.clang-format

+---
+# https://clang.llvm.org/docs/ClangFormatStyleOptions.html#
+# the "Visual Studio" style is similar to:
+BasedOnStyle: LLVM
+UseTab: Never
+IndentWidth: 4
+BreakBeforeBraces: Allman
+AccessModifierOffset: -4
+SortIncludes: false
+ColumnLimit: 0
+...

.editorconfig

+# EditorConfig is awesome: https://EditorConfig.org
+
+root = true
+
+[*]
+charset = utf-8
+indent_style = space
+indent_size = 4

.gitattributes

+*_lfs.msh filter=lfs diff=lfs merge=lfs -text
+*_lfs.apdl filter=lfs diff=lfs merge=lfs -text
+*_lfs.ansys filter=lfs diff=lfs merge=lfs -text
+*.brep filter=lfs diff=lfs merge=lfs -text
+*.stp filter=lfs diff=lfs merge=lfs -text
+

.gitignore

@@ -31,12 +31,19 @@ workspace.tar.gz
 # build dir
 build
 
-## Ansys
-#*.apdl
+# gitlab-ci / clang-format
+patches
+
+# Ansys
+*.apdl
+!*_lfs.apdl
+*.ansys
+!*_lfs.ansys
 
 # Gmsh
 *.pos
-*.msh
+*.msh # do not commit the mesh...
+!*_lfs.msh # ... except in the lfs
 #*.opt
 
 # sge output

.gitlab-ci.yml

 # gitlab-ci file for waves
 
 default:
-    image: rboman/waves
+    image: rboman/waves-py3:2020.3
     before_script:
         - source /opt/intel/mkl/bin/mklvars.sh intel64
         - source /opt/intel/tbb/bin/tbbvars.sh intel64
+        - echo $(nproc)
+        - printenv | sort
+
+.global_tag: &global_tag_def
+    tags:
+        - mn2l
+#        - warson   # you can choose a set of runners here
 
 stages:
     - build
     - test
 
-build-py2:
+format:
+    <<: *global_tag_def
+    stage: build
+    script:
+        - clang-format --version # we use clang-format-10 exclusively
+        - ./scripts/format_code.py
+        - mkdir -p patches
+        - if git diff --patch --exit-code > patches/clang-format.patch; then echo "Clang format changed nothing"; else echo "Clang format found changes to make!"; false; fi
+    artifacts:
+        paths:
+            - patches/
+        expire_in: 1 day
+        when: on_failure
+    allow_failure: true
+
+build-no-tlnos:
+    <<: *global_tag_def
     stage: build
     script:
-        - printenv | sort
         - rm -rf build workspace
         - mkdir build
         - cd build
-        - cmake -DUSE_PY3=OFF -Wno-dev ..
-        - make -j 4
-    artifacts:
-        paths:
-            - build/
-        expire_in: 1 hour
+        - cmake -Wno-dev -C ../CMake/disable-trilinos.cmake ..
+        - make -j 8
 
-build-py2-no-tlnos:
+build:
+    <<: *global_tag_def
     stage: build
     script:
-        - printenv | sort
         - rm -rf build workspace
         - mkdir build
         - cd build
-        - cmake -DUSE_PY3=OFF -Wno-dev -C ../CMake/disable-trilinos.cmake ..
-        - make -j 4
+        - cmake -Wno-dev ..
+        - make -j 8
+    artifacts:
+        paths:
+            - build/
+        expire_in: 1 day
 
-build-py3:
-    image: rboman/waves-py3
+build-red:
+    <<: *global_tag_def
+    image: rboman/waves-py3-red:2020.3
     stage: build
     script:
-        - printenv | sort
         - rm -rf build workspace
         - mkdir build
         - cd build
         - cmake -Wno-dev ..
-        - make -j 4
+        - make -j 8
     artifacts:
         paths:
             - build/
-        expire_in: 1 hour
-    
+        expire_in: 1 day
+            
 doxygen:
+    <<: *global_tag_def
     stage: test
     script:
         - cd build
@@ -57,27 +80,26 @@ doxygen:
     artifacts:
         paths:
             - build/doxygen/
-        expire_in: 1 day
+        expire_in: 1 week
     dependencies:
-        - build-py2
+        - build
 
-ctest-py2:
+ctest:
+    <<: *global_tag_def
     stage: test
     script:
         - cd build
-        - ctest -j 4 #--verbose
+        - ctest --output-on-failure -j 8
     #timeout: 10 hours  # will be available in 12.3
     dependencies:
-        - build-py2
-
-ctest-py3:
-    image: rboman/waves-py3
+        - build
+        
+ctest-red:
+    <<: *global_tag_def
+    image: rboman/waves-py3-red:2020.3
     stage: test
     script:
         - cd build
-        - ctest -j 4 #--verbose
+        - ctest --output-on-failure -j 8 -R katoptron
     dependencies:
-        - build-py3
-        
-
-
+        - build-red

CMake/FindEIGEN.cmake

@@ -12,11 +12,13 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-# FindEIGEN.cmake - try to find Eigen headers
+# FindEIGEN.cmake - try to find Eigen 3 headers
+# The logic that checks the version comes from FindEigen3.cmake (source dir)
 # ----------------------------------------------------------------------------   
 # output:
 #    EIGEN_FOUND             : TRUE/FALSE
 #    EIGEN_INCLUDE_DIRS      : where the Eigen/*.h are              [cached]
+#    EIGEN_VERSION           : version number of Eigen
 # ----------------------------------------------------------------------------
 # autodetection:
 #    utiliser "CMAKE_PREFIX_PATH=c:\local"
@@ -24,12 +26,53 @@
 #          ou "INCLUDE=c:\local\include"
 # ----------------------------------------------------------------------------   
 
+# Check version (only for Eigen 3)
+macro(_eigen3_check_version)
+    file(READ "${EIGEN_INCLUDE_DIRS}/Eigen/src/Core/util/Macros.h" _eigen3_version_header)
+
+    string(REGEX MATCH "define[ \t]+EIGEN_WORLD_VERSION[ \t]+([0-9]+)" _eigen3_world_version_match "${_eigen3_version_header}")
+    set(EIGEN_WORLD_VERSION "${CMAKE_MATCH_1}")
+    string(REGEX MATCH "define[ \t]+EIGEN_MAJOR_VERSION[ \t]+([0-9]+)" _eigen3_major_version_match "${_eigen3_version_header}")
+    set(EIGEN_MAJOR_VERSION "${CMAKE_MATCH_1}")
+    string(REGEX MATCH "define[ \t]+EIGEN_MINOR_VERSION[ \t]+([0-9]+)" _eigen3_minor_version_match "${_eigen3_version_header}")
+    set(EIGEN_MINOR_VERSION "${CMAKE_MATCH_1}")
+
+    set(EIGEN_VERSION ${EIGEN_WORLD_VERSION}.${EIGEN_MAJOR_VERSION}.${EIGEN_MINOR_VERSION})
+
+    if(${EIGEN_VERSION} VERSION_LESS ${EIGEN_FIND_VERSION})
+        message(FATAL_ERROR "Eigen version ${EIGEN_VERSION} found in ${EIGEN_INCLUDE_DIRS}, but at least version ${EIGEN_FIND_VERSION} is required!")
+    endif()
+endmacro()
+
+# Set a dummy version if not provided
+if(NOT EIGEN_FIND_VERSION)
+    if(NOT EIGEN_FIND_VERSION_MAJOR)
+        set(EIGEN_FIND_VERSION_MAJOR 3)
+    endif()
+    if(NOT EIGEN_FIND_VERSION_MINOR)
+        set(EIGEN_FIND_VERSION_MINOR 3)
+    endif()
+    if(NOT EIGEN_FIND_VERSION_PATCH)
+        set(EIGEN_FIND_VERSION_PATCH 4)
+    endif()
+
+    set(EIGEN_FIND_VERSION "${EIGEN_FIND_VERSION_MAJOR}.${EIGEN_FIND_VERSION_MINOR}.${EIGEN_FIND_VERSION_PATCH}")
+endif()
+
+# Find the header and check the version
 find_path(EIGEN_INCLUDE_DIRS "Eigen/Dense" PATHS "/usr/include/eigen3")
+if (EIGEN_INCLUDE_DIRS)
+    _eigen3_check_version()
+else()
+    message(FATAL_ERROR "Eigen3 headers not found! Define the path in the INCLUDE environment variable.")
+endif()
 
 # handle the QUIETLY and REQUIRED arguments and set EIGEN_FOUND to TRUE
 # if all listed variables are TRUE
 include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(EIGEN DEFAULT_MSG 
-				                  EIGEN_INCLUDE_DIRS)
+find_package_handle_standard_args(EIGEN
+                                  FOUND_VAR EIGEN_FOUND
+                                  REQUIRED_VARS EIGEN_INCLUDE_DIRS
+                                  VERSION_VAR EIGEN_VERSION)
 
 #MESSAGE(STATUS "EIGEN_FOUND = ${EIGEN_FOUND}")

CMake/FindMPI4PY.cmake

@@ -14,7 +14,7 @@
 
 if(NOT MPI4PY_INCLUDE_DIR)
     execute_process(COMMAND
-      "${PYTHON_EXECUTABLE}" "-c" "from __future__ import print_function; import mpi4py; print(mpi4py.get_include())"
+      "${PYTHON_EXECUTABLE}" "-c" "import mpi4py; print(mpi4py.get_include())"
       OUTPUT_VARIABLE MPI4PY_INCLUDE_DIR
       RESULT_VARIABLE MPI4PY_COMMAND_RESULT
       OUTPUT_STRIP_TRAILING_WHITESPACE)

CMake/disable-trilinos.cmake

@@ -13,5 +13,5 @@
 # limitations under the License.
 
 
-SET(WAVES_USE_MRSTLNOS OFF CACHE BOOL "" FORCE)
+SET(WAVES_USE_KATOPTRON OFF CACHE BOOL "" FORCE)
 SET(WAVES_USE_TLNOS    OFF CACHE BOOL "" FORCE)

CMake/fwkMacros.cmake

@@ -17,6 +17,19 @@
 
 MACRO(MACRO_AddTest srcDir)
     #message(STATUS "Adding test directory ${srcDir}")
+
+    #Extract the number of MPI processes used to 
+    #launch one test.
+    #If no extra arguments are given, the number
+    #is set to 1.
+    set (extra_macro_args ${ARGN})
+    list(LENGTH extra_macro_args num_extra_args)
+    if (${num_extra_args} GREATER 0)
+        list(GET extra_macro_args 0 nProcs)
+    else()
+        set(nProcs 1)
+    endif ()
+
     file(GLOB tfiles RELATIVE ${srcDir} ${srcDir}/*)
     #message(STATUS "tfiles=${tfiles}")
     foreach(tfile ${tfiles})
@@ -26,11 +39,18 @@ MACRO(MACRO_AddTest srcDir)
            NOT ${tfile} STREQUAL "__init__.py")
             string(REPLACE "${PROJECT_SOURCE_DIR}/" "" strip ${spath}) 
             message(STATUS "Adding test ${strip}")
-            add_test(NAME ${strip} 
-                     WORKING_DIRECTORY ${PROJECT_SOURCE_DIR} 
-                     COMMAND ${PYTHON_EXECUTABLE} run.py --nogui --clean ${strip})
+            if (${nProcs} GREATER 1)
+                add_test(NAME "${strip}-MPI${nProcs}"
+                        WORKING_DIRECTORY ${PROJECT_SOURCE_DIR} 
+                        COMMAND mpirun -np ${nProcs} --allow-run-as-root ${PYTHON_EXECUTABLE} run.py --nogui --clean ${strip})
+                # (mpi is run as root in docker)
+            else()
+                add_test(NAME ${strip} 
+                        WORKING_DIRECTORY ${PROJECT_SOURCE_DIR} 
+                        COMMAND ${PYTHON_EXECUTABLE} run.py --nogui --clean ${strip})            
+            endif ()
         else()
-            MACRO_AddTest(${srcDir}/${tfile})
+            MACRO_AddTest(${srcDir}/${tfile} ${nProcs})
         endif()
     endforeach()
 ENDMACRO()

CMake/gaston-clang.cmake → CMake/gaston-clang-Py3.cmake

@@ -14,8 +14,8 @@
 
 FIND_PROGRAM(CMAKE_CXX_COMPILER NAMES clang++)
 FIND_PROGRAM(CMAKE_C_COMPILER   NAMES clang)
-
+# vtk for py3
+SET(VTK_DIR "/opt/vtk/lib/cmake/vtk-7.1" CACHE PATH "" FORCE)
 # Trilinos not compiling with clang (check to wiki to fix)
 LIST(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR})
 INCLUDE(disable-trilinos)
-

CMake/msys2.cmake

+# Copyright 2020 University of Liège
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# 
+#     http://www.apache.org/licenses/LICENSE-2.0
+# 
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+# MSYS2 with MinGW (AC)
+
+SET(CMAKE_GENERATOR "MSYS Makefiles" CACHE INTERNAL "" FORCE)
+SET(WAVES_USE_MKL    OFF CACHE BOOL "" FORCE)
+SET(WAVES_USE_MUMPS  OFF CACHE BOOL "" FORCE)

CMake/spring.cmake

@@ -15,7 +15,7 @@
 FIND_PROGRAM(CMAKE_CXX_COMPILER NAMES icpc)
 FIND_PROGRAM(CMAKE_C_COMPILER   NAMES icc)
 
-# gmm automatically finds openblas, so we force to look for mkl
+# force to look for mkl
 SET(BLA_VENDOR "Intel10_64lp" CACHE STRING "" FORCE)
 
 # Trilinos not available on spring

CMake/win64-libsVs2017Py3.cmake

+# This file is used when PFEM is compiled on Windows x64
+# with Luc Papeleux's precompiled libraries
+
+
+SET(CMAKE_INSTALL_PREFIX  "../waves_INSTALL" CACHE PATH "" FORCE)
+
+STRING(REGEX REPLACE "\\\\" "/" MYLIBS $ENV{METAFORLIBS})
+SET(CMAKE_GENERATOR  "Visual Studio 15 2017 Win64" CACHE INTERNAL "" FORCE)
+
+SET(PYTHON_INCLUDE_DIR              "${MYLIBS}/Python/include"             CACHE PATH "" FORCE)
+SET(PYTHON_LIBRARY                       "${MYLIBS}/Python/Libs/python37.lib"     CACHE FILEPATH "" FORCE)
+SET(PYTHON_RELEASE_LIBRARY      "${MYLIBS}/Python/Libs/python37.lib"     CACHE FILEPATH "" FORCE)
+SET(PYTHON_DEBUG_LIBRARY         "${MYLIBS}/Python/Libs/python37_d.lib" CACHE FILEPATH "" FORCE)
+
+
+# Disable Trilinos (we should test with Trilinos/clang)
+LIST(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR})
+INCLUDE(disable-trilinos)

CMakeLists.txt

@@ -16,6 +16,10 @@
 PROJECT(Waves)
 # ----------------------------------------------------------------------------
 CMAKE_MINIMUM_REQUIRED(VERSION 3.1)
+IF(${CMAKE_VERSION} VERSION_GREATER "3.14.0") # we might want to update the project and use the NEW behavior here
+    cmake_policy(SET CMP0078 OLD)
+    cmake_policy(SET CMP0086 OLD)
+ENDIF()
 
 SET(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin CACHE PATH
                         "Single output directory for building all libraries.")
@@ -28,40 +32,38 @@ IF(NOT CMAKE_BUILD_TYPE)
          "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel."
          FORCE)
 ENDIF(NOT CMAKE_BUILD_TYPE)
+MESSAGE(STATUS "Build type: ${CMAKE_BUILD_TYPE}")
 
 LIST(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/CMake")
 
 # -- GENERAL OPTIONS
 
-#OPTION(WAVES_USE_MKL "Use Intel MKL for BLAS/LAPACK" OFF)
-
 # print OS
 MESSAGE(STATUS "CMAKE_SYSTEM_NAME=\"${CMAKE_SYSTEM_NAME}\"")
 MESSAGE(STATUS "CMAKE_CXX_COMPILER_ID=${CMAKE_CXX_COMPILER_ID}")
 
-# (de)activate python 3
-OPTION(USE_PY3               "Use python 3"                    ON)
 # (de)activate modules
 OPTION(WAVES_USE_FDTD        "Compile fdtd module"             ON)
 OPTION(WAVES_USE_FLOW        "Compile flow module"             ON)
 OPTION(WAVES_USE_HEAT        "Compile heat module"             ON)
 OPTION(WAVES_USE_MIRRORS     "Compile mirrors module"          ON)
-OPTION(WAVES_USE_MRSTLNOS    "Compile mrstlnos module"         ON)
+OPTION(WAVES_USE_KATOPTRON   "Compile katoptron module"        ON)
 OPTION(WAVES_USE_PARAMS      "Compile params module"           ON)
 OPTION(WAVES_USE_SPH         "Compile sph module"              ON)
 OPTION(WAVES_USE_TLNOS       "Compile tlnos module"            ON)
 OPTION(WAVES_USE_WAVES       "Compile waves module"            ON)
 # (de)activate extensions
 OPTION(WAVES_USE_TBOXVTK     "Compile tboxVtk module"          ON)
-
-# todo: should be removed
-OPTION(WAVES_USE_TBB         "Compile with TBB" ON)
+# (de)activate external packages
+OPTION(WAVES_USE_MKL         "Compile with Intel MKL"          ON)
+OPTION(WAVES_USE_MUMPS       "Compile with MUMPS"              ON)
+OPTION(WAVES_USE_TBB         "Compile with TBB"                ON) # todo: should be removed
 
 # --- Disable some Options on Windows
 IF(WIN32)
     # Trilinos is not available on Windows
     MESSAGE("Disabling TRILINOS on Windows")
-    SET(WAVES_USE_MRSTLNOS OFF CACHE BOOL "" FORCE)
+    SET(WAVES_USE_KATOPTRON OFF CACHE BOOL "" FORCE)
     SET(WAVES_USE_TLNOS OFF CACHE BOOL "" FORCE)
 ENDIF()
 
@@ -81,6 +83,7 @@ IF((CMAKE_CXX_COMPILER_ID MATCHES "GNU") OR (CMAKE_CXX_COMPILER_ID MATCHES "Inte
     SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp -Wno-unknown-pragmas -Wno-sign-compare") # merge trilinos
 ELSEIF(CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
     ADD_DEFINITIONS(-D_CRT_SECURE_NO_WARNINGS -D_SCL_SECURE_NO_DEPRECATE)
+    ADD_DEFINITIONS(-D_USE_MATH_DEFINES) # otherwise M_PI is undefined
     SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /MP")  # parallel build with MSVC
     #SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /W4")  # add verbosity
 ELSEIF(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
@@ -94,14 +97,17 @@ IF(APPLE)
 ENDIF()
 
 # -- Search for Python
-IF(USE_PY3)
-    SET(pyVersion 3.6)
+IF (CMAKE_VERSION VERSION_LESS 3.12.0)
+    FIND_PACKAGE(PythonInterp 3.6 REQUIRED)
+    FIND_PACKAGE(PythonLibs 3.6 REQUIRED)
 ELSE()
-    SET(pyVersion 2.7)
+    find_package (Python3 COMPONENTS Interpreter Development)
+    # use Python3_ROOT_DIR if wrong python found (e.g. anaconda)
+    SET(PYTHON_EXECUTABLE ${Python3_EXECUTABLE})
+    SET(PYTHON_LIBRARIES ${Python3_LIBRARIES})
+    SET(PYTHON_INCLUDE_PATH ${Python3_INCLUDE_DIRS}) 
+    SET(PYTHONLIBS_VERSION_STRING ${Python3_VERSION})     
 ENDIF()
-FIND_PACKAGE(PythonInterp ${pyVersion} REQUIRED)
-FIND_PACKAGE(PythonLibs ${pyVersion} REQUIRED)
-
 MESSAGE(STATUS "PYTHON_EXECUTABLE:FILEPATH=${PYTHON_EXECUTABLE}")
 MESSAGE(STATUS "PYTHON_LIBRARY:FILEPATH=${PYTHON_LIBRARY}")
 MESSAGE(STATUS "PYTHON_INCLUDE_DIR:FILEPATH=${PYTHON_INCLUDE_DIR}")
@@ -140,6 +146,11 @@ ELSE()
     MESSAGE("Doxygen need to be installed to generate the doxygen documentation")
 ENDIF()
 
+# -- Configure file (for SWIG to detect definitions)
+CONFIGURE_FILE(${PROJECT_SOURCE_DIR}/waves_config.h.in
+               ${PROJECT_BINARY_DIR}/waves_config.h)
+INCLUDE_DIRECTORIES(${PROJECT_BINARY_DIR}) # to find "waves_config.h"
+
 # -- CTest
 ENABLE_TESTING()
 
@@ -168,8 +179,8 @@ IF(WAVES_USE_MIRRORS)
     ADD_SUBDIRECTORY( mirrors )
 ENDIF()
 
-IF(WAVES_USE_MRSTLNOS)
-    ADD_SUBDIRECTORY( mrstlnos )
+IF(WAVES_USE_KATOPTRON)
+    ADD_SUBDIRECTORY( katoptron )
 ENDIF()
 
 IF(WAVES_USE_PARAMS)
@@ -188,4 +199,12 @@ IF(WAVES_USE_WAVES)
     ADD_SUBDIRECTORY( waves )
 ENDIF()
 
-
+# -- Packaging
+# set paths and target names
+SET(WAVES_INCLUDE_DIRS "${PROJECT_SOURCE_DIR}/fwk/src" "${PROJECT_SOURCE_DIR}/tbox/src" "${PROJECT_BINARY_DIR}")
+SET(WAVES_SWIG_DIRS "${PROJECT_SOURCE_DIR}/fwk/_src" "${PROJECT_SOURCE_DIR}/tbox/_src")
+SET(WAVES_LIBRARIES fwk tbox)
+# export target config
+EXPORT(TARGETS ${WAVES_LIBRARIES} FILE "${PROJECT_BINARY_DIR}/wavesTargets.cmake")
+# generate configuration file with absolute paths
+CONFIGURE_FILE(waves-config.cmake.in "${PROJECT_BINARY_DIR}/waves-config.cmake" @ONLY)

CODEOWNERS

@@ -11,7 +11,7 @@
 /flow/ @acrovato
 /heat/ @R.Boman
 /mirrors/ @Kim.Liegeois
-/mrstlnos/ @Kim.Liegeois
+/katoptron/ @Kim.Liegeois
 /sph/ @R.Boman
 /tlnos/ @R.Boman
 /waves/ @R.Boman

Doxyfile.in

@@ -787,6 +787,7 @@ INPUT                  = @PROJECT_SOURCE_DIR@/README.md \
                          @PROJECT_SOURCE_DIR@/fwk/src \
                          @PROJECT_SOURCE_DIR@/heat/src \
                          @PROJECT_SOURCE_DIR@/mirrors/src \
+                         @PROJECT_SOURCE_DIR@/katoptron/src \
                          @PROJECT_SOURCE_DIR@/sph/src \
                          @PROJECT_SOURCE_DIR@/tbox/src \
                          @PROJECT_SOURCE_DIR@/waves/src 
@@ -1726,7 +1727,7 @@ PAPER_TYPE             = a4
 # If left blank no extra packages will be included.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
-EXTRA_PACKAGES         = 
+EXTRA_PACKAGES         = amsmath
 
 # The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
 # generated LaTeX document. The header should contain everything until the first

Metafor/Mparams/Metafor_call.py

-#!/usr/bin/env python
-# -*- coding: latin-1; -*-
+#!/usr/bin/env python3
+# -*- coding: utf-8; -*-
 
 # Copyright 2020 University of Liège
 # 
@@ -16,7 +16,7 @@
 # limitations under the License.
 
 
-from __future__ import print_function
+
 import numpy as np
 import os
 import shutil

Metafor/Mparams/TaskManager.py

-#!/usr/bin/env python
-# -*- coding: latin-1; -*-
+#!/usr/bin/env python3
+# -*- coding: utf-8; -*-
 
 # Copyright 2020 University of Liège
 # 
@@ -16,13 +16,6 @@
 # limitations under the License.
 
 
-from __future__ import print_function
-from __future__ import division
-from builtins import zip
-from builtins import str
-from builtins import range
-from past.utils import old_div
-from builtins import object
 import tbox
 import math
 
@@ -60,7 +53,7 @@ tags = enum('READY', 'DONE', 'EXIT', 'START', 'WAKEUP', 'SUICIDE')
 
 
 
-class Job(object):
+class Job:
     """ Class containing data transmitted between MPI procs
     """
     def __init__(self, parameters, name, xi, m_i):
@@ -91,7 +84,7 @@ class Job(object):
         os.chdir('..')
 
 
-class Master(object):
+class Master:
     """
     MPI Process with rank #0
     """
@@ -218,7 +211,7 @@ class Master(object):
                             correlations = surrogate_parameters['correlations']
 
                             for j in range(0,d):
-                                xi[j] = old_div((X[m_i,j]-means[j]),(surrogate_parameters['nstddeviation']*np.sqrt(variances[j])))
+                                xi[j] = (X[m_i,j]-means[j]) / (surrogate_parameters['nstddeviation']*np.sqrt(variances[j]))
 
                     elif surrogate_parameters['training_points'] == 'gamma':
                         means = surrogate_parameters['means']
@@ -249,7 +242,7 @@ class Master(object):
                     elif surrogate_parameters['training_points'] == 'gamma':
                         xi2 = np.zeros((d,))
                         for j in range(0,d):
-                            xi2[j] = old_div((xi[j][0]-means[j]),np.sqrt(variances[j]))
+                            xi2[j] = (xi[j][0]-means[j]) / np.sqrt(variances[j])
                         Z[m_i,:] = np.transpose(phi(xi2,N,n_max,d))
                         #print xi2
                     else:
@@ -351,7 +344,7 @@ class Master(object):
             comm.send(None, dest=s, tag=tags.SUICIDE)
 
 
-class Worker(object):
+class Worker:
     """
     MPI Process with rank #1-#n
     """

Metafor/Mparams/__init__.py

-# -*- coding: latin-1; -*-
+# -*- coding: utf-8; -*-
 # mirrors MODULE initialization file
 
 import tbox

Metafor/Mparams/mparams.py

-#!/usr/bin/env python
-# -*- coding: latin-1; -*-
+#!/usr/bin/env python3
+# -*- coding: utf-8; -*-
 
 # Copyright 2020 University of Liège
 #