update dependencies, move examples etc

4 files changed, 495 insertions, 0 deletions

diff --git a/packages/base/CHANGELOG b/packages/base/CHANGELOG
new file mode 100644
index 0000000..99a6845
--- /dev/null
+++ b/packages/base/CHANGELOG
@@ -0,0 +1,219 @@
+0.16.0.0
+--------
+
+    * created hmatrix-base
+
+    * Added more organized reexport modules:
+      Numeric.HMatrix, Numeric.HMatrix.Data, Numeric.HMatrix.Devel
+      (The documentation is hidden for the other modules,
+       but they continue to be exposed and are not deprecated)
+
+    * added support for empty arrays
+
+    * join deprecated, use vjoin
+
+    * dot now conjugates the first input vector
+    * added udot (unconjugated dot product)
+    
+    * (<.>) overloaded to matrix and dot products
+    * added Monoid instance for Matrix using matrix product
+    
+    * improved build and konst
+
+    * improved linspace
+    
+    * improved error messages
+    * more usage examples
+
+    * simplified LSDiv
+    * Plot functions moved to Numeric.LinearAlgebra.Util
+    * removed (!) (use (¦)), added (——)
+
+0.15.2.0
+--------
+
+    * general pinvTol and improved pinv
+
+0.15.1.0
+--------
+
+    * One-dimensional minimization
+
+    * Doubly-adaptive quadrature for difficult integrands
+
+0.15.0.0
+--------
+
+    * Data.Packed.Foreign (additional FFI helpers)
+
+    * NFData instance of Matrix
+
+    * Unidimensional root finding
+
+    * In Numeric.LinearAlgebra.Util:
+      pairwise2D, rowOuters, null1, null1sym, size, unitary, mt, (¦), (?), (¿)
+
+    * diagBlock
+
+    * meanCov moved to Container
+
+0.14.1.0
+--------
+
+    * In Numeric.LinearAlgebra.Util:
+      convolution: corr, conv, corr2, conv2, separable, corrMin
+      kronecker: vec, vech, dup, vtrans
+
+0.14.0.0
+--------
+
+    * integration over infinite intervals
+
+    * msadams and msbdf methods for ode
+
+    * Numeric.LinearAlgebra.Util
+
+    * (<\>) extended to multiple right-hand sides
+
+    * orth
+
+0.13.0.0
+--------
+
+    * tests moved to new package hmatrix-tests
+
+0.11.2.0
+--------
+
+    * geigSH' (symmetric generalized eigensystem)
+
+    * mapVectorWithIndex
+
+0.11.1.0
+--------
+
+    * exported Mul
+
+    * mapMatrixWithIndex{,M,M_}
+
+0.11.0.0
+--------
+
+    * flag -fvector default = True
+
+    * invlndet (inverse and log of determinant)
+
+    * step, cond
+
+    * find
+
+    * assoc, accum
+
+0.10.0.0
+--------
+
+    * Module reorganization
+
+    * Support for Float and Complex Float elements (excluding LAPACK computations)
+
+    * Binary instances for Vector and Matrix
+
+    * optimiseMult
+
+    * mapVectorM, mapVectorWithIndexM, unzipVectorWith, and related functions.
+
+    * diagRect admits diagonal vectors of any length without producing an error,
+      and takes an additional argument for the off-diagonal elements.
+
+    * different signatures in some functions
+
+0.9.3.0
+--------
+
+    * flag -fvector to optionally use Data.Vector.Storable.Vector
+  without any conversion.
+
+    * Simpler module structure.
+
+    * toBlocks, toBlocksEvery
+
+    * cholSolve, mbCholSH
+
+    * GSL Nonlinear Least-Squares fitting using Levenberg-Marquardt.
+
+    * GSL special functions moved to separate package hmatrix-special.
+
+    * Added offset of Vector, allowing fast, noncopy subVector (slice).
+  Vector is now identical to Roman Leshchinskiy's Data.Vector.Storable.Vector,
+  so we can convert from/to them in O(1).
+
+    * Removed Data.Packed.Convert, see examples/vector.hs
+
+0.8.3.0
+--------
+
+    * odeSolve
+
+    * Matrix arithmetic automatically replicates matrix with single row/column
+
+    * latexFormat, dispcf
+
+0.8.2.0
+--------
+
+    * fromRows/fromColumns now automatically expand vectors of dim 1
+      to match the common dimension.
+      fromBlocks also replicates single row/column matrices.
+      Previously all dimensions had to be exactly the same.
+
+    * display utilities: dispf, disps, vecdisp
+
+    * scalar
+
+    * minimizeV, minimizeVD, using Vector instead of lists.
+
+0.8.1.0
+--------
+
+    * runBenchmarks
+
+0.8.0.0
+--------
+
+    * singularValues, fullSVD, thinSVD, compactSVD, leftSV, rightSV
+      and complete interface to [d|z]gesdd.
+      Algorithms based on the SVD of large matrices can now be
+      significantly faster.
+
+    * eigenvalues, eigenvaluesSH
+
+    * linearSolveLS, rq
+
+0.7.2.0
+--------
+
+    * ranksv
+
+0.7.1.0
+--------
+
+    * buildVector/buildMatrix
+
+    * removed NFData instances
+
+0.6.0.0
+--------
+
+    * added randomVector, gaussianSample, uniformSample, meanCov
+
+    * added rankSVD, nullspaceSVD
+
+    * rank, nullspacePrec, and economy svd defined in terms of ranksvd.
+
+    * economy svd now admits zero rank matrices and return a "degenerate
+      rank 1" decomposition with zero singular value.
+
+    * added NFData instances for Matrix and Vector.
+
+    * liftVector, liftVector2 replaced by mapVector, zipVector.
+
diff --git a/packages/base/INSTALL.md b/packages/base/INSTALL.md
new file mode 100644
index 0000000..ef51167
--- /dev/null
+++ b/packages/base/INSTALL.md
@@ -0,0 +1,117 @@
+# [hmatrix][hmatrix2] installation
+
+This package requires the [Glasgow Haskell Compiler](http://www.haskell.org/ghc/index.html) ghc >= 6.10, and [cabal-install](http://www.haskell.org/haskellwiki/Cabal-Install), conveniently available in the [Haskell Platform](http://hackage.haskell.org/platform), and the development packages for [GSL](http://www.gnu.org/software/gsl) and BLAS/[LAPACK](http://www.netlib.org/lapack). (The graphical functions also require **gnuplot** and **imagemagick**.)
+
+[hmatrix]: http://code.haskell.org/hmatrix
+[hmatrix2]: http://perception.inf.um.es/hmatrix
+
+
+## Linux ##################################################
+
+
+Ubuntu/Debian:
+
+    $ sudo apt-get install libgsl0-dev liblapack-dev
+    $ cabal install hmatrix
+
+Arch Linux: If the automatic installation from Hackage fails, install atlas-lapack and gsl, unpack the source, change the build-type to Simple in hmatrix.cabal (line 28) and add extra-libraries: gsl lapack (line 194). 
+
+Other distributions may require additional libraries. They can be given in a **--configure-option**.
+
+## Mac OS/X ###############################################
+
+
+GSL must be installed via Homebrew or MacPorts.
+
+Via Homebrew:
+
+    $ brew install gsl
+    $ cabal install hmatrix
+
+Via MacPorts:
+
+    $ sudo port install gsl +universal
+    $ cabal install hmatrix
+
+(Contributed by Heinrich Apfelmus, Torsten Kemps-Benedix and Ted Fujimoto).
+
+## Windows ###############################################
+
+We use this [GSL binary](http://www.miscdebris.net/blog/2009/04/20/mingw-345-binaries-of-gnu-scientific-library-112-for-use-with-mingw-and-visual-c/), and blas/lapack dlls built with g77 (contributed by Gilberto Camara). All required files are in [gsl-lapack-windows.zip][winpack].
+
+(Due to [issue 21](https://github.com/albertoruiz/hmatrix/issues/21) we need hmatrix-0.13.1.0.)
+
+1) Install the Haskell Platform (tested on 2011.2.0.1)
+
+    > cabal update
+
+2) Download and unzip the following file into a stable folder %GSL%
+
+    http://perception.inf.um.es/hmatrix/gsl-lapack-windows.zip
+
+3.a) In a msys shell the installation should be fully automatic:
+
+    $ cabal install hmatrix-0.13.1.0 --extra-lib-dir=${GSL} --extra-include-dir=${GSL}
+
+3.b) Alternatively, in a normal windows cmd:
+
+     > cabal unpack hmatrix-0.13.1.0
+
+   Edit hmatrix.cabal, in line 28 change build-type to "Simple", and then
+
+     > cabal install --extra-lib-dir=%GSL% --extra-include-dir=%GSL%
+
+   It may be necessary to put the dlls in the search path.
+
+
+NOTE: The examples using graphics do not yet work in windows.
+
+[install]: http://code.haskell.org/hmatrix/INSTALL
+[install2]: http://patch-tag.com/r/aruiz/hmatrix/snapshot/current/content/pretty/INSTALL
+[winpack2]: http://perception.inf.um.es/hmatrix/gsl-lapack-windows.zip
+[winpack]: https://github.com/downloads/AlbertoRuiz/hmatrix/gsl-lapack-windows.zip
+
+## Tests ###############################################
+
+After installation we must verify that the library works as expected:
+
+    $ cabal install hmatrix-tests --enable-tests
+    $ ghci
+    > Numeric.LinearAlgebra.Tests.runTests 20
+    OK, passed 100 tests. 
+    OK, passed 100 tests.
+    ... etc...
+
+If you get any failure please run lapack's own tests to confirm that your version is not broken. For instance, in ubuntu 9.04, **libatlas-sse2** does not work (see this [bug report](https://bugs.launchpad.net/ubuntu/+source/atlas/+bug/368478)). If your lapack library is ok but hmatrix's tests fail please send a bug report!
+
+
+## Optimized BLAS/LAPACK ##########################################
+
+I have successfully tested ATLAS and MKL on Linux.
+
+### [ATLAS](http://math-atlas.sourceforge.net/)  ####################
+
+In Ubuntu >= 9.04 we need:
+
+    $ sudo apt-get install libatlas-base-dev
+
+In older Ubuntu/Debian versions we needed:
+
+    $ sudo apt-get install refblas3-dev lapack3-dev atlas3-base-dev
+
+We may use a version (sse2, 3dnow, etc.) optimized for the machine.
+
+### Intel's MKL  ###############################################
+
+There is a free noncommercial download available from Intel's website. To use it I have added the following lines in my .bashrc configuration file:
+
+    export LD_LIBRARY_PATH=/path/to/mkl/lib/arch
+    export LIBRARY_PATH=/path/to/mkl/lib/arch
+
+where arch = 32 or em64t.
+
+The library must be installed with the -fmkl flag:
+
+    $ cabal install hmatrix -fmkl
+
+
diff --git a/packages/base/THANKS.md b/packages/base/THANKS.md
new file mode 100644
index 0000000..b1417a6
--- /dev/null
+++ b/packages/base/THANKS.md
@@ -0,0 +1,157 @@
+I thank Don Stewart, Henning Thielemann, Bulat Ziganshin, Heinrich Apfelmus,
+and all the people in the Haskell mailing lists for their help.
+
+I am particularly grateful to Vivian McPhail for his excellent
+contributions: improved configure.hs, Binary instances for
+Vector and Matrix, support for Float and Complex Float elements,
+module reorganization, monadic mapVectorM, and many other improvements.
+
+- Nico Mahlo discovered a bug in the eigendecomposition wrapper.
+
+- Frederik Eaton discovered a bug in the design of the wrappers.
+
+- Eric Kidd has created a wiki page explaining the installation on MacOS X:
+  http://www.haskell.org/haskellwiki/GSLHaskell_on_MacOS_X
+
+- Fawzi Mohamed discovered a portability bug in the lapack wrappers.
+
+- Pedro E. López de Teruel fixed the interface to lapack.
+
+- Antti Siira discovered a bug in the plotting functions.
+
+- Paulo Tanimoto helped to fix the configuration of the required libraries.
+  He also discovered the segfault of minimize.hs in ghci.
+
+- Xiao-Yong Jin reported a bug on x86_64 caused by the assumptions in f2c.h,
+  which are wrong for this architecture.
+
+- Jason Schroeder reported an error in the documentation.
+
+- Bulat Ziganshin gave invaluable help for the ST monad interface to
+  in-place modifications.
+
+- Don Stewart fixed the implementation of the internal data structures
+  to achieve excellent, C-like performance in Haskell functions which
+  explicitly work with the elements of vectors and matrices.
+
+- Dylan Alex Simon improved the numeric instances to allow optimized
+  implementations of signum and abs on Vectors.
+
+- Pedro E. López de Teruel discovered the need of asm("finit") to
+  avoid the wrong NaNs produced by foreign functions.
+
+- Reiner Pope added support for luSolve, based on (d|z)getrs.
+  Made Matrix a product type and added changes to improve the code generated
+  by hmatrix-syntax.
+
+- Simon Beaumont reported the need of QuickCheck<2 and the invalid
+  asm("finit") on ppc. He also contributed the configuration options
+  for the accelerate framework on OS X.
+
+- Daniel Schüssler added compatibility with QuickCheck 2 as well
+  as QuickCheck 1 using the C preprocessor. He also added some
+  implementations for the new "shrink" method of class Arbitrary.
+
+- Tracy Wadleigh improved the definitions of (|>) and (><), which now
+  apply an appropriate 'take' to the given lists so that they may be
+  safely used on lists that are too long (or infinite).
+
+- Chris Waterson improved the configure.hs program for OS/X.
+
+- Erik de Castro Lopo added buildVector and buildMatrix, which take a
+  size parameter(s) and a function that maps vector/matrix indices
+  to the values at that position.
+
+- Jean-Francois Tremblay discovered an error in the tutorial.
+
+- Gilberto Camara contributed improved blas and lapack dlls for Windows.
+
+- Heinrich Apfelmus fixed hmatrix.cabal for OS/X. He also tested the package
+  on PPC discovering a problem in zgesdd.
+
+- Felipe Lessa tested the performance of GSL special function bindings
+  and contributed the cabal flag "safe-cheap".
+
+- Ozgur Akgun suggested better symbols for the Bound constructors in the
+  Linear Programming package.
+
+- Tim Sears reported the zgesdd problem also in intel mac.
+
+- Max Suica simplified the installation on Windows and improved the instructions.
+
+- John Billings first reported an incompatibility with QuickCheck>=2.1.1
+
+- Alexey Khudyakov cleaned up PRAGMAS and fixed some hlint suggestions.
+
+- Torsten Kemps-Benedix reported an installation problem in OS/X.
+
+- Stefan Kersten fixed hmatrix.cabal for 64-bit ghc-7 in OS/X
+
+- Sacha Sokoloski reported an installation problem on Arch Linux and
+  helped with the configuration.
+
+- Carter Schonwald helped with the configuration for Homebrew OS X and
+  found a tolerance problem in test "1E5 rots". He also discovered
+  a bug in the signature of cmap.
+
+- Duncan Coutts reported a problem with configure.hs and contributed
+  a solution and a simplified Setup.lhs.
+
+- Mark Wright fixed the import of vector >= 0.8.
+
+- Bas van Dijk fixed the import of vector >= 0.8, got rid of some
+  deprecation warnings, used more explicit imports, and updated to ghc-7.4.
+
+- Tom Nielsen discovered a problem in Config.hs, exposed by link problems
+  in Ubuntu 11.10 beta.
+
+- Daniel Fischer reported some Haddock markup errors.
+
+- Danny Chan added support for integration over infinite intervals, and fixed
+  Configure.hs using platform independent functions.
+
+- Clark Gaebel removed superfluous thread safety.
+
+- Jeffrey Burdges reported a glpk link problem on OS/X
+
+- Jian Zhang reported the Windows installation problem due to new ODE interface.
+
+- Mihaly Barasz and Ben Gamari fixed mapMatrix* and mapMatrixWithIndex
+
+- Takano Akio fixed off-by-one errors in gsl-aux.c producing segfaults.
+
+- Alex Lang implemented uniRoot and uniRootJ for one-dimensional root-finding.
+
+- Mike Ledger contributed alternative FFI helpers for matrix interoperation with C
+
+- Stephen J. Barr suggested flipping argument order in the double integral example
+
+- Greg Horn fixed the bus error on ghci 64-bit.
+
+- Kristof Bastiaensen added bindings for one-dimensional minimization.
+
+- Matthew Peddie added bindings for gsl_integrate_cquad doubly-adaptive quadrature
+  for difficult integrands.
+
+- Ben Gamari exposed matrixFromVector for Development.
+
+- greg94301 reported tolerance issues in the tests.
+
+- Clemens Lang updated the MacPort installation instructions.
+
+- Henning Thielemann reported the pinv inefficient implementation.
+
+- bdoering reported the problem of zero absolute tolerance in the integration functions.
+
+- Alexei Uimanov replaced fromList by Vector.fromList.
+
+- Adam Vogt updated the code for ghc-7.7
+
+- Mike Meyer (mwm) added freeBSD library configuration information.
+
+- tfgit updated the OSX installation instructions via Homebrew
+
+- "yokto" and "ttylec" reported the problem with the dot product of complex vectors.
+
+- Samium Gromoff reported a build failure caused by a size_t - int mismatch.
+
diff --git a/packages/base/hmatrix-base.cabal b/packages/base/hmatrix.cabal
index 91dc0db..5f3c48e 100644
--- a/packages/base/hmatrix-base.cabal
+++ b/packages/base/hmatrix.cabal
@@ -15,6 +15,8 @@ cabal-version:      >=1.8
 
 build-type:         Simple
 
+extra-source-files: THANKS.md INSTALL.md CHANGELOG
+
 extra-source-files: src/C/lapack-aux.h
 
 library