ruby-netcdf 0.7.1 → 0.8.0

data/ruby-netcdf-bigmem.gemspec

@@ -0,0 +1,29 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'numru/netcdf/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "ruby-netcdf-bigmem"
+  spec.version       = NumRu::NetCDF::VERSION
+  spec.authors           = ["Takeshi Horinouchi", "Tsuyoshi Koshiro",\
+    "Shigenori Otsuka", "Seiya Nishizawa", "T Sakakima"]
+  spec.email            = ['eriko@gfd-dennou.org']
+
+  spec.summary          = %q{Ruby interface to NetCDF}
+  spec.description      = %q{RubyNetCDF is the Ruby interface to the NetCDF library built on the NArray library, which is an efficient multi-dimensional numeric array class for Ruby. This version works with Ruby2.0.}
+
+  spec.homepage         = 'http://www.gfd-dennou.org/arch/ruby/products/ruby-netcdf/'
+  spec.licenses         = ["BSD-2-Clause"]
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.test_files    = spec.files.grep(%r{^(test|demo)/})
+  spec.require_paths = ["ext","lib"]
+  spec.extensions << "ext/numru/extconf.rb"
+
+  spec.required_ruby_version = Gem::Requirement.new(">= 1.8")
+  spec.add_runtime_dependency(%q<narray-bigmem>, [">= 0"])
+  spec.add_runtime_dependency(%q<narray_miss-bigmem>, [">= 0"])
+  spec.add_development_dependency "test-unit"
+
+end

data/ruby-netcdf.gemspec

@@ -1,34 +1,29 @@
 # coding: utf-8
 lib = File.expand_path('../lib', __FILE__)
 $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
-require 'version'
+require 'numru/netcdf/version'
 
 Gem::Specification.new do |spec|
   spec.name          = "ruby-netcdf"
-  spec.version       = Ruby::Netcdf::VERSION
+  spec.version       = NumRu::NetCDF::VERSION
   spec.authors           = ["Takeshi Horinouchi", "Tsuyoshi Koshiro",\
     "Shigenori Otsuka", "Seiya Nishizawa", "T Sakakima"]
   spec.email            = ['eriko@gfd-dennou.org']
 
-  #if spec.respond_to?(:metadata)
-  #  spec.metadata['allowed_push_host'] = "TODO: Set to 'http://mygemserver.com' to prevent pushes to rubygems.org, or delete to allow pushes to any server."
-  #end
-
   spec.summary          = %q{Ruby interface to NetCDF}
-  spec.description      = %q{RubyNetCDF is the Ruby interface to the NetCDF library built on the NArray library, which is an efficient multi-dimensional numeric array class for Ruby.}
+  spec.description      = %q{RubyNetCDF is the Ruby interface to the NetCDF library built on the NArray library, which is an efficient multi-dimensional numeric array class for Ruby. This version works with Ruby2.0.}
 
   spec.homepage         = 'http://www.gfd-dennou.org/arch/ruby/products/ruby-netcdf/'
-  spec.licenses         = ["GFD Dennou Club"]
+  spec.licenses         = ["BSD-2-Clause"]
 
   spec.files         = `git ls-files -z`.split("\x0")
   spec.test_files    = spec.files.grep(%r{^(test|demo)/})
-  #spec.bindir        = "exe"
-  #spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
-  spec.require_paths = ["lib"]
+  spec.require_paths = ["ext","lib"]
+  spec.extensions << "ext/numru/extconf.rb"
 
-  spec.required_ruby_version = Gem::Requirement.new(">= 1.6")
+  spec.required_ruby_version = Gem::Requirement.new(">= 1.8")
   spec.add_runtime_dependency(%q<narray>, [">= 0"])
   spec.add_runtime_dependency(%q<narray_miss>, [">= 0"])
+  spec.add_development_dependency "test-unit"
 
-  spec.extensions << "extconf.rb"
 end

data/test/aref_aset.rb

@@ -1,37 +1,67 @@
+require 'test/unit'
 require 'numru/netcdf'
 include NumRu
-s = 'tmp.nc'
-f = NetCDF.create(s)
-f.redef
-dx = f.def_dim('x',5)
-dy = f.def_dim('y',3)
-v = f.def_var('x','sfloat',[dx])
-v2 = f.def_var('x2',NArray::SFLOAT,[dx])
-vxy = f.def_var('xy','sfloat',[dx,dy])
-f.enddef
-v.put([1,2,3,4,5])
-p 'testing []= ...'
-v[{0..3=>2}]=[100,500]
-v[1]=999
-v[3..4]=[-99,-99]
-v2.put(666)
-v2[0..2]=777
-vxy.put(NArray.sfloat(5,3).indgen!)
-vxy[[2,0],[0,2,1]] = [[1,2],[3,4],[5,6]]
-vxy[1,[2,0,1]] = [10,20,30]
-vxy[[4,3],2] = [100,200]
 
-f.close
+class TestArefAset < Test::Unit::TestCase
+  def startup  # call once before tests
+  end
+  def setup     # call before each test
+    @s = 'tmp.nc'
+  end
+  def teardown  # call after each test
+  end
+  def shutdown  # call once after tests
+  end
 
-f = NetCDF.open(s)
-v = f.var('x')
-p 'testing [] ...'
-p '*0*',v[{0..3=>2}]
-p '*1*',v[1]
-p '*2*',v[3..4],v.rank
-p '*3*',v[[2,0,0]]
-vxy = f.var('xy')
-p '*4*',vxy[[2,0],[0,2,1]]
-p '*5*',vxy[1,[2,0,1]]
-p '*6*',vxy[[4,3],2]
-f.close
+  def test_netcdf_create
+    f = NetCDF.create(@s)
+    f.redef
+    dx = f.def_dim('x',5)
+    dy = f.def_dim('y',3)
+    v = f.def_var('x','sfloat',[dx])
+    v2 = f.def_var('x2',NArray::SFLOAT,[dx])
+    vxy = f.def_var('xy','sfloat',[dx,dy])
+    f.enddef
+    v.put([1,2,3,4,5])
+    v[{0..3=>2}]=[100,500]
+    v[1]=999
+    v[3..4]=[-99,-99]
+    v2.put(666)
+    v2[0..2]=777
+    vxy.put(NArray.sfloat(5,3).indgen!)
+    vxy[[2,0],[0,2,1]] = [[1,2],[3,4],[5,6]]
+    vxy[1,[2,0,1]] = [10,20,30]
+    vxy[[4,3],2] = [100,200]
+    f.close
+  end
+
+  def test_netcdf_open
+    unless File.exist?(@s)
+      test_netcdf_create
+    else
+      f = NetCDF.open(@s)
+      v = f.var('x')
+      assert_equal v[{0..3=>2}], NArray[100.0,500.0].to_f
+      assert_equal v[1], NArray[999.0].to_f
+      assert_equal v[3..4], NArray[-99.0,-99.0].to_f
+      assert_equal v.rank, 1
+      assert_equal v[[2,0,0]], NArray[500.0,100.0,100.0].to_f
+      vxy = f.var('xy')
+      assert_equal vxy[[2,0],[0,2,1]],
+                   NArray[[1.0,2.0],[3.0,4.0],[5.0,6.0]].to_f
+      assert_equal vxy[1,[2,0,1]],
+                   NArray[10.0,20.0,30.0].to_f
+      assert_equal vxy[[4,3],2],
+                   NArray[100.0,200.0].to_f
+      f.close
+    end
+    if File.exist?(@s)
+      begin
+        File.delete(@s)
+      rescue
+        p $!
+      end
+    end
+  end
+
+end

data/test/char_var.rb

@@ -1,25 +1,36 @@
-## test of "char" variables
-
+require 'test/unit'
 require 'numru/netcdf'
 include NumRu
-s = 'tmp.nc'
-f = NetCDF.create(s)
-d = f.def_dim('x',5)
-v = f.def_var('x','char',[d])
-tv = f.def_var('text','char',[d])
-f.enddef
-v.put( NArray.byte(5).indgen! )
-tv.put( NArray.to_na("hello","byte",5) )
-tv.put( NArray.to_na("LO","byte",2), 'start'=>[3] )
-tv.put( NArray.to_na("H","byte",1), 'index'=>[0] )
-f.close
-
-f = NetCDF.open(s)
-v = f.var('x')
-p v.get
-tv = f.var('text')
-p tv.get
-p tv.get.to_s
-
+class TestCharVar < Test::Unit::TestCase
+  def setup
+    @s = 'tmp.nc'
+    f = NetCDF.create(@s)
+    d = f.def_dim('x',5)
+    v = f.def_var('x','char',[d])
+    tv = f.def_var('text','char',[d])
+    f.enddef
+    v.put( NArray.byte(5).indgen! )
+    tv.put( NArray.to_na("hello","byte",5) )
+    tv.put( NArray.to_na("LO","byte",2), 'start'=>[3] )
+    tv.put( NArray.to_na("H","byte",1), 'index'=>[0] )
+    f.close
+  end
+  def teardown
+    if File.exist?(@s)
+      begin
+        File.delete(@s)
+      rescue
+        p $!
+      end
+    end
+  end
 
+  def test_char_var
+  f = NetCDF.open(@s)
+  v = f.var('x')
+  assert_equal v.get, NArray.byte(5).indgen!
+  tv = f.var('text')
+  assert_equal tv.get.to_s, "HelLO"
+  end
 
+end

data/test/clone.rb

@@ -1,54 +1,49 @@
+require 'test/unit'
 require 'numru/netcdf'
 include NumRu
-s = 'tmp.nc'
-#f = NetCDF.new(s,'rw')
-f = NetCDF.create(s)
-f.redef
-d = f.def_dim('x',3)
-v = f.def_var('x','sfloat',[d])
-a = f.put_att('long_name','xx')
-f.enddef
-v.put([1,2,3])
-f.taint
-f.freeze
-f2 = f.clone
-p 'netcdf  clone'
-p f.path, f2.path   
-p f.tainted?, f2.tainted?, f.frozen?, f2.frozen?  
-
-p 'netcdf  dup'
-f3 = f.dup
-p f.tainted?, f3.tainted?, f.frozen?, f3.frozen?  
-
-p 'netcdfdim'
-d.taint
-d2 = d.clone
-d3 = d.dup
-p d.tainted?, d2.tainted?, d3.tainted?
-
-p 'netcdfvar'
-v.taint
-v2 = v.clone
-v3 = v.dup
-p v.tainted?, v2.tainted?, v3.tainted?
-
-p 'netcdfatt'
-a.taint
-a2 = a.clone
-a3 = a.dup
-p a.tainted?, a2.tainted?, a3.tainted?
-
-f.close
-
-p 'narray (for reference)'
-a = NArray.float(3)
-a.taint
-b = a.clone
-p a.tainted?, b.tainted?  
-b = a.dup
-p a.tainted?, b.tainted?  
-
-
-
-
 
+class TestClone < Test::Unit::TestCase
+  def setup
+    @s = 'tmp.nc'
+    @f = NetCDF.create(@s)
+    @f.redef
+    @d = @f.def_dim('x',3)
+    @v = @f.def_var('x','sfloat',[@d])
+    @a = @f.put_att('long_name','xx')
+    @f.enddef
+    @v.put([1,2,3])
+    @f.freeze
+  end
+
+  def teardown
+    @f.close
+    if File.exist?(@s)
+      begin
+        File.delete(@s)
+      rescue
+        p $!
+      end
+    end
+  end
+
+  def test_clone_netcdf_path
+    f = @f.clone
+    assert_equal @f.path, f.path
+    assert(@f.frozen? == f.frozen?)
+    d = @d.clone
+    assert_equal @d, d
+    v = @v.clone
+    assert_equal @v, v
+    a = @a.clone
+    assert_equal @a, a
+  end
+
+  def test_clone_netcdf_dup
+    f = @f.dup
+    assert(@f.frozen? != f.frozen?)
+    # d = @d.dup
+    # v = @v.dup
+    # a = @a.dup
+  end
+
+end

data/test/create_tmp.rb

@@ -1,15 +1,19 @@
+require 'test/unit'
 require 'numru/netcdf'
-
-$DEBUG = true
 include NumRu
-file = NetCDF.create_tmp
-file.def_dim('x',5)
-file.put_att("history", __FILE__ )
-p file.path
-p file.att("history").get
-print "environment variable TEMP ="+(ENV['TEMP'] || '')+"\n"
-file2=file
-print "000\n"
-file.close
-GC.start
-print "aaa\n"
+class CreateTMP < Test::Unit::TestCase
+  def setup
+    @file = NetCDF.create_tmp
+    @file.def_dim('x',5)
+    @file.put_att("history", __FILE__ )
+  end
+  def teardown
+    @file.close
+    GC.start
+  end
+  def test_create_tmp
+    assert_equal @file.att("history").get, __FILE__
+    # print "environment variable TEMP ="+(ENV['TEMP'] || '')+"\n"
+    # file2 = @file
+  end
+end

data/test/def_var_with_dim.rb

@@ -1,14 +1,32 @@
+require 'test/unit'
 require 'numru/netcdf'
 include NumRu
-file = NetCDF.create("tmp.nc")
-var1 = file.def_var_with_dim("var1","sfloat",[6],["x"])
-var2 = file.def_var_with_dim("var2","sfloat",[6,3],["x","y"])
-var3 = file.def_var_with_dim("var3","sfloat",[3],["y"])
-var3 = file.def_var_with_dim("var4","sfloat",[0],["t"])
-att = var1.put_att("long_name","test")
-file.close
+class TestDefVarWithDim < Test::Unit::TestCase
+  def setup
+    @fname = "tmp.nc"
+    @file = NetCDF.create(@fname)
+    @var1 = @file.def_var_with_dim("var1","sfloat",[6],["x"])
+    @var2 = @file.def_var_with_dim("var2","sfloat",[6,3],["x","y"])
+    @var3 = @file.def_var_with_dim("var3","sfloat",[3],["y"])
+    @var3 = @file.def_var_with_dim("var4","sfloat",[0],["t"])
+    @att = @var1.put_att("long_name","test")
+    @file.close
+  end
+  def teardown
+    if File.exist?(@fname)
+      begin
+        File.delete(@fname)
+      rescue
+        p $!
+      end
+    end
+  end
 
-p var1 == nil
-p file == nil
-p att == nil
-p att == att, var1 ==var1, file == file
+  def test_def_var_with_dim
+    assert_not_nil @var1
+    assert_not_nil @var2
+    assert_not_nil @var3
+    assert_not_nil @file
+    assert_not_nil @att
+  end
+end

data/test/factor_offset.rb

@@ -1,53 +1,84 @@
+require 'test/unit'
 require 'numru/netcdf'
 include NumRu
 
-s = 'tmp.nc'
-f = NetCDF.create(s)
+class TestFactorOffset < Test::Unit::TestCase
+  def setup
+    @s = 'tmp.nc'
+    f = NetCDF.create(@s)
+    nx = 10
+    d = f.def_dim('x',nx)
+    v1 = f.def_var('v1','sint',[d])
+    v2 = f.def_var('v2','sint',[d])
+    v3 = f.def_var('v3','int',[d])
+    v1.put_att('scale_factor',0.1,'sfloat')
+    v1.put_att('add_offset',100.0,'sfloat')
+    v2.put_att('scale_factor',0.1,'sfloat')
+    v2.put_att('add_offset',100.0,'sfloat')
+    v3.put_att('scale_factor',0.1,'sfloat')
+    v3.put_att('add_offset',100.0,'sfloat')
+    f.enddef
+    v1.put( NArray.sint(nx).indgen!+100 )
+    v2.scaled_put( NArray.float(nx).indgen!+100 )
+    v3.scaled_put( NArray.float(nx).indgen!+100 )
+    f.close
+  end
 
-nx = 10
-d = f.def_dim('x',nx)
-v1 = f.def_var('v1','sint',[d])
-v2 = f.def_var('v2','sint',[d])
-v3 = f.def_var('v3','int',[d])
-v1.put_att('scale_factor',0.1,'sfloat')
-v1.put_att('add_offset',100.0,'sfloat')
-v2.put_att('scale_factor',0.1,'sfloat')
-v2.put_att('add_offset',100.0,'sfloat')
-v3.put_att('scale_factor',0.1,'sfloat')
-v3.put_att('add_offset',100.0,'sfloat')
-f.enddef
-v1.put( NArray.sint(nx).indgen!+100 )
-v2.scaled_put( NArray.float(nx).indgen!+100 )
-v3.scaled_put( NArray.float(nx).indgen!+100 )
-f.close
+  def teardown
+    if File.exist?(@s)
+      begin
+        File.delete(@s)
+      rescue
+        p $!
+      end
+    end
+  end
+  def test_originally_uscaled
+    f = NetCDF.open(@s)
+    v1 = f.var('v1')
+    v11 = v1.get
+    assert_equal v11,
+                 NArray[ 100, 101, 102, 103, 104, 105, 106, 107, 108, 109 ].to_i
+    v12 = v1.scaled_get
+    assert_equal v12,
+                 NArray[ 110.0, 110.1, 110.2, 110.3, 110.4, 110.5, 110.6, 110.7, 110.8, 110.9 ].to_type(NArray::SFLOAT)
+    f.close
+  end
 
+  def test_originally_scaled
+    f = NetCDF.open(@s)
+    v2 = f.var('v2')
+    v21 = v2.get
+    assert_equal v21,
+                 NArray[ 0, 10, 20, 30, 40, 50, 60, 70, 80, 90 ].to_i
+    v22 = v2.scaled_get
+    assert_equal v22,
+                 NArray[ 100.0, 101.0, 102.0, 103.0, 104.0, 105.0, 106.0, 107.0, 108.0, 109.0 ].to_type(NArray::SFLOAT)
+    f.close
+  end
 
-print "** originally unscaled\n"
-f = NetCDF.open(s)
-v1 = f.var('v1')
-v11 = v1.get
-v12 = v1.scaled_get
-p v11
-p v12
+  def test_originally_scaled_int_to_double
+    f = NetCDF.open(@s)
+    v3 = f.var('v3')
+    v31 = v3.get
+    assert_equal v31,
+                 NArray[ 0, 10, 20, 30, 40, 50, 60, 70, 80, 90 ].to_i
+    v32 = v3.scaled_get
+    assert_equal v32,
+                 NArray[ 100.0, 101.0, 102.0, 103.0, 104.0, 105.0, 106.0, 107.0, 108.0, 109.0 ].to_type(NArray::SFLOAT)
+    f.close
+  end
 
-print "** originally scaled\n"
-v2 = f.var('v2')
-v21 = v2.get
-v22 = v2.scaled_get
-p v21
-p v22
-
-print "** originally sclaed (int --> double)\n"
-v3 = f.var('v3')
-v31 = v3.get
-v32 = v3.scaled_get
-p v31
-p v32
-
-print "** unpack type fixed to sfloat\n"
-NetCDFVar.unpack_type = NArray::SFLOAT
-v33 = v3.scaled_get
-p v33
-NetCDFVar.unpack_type = NArray::INT
-v33 = v3.scaled_get
-p v33
+  def test_unpack_type_fixed_to_sfloat
+    f = NetCDF.open(@s)
+    v3 = f.var('v3')
+    NetCDFVar.unpack_type = NArray::SFLOAT
+    v33 = v3.scaled_get
+    assert_equal v33,
+                 NArray[ 100.0, 101.0, 102.0, 103.0, 104.0, 105.0, 106.0, 107.0, 108.0, 109.0 ].to_type(NArray::SFLOAT)
+    NetCDFVar.unpack_type = NArray::INT
+    v33 = v3.scaled_get
+    assert_equal v33,
+                 NArray[ 100, 101, 102, 103, 104, 105, 106, 107, 108, 109 ].to_i
+  end
+end

data/test/putatt.rb

@@ -1,56 +1,78 @@
+require 'test/unit'
 require 'numru/netcdf'
-include NumRu
-s = 'tmp.nc'
-f = NetCDF.create(s)
-d = f.def_dim('x',5)
-v = f.def_var('x','sfloat',[d])
-
 require 'date'
-att = f.put_att("history", Date.today.to_s )
-p att.get, f.att("history").get
-att = f.put_att("int_att",123)
-att = f.put_att("sfloat_att",1.0/3.0,'sfloat')
-att = f.put_att("sfloat_att2",2.0/3.0,NArray::SFLOAT)
-att = v.put_att("long_name",'test variable')
-att = v.put_att("int_att",123)
-p att.get, v.att("int_att").get
-att = v.put_att("float_att",1.0/3.0)
-att = v.put_att("float_array",[0.1, 0.2, 30])
-att = v.put_att("sfloat_narray",NArray.sfloat(3).indgen!/3)
-att = v.put_att("float_narray",NArray.float(3).indgen!)
-att = v.put_att("sint_narray",NArray.sint(3).indgen!)
-att = v.put_att("int2float",10,'float')
-att = att = v.put_att("dummy",10,'float')
-att.put('changed to text')
-att.name = 'changed'
-begin
-   v.put_att("destined_to_fail",9.8,'complex')
-rescue
-   print "*1* exception raised as expected -- (",
-         __FILE__,":",__LINE__,") ", $!,"\n"
-end
-begin
-   v.put_att("destined_to_fail",9.8,'string')
-rescue
-   print "*2* exception raised as expected -- (",
-         __FILE__,":",__LINE__,") ", $!,"\n"
-end
+include NumRu
+class TestPutAttr < Test::Unit::TestCase
+  def setup
+    @s = 'tmp.nc'
+    @f = NetCDF.create(@s)
+    @d = @f.def_dim('x',5)
+    @v = @f.def_var('x','sfloat',[@d])
+  end
+  def teardown
+    @f.close
+    if File.exist?(@s)
+      begin
+        File.delete(@s)
+      rescue
+        p $!
+      end
+    end
+  end
+  def test_att_history_get
+    att = @f.put_att("history", Date.today.to_s )
+    assert_equal att.get,
+                 @f.att("history").get
+  end
+  def test_att_int_att_get
+    att = @f.put_att("int_att",123)
+    att = @f.put_att("sfloat_att",1.0/3.0,'sfloat')
+    att = @f.put_att("sfloat_att2",2.0/3.0,NArray::SFLOAT)
+    att = @v.put_att("long_name",'test variable')
+    att = @v.put_att("int_att",123)
+    assert_equal att.get,
+                 @v.att("int_att").get
+  end
 
-begin
-   v.put_att("destined_to_fail",'hello','int')
-rescue
-   print "*3* exception raised as expected -- (",
-         __FILE__,":",__LINE__,") ", $!,"\n"
-end
+  def test_att_changed_to_text
+    att = @v.put_att("float_att",1.0/3.0)
+    att = @v.put_att("float_array",[0.1, 0.2, 30])
+    tmp = NArray.sfloat(3).indgen!
+    tmp = tmp/3
+    att = @v.put_att("sfloat_narray",tmp)
+    att = @v.put_att("float_narray",NArray.float(3).indgen!)
+    att = @v.put_att("sint_narray",NArray.sint(3).indgen!)
+    att = @v.put_att("int2float",10,'float')
+    att = att = @v.put_att("dummy",10,'float')
+    assert att.put('changed to text')
+    att.name = 'changed'
+  end
 
-begin
-   v.put_att("destined_to_fail",[10,30,'sss'])
-rescue
-   print "*4* exception raised as expected -- (",
-         __FILE__,":",__LINE__,") ", $!,"\n"
-end
+  def test_destined_to_fail_complex
+    assert_raise(NetcdfError) do
+      @v.put_att("destined_to_fail", 9.8, 'complex')
+      # "unsupported type. code = 7"
+    end
+  end
 
+  def test_destined_to_fail_string
+    assert_raise(ArgumentError) do
+      @v.put_att("destined_to_fail", 9.8, 'string')
+      # Unrecognized NArray type>
+    end
+  end
 
-f.close
+  def test_destined_to_fail_int
+    assert_raise(NetcdfError) do
+      @v.put_att("destined_to_fail", 'hello', 'int')
+      # attribute type must be 'char' (or nil) for a String value
+    end
+  end
 
-print `ncdump tmp.nc`
+  def test_destined_to_fail_mixed_array
+    assert_raise(TypeError) do
+      @v.put_att("destined_to_fail",[10,30,'sss'])
+      # no implicit conversion of String into Integer
+    end
+  end
+end