Merge branch 'release/2.0.alpha3'

.gitignore

@@ -1,9 +1,59 @@
+# http://www.gnu.org/software/automake
+
+Makefile.in
+
+# http://www.gnu.org/software/autoconf
+
+/autom4te.cache
+/aclocal.m4
+/compile
+/configure
+/depcomp
+/install-sh
+/missing
+/stamp-h1
+
 *.sublime-workspace
 
-.DS_Store
+config.*
+
+libtool
+Makefile
+
+*.sublime-workspace
+
+bertini2
+b2_class_test
+b2_classic_compatibility_test
+b2_timing_test
+test_tree_interactive
+
+m4/libtool.m4
+m4/ltoptions.m4
+m4/ltsugar.m4
+m4/ltversion.m4
+m4/lt~obsolete.m4
+
+serialization_test*
+
+/config
+
+# Python folders
+/python/test/.idea
+/.deps/*
+
+# Python files
+*.pyc
+
+
+
+*.dirstamp
+*.deps
 
 *~
 
+.DS_Store
+
 # Compiled Object files
 *.slo
 *.lo
@@ -33,3 +83,4 @@
 *.exe
 *.out
 *.app
+python/autom4te.cache

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "python/minieigen"]
+	path = python/minieigen
+url=https://github.com/eudoxos/minieigen.git

core/.gitignore

@@ -18,9 +18,12 @@ config.*
 libtool
 Makefile
 
+b2_timing_test
 b2_class_test
 test_tree_interactive
-
+settings_test
+tracking_basics_test
+b2_classic_compatibility_test
 
 m4/libtool.m4
 m4/ltoptions.m4
@@ -29,13 +32,18 @@ m4/ltversion.m4
 m4/lt~obsolete.m4
 
 serialization_test*
+*.log
+.libs/*
+
+*.trs
 
 /config
 
 .DS_Store
 *.dirstamp
 *.deps
 
+
 *~
 
 
@@ -66,4 +74,4 @@ serialization_test*
 # Executables
 *.exe
 *.out
-*.app
+*.app

core/configure.ac

@@ -3,8 +3,8 @@
 
 
 
-#we're building b2, version 2.0-alpha2, and the corresponding email is dan brake's
-AC_INIT([b2], [2.0-alpha2], [[email protected]],[b2], [http://github.com/bertiniteam/b2])
+#we're building b2, version 2.0-alpha3, and the corresponding email is dan brake's
+AC_INIT([b2], [2.0-alpha3], [[email protected]],[b2], [http://github.com/bertiniteam/b2])
 
 
 # Force autoconf to be at least this version number:

core/doc/b2_review_CODE_NAME.tex

@@ -0,0 +1,160 @@
+\documentclass{article}
+
+\usepackage{amssymb,amsmath}
+
+\oddsidemargin 0.0in
+\textwidth 6.5in
+\headheight -0.5in
+\topmargin 0.5in
+\headsep 0.0in
+\textheight 9.2in
+\parskip 3mm
+\pagestyle{empty}
+
+
+%%%%%%%%%%%%%%%%%%%
+%%%%% INSTRUCTIONS %%%%%
+%%%%%%%%%%%%%%%%%%%
+
+% REVIEWER:  Please fill out the following fields.  The form will then be filled in automatically upon compilation.
+% The goal of this review is to determine whether the code under review is adequate for inclusion into the develop branch of b2.
+% If you have any hesitations on any yes/no question, mark no and explain your concerns.
+% Please work with the author(s) of the code under review to resolve any issues.
+% A final copy of all reviews must be submitted to Dan Bates before the pull request for the code under review is accepted.
+% Copies of the final review forms will be kept in the repo for future reference.
+%
+% If you have questions, please contact Dan Bates.
+
+
+\newcommand\you{  Dan Bates, [email protected]  }  %your name, email
+\newcommand\class{  Example Class  }  %name of the class, file, or module you are reviewing
+\newcommand\revdate{  21 February 2015  }  %date you are completing the review
+
+%SCOPE
+\newcommand\goals{  a,b,c  }  %brief but complete list of goals for the code under review
+\newcommand\goalsAppropriate{  y/n  } %Are these goals appropriate for this code -- yes or no?
+\newcommand\goalsMet{  y/n  } %Were all goals met -- yes or no?
+\newcommand\goalsComments{  asdf  } %Comments about goals and scope
+
+%COMPILATION
+\newcommand\compileSuccess{  y/n  } %Does the code compile -- yes or no?
+\newcommand\compileComments{  asdf  }  %Comments about compilation
+
+%TESTING
+\newcommand\testSuccess{  y/n  } %Does the code pass the provided tests -- yes or no?
+\newcommand\testGeneral{  y/n  } %Do the provided tests adequately measure general circumstances -- yes or no?
+\newcommand\testEdge {  y/n  } %Do the provided tests adequately include edge cases -- yes or no?
+\newcommand\testComments{  asdf  } %Comments about tests
+
+%DOCUMENTATION
+\newcommand\docAdequate{  y/n  } %Is the code adequately commented -- yes or no?
+\newcommand\docComments{  asdf  }  %Comments about documentation
+
+%STYLE
+\newcommand\styleAdequate{  y/n  } %Does the code conform adequately to the b2 style conventions -- yes or no?
+\newcommand\styleComments{  asdf  } %Comments about style
+
+%OTHER COMMENTS
+\newcommand\otherComments{  asdf  } %Other comments
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%% END OF REVIEWER SECTION %%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+
+
+\newcommand\bb{{bertini2\ }}
+
+\begin{document}
+
+\noindent
+{\bf \bb review}\\
+Code: \class\\
+Reviewer:  \you \\
+Date:  \revdate
+
+\noindent\hrulefill
+
+\noindent
+{\bf Scope}
+
+\noindent
+\underbar{Goals}: \goals
+
+\noindent
+\underbar{Are these goals appropriate}? \goalsAppropriate
+
+\noindent
+\underbar{Were these goals met}? \goalsMet
+
+\noindent
+\underbar{Comments}: \\ \goalsComments
+
+\noindent\hrulefill
+
+
+
+\noindent
+{\bf Compilation}
+
+\noindent
+\underbar{Does the code compile?} \compileSuccess
+
+\noindent
+\underbar{Comments}:\\ \compileComments
+
+\noindent\hrulefill
+
+
+
+\noindent
+{\bf Testing}
+
+\noindent
+\underbar{Does the code pass the provided tests?} \testSuccess
+
+\noindent
+\underbar{Do the provided tests adequately measure general circumstances?} \testGeneral
+
+\noindent
+\underbar{Do the provided tests adequately include edge cases?} \testEdge
+
+\noindent
+\underbar{Comments}: \\ \testComments
+
+\noindent\hrulefill
+
+
+
+\noindent
+{\bf Documentation}
+
+\noindent
+\underbar{Is the code adequately commented?} \docAdequate
+
+\noindent
+\underbar{Comments}: \\ \docComments
+
+\noindent\hrulefill
+
+
+
+\noindent
+{\bf Style}
+
+\noindent
+\underbar{Does the code conform adequately to the b2 style conventions?} \styleAdequate
+
+\noindent
+\underbar{Comments}:\\ \styleComments
+
+\noindent\hrulefill
+
+
+
+\noindent
+{\bf Other comments}\\  \otherComments
+
+
+\end{document}

core/include/bertini2/mpfr_complex.hpp

@@ -1079,7 +1079,51 @@ namespace Eigen {
 
 
 
-
+	namespace internal {
+		template<>
+		struct abs2_impl<bertini::complex>
+		{
+			static inline mpfr_float run(const bertini::complex& x)
+			{
+				return real(x)*real(x) + imag(x)*imag(x);
+			}
+		};
+
+
+		template<> inline bertini::complex random<bertini::complex>()
+		{
+			return bertini::complex::rand();
+		}
+
+		template<> inline bertini::complex random<bertini::complex>(const bertini::complex& a, const bertini::complex& b)
+		{
+			return a + (b-a) * random<bertini::complex>();
+		}
+
+		template<>
+		struct conj_helper<bertini::complex, bertini::complex, false, true>
+		{
+			typedef bertini::complex Scalar;
+			EIGEN_STRONG_INLINE Scalar pmadd(const Scalar& x, const Scalar& y, const Scalar& c) const
+			{ return c + pmul(x,y); }
+
+			EIGEN_STRONG_INLINE Scalar pmul(const Scalar& x, const Scalar& y) const
+			{ return Scalar(numext::real(x)*numext::real(y) + numext::imag(x)*numext::imag(y), numext::imag(x)*numext::real(y) - numext::real(x)*numext::imag(y)); }
+		};
+
+		template<>
+		struct conj_helper<bertini::complex, bertini::complex, true, false>
+		{
+			typedef bertini::complex Scalar;
+			EIGEN_STRONG_INLINE Scalar pmadd(const Scalar& x, const Scalar& y, const Scalar& c) const
+			{ return c + pmul(x,y); }
+
+			EIGEN_STRONG_INLINE Scalar pmul(const Scalar& x, const Scalar& y) const
+			{ return Scalar(numext::real(x)*numext::real(y) + numext::imag(x)*numext::imag(y), numext::real(x)*numext::imag(y) - numext::imag(x)*numext::real(y)); }
+		};
+
+	} // re: namespace internal
+
 
 
 }