Merge pull request #3 from htm-community/master

update from htm-community

.travis.yml

@@ -1,4 +1,4 @@
-language: cpp
+language: python
 python: 
  - 2.7 #TODO change  to 3.x later
 
@@ -15,13 +15,14 @@ matrix:
           sources:
             - ubuntu-toolchain-r-test
           packages:
-            - g++-7
+            - build-essential 
+            - g++-8
+            - cmake
+            - cmake-data
             - xsltproc #only for doc transform to html , can be removed
-            - python-pip-whl
-            - python2.7
             - libboost-all-dev
       env:
-        - MATRIX_EVAL="CC=gcc-7 && CXX=g++-7"
+        - MATRIX_EVAL="CC=gcc-8 && CXX=g++-8"
         - PLATFORM="linux"
 #    ## OSX builds take very long to start on OSX
 #    # moved to CircleCI for OSX
@@ -105,9 +106,9 @@ before_install:
   - eval "${MATRIX_EVAL}"
   - $CXX --version
   - echo "Installing pip, setuptools, and wheel"
-  - pip2 install  --user pip setuptools wheel || exit
+  - pip install --upgrade pip setuptools wheel || exit
   - echo "Installing Python dependencies"
-  - sudo pip2 install -r $TRAVIS_BUILD_DIR/bindings/py/requirements.txt --only-binary --quiet || exit
+  - pip install -r $TRAVIS_BUILD_DIR/bindings/py/requirements.txt --only-binary --quiet || exit
 
 install:
   # Prepare directories
@@ -119,11 +120,10 @@ install:
   - "cmake $TRAVIS_BUILD_DIR -DCMAKE_BUILD_TYPE=Release -DNTA_COV_ENABLED=ON"
   # Configure bash such that a failure in any link in the pipe causes the whole pipe to fail
   - "set -o pipefail"
-  - "VERBOSE=1 make |grep -v -F '\\-\\- Installing:'"
+  - "VERBOSE=0 make |grep -v -F '\\-\\- Installing:'"
   - "make install 2>&1|grep -v -F 'Installing:'"
   - "cd $TRAVIS_BUILD_DIR"
-  # TODO later remove, --prefix= is workaround for https://stackoverflow.com/questions/4495120/combine-user-with-prefix-error-with-setup-py-install
-  - "python setup.py install --user --prefix="
+  - "python setup.py install"
 
 script:
   # Some tests (e.g., helloregion) expect this to be the current directory and
@@ -132,7 +132,7 @@ script:
   # unit tests
   - "${TRAVIS_BUILD_DIR}/build/release/bin/unit_tests --gtest_output=xml:${TRAVIS_BUILD_DIR}/build/artifacts/unit_tests_report.xml"
   # run python tests
-  - "py.test ${TRAVIS_BUILD_DIR}/bindings/py/tests"
+  - "python ${TRAVIS_BUILD_DIR}/setup.py test"
   # output unit tests report
   - "cd $TRAVIS_BUILD_DIR/build/artifacts/"
   # transform the JUnit-style xml report to html

external/common/include/Eigen/CMakeLists.txt

@@ -0,0 +1,19 @@
+include(RegexUtils)
+test_escape_string_as_regex()
+
+file(GLOB Eigen_directory_files "*")
+
+escape_string_as_regex(ESCAPED_CMAKE_CURRENT_SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}")
+
+foreach(f ${Eigen_directory_files})
+  if(NOT f MATCHES "\\.txt" AND NOT f MATCHES "${ESCAPED_CMAKE_CURRENT_SOURCE_DIR}/[.].+" AND NOT f MATCHES "${ESCAPED_CMAKE_CURRENT_SOURCE_DIR}/src")
+    list(APPEND Eigen_directory_files_to_install ${f})
+  endif()
+endforeach(f ${Eigen_directory_files})
+
+install(FILES
+  ${Eigen_directory_files_to_install}
+  DESTINATION ${INCLUDE_INSTALL_DIR}/Eigen COMPONENT Devel
+  )
+
+install(DIRECTORY src DESTINATION ${INCLUDE_INSTALL_DIR}/Eigen COMPONENT Devel FILES_MATCHING PATTERN "*.h")

external/common/include/Eigen/Cholesky

@@ -0,0 +1,46 @@
+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+#ifndef EIGEN_CHOLESKY_MODULE_H
+#define EIGEN_CHOLESKY_MODULE_H
+
+#include "Core"
+#include "Jacobi"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+/** \defgroup Cholesky_Module Cholesky module
+  *
+  *
+  *
+  * This module provides two variants of the Cholesky decomposition for selfadjoint (hermitian) matrices.
+  * Those decompositions are also accessible via the following methods:
+  *  - MatrixBase::llt()
+  *  - MatrixBase::ldlt()
+  *  - SelfAdjointView::llt()
+  *  - SelfAdjointView::ldlt()
+  *
+  * \code
+  * #include <Eigen/Cholesky>
+  * \endcode
+  */
+
+#include "src/Cholesky/LLT.h"
+#include "src/Cholesky/LDLT.h"
+#ifdef EIGEN_USE_LAPACKE
+#ifdef EIGEN_USE_MKL
+#include "mkl_lapacke.h"
+#else
+#include "src/misc/lapacke.h"
+#endif
+#include "src/Cholesky/LLT_LAPACKE.h"
+#endif
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN_CHOLESKY_MODULE_H
+/* vim: set filetype=cpp et sw=2 ts=2 ai: */

external/common/include/Eigen/CholmodSupport

@@ -0,0 +1,48 @@
+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+#ifndef EIGEN_CHOLMODSUPPORT_MODULE_H
+#define EIGEN_CHOLMODSUPPORT_MODULE_H
+
+#include "SparseCore"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+extern "C" {
+  #include <cholmod.h>
+}
+
+/** \ingroup Support_modules
+  * \defgroup CholmodSupport_Module CholmodSupport module
+  *
+  * This module provides an interface to the Cholmod library which is part of the <a href="http://www.suitesparse.com">suitesparse</a> package.
+  * It provides the two following main factorization classes:
+  * - class CholmodSupernodalLLT: a supernodal LLT Cholesky factorization.
+  * - class CholmodDecomposiiton: a general L(D)LT Cholesky factorization with automatic or explicit runtime selection of the underlying factorization method (supernodal or simplicial).
+  *
+  * For the sake of completeness, this module also propose the two following classes:
+  * - class CholmodSimplicialLLT
+  * - class CholmodSimplicialLDLT
+  * Note that these classes does not bring any particular advantage compared to the built-in
+  * SimplicialLLT and SimplicialLDLT factorization classes.
+  *
+  * \code
+  * #include <Eigen/CholmodSupport>
+  * \endcode
+  *
+  * In order to use this module, the cholmod headers must be accessible from the include paths, and your binary must be linked to the cholmod library and its dependencies.
+  * The dependencies depend on how cholmod has been compiled.
+  * For a cmake based project, you can use our FindCholmod.cmake module to help you in this task.
+  *
+  */
+
+#include "src/CholmodSupport/CholmodSupport.h"
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN_CHOLMODSUPPORT_MODULE_H
+