thera 0.0.6 → 0.0.7

data/lib/quarry/src/data_set/data_set.cpp

@@ -76,10 +76,12 @@ void DataSet::DataSet::index() {
 // TODO: this isn't really stratification; categories should be proportionally represented
 vector<vector<DataSet::Example *> > *DataSet::DataSet::stratify(int number_of_folds) {
   int examples_per_fold = examples.size() / number_of_folds;
+  vector<vector<Example *> > *folds = new vector<vector<Example *> >();
+  folds->resize(number_of_folds);
   Example *example;
-  vector<vector<Example *> > *folds = new vector<vector<Example *> >(number_of_folds, vector<Example *>(examples_per_fold, NULL));
   
   for(int fold = 0; fold < number_of_folds; fold++) {
+    (*folds)[fold].resize(examples_per_fold);
     for(int i = 0; i < examples_per_fold; i++) {
       (*folds)[fold][i] = examples[fold + (i * number_of_folds)];
     }

data/lib/quarry/src/data_set/features/numeric_feature.cpp

@@ -59,7 +59,7 @@ void DataSet::NumericFeature::index_example(double value, Example *example) {
 
 void DataSet::NumericFeature::finalise_indexing(DataSet *data_set) {}
 
-void DataSet::NumericFeature::print(DataSet::DataSet *data_set) {
+void DataSet::NumericFeature::print(DataSet *data_set) {
   cout << "F" << index << ", " << name << endl;
   print_counts(&counts);
   for(int i = 0; i < (data_set->categories_size() + 1); i++) {

data/thera.gemspec

@@ -9,7 +9,7 @@ Gem::Specification.new do |s|
   s.description = "C++ Data Mining Library for Ruby"
   s.email = "me@willcannings.com"
   s.authors = ["Will Cannings"]
-  s.version = '0.0.6'
+  s.version = '0.0.7'
   s.extensions = ["ext/extconf.rb"]
 
   s.files         = `git ls-files`.split("\n")

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: thera
 version: !ruby/object:Gem::Version
-  version: 0.0.6
+  version: 0.0.7
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-12-13 00:00:00.000000000Z
+date: 2011-12-22 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rice
-  requirement: &70149523474660 !ruby/object:Gem::Requirement
+  requirement: &70195705116960 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,7 +21,7 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70149523474660
+  version_requirements: *70195705116960
 description: C++ Data Mining Library for Ruby
 email: me@willcannings.com
 executables: []
@@ -36,7 +36,6 @@ files:
 - LICENSE.txt
 - README.rdoc
 - Rakefile
-- ext/Makefile
 - ext/extconf.rb
 - ext/quarry/quarry_toolkit.cpp
 - lib/quarry/Makefile.linux

data/ext/Makefile

@@ -1,225 +0,0 @@
-
-SHELL = /bin/sh
-
-#### Start of system configuration section. ####
-
-srcdir = quarry
-topdir = /Users/will/.rvm/rubies/ruby-1.9.2-p290/include/ruby-1.9.1
-hdrdir = /Users/will/.rvm/rubies/ruby-1.9.2-p290/include/ruby-1.9.1
-arch_hdrdir = /Users/will/.rvm/rubies/ruby-1.9.2-p290/include/ruby-1.9.1/$(arch)
-VPATH = $(srcdir):$(arch_hdrdir)/ruby:$(hdrdir)/ruby
-
-prefix = $(DESTDIR)/Users/will/.rvm/rubies/ruby-1.9.2-p290
-
-rubylibprefix = $(libdir)/$(RUBY_BASE_NAME)
-
-exec_prefix = $(prefix)
-
-vendorhdrdir = $(rubyhdrdir)/vendor_ruby
-
-sitehdrdir = $(rubyhdrdir)/site_ruby
-
-rubyhdrdir = $(includedir)/$(RUBY_BASE_NAME)-$(ruby_version)
-
-vendordir = $(rubylibprefix)/vendor_ruby
-
-sitedir = $(rubylibprefix)/site_ruby
-
-ridir = $(datarootdir)/$(RI_BASE_NAME)
-
-mandir = $(datarootdir)/man
-
-localedir = $(datarootdir)/locale
-
-libdir = $(exec_prefix)/lib
-
-psdir = $(docdir)
-
-pdfdir = $(docdir)
-
-dvidir = $(docdir)
-
-htmldir = $(docdir)
-
-infodir = $(datarootdir)/info
-
-docdir = $(datarootdir)/doc/$(PACKAGE)
-
-oldincludedir = $(DESTDIR)/usr/include
-
-includedir = $(prefix)/include
-
-localstatedir = $(prefix)/var
-
-sharedstatedir = $(prefix)/com
-
-sysconfdir = $(prefix)/etc
-
-datadir = $(datarootdir)
-
-datarootdir = $(prefix)/share
-
-libexecdir = $(exec_prefix)/libexec
-
-sbindir = $(exec_prefix)/sbin
-
-bindir = $(exec_prefix)/bin
-
-rubylibdir = $(rubylibprefix)/$(ruby_version)
-
-archdir = $(rubylibdir)/$(arch)
-
-sitelibdir = $(sitedir)/$(ruby_version)
-
-sitearchdir = $(sitelibdir)/$(sitearch)
-
-vendorlibdir = $(vendordir)/$(ruby_version)
-
-vendorarchdir = $(vendorlibdir)/$(sitearch)
-
-
-CC = /usr/bin/gcc-4.2
-CXX = g++
-LIBRUBY = $(LIBRUBY_SO)
-LIBRUBY_A = lib$(RUBY_SO_NAME)-static.a
-LIBRUBYARG_SHARED = -l$(RUBY_SO_NAME)
-LIBRUBYARG_STATIC = -lruby.1.9.1-static
-OUTFLAG = -o 
-COUTFLAG = -o 
-
-RUBY_EXTCONF_H = 
-cflags   =  $(optflags) $(debugflags) $(warnflags)
-optflags = -O3
-debugflags = -ggdb
-warnflags = -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wshorten-64-to-32 -Wno-long-long
-CFLAGS   = -fno-common -x c++ 
-INCFLAGS = -I. -I$(arch_hdrdir) -I$(hdrdir)/ruby/backward -I$(hdrdir) -I$(srcdir) -I./../lib/quarry/src
-DEFS     = 
-CPPFLAGS =  -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE $(DEFS) $(cppflags)  -I/Users/will/.rvm/gems/ruby-1.9.2-p290/gems/rice-1.4.3/ruby/lib/include
-CXXFLAGS = $(CFLAGS)  -Wall -g
-ldflags  = -L. -L/usr/local/lib  -L/Users/will/.rvm/gems/ruby-1.9.2-p290/gems/rice-1.4.3/ruby/lib/lib
-dldflags = -Wl,-undefined,dynamic_lookup -Wl,-multiply_defined,suppress -Wl,-flat_namespace
-ARCH_FLAG = 
-DLDFLAGS = $(ldflags) $(dldflags)
-LDSHARED = g++ -dynamic -bundle
-LDSHAREDXX = $(CXX) -dynamic -bundle
-AR = ar
-EXEEXT = 
-
-RUBY_BASE_NAME = ruby
-RUBY_INSTALL_NAME = ruby
-RUBY_SO_NAME = ruby.1.9.1
-arch = x86_64-darwin11.1.0
-sitearch = $(arch)
-ruby_version = 1.9.1
-ruby = /Users/will/.rvm/rubies/ruby-1.9.2-p290/bin/ruby
-RUBY = $(ruby)
-RM = rm -f
-RM_RF = $(RUBY) -run -e rm -- -rf
-RMDIRS = $(RUBY) -run -e rmdir -- -p
-MAKEDIRS = mkdir -p
-INSTALL = /usr/bin/install -c
-INSTALL_PROG = $(INSTALL) -m 0755
-INSTALL_DATA = $(INSTALL) -m 644
-COPY = cp
-
-#### End of system configuration section. ####
-
-preload = 
-
-
-CXX = g++
-
-libpath = . $(libdir) ./../lib/quarry/obj
-LIBPATH =  -L. -L$(libdir) -L./../lib/quarry/obj
-DEFFILE = 
-
-CLEANFILES = mkmf.log
-DISTCLEANFILES = 
-DISTCLEANDIRS = 
-
-extout = 
-extout_prefix = 
-target_prefix = 
-LOCAL_LIBS = 
-LIBS = -lquarry -lrice -lruby.1.9.1 -lpthread -ldl -lobjc 
-SRCS = quarry_toolkit.cpp
-OBJS = quarry_toolkit.o
-TARGET = quarry_toolkit
-DLLIB = $(TARGET).bundle
-EXTSTATIC = 
-STATIC_LIB = 
-
-BINDIR        = $(bindir)
-RUBYCOMMONDIR = $(sitedir)$(target_prefix)
-RUBYLIBDIR    = $(sitelibdir)$(target_prefix)
-RUBYARCHDIR   = $(sitearchdir)$(target_prefix)
-HDRDIR        = $(rubyhdrdir)/ruby$(target_prefix)
-ARCHHDRDIR    = $(rubyhdrdir)/$(arch)/ruby$(target_prefix)
-
-TARGET_SO     = $(DLLIB)
-CLEANLIBS     = $(TARGET).bundle 
-CLEANOBJS     = *.o  *.bak
-
-all:    $(DLLIB)
-static: $(STATIC_LIB)
-.PHONY: all install static install-so install-rb
-.PHONY: clean clean-so clean-rb
-
-clean-rb-default::
-clean-rb::
-clean-so::
-clean: clean-so clean-rb-default clean-rb
-		@-$(RM) $(CLEANLIBS) $(CLEANOBJS) $(CLEANFILES)
-
-distclean-rb-default::
-distclean-rb::
-distclean-so::
-distclean: clean distclean-so distclean-rb-default distclean-rb
-		@-$(RM) Makefile $(RUBY_EXTCONF_H) conftest.* mkmf.log
-		@-$(RM) core ruby$(EXEEXT) *~ $(DISTCLEANFILES)
-		@-$(RMDIRS) $(DISTCLEANDIRS)
-
-realclean: distclean
-install: install-so install-rb
-
-install-so: $(RUBYARCHDIR)
-install-so: $(RUBYARCHDIR)/$(DLLIB)
-$(RUBYARCHDIR)/$(DLLIB): $(DLLIB)
-	@-$(MAKEDIRS) $(@D)
-	$(INSTALL_PROG) $(DLLIB) $(@D)
-install-rb: pre-install-rb install-rb-default
-install-rb-default: pre-install-rb-default
-pre-install-rb: Makefile
-pre-install-rb-default: Makefile
-$(RUBYARCHDIR):
-	$(MAKEDIRS) $@
-
-site-install: site-install-so site-install-rb
-site-install-so: install-so
-site-install-rb: install-rb
-
-.SUFFIXES: .c .m .cc .cxx .cpp .C .o
-
-.cc.o:
-	$(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
-
-.cxx.o:
-	$(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
-
-.cpp.o:
-	$(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
-
-.C.o:
-	$(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
-
-.c.o:
-	$(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -c $<
-
-$(DLLIB): $(OBJS) Makefile
-	@-$(RM) $(@)
-	$(LDSHAREDXX) -o $@ $(OBJS) $(LIBPATH) $(DLDFLAGS) $(LOCAL_LIBS) $(LIBS)
-
-
-
-$(OBJS): $(hdrdir)/ruby.h $(hdrdir)/ruby/defines.h $(arch_hdrdir)/ruby/config.h