORY
 #
+#   2010/03/10  Y SASAKI (change help block into RD format)
 #   2007/07/18  Y. Morikawa  'gpattr' is renamed to 'gpedit'
 #   2006/09/29  Y. Morikawa  A value looks like numeric is treated as a numerical value
 #   2005/01/09  Y. Morikawa
@@ -110,8 +143,11 @@ def parse_gturl_for_attr(gturl)
   if /(.*)@(.*)/ =~ gturl
     file = $1
     var = $2
+  elsif /(.*)\/(.*)/ =~ gturl
+    file = $1
+    var = $2
   else
-    url_error "'@' between path & variable is not found"
+    url_error "'[@|/]' between path & variable is not found"
   end
   if /(.*):(.*)/ =~ var
     var_name = var.split(":")[0]

data/bin/gplist

@@ -1,22 +1,23 @@
 #!/usr/bin/env ruby
 =begin
-=gplist
+= NAME
 
-Print out info on GPhys-compatible variables in specified files.
+gplist - print out info on GPhys-compatible variables in specified files.
 
-==Usage 
+= Usage 
 
    % gplist [-h] [ FILES... ]
 
 where FILES are plane files (NetCDF, grib, GrADS control..) or directories. 
 If omitted, equivalent to specifing the current directory.
 
-==HISTORY
+= HISTORY
 
   2005/05/15  S Takehiro (created)
   2005/06/21  T Horinouchi (modified to use GDir (non-recursive version))
   2005/08/10  S Takehiro (utilize internal function for printing help message)
   2005/08/23  S Takehiro (common methods to gp* command moved to gpcommon.rb)
+  2010/03/10  Y SASAKI (change help block into RD format)
 
 =end