Merge branch 'release-1.3.x'

AUTHORS

+MDANSE project has been created by:
+
+* Eric Pellegrini
+
+MDANSE source code is currently developed by
+
+* Eric Pellegrini
+* Remi Perenon
+
+MDANSE former contributors:
+
+* Bachir Aoun
+* Gael Goret
+

BuildServer/Docker/Builder/Ubuntu-bionic/Dockerfile_deploy

@@ -4,6 +4,6 @@ SHELL ["/bin/bash", "-c"]
 
 VOLUME builds
 
-RUN source ./BuildServer/Unix/Debian/definitions.sh; source ./BuildServer/Unix/setup_ci.sh ; ./BuildServer/Unix/Debian/deploy.sh
+RUN source ./BuildServer/Unix/Debian/definitions.sh; source ./BuildServer/Unix/setup_ci.sh ; source ./BuildServer/Unix/bionic_dependencies_modification.sh ; ./BuildServer/Unix/Debian/deploy.sh
 
 

BuildServer/Unix/bionic_dependencies_modification.sh

+#!/bin/bash
+
+cd ${CI_PROJECT_DIR}
+
+# Modifying python-vtk to python-vtk6 in CONTROL FILE
+cd ${CI_PROJECT_DIR}
+sed -i "s/python-vtk/python-vtk6/" BuildServer/Unix/Debian/Resources/DEBIAN/control
+
+status=$?
+if [ $status -ne 0 ]; then
+	echo -e "${RED}" "Failed to build/install MDANSE""${NORMAL}"
+	exit $status
+fi

CHANGELOG

+version 1.3.0
+--------------
+* ADDED Neutron Dynamic Total Structure Factor analysis
+* ADDED User can now launch a script with qvector parameters instead of saved qvector definition
+* FIXED issue #45 MSD computing on non-orthorombic universe was wrong (fixed with new mmtk version) /!\ Modifies MSD, VACF and DoS, and maybe others... /!\ Units in MMTK have slightly changed
+* FIXED issue #44 An error message appeared when display, close and reopen molecular viewer and animation plugins
+* FIXED issue #43 The weights are no more normalized with absolute sum /!\ Modifies at least CCF, DCSF and SSF job behavior
+* FIXED issue #42 Plotter units could be inconsistent
+* FIXED issue #41 Instrument resolution window froze GUI on macOS
+* FIXED issue #40 MDANSE could not be used on Ubuntu Bionic systems (due to vtk dependency name)
+* FIXED issue #38 Interface was frozen when jobs were launched. A delay of 2s is added at the end of jobs before suppressing the status file
+
 version 1.2.1
 --------------
 * FIXED issue #39 Time scale in Gromacs converter was incorrect

CITATION

+Citing MDANSE
+
+MDANSE: An Interactive Analysis Environment for Molecular Dynamics Simulations.
+G. Goret, B. Aoun, E. Pellegrini. J Chem Inf Model. (2017) 57(1):1-5.
+
+

Extensions/distance_histogram.pyx

+# **************************************************************************
+#
+# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
+#
+# @file      Extensions/distance_histogram.pyx
+# @brief     Implements module/class/test distance_histogram
+#
+# @homepage  https://mdanse.org
+# @license   GNU General Public License v3 or higher (see LICENSE)
+# @copyright Institut Laue Langevin 2013-now
+# @authors   Scientific Computing Group at ILL (see AUTHORS)
+#
+# **************************************************************************
+
 import cython
 cimport numpy as np 
 from numpy cimport ndarray

Extensions/fast_calculation.pyx

-# -*- coding: utf-8 -*-
-#################################################
-# fast calculation module of trajectory-viewer  #
-# Gael Goret for the Institut Laue-Langevin     #
-# gael.goret@ill.eu                             #
-#################################################
-
+# **************************************************************************
+#
+# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
+#
+# @file      Extensions/fast_calculation.pyx
+# @brief     Implements module/class/test fast_calculation
+#
+# @homepage  https://mdanse.org
+# @license   GNU General Public License v3 or higher (see LICENSE)
+# @copyright Institut Laue Langevin 2013-now
+# @authors   Scientific Computing Group at ILL (see AUTHORS)
+#
+# **************************************************************************
 
 import cython
 cimport numpy as np
@@ -37,4 +43,4 @@ def cpt_cluster_connectivity(ndarray[np.float64_t, ndim=2] coords,
                 bonds.append([i,j])
     return bonds
 
-                
\ No newline at end of file
+                

Extensions/mic_fast_calc.pyx

+# **************************************************************************
+#
+# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
+#
+# @file      Extensions/mic_fast_calc.pyx
+# @brief     Implements module/class/test mic_fast_calc
+#
+# @homepage  https://mdanse.org
+# @license   GNU General Public License v3 or higher (see LICENSE)
+# @copyright Institut Laue Langevin 2013-now
+# @authors   Scientific Computing Group at ILL (see AUTHORS)
+#
+# **************************************************************************
+
 cimport numpy as np 
 import numpy as np
 from numpy cimport ndarray

Extensions/mt_fast_calc.pyx

+# **************************************************************************
+#
+# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
+#
+# @file      Extensions/mt_fast_calc.pyx
+# @brief     Implements module/class/test mt_fast_calc
+#
+# @homepage  https://mdanse.org
+# @license   GNU General Public License v3 or higher (see LICENSE)
+# @copyright Institut Laue Langevin 2013-now
+# @authors   Scientific Computing Group at ILL (see AUTHORS)
+#
+# **************************************************************************
+
 import cython
 cimport numpy as np 
 import numpy as np

Extensions/qhull.pyx

-"""
-Wrappers for Qhull triangulation, plus some additional N-D geometry utilities
-
-.. versionadded:: 0.9
+# **************************************************************************
+#
+# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
+#
+# @file      Extensions/qhull.pyx
+# @brief     Implements module/class/test qhull
+#
+# @homepage  https://mdanse.org
+# @license   GNU General Public License v3 or higher (see LICENSE)
+# @copyright Institut Laue Langevin 2013-now
+# @authors   Scientific Computing Group at ILL (see AUTHORS)
+#
+# **************************************************************************
 
-"""
 #
 # Copyright (C)  Pauli Virtanen, 2010.
 #

Extensions/sas_fast_calc.pyx

+# **************************************************************************
+#
+# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
+#
+# @file      Extensions/sas_fast_calc.pyx
+# @brief     Implements module/class/test sas_fast_calc
+#
+# @homepage  https://mdanse.org
+# @license   GNU General Public License v3 or higher (see LICENSE)
+# @copyright Institut Laue Langevin 2013-now
+# @authors   Scientific Computing Group at ILL (see AUTHORS)
+#
+# **************************************************************************
+
 import cython
 import numpy as np
 cimport numpy as np 

Extensions/sd_fast_calc.pyx

+# **************************************************************************
+#
+# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
+#
+# @file      Extensions/sd_fast_calc.pyx
+# @brief     Implements module/class/test sd_fast_calc
+#
+# @homepage  https://mdanse.org
+# @license   GNU General Public License v3 or higher (see LICENSE)
+# @copyright Institut Laue Langevin 2013-now
+# @authors   Scientific Computing Group at ILL (see AUTHORS)
+#
+# **************************************************************************
+
 import cython
 cimport numpy as np 
 import numpy as np

Extensions/setup.py

-# Pour compiler:
-#      python setup.py build_ext --inplace
+# **************************************************************************
+#
+# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
+#
+# @file      Extensions/setup.py
+# @brief     Implements module/class/test setup
+#
+# @homepage  https://mdanse.org
+# @license   GNU General Public License v3 or higher (see LICENSE)
+# @copyright Institut Laue Langevin 2013-now
+# @authors   Scientific Computing Group at ILL (see AUTHORS)
+#
+# **************************************************************************
 
 import glob
 import os

Extensions/xtc/trr.pyx

+# **************************************************************************
+#
+# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
+#
+# @file      Extensions/xtc/trr.pyx
+# @brief     Implements module/class/test trr
+#
+# @homepage  https://mdanse.org
+# @license   GNU General Public License v3 or higher (see LICENSE)
+# @copyright Institut Laue Langevin 2013-now
+# @authors   Scientific Computing Group at ILL (see AUTHORS)
+#
+# **************************************************************************
+
 # cython: c_string_type=str, c_string_encoding=ascii
 ##############################################################################
 # MDTraj: A Python Library for Loading, Saving, and Manipulating

Extensions/xtc/xtc.pyx

+# **************************************************************************
+#
+# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
+#
+# @file      Extensions/xtc/xtc.pyx
+# @brief     Implements module/class/test xtc
+#
+# @homepage  https://mdanse.org
+# @license   GNU General Public License v3 or higher (see LICENSE)
+# @copyright Institut Laue Langevin 2013-now
+# @authors   Scientific Computing Group at ILL (see AUTHORS)
+#
+# **************************************************************************
+
 # cython: c_string_type=str, c_string_encoding=ascii
 ##############################################################################
 # MDTraj: A Python Library for Loading, Saving, and Manipulating

Scripts/mdanse

 #!/usr/bin/env python
 
+# **************************************************************************
+#
+# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
+#
+# @file      Src/__init__.py
+# @brief     Implements module/class/test __init__
+#
+# @homepage  https://mdanse.org
+# @license   GNU General Public License v3 or higher (see LICENSE)
+# @copyright Institut Laue Langevin 2013-now
+# @authors   Scientific Computing Group at ILL (see AUTHORS)
+#
+# **************************************************************************
+
 import cPickle
 import glob
 import optparse

Scripts/mdanse_elements_database

 #!/usr/bin/env python
 
+# **************************************************************************
+#
+# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
+#
+# @file      Src/__init__.py
+# @brief     Implements module/class/test __init__
+#
+# @homepage  https://mdanse.org
+# @license   GNU General Public License v3 or higher (see LICENSE)
+# @copyright Institut Laue Langevin 2013-now
+# @authors   Scientific Computing Group at ILL (see AUTHORS)
+#
+# **************************************************************************
+
 if __name__ == "__main__":
 
     from MDANSE.GUI.Apps import ElementsDatabaseEditorApp

Scripts/mdanse_gui

 #!/usr/bin/env python
 
+# **************************************************************************
+#
+# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
+#
+# @file      Src/__init__.py
+# @brief     Implements module/class/test __init__
+#
+# @homepage  https://mdanse.org
+# @license   GNU General Public License v3 or higher (see LICENSE)
+# @copyright Institut Laue Langevin 2013-now
+# @authors   Scientific Computing Group at ILL (see AUTHORS)
+#
+# **************************************************************************
+
 if __name__ == "__main__":
 
     from MDANSE.GUI.Apps import MainApplication

Scripts/mdanse_periodic_table

 #!/usr/bin/env python
 
+# **************************************************************************
+#
+# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
+#
+# @file      Src/__init__.py
+# @brief     Implements module/class/test __init__
+#
+# @homepage  https://mdanse.org
+# @license   GNU General Public License v3 or higher (see LICENSE)
+# @copyright Institut Laue Langevin 2013-now
+# @authors   Scientific Computing Group at ILL (see AUTHORS)
+#
+# **************************************************************************
+
 if __name__ == "__main__":
 
     from MDANSE.GUI.Apps import PeriodicTableViewerApp

Scripts/mdanse_plotter

 #!/usr/bin/env python
 
+# **************************************************************************
+#
+# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
+#
+# @file      Src/__init__.py
+# @brief     Implements module/class/test __init__
+#
+# @homepage  https://mdanse.org
+# @license   GNU General Public License v3 or higher (see LICENSE)
+# @copyright Institut Laue Langevin 2013-now
+# @authors   Scientific Computing Group at ILL (see AUTHORS)
+#
+# **************************************************************************
+
 if __name__ == "__main__":
     
     from MDANSE.GUI.Apps import PlotterApp

Scripts/mdanse_ud_editor

 #!/usr/bin/env python
 
+# **************************************************************************
+#
+# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
+#
+# @file      Src/__init__.py
+# @brief     Implements module/class/test __init__
+#
+# @homepage  https://mdanse.org
+# @license   GNU General Public License v3 or higher (see LICENSE)
+# @copyright Institut Laue Langevin 2013-now
+# @authors   Scientific Computing Group at ILL (see AUTHORS)
+#
+# **************************************************************************
+
 if __name__ == "__main__":
     
     from MDANSE.GUI.Apps import UserDefinitionViewerApp

Src/Core/ClassRegistry.py

-#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
-#------------------------------------------------------------------------------------------
-#Copyright (C)
-#2015- Eric C. Pellegrini Institut Laue-Langevin
-#BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
-#France
-#pellegrini[at]ill.fr
-#goret[at]ill.fr
-#aoun[at]ill.fr
-#
-#This library is free software; you can redistribute it and/or
-#modify it under the terms of the GNU Lesser General Public
-#License as published by the Free Software Foundation; either
-#version 2.1 of the License, or (at your option) any later version.
-#
-#This library is distributed in the hope that it will be useful,
-#but WITHOUT ANY WARRANTY; without even the implied warranty of
-#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#Lesser General Public License for more details.
-#
-#You should have received a copy of the GNU Lesser General Public
-#License along with this library; if not, write to the Free Software
-#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-
-''' 
-Created on Mar 30, 2015
-
-:author: Eric C. Pellegrini
-'''
-
+# **************************************************************************
+#
+# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
+#
+# @file      Src/Core/ClassRegistry.py
+# @brief     Implements module/class/test ClassRegistry
+#
+# @homepage  https://mdanse.org
+# @license   GNU General Public License v3 or higher (see LICENSE)
+# @copyright Institut Laue Langevin 2013-now
+# @authors   Scientific Computing Group at ILL (see AUTHORS)
+#
+# **************************************************************************
+
 import glob
 import imp
 import inspect

Src/Core/Error.py

-#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
-#------------------------------------------------------------------------------------------
-#Copyright (C)
-#2015- Eric C. Pellegrini Institut Laue-Langevin
-#BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
-#France
-#pellegrini[at]ill.fr
-#goret[at]ill.fr
-#aoun[at]ill.fr
+# **************************************************************************
 #
-#This library is free software; you can redistribute it and/or
-#modify it under the terms of the GNU Lesser General Public
-#License as published by the Free Software Foundation; either
-#version 2.1 of the License, or (at your option) any later version.
+# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
 #
-#This library is distributed in the hope that it will be useful,
-#but WITHOUT ANY WARRANTY; without even the implied warranty of
-#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#Lesser General Public License for more details.
+# @file      Src/Core/Error.py
+# @brief     Implements module/class/test Error
 #
-#You should have received a copy of the GNU Lesser General Public
-#License along with this library; if not, write to the Free Software
-#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-
-''' 
-Created on Mar 30, 2015
-
-:author: Eric C. Pellegrini
-'''
+# @homepage  https://mdanse.org