update index.html to match README.md

Former-commit-id: 68f4ef0f5973eb197da8ca64ef744b1467cf9d1b

README.md

@@ -64,8 +64,9 @@ Hello, mesh:
 
 ## Tutorial ##
 
-As of version 1.0, libigl includes an introductory tutorial that covers its basic
-functionalities. See [tutorial/tutorial.md](./tutorial/tutorial.md) to get started.
+As of version 1.0, libigl includes an introductory
+[tutorial](http://libigl.github.io/libigl/tutorial/tutorial.html) that covers
+its basic functionalities.
 
 ## Dependencies ##
 - Eigen3  Last tested with Eigen Version 3.2

index.html

@@ -1 +1,570 @@
-<a href=tutorial/tutorial.html>Tutorial</a>
+<h1 id="libigl-asimplecgeometryprocessinglibrary">libigl - A simple c++ geometry processing library</h1>
+
+<p><a href="http://igl.ethz.ch/projects/libigl/">http://igl.ethz.ch/projects/libigl/</a>
+<a href="https://github.com/alecjacobson/libigl/">https://github.com/alecjacobson/libigl/</a></p>
+
+<p>Copyright 2014 - Alec Jacobson, Daniele Panozzo, Olga Diamanti, Kenshi
+Takayama, Leo Sacht, Wenzel Jacob, etc.</p>
+
+<p>This is first and foremost a <em>header</em> library. Each header file should contain
+a single function. The function may have multiple prototypes. All functions
+should use the igl namespace and should adhere to the conventions and styles
+listed below.</p>
+
+<blockquote>
+<p><strong>New:</strong> As of 1 July 2014, we have released libigl as beta version 1.0.
+There are a number of changes we collected for this release to minimize
+confusion and changes to how you use libigl. See <a href="#version1.0changes">Version 1.0
+Changes</a>.</p>
+</blockquote>
+
+<h2 id="installation">Installation</h2>
+
+<p>Libigl is a <em>header</em> library. You do <strong>not</strong> need to build anything to install.
+Simple add <code>igl/</code> to your include path and include relevant headers. Here&#8217;s a
+small &#8220;Hello, World&#8221; program:</p>
+
+<pre><code class="cpp">#include &lt;igl/cotmatrix.h&gt;
+#include &lt;Eigen/Dense&gt;
+#include &lt;Eigen/Sparse&gt;
+#include &lt;iostream&gt;
+int main()
+{
+  Eigen::MatrixXd V(4,2);
+  V&lt;&lt;0,0,
+     1,0,
+     1,1,
+     0,1;
+  Eigen::MatrixXi F(2,3);
+  F&lt;&lt;0,1,2,
+     0,2,3;
+  Eigen::SparseMatrix&lt;double&gt; L;
+  igl::cotmatrix(V,F,L);
+  std::cout&lt;&lt;&quot;Hello, mesh: &quot;&lt;&lt;std::endl&lt;&lt;L*V&lt;&lt;std::endl;
+  return 0;
+}
+</code></pre>
+
+<p>If you save this in <code>hello.cpp</code>, then on <code>gcc</code> with Eigen installed via
+macports for example you could compile this with:</p>
+
+<pre><code class="bash">gcc -I/opt/local/include/eigen3 -I./igl/ hello.cpp -o hello
+</code></pre>
+
+<p>Running <code>./hello</code> would then produce</p>
+
+<pre><code>Hello, mesh:
+ 0.5  0.5
+-0.5  0.5
+-0.5 -0.5
+ 0.5 -0.5
+</code></pre>
+
+<h2 id="tutorial">Tutorial</h2>
+
+<p>As of version 1.0, libigl includes an introductory
+<a href="http://libigl.github.io/libigl/tutorial/tutorial.html">tutorial</a> that covers
+its basic functionalities.</p>
+
+<h2 id="dependencies">Dependencies</h2>
+
+<ul>
+<li>Eigen3 Last tested with Eigen Version 3.2</li>
+</ul>
+
+<h3 id="optional">Optional</h3>
+
+<ul>
+<li>OpenGL (disable with <code>IGL_NO_OPENGL</code>)
+
+<ul>
+<li>OpenGL &gt;= 4 (enable with <code>IGL_OPENGL_4</code>)</li>
+</ul></li>
+<li>AntTweakBar (disable with <code>IGL_NO_ANTTWEAKBAR</code>) Last tested 1.16 (see
+ <code>libigl/external/AntTweakBar</code>)</li>
+<li>GLEW Windows and Linux</li>
+<li>OpenMP</li>
+<li>libpng libiglpng extra only</li>
+<li>Mosek libiglmosek extra only</li>
+<li>Matlab libiglmatlab extra only</li>
+<li>boost libiglboost, libiglcgal extra only</li>
+<li>SSE/AVX libiglsvd3x3 extra only</li>
+<li>CGAL libiglcgal extra only
+
+<ul>
+<li>boost</li>
+<li>gmp</li>
+<li>mpfr</li>
+</ul></li>
+<li>CoMiSo libcomiso extra only</li>
+</ul>
+
+<h3 id="optionalincludedinexternal">Optional (included in external/)</h3>
+
+<ul>
+<li>TetGen libigltetgen extra only</li>
+<li>Embree libiglembree extra only</li>
+<li>tinyxml2 libiglxml extra only</li>
+<li>glfw libviewer extra only</li>
+<li>LIM liblim extra only</li>
+</ul>
+
+<h2 id="headeronly">Header only</h2>
+
+<p>Libigl is designed to work &#8220;out-of-the-box&#8221; as a headers only library. To
+include libigl in your project. You need only include the libigl/include/
+directory in your include path. To
+compile a hello-word example.cpp:</p>
+
+<pre><code>#include &lt;Eigen/Dense&gt;
+#include &lt;igl/readOBJ.h&gt;
+#include &lt;iostream&gt;
+int main(int argc, char * argv[])
+{
+  if(argc&gt;1)
+  {
+    Eigen::MatrixXd V;
+    Eigen::MatrixXi F;
+    igl::readOBJ(argv[1],V,F);
+    std::cout&lt;&lt;&quot;Hello, mesh with &quot;&lt;&lt;V.rows()&lt;&lt;&quot; vertices!&quot;&lt;&lt;std::endl;
+  }else{
+    std::cout&lt;&lt;&quot;Hello, world!&quot;&lt;&lt;std::endl;
+  }
+  return 0;
+}
+</code></pre>
+
+<p>using gcc (replacing appropriate paths):</p>
+
+<pre><code>g++ -I/usr/local/igl/libigl/include \
+  -I/opt/local/include/eigen3 example.cpp -o example
+</code></pre>
+
+<p>Then run this example with:</p>
+
+<pre><code>./example examples/shared/TinyTorus.obj
+</code></pre>
+
+<h2 id="compilationasastaticlibrary">Compilation as a static library</h2>
+
+<p>Libigl is developed most often on Mac OS X, though has current users in Linux
+and Windows.</p>
+
+<h3 id="linuxmacosxcygwin">Linux/Mac OS X/Cygwin</h3>
+
+<p>Libigl may also be compiled to a static library. This is advantageous when
+building a project with libigl, since when used as an header-only library can
+slow down compile times.</p>
+
+<p>To build the entire libigl library producing lib/libigl.a, issue:</p>
+
+<pre><code>cd build
+make lib
+</code></pre>
+
+<p>You may need to edit Makefile.conf accordingly. Best to give yourself an
+<code>IGL_USERNAME</code> and add a custom install suite for yourself. Then you can enable
+appropriate extras.</p>
+
+<h4 id="extras">Extras</h4>
+
+<p>Once you&#8217;ve set up an <code>IGL_USERNAME</code> and enabled extras within Makefile.conf.
+You can build the extra libraries (into lib/ligiglpng.a, lib/libiglmatlab.a,
+lib/libigltetgen.a, lib/libiglmosek.a, etc.) by issuing:</p>
+
+<pre><code>cd build
+make extras
+</code></pre>
+
+<h4 id="examples">Examples</h4>
+
+<p>You can make a slew of examples by issuing:</p>
+
+<pre><code>cd build
+make examples
+</code></pre>
+
+<h4 id="external">External</h4>
+
+<p>Finally there are a number of external libraries that we include in
+./external/ because they are either difficult to obtain or they have been
+patched for easier use with libigl. Please see the respective readmes in
+those directories.</p>
+
+<h5 id="installinganttweakbar">Installing AntTweakBar</h5>
+
+<p>To build the a static AntTweakBar library on Mac OS X issue:</p>
+
+<pre><code>cd external/AntTweakBar/src
+make -f Makefile.osx.igl
+</code></pre>
+
+<h5 id="installingtetgen">Installing Tetgen</h5>
+
+<p>To build the tetgen library and executable on Mac OS X issue:</p>
+
+<pre><code>cd external/tetgen
+make clean
+rm -f obj/*.o
+make -f Makefile.igl tetgen
+rm -f obj/*.o
+make -f Makefile.igl tetlib
+</code></pre>
+
+<h5 id="installingmedit">Installing medit</h5>
+
+<p>To build the igl version of the medit executable on Mac OS X issue:</p>
+
+<pre><code>cd external/medit
+make -C libmesh
+make -f Makefile.igl medit
+</code></pre>
+
+<h5 id="installingembree2.0">Installing Embree 2.0</h5>
+
+<p>To build the embree library and executables on Mac OS X issue:</p>
+
+<pre><code>cd external/embree
+mkdir build
+cd build
+cmake ..
+# Or using a different compiler
+#cmake .. -DCMAKE_C_COMPILER=/opt/local/bin/gcc -DCMAKE_CXX_COMPILER=/opt/local/bin/g++
+make
+# Could also install embree to your root, but libigl examples don't expect
+# this
+#sudo make install
+</code></pre>
+
+<h5 id="installingtinyxml2">Installing tinyxml2</h5>
+
+<p>To build the a static tinyxml2 library on Mac OS X issue:</p>
+
+<pre><code>cd external/tinyxml2
+cmake .
+make
+</code></pre>
+
+<h5 id="installingyimg">Installing YImg</h5>
+
+<p>To build the a static YImg library on Mac OS X issue:</p>
+
+<pre><code>cd external/yimg
+make
+</code></pre>
+
+<p>You may need to install libpng. Systems with X11 might find this already
+installed at <code>/usr/X11/lib</code>.</p>
+
+<h3 id="windowsexperimental">Windows (Experimental)</h3>
+
+<p>To build a static library (.lib) on windows, open Visual Studio 2010.</p>
+
+<ul>
+<li>New &gt; Project &#8230;</li>
+<li>Visual C++ &gt; Win32</li>
+<li>Win32 Console Application</li>
+<li>Name: libiglVisualStudio</li>
+<li>Uncheck &#8220;Create directory for solution&#8221;</li>
+<li>Then hit OK, and then Next</li>
+<li>Check &#8220;Static Library&#8221;</li>
+<li>Uncheck &#8220;Precompiled headers&#8221;</li>
+<li>Add all include/igl/*.cpp to the sources directory</li>
+<li>Add all include/igl/*.h to the headers directory</li>
+<li>Open Project &gt; libigl Properties&#8230;</li>
+<li>Add the path to eigen3 to the include paths</li>
+<li>Change the target name to libigl</li>
+<li>Build and pray (this should create libigl.lib</li>
+</ul>
+
+<p><a href="http://msdn.microsoft.com/en-us/library/ms235627(v=vs.80).aspx">Source</a></p>
+
+<h2 id="examples">Examples</h2>
+
+<p>To get started, we advise that you take a look at a few examples:</p>
+
+<pre><code>./examples/hello-world/
+
+./examples/meshio/
+
+./examples/basic-topology/
+
+./examples/ReAntTweakBar/
+</code></pre>
+
+<h2 id="extras">Extras</h2>
+
+<p>Libigl compartmentalizes dependences via its organization into a <em>main</em> libigl
+library and &#8220;extras.&#8221;</p>
+
+<h3 id="bbw">bbw</h3>
+
+<p>This library extra contains functions for computing Bounded Biharmonic Weights, can
+be used with and without the <a href="#mosek">mosek</a> extra via the <code>IGL_NO_MOSEK</code>
+macro.</p>
+
+<h3 id="boost">boost</h3>
+
+<p>This library extra utilizes the graph functions in the boost library for find
+connected components and performing breadth-first traversals.</p>
+
+<h3 id="cgal">cgal</h3>
+
+<p>This library extra utilizes CGAL&#8217;s efficient and exact intersection and
+proximity queries.</p>
+
+<h3 id="embree">embree</h3>
+
+<p>This library extra utilizes embree&#8217;s efficient ray tracing queries.</p>
+
+<h3 id="matlab">matlab</h3>
+
+<p>This library extra provides support for reading and writing <code>.mat</code> workspace
+files, interfacing with Matlab at run time and compiling mex functions.</p>
+
+<h3 id="mosek">mosek</h3>
+
+<p>This library extra utilizes mosek&#8217;s efficient interior-point solver for
+quadratic programs.</p>
+
+<h3 id="png">png</h3>
+
+<p>This library extra uses <code>libpng</code> and <code>YImage</code> to read and write <code>.png</code> files.</p>
+
+<h3 id="svd3x3">svd3x3</h3>
+
+<p>This library extra implements &#8220;as-rigid-as-possible&#8221; (ARAP) deformation
+techniques using the fast singular value decomposition routines
+written specifically for 3x3 matrices to use <code>SSE</code> intrinsics. This extra can
+still be compiled without sse support and support should be determined
+automatically at compile time via the <code>__SSE__</code> macro.</p>
+
+<h3 id="tetgen">tetgen</h3>
+
+<p>This library extra provides a simplified wrapper to the tetgen 3d tetrahedral meshing
+library.</p>
+
+<h3 id="viewer">viewer</h3>
+
+<p>This library extra utilizes glfw and glew to open an opengl context and launch
+a simple mesh viewer.</p>
+
+<h3 id="xml">xml</h3>
+
+<p>This library extra utilizes tinyxml2 to read and write serialized classes
+containing Eigen matrices and other standard simple data-structures.</p>
+
+<h2 id="development">Development</h2>
+
+<p>Further documentation for developers is listed in tutorial.html,
+style_guidelines.html</p>
+
+<h2 id="license">License</h2>
+
+<p>See <code>LICENSE.txt</code></p>
+
+<h2 id="zipping">Zipping</h2>
+
+<p>Zip this directory without .git litter and binaries using:</p>
+
+<pre><code>git archive -prefix=libigl/ -o libigl.zip master
+</code></pre>
+
+<h2 id="version1.0changes">Version 1.0 Changes</h2>
+
+<p>Our beta release marks our confidence that this library can be used outside of
+casual experimenting. To maintain order, we have made a few changes which
+current users should read and adapt their code accordingly.</p>
+
+<h3 id="renamedfunctions">Renamed functions</h3>
+
+<p>The following table lists functions which have changed name as of version
+1.0.0:</p>
+
+<table>
+<colgroup>
+<col style="text-align:left;"/>
+<col style="text-align:left;"/>
+</colgroup>
+
+<thead>
+<tr>
+	<th style="text-align:left;">Old</th>
+	<th style="text-align:left;">New</th>
+</tr>
+</thead>
+
+<tbody>
+<tr>
+	<td style="text-align:left;"><code>igl::add_barycenter</code></td>
+	<td style="text-align:left;"><code>igl::false_barycentric_subdivision</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::areamatrix</code></td>
+	<td style="text-align:left;"><code>igl::vector_area_matrix</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::barycentric2global</code></td>
+	<td style="text-align:left;"><code>igl::barycentric_to_global</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::boundary_faces</code></td>
+	<td style="text-align:left;"><code>igl::boundary_facets</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::boundary_vertices_sorted</code></td>
+	<td style="text-align:left;"><code>igl::boundary_loop</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::cotangent</code></td>
+	<td style="text-align:left;"><code>igl::cotmatrix_entries</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::edgetopology</code></td>
+	<td style="text-align:left;"><code>igl::edge_topology</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::gradMat</code></td>
+	<td style="text-align:left;"><code>igl::grad</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::is_manifold</code></td>
+	<td style="text-align:left;"><code>igl::is_edge_manifold</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::mexStream</code></td>
+	<td style="text-align:left;"><code>igl::MexStream</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::moveFV</code></td>
+	<td style="text-align:left;"><code>igl::average_onto_vertices</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::moveVF</code></td>
+	<td style="text-align:left;"><code>igl::average_onto_faces</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::plot_vector</code></td>
+	<td style="text-align:left;"><code>igl::print_vector</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::pos</code></td>
+	<td style="text-align:left;"><code>igl::HalfEdgeIterator</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::plane_project</code></td>
+	<td style="text-align:left;"><code>igl::project_isometrically_to_plane</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::project_points_mesh</code></td>
+	<td style="text-align:left;"><code>igl::line_mesh_intersection</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::read</code></td>
+	<td style="text-align:left;"><code>igl::read_triangle_mesh</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::removeDuplicates.cpp</code></td>
+	<td style="text-align:left;"><code>igl::remove_duplicates</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::removeUnreferenced</code></td>
+	<td style="text-align:left;"><code>igl::remove_unreferenced</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::tt</code></td>
+	<td style="text-align:left;"><code>igl::triangle_triangle_adjacency</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::vf</code></td>
+	<td style="text-align:left;"><code>igl::vertex_triangle_adjacency</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::write</code></td>
+	<td style="text-align:left;"><code>igl::write_triangle_mesh</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::manifold_patches</code></td>
+	<td style="text-align:left;"><code>igl::orientable_patches</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::selfintersect</code></td>
+	<td style="text-align:left;"><code>igl::remesh_self_intersections</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::project_mesh</code></td>
+	<td style="text-align:left;"><code>igl::line_mesh_intersection</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::triangulate</code></td>
+	<td style="text-align:left;"><code>igl::polygon_mesh_to_triangle_mesh</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::is_manifold</code></td>
+	<td style="text-align:left;"><code>igl::is_edge_manifold</code></td>
+</tr>
+<tr>
+	<td style="text-align:left;"><code>igl::triangle_wrapper</code></td>
+	<td style="text-align:left;"><code>igl::triangulate</code></td>
+</tr>
+</tbody>
+</table>
+
+<h3 id="miscellaneous">Miscellaneous</h3>
+
+<ul>
+<li>To match interfaces provided by (all) other quadratic optimization
+ libraries, <code>igl::min_quad_with_fixed</code> and <code>igl::active_set</code> now expect as
+ input twice the quadratic coefficients matrix, i.e. the Hessian. For
+ example, <code>igl::min_quad_with_fixed(H,B,...)</code> minimizes <span class="math">\(\frac{1}{2}x^T H
+   x+x^T B\)</span>.</li>
+<li>We have inverted the <code>IGL_HEADER_ONLY</code> macro to <code>IGL_STATIC_LIBRARY</code>. To
+ compile using libigl as a header-only library, simply include headers and
+ libigl in the header search path. To link to libigl, you must define the
+ <code>IGL_STATIC_LIBRARY</code> macro at compile time and link to the <code>libigl*.a</code>
+ libraries.</li>
+<li>Building libigl as a static library is now more organized. There is a
+ <code>build/</code> directory with Makefiles for the main library (<code>Makefile</code>) and each
+ dependency (e.g. <code>Makefile_mosek</code> for <code>libiglmosek.a</code>)</li>
+<li><code>igl::polar_svd</code> now always returns a rotation in <code>R</code>, never a reflection.
+ This mirrors the behavior of <code>igl::polar_svd3x3</code>. Consequently the <code>T</code>
+ part may have negative skews.</li>
+<li>We have organized the static</li>
+<li>The previous <code>igl::grad</code> function, which computed the per-triangle gradient
+ of a per-vertex scalar function has been replaced. Now <code>igl::grad</code> computes
+ the linear operator (previous computed using <code>igl::gradMat</code>). The gradient
+ values can still be recovered by multiplying the operator against the scalar
+ field as a vector and reshaping to have gradients per row.</li>
+<li><code>MASSMATRIX_*</code> has become <code>MASSMATRIX_TYPE_*</code></li>
+<li>The function <code>igl::project_normals</code>, which cast a line for each vertex of
+ mesh <em>A</em> in the normal direction and found the closest intersection along
+ these lines with mesh <em>B</em>, has been removed.</li>
+</ul>
+
+<h2 id="contact">Contact</h2>
+
+<p>Libigl is a group endeavor led by Alec Jacobson and Daniele Panozzo. Please
+contact <a href="&#109;&#97;&#105;&#108;&#x74;&#111;&#x3a;&#x61;&#x6c;&#101;&#x63;&#x6a;&#x61;&#x63;&#111;&#98;&#115;&#111;&#110;&#64;&#103;&#109;&#x61;&#105;&#108;&#x2e;&#x63;&#x6f;&#x6d;">&#97;&#x6c;&#x65;&#99;&#106;&#97;&#x63;&#111;&#x62;&#x73;&#x6f;&#110;&#x40;&#103;&#x6d;&#x61;&#105;&#x6c;&#x2e;&#x63;&#x6f;&#x6d;</a> if you have
+questions or comments. We are happy to get feedback! Enjoy!</p>
+
+<p>If you&#8217;re using libigl in your projects, quickly <a href="&#x6d;&#97;&#x69;&#x6c;&#116;&#x6f;&#x3a;&#97;&#x6c;&#101;&#x63;&#106;&#97;&#x63;&#x6f;&#98;&#115;&#x6f;&#x6e;&#64;&#103;&#x6d;&#97;&#105;&#108;&#x2e;&#x63;&#111;&#x6d;">&#x64;&#x72;&#111;&#112; &#117;&#x73; &#x61;
+&#x6e;&#x6f;&#116;&#101;</a>. Tell us who you are and what you&#8217;re using
+it for. This helps us apply for funding and justify spending time maintaining
+this.</p>
+
+<p>If you find bugs or have problems please use our <a href="https://github.com/libigl/libigl/issues">github issue tracking
+page</a>.</p>
+
+<h2 id="academiccitation">Academic citation</h2>
+
+<p>If you use libigl in your research projects, please cite the papers we
+implement as appropriate. To cite the library in general, you could use this
+BibTeX entry:</p>
+
+<pre><code class="bibtex">@misc{libigl,
+  title = {{libigl}: A simple {C++} geometry processing library},
+  author = {Alec Jacobson and Daniele Panozzo and others},
+  note = {http://igl.ethz.ch/projects/libigl/},
+  year = {2014},
+}
+</code></pre>