cdo 1.2.3 → 1.2.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 41b9ed1d2a5441fa063aaa7f3c341e825662b2d5
+  metadata.gz: 0596d2635271ae69ea1ea758d38f8481c3f04e13
+  data.tar.gz: 3ca1b3a218e5797071abaa01174fc68fb00f8095
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+  data.tar.gz: f1b5fed0c1909a7ad84ff504b24c76232c78d1d72f741ec76dc73c2b7c4098aae2852942a75f2595c8fef47cfadf5a33244cc484837a2a3288b63d639488a07c

data/gemspec

@@ -3,18 +3,18 @@ $:.unshift File.join(File.dirname(__FILE__),"..","lib")
 
 spec = Gem::Specification.new do |s|
   s.name              = "cdo"
-  s.version           = '1.2.3'
+  s.version           = '1.2.5'
   s.platform          = Gem::Platform::RUBY
-  s.files             = ["lib/cdo.rb"] + ["gemspec","COPYING","README.rdoc","ChangeLog"]
+  s.files             = ["lib/cdo.rb"] + ["gemspec","LICENSE"]
   s.test_file         = "test/test_cdo.rb"
   s.description       = "Easy access to the Climate Data operators"
   s.summary           = "Easy access to the Climate Data operators"
   s.author            = "Ralf Mueller"
   s.email             = "stark.dreamdetective@gmail.com"
   s.homepage          = "https://code.zmaw.de/projects/cdo/wiki/Cdo%7Brbpy%7D"
-  s.extra_rdoc_files  = ["README.rdoc","COPYING"]
   s.license           = "GPLv2"
-  s.required_ruby_version = ">= 1.9"
+  s.required_ruby_version = ">= 2.0"
+  s.add_development_dependency('unifiedPlot')
 end
 
 # vim:ft=ruby

data/lib/cdo.rb

@@ -1,7 +1,9 @@
 require 'pp'
 require 'open3'
+require 'logger'
+require 'stringio'
 
-# Copyright (C) 2011-2012 Ralf Mueller, ralf.mueller@zmaw.de
+# Copyright (C) 2011-2013 Ralf Mueller, ralf.mueller@zmaw.de
 # See COPYING file for copying and redistribution conditions.
 # 
 # This program is free software; you can redistribute it and/or modify
@@ -17,15 +19,22 @@ require 'open3'
 # CDO calling mechnism
 module Cdo
 
-  VERSION = "1.2.3"
+  VERSION = "1.2.5"
+  @@file  = StringIO.new
 
   State = {
     :debug       => false,
     :returnCdf   => false,
     :operators   => [],
-    :forceOutput => true
+    :forceOutput => true,
+    :env         => {},
+    :log         => false,
+    :logger      => Logger.new(@@file),
   }
-  State[:debug] = true unless ENV['DEBUG'].nil?
+  State[:debug] = ENV.has_key?('DEBUG')
+  State[:logger].formatter = proc do |serverity, time, progname, msg|
+    msg
+  end
 
   @@CDO = ENV['CDO'].nil? ? 'cdo' : ENV['CDO']
 
@@ -89,17 +98,24 @@ module Cdo
     end
   end
 
+  def Cdo.env=(envHash)
+    State[:env] = envHash
+  end
+  def Cdo.env; State[:env]; end
+
   def Cdo.call(cmd)
     if (State[:debug])
       puts '# DEBUG ====================================================================='
+      pp Cdo.env unless Cdo.env.empty?
+      puts 'CMD: '
       puts cmd
       puts '# DEBUG ====================================================================='
     end
-    stdin, stdout, stderr, wait_thr = Open3.popen3(cmd)
+    stdin, stdout, stderr, wait_thr = Open3.popen3(Cdo.env,cmd)
 
     {
-      :stdout => stdout.read,
-      :stderr => stderr.read,
+      :stdout     => stdout.read,
+      :stderr     => stderr.read,
       :returncode => wait_thr.value.exitstatus
     }
   end
@@ -109,6 +125,7 @@ module Cdo
     case ofile
     when $stdout
       retvals = Cdo.call(cmd)
+      State[:logger].info(cmd+"\n") if State[:log]
       unless hasError(cmd,retvals)
         return retvals[:stdout].split($/).map {|l| l.chomp.strip}
       else
@@ -120,6 +137,7 @@ module Cdo
         ofile = MyTempfile.path if ofile.nil?
         cmd << "#{ofile}"
         retvals = call(cmd)
+        State[:logger].info(cmd+"\n") if State[:log]
         if hasError(cmd,retvals)
           raise ArgumentError,"CDO did NOT run successfully!"
         end
@@ -155,7 +173,7 @@ module Cdo
     # iStream could be another CDO call (timmax(selname(Temp,U,V,ifile.nc))
     puts "Operator #{sym.to_s} is called" if State[:debug]
     if getOperators.include?(sym.to_s)
-      io,opts = Cdo.parseArgs(args)
+      io, opts = Cdo.parseArgs(args)
       if @@outputOperatorsPattern.match(sym)
         run(" -#{sym.to_s}#{opts} #{io[:input]} ",$stdout)
       else
@@ -195,18 +213,22 @@ module Cdo
   def Cdo.debug=(value)
     State[:debug] = value
   end
-
   def Cdo.debug
     State[:debug]
   end
-
   def Cdo.forceOutput=(value)
     State[:forceOutput] = value
   end
-
   def Cdo.forceOutput
     State[:forceOutput]
   end
+  def Cdo.log=(value)
+    State[:log] = value
+  end
+
+  def Cdo.log
+    State[:log]
+  end
 
   def Cdo.version
     cmd     = @@CDO + ' 2>&1'
@@ -289,6 +311,11 @@ module Cdo
     end
   end
 
+  def Cdo.showlog
+    @@file.rewind
+    puts @@file.read
+  end
+
   #==================================================================
   # Addional operotors:
   #------------------------------------------------------------------
@@ -317,6 +344,11 @@ module Cdo
     NetCDF.open(iFile)
   end
 
+  def Cdo.openCdf(iFile)
+    Cdo.loadCdf unless State[:returnCdf] 
+    NetCDF.open(iFile,'r+')
+  end
+
   def Cdo.readArray(iFile,varname)
     filehandle = Cdo.readCdf(iFile)
     if filehandle.var_names.include?(varname)

data/test/test_cdo.rb

@@ -1,9 +1,15 @@
 $:.unshift File.join(File.dirname(__FILE__),"..","lib")
-require 'test/unit'
+
+require 'minitest/autorun'
 require 'cdo'
+require 'unifiedPlot'
 require 'pp'
 
-class TestCdo < Test::Unit::TestCase
+
+#===============================================================================
+def rm(files); files.each {|f| FileUtils.rm(f) if File.exists?(f)};end
+
+class TestCdo < Minitest::Test
 
   DEFAULT_CDO_PATH = 'cdo'
 
@@ -14,7 +20,7 @@ class TestCdo < Test::Unit::TestCase
     else
       assert_equal(DEFAULT_CDO_PATH,Cdo.getCdo)
     end
-    newCDO="#{ENV['HOME']}/bin/cdo"
+    newCDO="#{ENV['HOME']}/local/bin/cdo"
     if File.exist?(newCDO) then
       Cdo.setCdo(newCDO)
       assert_equal(true,Cdo.checkCdo)
@@ -29,6 +35,7 @@ class TestCdo < Test::Unit::TestCase
         assert(Cdo.getOperators.include?(op),"Operator '#{op}' not found")
       end
     }
+    assert(Cdo.respond_to?('diff')) # an alias
   end
   def test_listAllOperators
     print Cdo.operators.join("\n")
@@ -53,16 +60,10 @@ class TestCdo < Test::Unit::TestCase
     assert("1.4.3.1" < Cdo.version,"Version to low: #{Cdo.version}")
   end
   def test_args
-    #Cdo.Debug = true
-    #MyTempfile.setPersist(true)
-    ofile0 = MyTempfile.path
-    ofile1 = MyTempfile.path
-    ofile2 = MyTempfile.path
-    ofile3 = MyTempfile.path
-    Cdo.stdatm(0,20,40,80,200,230,400,600,1100,:output => ofile0)
-    Cdo.intlevel(0,10,50,100,500,1000,  :input => ofile0,:output => ofile1)
-    Cdo.intlevel([0,10,50,100,500,1000],:input => ofile0,:output => ofile2)
-    Cdo.sub(:input => [ofile1,ofile2].join(' '),:output => ofile3)
+    ofile0 = Cdo.stdatm(0,20,40,80,200,230,400,600,1100)
+    ofile1 = Cdo.intlevel(0,10,50,100,500,1000,  :input => ofile0)
+    ofile2 = Cdo.intlevel([0,10,50,100,500,1000],:input => ofile0)
+    ofile3 = Cdo.sub(:input => [ofile1,ofile2].join(' '))
     info = Cdo.infon(:input => ofile3)
     (1...info.size).each {|i| assert_equal(0.0,info[i].split[-1].to_f)}
   end
@@ -79,6 +80,9 @@ class TestCdo < Test::Unit::TestCase
     if Cdo.hasLib?("sz")
       ofile = Cdo.topo(:output => ofile,:options => "-z szip")
       assert_equal(["GRIB SZIP"],Cdo.showformat(:input => ofile))
+    else
+      ofile = Cdo.topo
+      assert_equal(["GRIB"],Cdo.showformat(:input => ofile))
     end
   end
   def test_chain
@@ -88,11 +92,13 @@ class TestCdo < Test::Unit::TestCase
   end
 
   def test_diff
-    Cdo.debug = true
-    diffv = Cdo.diffn(:input => "-random,r1x1 -random,r1x1")
+    diffv_ = Cdo.diffn(:input => "-random,r1x1 -random,r1x1")
+    diff_  = Cdo.diffv(:input => "-random,r1x1 -random,r1x1")
+    return
+
     assert_equal(diffv[1].split(' ')[-1],"random")
     assert_equal(diffv[1].split(' ')[-3],"0.53060")
-    diff  = Cdo.diff(:input => "-random,r1x1 -random,r1x1")
+    pp diff
     assert_equal(diff[1].split(' ')[-3],"0.53060")
   end
 
@@ -291,11 +297,11 @@ class TestCdo < Test::Unit::TestCase
     files = [fileA,fileB]
     assert_equal(Cdo.diffv(:input => files.join(' ')),
                  Cdo.diffv(:input => files))
-    assert_equal("0 of 2 records differ",Cdo.diffv(:input => files).last)
+    assert_nil(Cdo.diffv(:input => files).last)
     # check for operator input
-    assert_equal("0 of 2 records differ",Cdo.diffv(:input => ["-stdatm,0","-stdatm,0"]).last)
+    assert_nil(Cdo.diffv(:input => ["-stdatm,0","-stdatm,0"]).last)
     # check for operator input and files
-    assert_equal("0 of 2 records differ",Cdo.diffv(:input => ["-stdatm,0",fileB]).last)
+    assert_nil(Cdo.diffv(:input => ["-stdatm,0",fileB]).last)
   end
 
   def test_libs
@@ -303,13 +309,13 @@ class TestCdo < Test::Unit::TestCase
     assert(Cdo.hasLib?("nc4"),"netcdf4 support missing")
     assert(Cdo.hasLib?("netcdf"),"netcdf support missing")
     assert_equal(false,Cdo.hasLib?("boost"))
-    if 'thingol' == `hostname`.chomp
-      assert_equal('1.10.0',Cdo.libsVersion("grib_api")) if Cdo.hasLib?("grib_api") 
-      Cdo.debug  = true
-      assert(! Cdo.libs.has_key?('magics'),"Magics support shoud not be build in the system wide installation")
-      Cdo.setCdo('../../src/cdo')
-      assert(Cdo.libs.has_key?('magics'),"Magics support is expected in the local development binary")
-    end
+   #if 'thingol' == `hostname`.chomp
+   #  assert_equal('1.10.0',Cdo.libsVersion("grib_api")) if Cdo.hasLib?("grib_api") 
+   #  Cdo.debug  = true
+   #  warn "Found magics support" if Cdo.libs.has_key?('magics')
+   #  Cdo.setCdo('../../src/cdo')
+   #  assert(Cdo.libs.has_key?('magics'),"Magics support is expected in the local development binary")
+   #end
     assert_raise ArgumentError do
       Cdo.libsVersion("foo")
     end
@@ -342,10 +348,92 @@ class TestCdo < Test::Unit::TestCase
       Cdo.help(:notDefinedOP)
       Cdo.help
     end
+    def test_fillmiss
+      Cdo.debug = true
+      # check up-down replacement
+      rand = Cdo.setname('v',:input => '-random,r1x10 ', :options => ' -f nc',:output => '/tmp/rand.nc')
+      cdf  = Cdo.openCdf(rand)
+      vals = cdf.var('v').get
+      cdf.var('v').put(vals.sort)
+      cdf.sync
+      cdf.close
 
+      missRange = '0.3,0.8'
+      arOrg = Cdo.setrtomiss(missRange,:input => cdf.path,:returnMaArray => 'v')
+      arFm  = Cdo.fillmiss(:input => "-setrtomiss,#{missRange} #{cdf.path}",:returnMaArray => 'v')
+      arFm1s= Cdo.fillmiss2(:input => "-setrtomiss,#{missRange} #{cdf.path}",:returnMaArray => 'v')
+      vOrg  = arOrg[0,0..-1]
+      vFm   = arFm[0,0..-1]
+      vFm1s = arFm1s[0,0..-1]
+      UnifiedPlot.linePlot([{:y => vOrg, :style => 'line',:title => 'org'},
+                            {:y => vFm,  :style => 'points',:title => 'fillmiss'},
+                            {:y => vFm1s,:style => 'points',:title => 'fillmiss2'}],
+                            plotConf: {:yrange => '[0:1]'},title: 'r1x10')
+      # check left-right replacement
+      rand = Cdo.setname('v',:input => '-random,r10x1 ', :options => ' -f nc',:output => '/tmp/rand.nc')
+      cdf  = Cdo.openCdf(rand)
+      vals = cdf.var('v').get
+      cdf.var('v').put(vals.sort)
+      cdf.sync
+      cdf.close
 
+      missRange = '0.3,0.8'
+      arOrg = Cdo.setrtomiss(missRange,:input => cdf.path,:returnMaArray => 'v')
+      arFm  = Cdo.fillmiss(:input => "-setrtomiss,#{missRange} #{cdf.path}",:returnMaArray => 'v')
+      arFm1s= Cdo.fillmiss2(:input => "-setrtomiss,#{missRange} #{cdf.path}",:returnMaArray => 'v')
+      vOrg  =  arOrg[0..-1,0]
+      vFm   =   arFm[0..-1,0]
+      vFm1s = arFm1s[0..-1,0]
+      UnifiedPlot.linePlot([{:y => vOrg, :style => 'line',:title => 'org'},
+                            {:y => vFm,  :style => 'points',:title => 'fillmiss'},
+                            {:y => vFm1s,:style => 'points',:title => 'fillmiss2'}],
+                            plotConf: {:yrange => '[0:1]'},title: 'r10x1')
+    end
   end
 
+  def test_env
+    oTag     = 'test_env_with_splitlevel_'
+    levels   = [0,10,100]
+    expected = levels.map {|l| "test_env_with_splitlevel_000#{l.to_s.rjust(3,'0')}"}
+    # clean up first
+    rm(Dir.glob(oTag+'*'))
+
+    # oType = grb (default)
+    ofiles = expected.map {|f| f += '.grb'}
+    Cdo.splitlevel(input: "-stdatm,0,10,100",output: oTag)
+    assert_equal(ofiles,Dir.glob(oTag+'*').sort)
+    rm(ofiles)
+
+    # oType = nc, from cdo options
+    ofiles = expected.map {|f| f += '.nc'}
+    Cdo.splitlevel(input: "-stdatm,0,10,100",output: oTag,options: '-f nc')
+    assert_equal(ofiles,Dir.glob(oTag+'*').sort)
+    rm(ofiles)
+
+    # oType = nc, from input type
+    ofiles = expected.map {|f| f += '.nc'}
+    Cdo.splitlevel(input: Cdo.stdatm(0,10,100,options: '-f nc'),output: oTag)
+    assert_equal(ofiles,Dir.glob(oTag+'*').sort)
+    rm(ofiles)
+
+    # oType = nc, from input ENV
+    ofiles = expected.map {|f| f += '.nc2'}
+    Cdo.env = {'CDO_FILE_SUFFIX' => '.nc2'}
+    Cdo.splitlevel(input: Cdo.stdatm(0,10,100,options: '-f nc'),output: oTag)
+    assert_equal(ofiles,Dir.glob(oTag+'*').sort)
+    rm(ofiles)
+
+    # oType = nc, from input ENV setting for each call
+    ofiles = expected.map {|f| f += '.nc2'}
+    Cdo.splitlevel(input: Cdo.stdatm(0,10,100,options: '-f nc'),output: oTag,env: {'CDO_FILE_SUFFIX' => '.nc2'})
+    assert_equal(ofiles,Dir.glob(oTag+'*').sort)
+    rm(ofiles)
+  end
+  def test_log
+    Cdo.log = true
+    Cdo.topo
+    Cdo.showlog
+  end
 end
 
 #  # Calling simple operators

metadata

@@ -1,28 +1,38 @@
 --- !ruby/object:Gem::Specification
 name: cdo
 version: !ruby/object:Gem::Version
-  version: 1.2.3
+  version: 1.2.5
 platform: ruby
 authors:
 - Ralf Mueller
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-09-23 00:00:00.000000000 Z
-dependencies: []
+date: 2015-06-02 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: unifiedPlot
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 description: Easy access to the Climate Data operators
 email: stark.dreamdetective@gmail.com
 executables: []
 extensions: []
-extra_rdoc_files:
-- README.rdoc
-- COPYING
+extra_rdoc_files: []
 files:
-- lib/cdo.rb
+- LICENSE
 - gemspec
-- COPYING
-- README.rdoc
-- ChangeLog
+- lib/cdo.rb
 - test/test_cdo.rb
 homepage: https://code.zmaw.de/projects/cdo/wiki/Cdo%7Brbpy%7D
 licenses:
@@ -34,20 +44,19 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
-      version: '1.9'
+      version: '2.0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.3
+rubygems_version: 2.4.5
 signing_key: 
 specification_version: 4
 summary: Easy access to the Climate Data operators
 test_files:
 - test/test_cdo.rb
-has_rdoc: 

data/ChangeLog

@@ -1,7 +0,0 @@
-1.0.0 2011-12-14: initial version 
-1.0.1 2011-12-15: bugix release
-1.0.2 2012-01-11: return NetCDF/NArray (optional)
-1.0.3 2012-01-17: bugfix for NArray return values
-		  remove chainCall method - can be replaced by setting :in
-		  speed up by reuse operator list instead of computing it
-		  every time

data/README.rdoc

@@ -1,64 +0,0 @@
-= Cdo.rb - Use Ruby to access the power of CDO
-
-This package contains the module Cdo, which implements a ruby style access to
-the Climate Data operators CDO. CDO is a command line tool for processing
-gridded data. Its main focus if climate data, but it can by used for other
-purposes to. It accepts input formats GRIB1, GRIB2, NetCDF and several Fortran
-binary formats.
-
-== Installation
-
-=== Gem Installation
-
-Download and installCdo with the following:
-
-   gem install cdo
-
-=== Requirements
-
-Cdo.rb requires a working CDO binary, but has not special requirement to Ruby
-
-== Usage
-
-=== Run operators
-
-* File information
-    
-    Cdo.infov(:input => ifile)
-    Cdo.showlevels(:input => ifile)
-
-* Operators with regular output files
-
-    Cdo.timmin(:input => ifile,:output => ofile)
-
-* Operators with options
-
-    Cdo.remap([gridfile,weightfile],:input => ifile, :output => ofile)
-
-* Set global CDO options
-
-   Cdo.copy(:input => ifile, :output => ofile,:options => "-f nc4")
-
-More examples can be found in test/cdo-examples.rb.
-
-=== Tempfile helpers
-
-Cdo.rb includes a simple tempfile wrapperm, which make live easier, when write your own scripts with Cdo.rb,m
-
-== Support, Issues, Bugs, ...
-
-Please use the forum or ticket system of CDOs official web page: http://code.zmaw.de/projects/cdo
-
-== License
-
-Cdo.rb makes use of the GPLv2D License, see COPYING
-
----
-
-= Other stuff
-
-Author::   Ralf Mueller <stark.dreamdetective@gmail.com>
-Requires:: CDO version 1.5.x
-License::  Copyright 2011-2012 by Ralf Mueller
-           Released under GPLv2 license.  See the COPYING
-           file included in the distribution.