Merge branch 'hotfix-6.1.4'

Author: karlnapf

NEWS

@@ -1,3 +1,10 @@
+2017-12-05 Heiko Strathmann <heiko.strathmann@gmail.com>
+
+	* SHOGUN Release version 6.1.4 (libshogun 18.0, data 0.11, parameter 1)
+
+	* Bugfixes:
+        - Fix cookbookx examples for website
+
 2017-12-05 Viktor Gal <viktor.gal@shogun-toolbox.org>
 
 	* SHOGUN Release version 6.1.3 (libshogun 18.0, data 0.11, parameter 1)

doc/cookbook/source/references.bib

@@ -35,9 +35,8 @@ @article{fan2008liblinear
 @book{Rasmussen2005GPM,
   author = {Rasmussen, C. E. and Williams, C. K. I.},
   title = {Gaussian Processes for Machine Learning},
-  year = {2005},
   publisher = {The MIT Press},
-  year={2008},
+  year={2006},
 }
 
 @article{gretton2012kernel,

doc/cookbook/source/static/mathconf.js

@@ -1,8 +1,8 @@
-MathJax.Hub.Config({
+window.MathJax = {
   TeX: {
     Macros: {
       argmax: ["\\mathop{\\rm arg\\,max}\\limits"],
       argmin: ["\\mathop{\\rm arg\\,min}\\limits"]
     }
   }
-});
+};

doc/cookbook/source/static/shogun-style.css

@@ -57,3 +57,8 @@ div.toctree-wrapper > p.caption {
     font-weight: 300;
     margin-bottom: 0.5em;
 }
+
+.citation td.label {
+    display: block;
+}
+

doc/cookbook/source/templates/layout.html

@@ -1,11 +1,6 @@
 {% extends "!layout.html" %}
 {% set script_files = script_files + ["_static/mathconf.js"] %}
 
-{% set bootswatch_css_custom = ['_static/shogun-style.css'] %}
-{#
-    bootswatch_css_custom is removed in sphinx-bootstrap-theme v0.5.0
-    css_files should be used instead
-#}
 {% set css_files = (css_files or []) + ['_static/shogun-style.css'] %}
 
 {% block rootrellink %}

doc/readme/INSTALL.md

@@ -82,17 +82,17 @@ Install as
 
 
 ### MacOS <a name="mac"></a>
-Shogun is part of [homebrew-science](https://github.com/Homebrew/homebrew-science).
+Shogun is part of [Homebrew](https://formulae.brew.sh/formula/shogun).
 Install the latest stable version as
 
-    brew install homebrew/science/shogun
+    brew install shogun
 
 ### Windows <a name="windows"></a>
 Shogun natively compiles under Windows using MSVC, see the [AppVeyor CI build](https://ci.appveyor.com/project/vigsterkr/shogun) and the [Windows section](#manual-windows). We currently only support binary packages via conda.
 If you are interested in packaging, documenting, or contributing otherwise, please contact us.
 
 ## Docker images <a name="docker"></a>
-You can run Shogun in [our own cloud](cloud.shogun.ml) or set up your own using our
+You can set up Shogun using our
 [Docker images](https://hub.docker.com/r/shogun/shogun/) as:
 
     sudo docker pull shogun/shogun:master
@@ -142,7 +142,7 @@ You need at least 1GB free disk space. If you compile any interface, roughly 4 G
 
 ## Basics <a name="manual-basics"></a>
 Shogun uses [CMake](https://cmake.org/) for its build. The general workflow is now explained.
-For further details on testing etc, see [DEVELOPING.md](DEVELOPING.md).
+For further details on testing etc, see [DEVELOPING.md](docs/DEVELOPING.md).
 
 Download the latest [stable release source code](https://github.com/shogun-toolbox/shogun/releases/latest), or (as demonstrated here) clone the latest develop code.
 Potentially update submodules

doc/readme/INTERFACES.md

@@ -1,7 +1,7 @@
 Running Shogun from the interfaces
 ==================================
 
-We assume that installation (including the interfaces) was successful and all dependencies are installed. See [INSTALL.md](INSTALL.md) and our website.
+We assume that installation (including the interfaces) was successful and all dependencies are installed. See [INSTALL.md][installation-page].
 
 Note that setting some the enviromental variables should not be necessary in case you installed Shogun to the default folder or installed it from a binary package.
 
@@ -110,7 +110,7 @@ Running it again requires the above class path and some more options
     java -Xmx1024m -cp /path/to/jblas.jar:/path/to/shogun.jar:path/to/java_example.java -Djava.library.path=/path/to/shogun.jar java_example
 
 ### Provided Examples
-Stand-alone, executable code for all interface examples on our website (and more) can be generated locally, see [INSTALL.md](INSTALL.md).
+Stand-alone, executable code for all interface examples on our website (and more) can be generated locally, [see INSTALL.md][installation-page].
 As the examples load data files, they requires the `shogun-data` submodule to be checked out.
 
 All examples should be run in the respective folder they are located in, for example (assuming that all described variables are set)
@@ -122,3 +122,5 @@ Or, for a compiled language with a manually compiled, not yet installed Shogun,
 
     cd /path/to/shogun-source/build/examples/meta/csharp/regression/
     mono linear_ridge_regression.cs
+
+[installation-page]: docs/INSTALL.md

doc/readme/MISSION.md

@@ -72,6 +72,6 @@ The original focus was on large-scale kernel methods and bioinformatics.
 Since then, Shogun has continuously been used for scientific research (a list of papers citing Shogun can be found [here](http://scholar.google.com/scholar?hl=en&q=shogun+toolbox&btnG=&as_sdt=1%2C33&as_sdtp=)) and massively expanded.
 Shogun joined [NumFocus](https://www.numfocus.org/) in early 2017.
 
-Currently, Shogun is developed by a diverse team of students, scientists and professionals, see the [website](http://shogun-toolbox.org/page/about/ourteam) and Shogun's [AUTHORS](https://github.com/shogun-toolbox/shogun/wiki/AUTHORS). 
+Currently, Shogun is developed by a diverse team of students, scientists and professionals, see Shogun's [AUTHORS](https://github.com/shogun-toolbox/shogun/wiki/AUTHORS). 
 None of their work would have been possible without the patches and bug reports by various contributors.