make into standard folder structure, not usable yet

.gitignore

@@ -0,0 +1,75 @@
+# Created by http://www.gitignore.io
+
+### Emacs ###
+# -*- mode: gitignore; -*-
+*~
+\#*\#
+/.emacs.desktop
+/.emacs.desktop.lock
+*.elc
+auto-save-list
+tramp
+.\#*
+
+# Org-mode
+.org-id-locations
+*_archive
+
+# flymake-mode
+*_flymake.*
+
+# eshell files
+/eshell/history
+/eshell/lastdir
+
+# elpa packages
+/elpa/
+
+# reftex files
+*.rel
+
+# AUCTeX auto folder
+/auto/
+
+
+### C++ ###
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+
+### CMake ###
+CMakeCache.txt
+CMakeFiles
+Makefile
+cmake_install.cmake
+install_manifest.txt
+
+### build ### 
+/build/*
+/bin/*
+/emacs-build/*
+/output/*
+/viewer.py
+# /python/*
+/test/*
+libpysegfit.so
+segfit

.travis.yml

@@ -0,0 +1,17 @@
+language: cpp
+compiler:
+  - clang
+notifications:
+  email: false
+env:
+  matrix:
+    - JULIAVERSION="juliareleases"
+    - JULIAVERSION="julianightlies"
+before_install:
+  - sudo add-apt-repository ppa:staticfloat/julia-deps -y
+  - sudo add-apt-repository ppa:staticfloat/${JULIAVERSION} -y
+  - sudo apt-get update -qq -y
+  - sudo apt-get install libpcre3-dev julia -y
+  - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
+script:
+  - julia -e 'Pkg.init(); Pkg.clone(pwd()); Pkg.test("Lbfgsb")'

LICENSE.md

@@ -0,0 +1,25 @@
+The Lbfgsb.jl package is licensed under the Simplified "2-clause" BSD License:
+
+> Copyright (c) 2014: Honglin Yu.
+>
+> Redistribution and use in source and binary forms, with or without
+> modification, are permitted provided that the following conditions are
+> met:
+>
+> 1. Redistributions of source code must retain the above copyright
+>    notice, this list of conditions and the following disclaimer.
+> 2. Redistributions in binary form must reproduce the above copyright
+>    notice, this list of conditions and the following disclaimer in the
+>    documentation and/or other materials provided with the distribution.
+>
+> THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+> "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+> LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+> A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+> OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+> SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+> LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+> DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+> THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+> (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+> OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -47,3 +47,4 @@ BSD-3
 
 [lbfgsb fortran library]:http://users.iems.northwestern.edu/~nocedal/lbfgsb.html
 [this wrapper]:http://hannes.nickisch.org/code/glm-ie/pls/lbfgsb/README.html
+

src/Lbfgsb.jl

@@ -0,0 +1,137 @@
+module Lbfgsb
+
+# package code goes here
+macro callLBFGS(cmd)
+    quote
+        if length($cmd) != 0
+            @simd for i = 1:length($cmd)
+                task[i] = ($cmd)[i];
+            end
+            @simd for i = length($cmd)+1:60
+                task[i] = ' ';
+            end
+        end
+
+        ccall((:setulb_, "./liblbfgsb.so"),
+              Void,
+              (Ptr{Int32},
+               Ptr{Int32},
+               Ptr{Float64},
+               Ptr{Float64},
+               Ptr{Float64},
+               Ptr{Int32},
+               Ptr{Float64},
+               Ptr{Float64},
+               Ptr{Float64},
+               Ptr{Float64},
+               Ptr{Float64},
+               Ptr{Int32},
+               Ptr{Uint8},
+               Ptr{Int32},
+               Ptr{Uint8},
+               Ptr{Bool},
+               Ptr{Int32},
+               Ptr{Float64} ),
+              n,
+              m,
+              x,
+              lb,
+              ub,
+              btype,
+              f,
+              g,
+              factr,
+              pgtol,
+              wa,
+              iwa,
+              task,
+              iprint,
+              csave,
+              lsave,
+              isave,
+              dsave );
+    end
+end
+
+function lbfgsb (ogFunc,
+                 x;
+                 lb = [],
+                 ub = [],
+                 btype = [],
+                 m::Int64 = 5,
+                 maxiter::Int64 = 100,
+                 factr::Float64 = 1e7,
+                 pgtol::Float64 = 1e-5,
+                 iprint::Int64 = -1 # does not print
+                 )
+    m = [convert(Int32, m)]
+    factr = [convert(Float64, factr)];
+    pgtol = [convert(Float64, pgtol)];
+    iprint = [convert(Int32, iprint)];
+
+    n = [convert(Int32, length(x))]; # number of variables
+    f = [convert(Float64, 0.0)]; # The value of the objective.
+    g = [convert(Float64, 0.0) for i=1:(n[1])]; # The value of the gradient.
+
+    if length(lb) == 0
+        lb = [-Inf for i=1:(n[1])];
+    else
+        lb = [convert(Float64, i) for i in lb]
+    end
+
+    if length(ub) == 0
+        ub = [Inf for i=1:(n[1])];
+    else
+        ub = [convert(Float64, i) for i in ub]
+    end
+
+    if length(btype) == 0
+        btype = [convert(Int32, 2) for i=1:(n[1])];
+    else
+        btype = [convert(Int32, i) for i in btype];
+    end
+
+    # structures used by the L-BFGS-B routine.
+    wa = [convert(Float64, 0.0) for i = 1:(2*m[1] + 5)*n[1] + 12*m[1]*(m[1] + 1)];
+    iwa = [convert(Int32, 0) for i = 1:3*n[1]];
+    task = [convert(Uint8, 0) for i =1:60];
+    csave = [convert(Uint8, 0) for i =1:60];
+    lsave = [convert(Bool, 0) for i=1:4];
+    isave = [convert(Int32, 0) for i=1:44];
+    dsave = [convert(Float64, 0.0) for i=1:29];
+
+    @callLBFGS "START"
+
+    status = "success";
+
+    t = 0;
+
+    while true
+
+        if task[1] == 'F'
+            tf, g = ogFunc(x);
+            f[1] = convert(Float64, tf);
+
+        elseif task[1] == 'N'
+            t += 1;
+            if t >= maxiter # exceed maximum number of iteration
+                @callLBFGS "STOP"
+                break;
+            end
+        elseif task[1] == 'C' # convergence
+            break;
+        elseif task[1] == 'A'
+            status = "abnormal";
+            break;
+        elseif task[1] == 'E'
+            status = "error";
+            break;
+        end
+
+        @callLBFGS ""
+    end
+
+    return (f, x, status, t);
+end
+
+end # module