Merge branch 'master' into mlpack-3.x

CMakeLists.txt

@@ -479,7 +479,7 @@ endif ()
 
 # Make a target to generate the man page documentation, but only if we are on a
 # UNIX-like system.
-if (UNIX)
+if (BUILD_CLI_EXECUTABLES AND UNIX)
   find_program(TXT2MAN txt2man)
 
   # It's not a requirement that we make man pages.

COPYRIGHT.txt

@@ -24,7 +24,7 @@ Copyright:
   Copyright 2012, Patrick Mason <patrick.s.mason@gmail.com>
   Copyright 2013-2018, Marcus Edel <marcus.edel@fu-berlin.de>
   Copyright 2013, Mudit Raj Gupta <mudit.raaj.gupta@gmail.com>
-  Copyright 2013, Sumedh Ghaisas <sumedhghaisas@gmail.com>
+  Copyright 2013-2018, Sumedh Ghaisas <sumedhghaisas@gmail.com>
   Copyright 2014, Michael Fox <michaelfox99@gmail.com>
   Copyright 2014, Ryan Birmingham <birm@gatech.edu>
   Copyright 2014, Siddharth Agrawal <siddharth.950@gmail.com>
@@ -48,14 +48,14 @@ Copyright:
   Copyright 2015, Joseph Mariadassou <joe.mariadassou@gmail.com>
   Copyright 2015, Pavel Zhigulin <pashaworking@gmail.com>
   Copyright 2016, Andy Fang <AndyFang.DZ@gmail.com>
-  Copyright 2016, Barak Pearlmutter <barak+git@pearlmutter.net>
+  Copyright 2016-2018, Barak Pearlmutter <barak+git@pearlmutter.net>
   Copyright 2016, Ivari Horm <ivari@risk.ee>
   Copyright 2016, Dhawal Arora <d.p.arora1@gmail.com>
   Copyright 2016, Alexander Leinoff <alexander-leinoff@uiowa.edu>
   Copyright 2016, Palash Ahuja <abhor902@gmail.com>
   Copyright 2016, Yannis Mentekidis <mentekid@gmail.com>
   Copyright 2016, Ranjan Mondal <ranjan.rev@gmail.com>
-  Copyright 2016, Mikhail Lozhnikov <lozhnikovma@gmail.com>
+  Copyright 2016-2018, Mikhail Lozhnikov <lozhnikovma@gmail.com>
   Copyright 2016, Marcos Pividori <marcos.pividori@gmail.com>
   Copyright 2016, Keon Kim <kwk236@gmail.com>
   Copyright 2016, Nilay Jain <nilayjain13@gmail.com>
@@ -84,9 +84,9 @@ Copyright:
   Copyright 2017, N Rajiv Vaidyanathan <rajivvaidyanathan4@gmail.com>
   Copyright 2017, Kartik Nighania <kartiknighania@gmail.com>
   Copyright 2017-2018, Eugene Freyman <evg.freyman@gmail.com>
-  Copyright 2017, Manish Kumar <manish887kr@gmail.com>
-  Copyright 2017, Haritha Sreedharan Nair <haritha1313@gmail.com>
-  Copyright 2017&2018, Sourabh Varshney <sourabhvarshney111@gmail.com>
+  Copyright 2017-2018, Manish Kumar <manish887kr@gmail.com>
+  Copyright 2017-2018, Haritha Sreedharan Nair <haritha1313@gmail.com>
+  Copyright 2017-2018, Sourabh Varshney <sourabhvarshney111@gmail.com>
   Copyright 2018, Projyal Dev <projyal@gmail.com>
   Copyright 2018, Nikhil Goel <nikhilgoel199797@gmail.com>
   Copyright 2018, Shikhar Jaiswal <jaiswalshikhar87@gmail.com>
@@ -101,6 +101,8 @@ Copyright:
   Copyright 2018, Namrata Mukhija <namratamukhija@gmail.com>
   Copyright 2018, Conrad Sanderson
   Copyright 2018, Thanasis Mattas <mattasa@auth.gr>
+  Copyright 2018, Shashank Shekhar <contactshashankshekhar@gmail.com>
+  Copyright 2018, Yasmine Dumouchel <yasmine.dumouchel@gmail.com>
 
 License: BSD-3-clause
   All rights reserved.

Doxyfile

@@ -4,7 +4,7 @@
 # Project related configuration options
 #---------------------------------------------------------------------------
 PROJECT_NAME           = mlpack
-PROJECT_NUMBER         = 3.0.1
+PROJECT_NUMBER         = 3.0.2
 OUTPUT_DIRECTORY       = ./doc
 CREATE_SUBDIRS         = NO
 OUTPUT_LANGUAGE        = English

HISTORY.md

@@ -1,3 +1,20 @@
+### mlpack 3.0.2
+###### 2018-06-08
+  * Documentation generation fixes for Python bindings (#1421).
+
+  * Fix build error for man pages if command-line bindings are not being built
+    (#1424).
+
+  * Add 'shuffle' parameter and Shuffle() method to KFoldCV (#1412).  This will
+    shuffle the data when the object is constructed, or when Shuffle() is
+    called.
+
+  * Added neural network layers: AtrousConvolution (#1390), Embedding (#1401),
+    and LayerNorm (layer normalization) (#1389).
+
+  * Add Pendulum environment for reinforcement learning (#1388) and update
+    Mountain Car environment (#1394).
+
 ### mlpack 3.0.1
 ###### 2018-05-10
   * Fix intermittently failing tests (#1387).

LICENSE.txt

@@ -13,7 +13,7 @@ src/mlpack/core/boost_backport/ and more details on the licensing are available
 there.
 
 ----
-Copyright (c) 2007-2016, mlpack contributors (see COPYRIGHT.txt)
+Copyright (c) 2007-2018, mlpack contributors (see COPYRIGHT.txt)
 All rights reserved.
 
 Redistribution and use of mlpack in source and binary forms, with or without

README.md

@@ -22,7 +22,7 @@ src="https://cdn.rawgit.com/mlpack/mlpack.org/e7d36ed8/mlpack-black.svg" style="
 <p align="center">
   <em>
     Download:
-    <a href="http://www.mlpack.org/files/mlpack-3.0.0.tar.gz">current stable version (3.0.0)</a>
+    <a href="http://www.mlpack.org/files/mlpack-3.0.2.tar.gz">current stable version (3.0.2)</a>
   </em>
 </p>
 
@@ -106,6 +106,11 @@ with the following command:
 
     $ sudo apt-get install libmlpack-dev
 
+Note: Older Ubuntu versions may not have the most recent version of mlpack
+available---for instance, at the time of this writing, Ubuntu 16.04 only has
+mlpack 2.0.1 available.  Options include upgrading your Ubuntu version, finding
+a PPA or other non-official sources, or installing with a manual build.
+
 There are some other useful pages to consult in addition to this section:
 
   - [Building mlpack From Source](http://www.mlpack.org/docs/mlpack-git/doxygen/build.html)

doc/guide/build.hpp

@@ -11,6 +11,12 @@ with the following command:
 $ sudo apt-get install libmlpack-dev
 @endcode
 
+@note Older Ubuntu versions may not have the most recent version of mlpack
+available---for instance, at the time of this writing, Ubuntu 16.04 only has
+mlpack 2.0.1 available.  Options include upgrading Ubuntu to a newer release,
+finding a PPA or other non-official sources, or installing with a manual build
+(below).
+
 If mlpack is not available in your system's package manager, then you can follow
 this document for how to compile and install mlpack from source.
 
@@ -22,17 +28,17 @@ to build mlpack on Windows, see <a
 href="https://keon.io/mlpack-on-windows/">Keon's excellent tutorial</a>.
 
 You can download the latest mlpack release from here:
-<a href="http://www.mlpack.org/files/mlpack-3.0.1.tar.gz">mlpack-3.0.1</a>
+<a href="http://www.mlpack.org/files/mlpack-3.0.2.tar.gz">mlpack-3.0.2</a>
 
 @section build_simple Simple Linux build instructions
 
 Assuming all dependencies are installed in the system, you can run the commands
 below directly to build and install mlpack.
 
 @code
-$ wget http://www.mlpack.org/files/mlpack-3.0.1.tar.gz
-$ tar -xvzpf mlpack-3.0.1.tar.gz
-$ mkdir mlpack-3.0.1/build && cd mlpack-3.0.1/build
+$ wget http://www.mlpack.org/files/mlpack-3.0.2.tar.gz
+$ tar -xvzpf mlpack-3.0.2.tar.gz
+$ mkdir mlpack-3.0.2/build && cd mlpack-3.0.2/build
 $ cmake ../
 $ make -j4  # The -j is the number of cores you want to use for a build.
 $ sudo make install
@@ -41,6 +47,13 @@ below directly to build and install mlpack.
 If the \c cmake \c .. command fails, you are probably missing a dependency, so
 check the output and install any necessary libraries.  (See \ref build_dep.)
 
+On many Linux systems, mlpack will install by default to @c /usr/local/lib and
+you may need to set the @c LD_LIBRARY_PATH environment variable:
+
+@code
+export LD_LIBRARY_PATH=/usr/local/lib
+@endcode
+
 The instructions above are the simplest way to get, build, and install mlpack.
 The sections below discuss each of those steps in further detail and show how to
 configure mlpack.
@@ -50,8 +63,8 @@ configure mlpack.
 First we should unpack the mlpack source and create a build directory.
 
 @code
-$ tar -xvzpf mlpack-3.0.1.tar.gz
-$ cd mlpack-3.0.1
+$ tar -xvzpf mlpack-3.0.2.tar.gz
+$ cd mlpack-3.0.2
 $ mkdir build
 @endcode
 
@@ -195,6 +208,27 @@ If you wish to install mlpack to the system, make sure you have root privileges
 
 You can now run the executables by name; you can link against mlpack with
 \c -lmlpack, and the mlpack headers are found in \c /usr/include or
-\c /usr/local/include (depending on the system and CMake configuration).
+\c /usr/local/include (depending on the system and CMake configuration).  If
+Python bindings were installed, they should be available when you start Python.
+
+@section build_run Using mlpack without installing
+
+If you would prefer to use mlpack after building but without installing it to
+the system, this is possible.  All of the command-line programs in the
+@c build/bin/ directory will run directly with no modification.
+
+For running the Python bindings from the build directory, the situation is a
+little bit different.  You will need to set the following environment variables:
+
+@code
+export LD_LIBRARY_PATH=/path/to/mlpack/build/lib/:${LD_LIBRARY_PATH}
+export PYTHONPATH=/path/to/mlpack/build/src/mlpack/bindings/python/:${PYTHONPATH}
+@endcode
+
+(Be sure to substitute the correct path to your build directory for
+`/path/to/mlpack/build/`.)
+
+Once those environment variables are set, you should be able to start a Python
+interpreter and `import mlpack`, then use the Python bindings.
 
 */

doc/guide/python_quickstart.hpp

@@ -31,12 +31,20 @@ build and install mlpack.  You can copy-paste the commands into your shell.
 @code{.sh}
 sudo apt-get install libboost-all-dev g++ cmake libarmadillo-dev python-pip wget
 sudo pip install cython setuptools distutils numpy pandas
-wget http://www.mlpack.org/files/mlpack-3.0.1.tar.gz
-tar -xvzpf mlpack-3.0.1.tar.gz
-mkdir -p mlpack-3.0.1/build/ && cd mlpack-3.0.1/build/
+wget http://www.mlpack.org/files/mlpack-3.0.2.tar.gz
+tar -xvzpf mlpack-3.0.2.tar.gz
+mkdir -p mlpack-3.0.2/build/ && cd mlpack-3.0.2/build/
 cmake ../ && make -j4 && sudo make install
 @endcode
 
+More information on the build process and details can be found on the @ref build
+page.  You may also need to set the environment variable @c LD_LIBRARY_PATH to
+include @c /usr/local/lib/ on most Linux systems.
+
+@code
+export LD_LIBRARY_PATH=/usr/local/lib/
+@endcode
+
 You can also use the mlpack Docker image on Dockerhub, which has all of the
 Python bindings pre-installed:
 

doc/joss_paper/paper.bib

@@ -6,7 +6,8 @@ @article{halevy2009unreasonable
   number={2},
   pages={8--12},
   year={2009},
-  publisher={IEEE}
+  publisher={IEEE},
+  doi={10.1109/MIS.2009.36}
 }
 
 @inproceedings{mlpack2011,
@@ -15,7 +16,8 @@ @inproceedings{mlpack2011
   title={{mlpack: A Scalable C++ Machine Learning Library}},
   booktitle={{BigLearning: Algorithms, Systems, and Tools for Learning at
               Scale}},
-  year = 2011
+  year = 2011,
+  doi = {10.1.1.676.5625}
 }
 
 @article{mlpack2013,
@@ -40,7 +42,8 @@ @article{sanderson2016armadillo
   author={Sanderson, C. and Curtin, R.R.},
   journal={Journal of Open Source Software},
   year={2016},
-  publisher={Journal of Open Source Software}
+  publisher={Journal of Open Source Software},
+  doi={10.21105/joss.00026}
 }
 
 @misc{xianyi2018openblas,
@@ -54,7 +57,7 @@ @misc{nvblas
   title={{NVBLAS Library}},
   author={{NVIDIA}},
   year={2015},
-  howpublished={\ur;{http://docs.nvidia.com/cuda/nvblas}}
+  howpublished={\url{http://docs.nvidia.com/cuda/nvblas}}
 }
 
 @inproceedings{curtin2013tree,

doc/joss_paper/paper.md

@@ -22,9 +22,11 @@ authors:
 
 - name: Yannis Mentekidis
   orcid: 0000-0003-3860-9885
+  affiliation: 5
 
 - name: Sumedh Ghaisas
   orcid: 0000-0003-3753-9029
+  affiliation: 5
 
 - name: Shangtong Zhang
   orcid: 0000-0003-4255-1364
@@ -39,6 +41,8 @@ affiliations:
   index: 3
 - name: University of Alberta
   index: 4
+- name: None
+  index: 5
 
 date: 5 April 2018
 bibliography: paper.bib

src/mlpack/bindings/python/print_doc_functions_impl.hpp

@@ -142,7 +142,14 @@ template<typename... Args>
 std::string ProgramCall(const std::string& programName, Args... args)
 {
   std::ostringstream oss;
-  oss << ">>> " << programName << "(";
+  oss << ">>> ";
+
+  // Find out if we have any output options first.
+  std::ostringstream ossOutput;
+  ossOutput << PrintOutputOptions(args...);
+  if (ossOutput.str() != "")
+    oss << "output = ";
+  oss << programName << "(";
 
   // Now process each input option.
   oss << PrintInputOptions(args...);

src/mlpack/core.hpp

@@ -245,6 +245,8 @@
  *   - Rohan Raj <rajrohan1108@gmail.com>
  *   - Conrad Sanderson
  *   - Thanasis Mattas <mattasa@auth.gr>
+ *   - Shashank Shekhar <contactshashankshekhar@gmail.com>
+ *   - Yasmine Dumouchel <yasmine.dumouchel@gmail.com>
  */
 
 // First, include all of the prerequisites.