lulu 0.0.2 → 0.0.3

data/lib/lulu/version.rb

@@ -1,3 +1,3 @@
 module Lulu
-  VERSION = "0.0.2"
+  VERSION = "0.0.3"
 end

data/lulu.gemspec

@@ -4,10 +4,10 @@ $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
 require 'lulu/version'
 
 Gem::Specification.new do |spec|
-  spec.name          = "lulu"
+  spec.name          = 'lulu'
   spec.version       = Lulu::VERSION
-  spec.authors       = ["Gene Ressler"]
-  spec.email         = ["gene.ressler@gmail.com"]
+  spec.authors       = ['Gene Ressler']
+  spec.email         = ['gene.ressler@gmail.com']
   spec.summary       = %q{Merge map markers by agglomerative clustering.}
   spec.description   =
 %q{Lulu merges the closest overlapping pair of map markers into a one whose
@@ -16,17 +16,17 @@ this until no overlaps remain. Some interesting data structures make this
 quite fast for all but pathologically bad data. Markers can be circles or
 squares. The user may provide a scale factor allowing the marker radius to
 have a different scale than distance between markers.}
-  spec.homepage      = "https://github.com/gene-ressler/lulu/wiki"
-  spec.licenses      = "GPL-3.0"
+  spec.homepage      = 'https://github.com/gene-ressler/lulu/wiki'
+  spec.licenses      = 'GPL-3.0'
 
   spec.files         = `git ls-files`.split($/)
   spec.extensions  = ['ext/lulu/extconf.rb']
   spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
   spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
-  spec.require_paths = ["lib"]
+  spec.require_paths = ['lib']
 
-  spec.add_development_dependency "bundler", "~> 1.5"
-  spec.add_development_dependency "rake", "~> 10.1"
-  spec.add_development_dependency "rake-compiler"
-  spec.add_development_dependency "rspec", "~> 2.14"
+  spec.add_development_dependency 'bundler', '~> 1.5'
+  spec.add_development_dependency 'rake', '~> 10.1'
+  spec.add_development_dependency 'rake-compiler', '~> 0.9'
+  spec.add_development_dependency 'rspec', '~> 2.14'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: lulu
 version: !ruby/object:Gem::Version
-  version: 0.0.2
+  version: 0.0.3
 platform: ruby
 authors:
 - Gene Ressler
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-04-02 00:00:00.000000000 Z
+date: 2014-04-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -42,16 +42,16 @@ dependencies:
   name: rake-compiler
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.9'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.9'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -90,7 +90,6 @@ files:
 - LICENSE.txt
 - README.md
 - Rakefile
-- ext/lulu/Makefile
 - ext/lulu/extconf.rb
 - ext/lulu/lulu.c
 - ext/lulu/marker.c
@@ -106,7 +105,6 @@ files:
 - ext/lulu/utility.c
 - ext/lulu/utility.h
 - lib/lulu.rb
-- lib/lulu/lulu.bundle
 - lib/lulu/version.rb
 - lulu.gemspec
 - spec/lib/lulu_spec.rb

data/ext/lulu/Makefile

@@ -1,220 +0,0 @@
-
-SHELL = /bin/sh
-
-# V=0 quiet, V=1 verbose.  other values don't work.
-V = 0
-Q1 = $(V:1=)
-Q = $(Q1:0=@)
-n=$(NULLCMD)
-ECHO1 = $(V:1=@$n)
-ECHO = $(ECHO1:0=@echo)
-
-#### Start of system configuration section. ####
-
-srcdir = .
-topdir = /usr/local/rvm/rubies/ruby-1.9.3-p484/include/ruby-1.9.1
-hdrdir = /usr/local/rvm/rubies/ruby-1.9.3-p484/include/ruby-1.9.1
-arch_hdrdir = /usr/local/rvm/rubies/ruby-1.9.3-p484/include/ruby-1.9.1/$(arch)
-VPATH = $(srcdir):$(arch_hdrdir)/ruby:$(hdrdir)/ruby
-prefix = $(DESTDIR)/usr/local/rvm/rubies/ruby-1.9.3-p484
-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)
-
-NULLCMD = :
-
-CC = /usr/local/opt/apple-gcc42/bin/gcc-4.2
-CXX = g++
-LIBRUBY = $(LIBRUBY_SO)
-LIBRUBY_A = lib$(RUBY_SO_NAME)-static.a
-LIBRUBYARG_SHARED = -l$(RUBY_SO_NAME)
-LIBRUBYARG_STATIC = -l$(RUBY_SO_NAME)-static
-empty =
-OUTFLAG = -o $(empty)
-COUTFLAG = -o $(empty)
-
-RUBY_EXTCONF_H = 
-cflags   =  $(optflags) $(debugflags) $(warnflags)
-optflags = -O3
-debugflags = -ggdb
-warnflags = -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wshorten-64-to-32 -Wimplicit-function-declaration
-CFLAGS   = -fno-common $(cflags)  -fno-common -pipe -std=c99 -Wno-declaration-after-statement $(ARCH_FLAG)
-INCFLAGS = -I. -I$(arch_hdrdir) -I$(hdrdir)/ruby/backward -I$(hdrdir) -I$(srcdir)
-DEFS     = 
-CPPFLAGS =  -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE $(DEFS) $(cppflags) -I/usr/local/opt/libyaml/include -I/usr/local/opt/readline/include -I/usr/local/opt/libksba/include -I/usr/local/opt/openssl/include
-CXXFLAGS = $(CFLAGS) $(cxxflags)
-ldflags  = -L. -L/usr/local/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libksba/lib -L/usr/local/opt/openssl/lib 
-dldflags = -Wl,-undefined,dynamic_lookup -Wl,-multiply_defined,suppress -Wl,-flat_namespace -L/usr/local/opt/libyaml/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libksba/lib -L/usr/local/opt/openssl/lib  
-ARCH_FLAG = 
-DLDFLAGS = $(ldflags) $(dldflags) $(ARCH_FLAG)
-LDSHARED = $(CC) -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-darwin13.0.0
-sitearch = $(arch)
-ruby_version = 1.9.1
-ruby = /usr/local/rvm/rubies/ruby-1.9.3-p484/bin/ruby
-RUBY = $(ruby)
-RM = rm -f
-RM_RF = $(RUBY) -run -e rm -- -rf
-RMDIRS = rmdir -p
-MAKEDIRS = mkdir -p
-INSTALL = /usr/bin/install -c
-INSTALL_PROG = $(INSTALL) -m 0755
-INSTALL_DATA = $(INSTALL) -m 644
-COPY = cp
-TOUCH = exit >
-
-#### End of system configuration section. ####
-
-preload = 
-
-libpath = . $(libdir) /usr/local/opt/libyaml/lib /usr/local/opt/readline/lib /usr/local/opt/libksba/lib /usr/local/opt/openssl/lib
-LIBPATH =  -L. -L$(libdir) -L/usr/local/opt/libyaml/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libksba/lib -L/usr/local/opt/openssl/lib
-DEFFILE = 
-
-CLEANFILES = mkmf.log
-DISTCLEANFILES = 
-DISTCLEANDIRS = 
-
-extout = 
-extout_prefix = 
-target_prefix = /lulu
-LOCAL_LIBS = 
-LIBS = $(LIBRUBYARG_SHARED)  -lpthread -ldl -lobjc 
-SRCS = lulu.c marker.c merger.c pq.c qt.c test.c utility.c
-OBJS = lulu.o marker.o merger.o pq.o qt.o test.o utility.o
-TARGET = lulu
-TARGET_NAME = lulu
-TARGET_ENTRY = Init_$(TARGET_NAME)
-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: $(STATIC_LIB)
-.PHONY: all install static install-so install-rb
-.PHONY: clean clean-so clean-rb
-
-clean-static::
-clean-rb-default::
-clean-rb::
-clean-so::
-clean: clean-so clean-static clean-rb-default clean-rb
-		-$(Q)$(RM) $(CLEANLIBS) $(CLEANOBJS) $(CLEANFILES) .*.time
-
-distclean-rb-default::
-distclean-rb::
-distclean-so::
-distclean: clean distclean-so distclean-rb-default distclean-rb
-		@-$(RM) Makefile $(RUBY_EXTCONF_H) conftest.* mkmf.log
-		@-$(RM) core ruby$(EXEEXT) *~ $(DISTCLEANFILES)
-		@-$(RMDIRS) $(DISTCLEANDIRS) 2> /dev/null || true
-
-realclean: distclean
-install: install-so install-rb
-
-install-so: $(RUBYARCHDIR)/$(DLLIB)
-$(RUBYARCHDIR)/$(DLLIB): $(DLLIB)
-	-$(Q)$(MAKEDIRS) $(@D)
-	$(INSTALL_PROG) $(DLLIB) $(@D)
-clean-static::
-	-$(Q)$(RM) $(STATIC_LIB)
-install-rb: pre-install-rb install-rb-default
-install-rb-default: pre-install-rb-default
-pre-install-rb: Makefile
-pre-install-rb-default: Makefile
-pre-install-rb-default:
-	$(ECHO) installing default lulu libraries
-./.RUBYARCHDIR.time:
-	$(Q) $(MAKEDIRS) $(RUBYARCHDIR)
-	$(Q) $(TOUCH) $@
-
-site-install: site-install-so site-install-rb
-site-install-so: install-so
-site-install-rb: install-rb
-
-.SUFFIXES: .c .m .cc .mm .cxx .cpp .C .o
-
-.cc.o:
-	$(ECHO) compiling $(<)
-	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
-
-.mm.o:
-	$(ECHO) compiling $(<)
-	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
-
-.cxx.o:
-	$(ECHO) compiling $(<)
-	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
-
-.cpp.o:
-	$(ECHO) compiling $(<)
-	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
-
-.C.o:
-	$(ECHO) compiling $(<)
-	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
-
-.c.o:
-	$(ECHO) compiling $(<)
-	$(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -c $<
-
-.m.o:
-	$(ECHO) compiling $(<)
-	$(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -c $<
-
-$(DLLIB): $(OBJS) Makefile
-	$(ECHO) linking shared-object lulu/$(DLLIB)
-	-$(Q)$(RM) $(@)
-	$(Q) $(LDSHARED) -o $@ $(OBJS) $(LIBPATH) $(DLDFLAGS) $(LOCAL_LIBS) $(LIBS)
-
-
-
-$(OBJS): $(hdrdir)/ruby.h $(hdrdir)/ruby/defines.h $(arch_hdrdir)/ruby/config.h