Fixed merge conflicts

.gitignore

-/.project
-/.pydevproject
-/build/
-*.pyc
+.DS_Store
 .env
 .eggs
+.gitignore
+.project
+.pydevproject
+.settings
+MANIFEST
+*.pyc
+build/
 dist/
-.DS_Store
-Tests/FunctionalTests/Jobs
-/.gitignore
-/MANIFEST
+

.gitlab-ci.yml

 stages:
-  - build
-  - test
+  - docker_login
+  - ci
   - deploy
- 
-# trusty pipeline
-build:trusty:
-  stage: build
+  - clean
+
+docker_login:
+  stage: docker_login
   script:
-    - ./BuildServer/Debian/run_build.sh
-  allow_failure: false
-  only:
-    - triggers
-    - tags
-    - /^feature-.*$/
-    - /^release-.*$/
-    - /^hotfix-.*$/
-    - /^bugfix-.*$/
-    - develop
-  artifacts:
-    paths:
-    - build
-    expire_in: 1 day
+    - docker login -u gitlab-ci-token -p ${CI_JOB_TOKEN} ${CI_REGISTRY}
   tags:
-    - ubuntu14.04
-
-test:trusty:
-  stage: test
+    - docker
+    - sci
+    - ubuntu
+  
+############################
+# ubuntu trusty  pipeline
+############################
+ci:ubuntu_trusty:
+  stage: ci
   script:
-    - ./BuildServer/Debian/run_tests.sh
+    - docker build --force-rm --build-arg MDANSE_GIT_COMMIT=${CI_COMMIT_SHA} -t ci_mdanse_trusty -f ${CI_PROJECT_DIR}/BuildServer/Docker/Builder/Ubuntu-trusty/Dockerfile_build .
   allow_failure: false
-  only:
-    - triggers
-    - tags
-    - /^feature-.*$/
-    - /^release-.*$/
-    - /^hotfix-.*$/
-    - /^bugfix-.*$/
-    - develop
-  dependencies:
-    - build:trusty
   tags:
-    - ubuntu14.04
+    - docker
+    - sci
+    - ubuntu
 
-deploy:trusty:
+deploy:ubuntu_trusty:
   stage: deploy
   script:
-    - ./BuildServer/Debian/run_deploy.sh amd64 trusty
+    - docker build --force-rm -t deploy_mdanse_trusty -f ${CI_PROJECT_DIR}/BuildServer/Docker/Builder/Ubuntu-trusty/Dockerfile_deploy .
+    - chmod 755 ${CI_PROJECT_DIR}/BuildServer/Docker/upload_artefacts.sh
+    - ${CI_PROJECT_DIR}/BuildServer/Docker/upload_artefacts.sh trusty
+  dependencies:
+    - ci:ubuntu_trusty
+  allow_failure: false
   only:
-    - triggers
-    - tags
+    - master
     - develop
+    - /^release-.*$/
+    - /^hotfix-.*$/
+    - web
   when: on_success
   artifacts:
     paths:
-    - ./BuildServer/Debian/Build/*.deb
+    - ./*.deb
   tags:
-    - ubuntu14.04
+    - docker
+    - sci
+    - ubuntu
 
-# osx pipeline
+############################
+# ubuntu xenial  pipeline
+############################
+ci:ubuntu_xenial:
+  stage: ci
+  script:
+    - docker build --force-rm --build-arg MDANSE_GIT_COMMIT=${CI_COMMIT_SHA} -t ci_mdanse_xenial -f ${CI_PROJECT_DIR}/BuildServer/Docker/Builder/Ubuntu-xenial/Dockerfile_build .
+  allow_failure: false
+  tags:
+    - docker
+    - sci
+    - ubuntu
 
-build:osx:
-  stage: build
+deploy:ubuntu_xenial:
+  stage: deploy
   script:
-    - ./BuildServer/Darwin/Scripts/run_build.sh
+    - docker build --force-rm -t deploy_mdanse_xenial -f ${CI_PROJECT_DIR}/BuildServer/Docker/Builder/Ubuntu-xenial/Dockerfile_deploy .
+    - chmod 755 ${CI_PROJECT_DIR}/BuildServer/Docker/upload_artefacts.sh
+    - ${CI_PROJECT_DIR}/BuildServer/Docker/upload_artefacts.sh xenial
+  dependencies:
+    - ci:ubuntu_xenial
   allow_failure: false
   only:
-    - triggers
-    - tags
-    - /^feature-.*$/
+    - master
+    - develop
     - /^release-.*$/
     - /^hotfix-.*$/
-    - /^bugfix-.*$/
-    - develop
+    - web
+  when: on_success
   artifacts:
     paths:
-    - build
-    expire_in: 1 day
+    - ./*.deb
   tags:
-    - mac
+    - docker
+    - sci
+    - ubuntu
 
-test:osx:
-  stage: test
+############################
+# ubuntu bionic pipeline
+############################
+ci:ubuntu_bionic:
+  stage: ci
   script:
-    - ./BuildServer/Darwin/Scripts/run_tests.sh
+    - docker build --force-rm --build-arg MDANSE_GIT_COMMIT=${CI_COMMIT_SHA} -t ci_mdanse_bionic -f ${CI_PROJECT_DIR}/BuildServer/Docker/Builder/Ubuntu-bionic/Dockerfile_build .
   allow_failure: false
-  only:
-    - triggers
-    - tags
-    - /^feature-.*$/
-    - /^release-.*$/
-    - /^hotfix-.*$/
-    - /^bugfix-.*$/
-    - develop
-  dependencies:
-    - build:osx
   tags:
-    - mac
+    - docker
+    - sci
+    - ubuntu
 
-deploy:osx:
+deploy:ubuntu_bionic:
   stage: deploy
   script:
-    - ./BuildServer/Darwin/Scripts/run_deploy.sh
+    - docker build --force-rm -t deploy_mdanse_bionic -f ${CI_PROJECT_DIR}/BuildServer/Docker/Builder/Ubuntu-bionic/Dockerfile_deploy .
+    - chmod 755 ${CI_PROJECT_DIR}/BuildServer/Docker/upload_artefacts.sh
+    - ${CI_PROJECT_DIR}/BuildServer/Docker/upload_artefacts.sh bionic
+  dependencies:
+    - ci:ubuntu_bionic
+  allow_failure: false
   only:
-    - triggers
-    - tags
+    - master
     - develop
+    - /^release-.*$/
+    - /^hotfix-.*$/
+    - web
   when: on_success
   artifacts:
     paths:
-     - BuildServer/Darwin/Build/*.dmg
+    - ${CI_PROJECT_DIR}/*.deb
   tags:
-    - mac
+    - docker
+    - sci
+    - ubuntu
 
-# # windows 7 pipeline
+############################
+# osx high sierra pipeline
+############################
+ci:osx:
+  stage: ci
+  script:
+    - source ${CI_PROJECT_DIR}/BuildServer/Unix/definitions_macos.sh
+    - source ${CI_PROJECT_DIR}/BuildServer/Unix/version.sh
+    - ${CI_PROJECT_DIR}/BuildServer/Unix/build.sh
+    - ${CI_PROJECT_DIR}/BuildServer/Unix/tests.sh
+  allow_failure: false
+  artifacts:
+    paths:
+    - ${CI_PROJECT_DIR}/BuildServer/Unix/Build_macOS
+    expire_in: 1 hrs
+  tags:
+    - sci
+    - osx-10.13
 
-build:windows:
-  stage: build
+deploy:osx:
+  stage: deploy
   script:
-    - c:\cygwin64\bin\bash -c "dos2unix.exe ./BuildServer/Windows/run_build.sh"
-    - c:\cygwin64\bin\bash -c "chmod a+x ./BuildServer/Windows/run_build.sh"
-    - c:\cygwin64\bin\bash -c "./BuildServer/Windows/run_build.sh"
+    - source ${CI_PROJECT_DIR}/BuildServer/Unix/definitions_macos.sh
+    - source ${CI_PROJECT_DIR}/BuildServer/Unix/version.sh
+    - ${CI_PROJECT_DIR}/BuildServer/Unix/deploy_macos.sh
+  dependencies:
+    - ci:osx
   allow_failure: false
   only:
-    - triggers
-    - tags
-    - /^feature-.*$/
+    - master
+    - develop
     - /^release-.*$/
     - /^hotfix-.*$/
-    - /^bugfix-.*$/
-    - develop
+    - web
+  when: on_success
   artifacts:
     paths:
-    - .\BuildServer\Windows\Build
-    expire_in: 1 day
+     - ${CI_PROJECT_DIR}/BuildServer/*.dmg
   tags:
-    - windows
+    - sci
+    - osx-10.13
 
-test:windows:
-  stage: test
+############################
+# windows 10 pipeline
+# "call" is mandatory, see https://gitlab.com/gitlab-org/gitlab-runner/issues/1051
+############################
+ci:windows:
+  stage: ci
   script:
-    - c:\cygwin64\bin\bash -c "dos2unix.exe ./BuildServer/Windows/run_tests.sh"
-    - c:\cygwin64\bin\bash -c "chmod a+x ./BuildServer/Windows/run_tests.sh"
-    - c:\cygwin64\bin\bash -c "./BuildServer/Windows/run_tests.sh"
+    - call "%CI_PROJECT_DIR%\\BuildServer\\Windows\\definitions.bat"
+    - call "%CI_PROJECT_DIR%\\BuildServer\\Windows\\version.bat"
+    - call "%CI_PROJECT_DIR%\\BuildServer\\Windows\\build.bat"
+    - call "%CI_PROJECT_DIR%\\BuildServer\\Windows\\tests.bat"
   allow_failure: false
-  only:
-    - triggers
-    - tags
-    - /^feature-.*$/
-    - /^release-.*$/
-    - /^hotfix-.*$/
-    - /^bugfix-.*$/
-    - develop
-  dependencies:
-    - build:windows
+  artifacts:
+    paths:
+    - "%CI_PROJECT_DIR%\\BuildServer\\Windows\\Build"
+    expire_in: 1 hrs
   tags:
-    - windows
+    - sci
+    - windows-10
 
 deploy:windows:
   stage: deploy
   script:
-    - c:\cygwin64\bin\bash -c "dos2unix.exe ./BuildServer/Windows/run_deploy.sh"
-    - c:\cygwin64\bin\bash -c "chmod a+x ./BuildServer/Windows/run_deploy.sh"
-    - c:\cygwin64\bin\bash -c "./BuildServer/Windows/run_deploy.sh"
+    - call "%CI_PROJECT_DIR%\\BuildServer\\Windows\\definitions.bat"
+    - call "%CI_PROJECT_DIR%\\BuildServer\\Windows\\version.bat"
+    - call "%CI_PROJECT_DIR%\\BuildServer\\Windows\\deploy.bat"
+  dependencies:
+    - ci:windows
+  allow_failure: false
   only:
-    - triggers
-    - tags
+    - master
     - develop
+    - /^release-.*$/
+    - /^hotfix-.*$/
+    - web
   when: on_success
   artifacts:
     paths:
-     - BuildServer/Windows/Build/MDANSE*.exe
+     - "%CI_PROJECT_DIR%\\BuildServer\\*.exe"
+  tags:
+    - sci
+    - windows-10
+
+clean:docker:
+  stage: clean
+  when: always
+  script:
+    - chmod 755 ${CI_PROJECT_DIR}/BuildServer/Docker/clean.sh
+    - ${CI_PROJECT_DIR}/BuildServer/Docker/clean.sh
+  after_script:
+    - docker logout
   tags:
-    - windows
+    - docker
+    - sci
+    - ubuntu
 
+clean:osx:
+  stage: clean
+  when: always
+  script:
+    - source ${CI_PROJECT_DIR}/BuildServer/Unix/definitions_macos.sh
+    - ${CI_PROJECT_DIR}/BuildServer/Unix/clean.sh
+  tags:
+    - sci
+    - osx-10.13
+    
+clean:windows:
+  stage: clean
+  when: always
+  script:
+    - call "%CI_PROJECT_DIR%\\BuildServer\\Windows\\definitions.bat"
+    - call "%CI_PROJECT_DIR%\\BuildServer\\Windows\\clean.bat"
+  tags:
+    - sci
+    - windows-10

BuildServer/.gitignore

+*.deb
+*.dmg
+*.exe
+Unix/Build*
+Windows/Build*
+

BuildServer/Darwin/.gitignore

-Build

BuildServer/Darwin/Scripts/run_build.sh

-#!/bin/bash
-
-# This script is to package the MDANSE package for Mac OS X
-
-#############################
-# CONFIGURATION
-#############################
-
-## Add some colors
-ROUGE="\\033[1;31m"
-BLEU="\\033[1;34m"
-
-##Select the build target
-BUILD_TARGET=darwin
-
-# take the latest version of nmoldyn available on the forge
-echo -e "$BLEU""Getting last MDANSE revision" "$NORMAL"
-
-# Update the __pkginfo__ file with the current commit. The sed -i "" is compulsory other crashes on macos
-COMMIT_ID=$(git rev-parse --short HEAD)
-sed -i "" "s/.*__commit__.*/__commit__ = \"${COMMIT_ID}\"/" MDANSE/__pkginfo__.py
-
-# Get revision number from git (without trailing newline)
-echo -e "$BLEU""Commit id = ${COMMIT_ID}" "$NORMAL"
-
-# Now build last version and install it in our homebrewed python
-echo -e "$BLEU""Building MDANSE" "$NORMAL"
-
-# Clean up temporary build directories
-rm -rf build
-rm -rf dist
-
-# Remove previous install of MDANSE
-rm /usr/local/bin/mdanse*
-rm /usr/local/lib/python2.7/site-packages/MDANSE*.egg-info
-rm -rf /usr/local/lib/python2.7/site-packages/MDANSE
-
-# Build and install MDANSE to the homebrewed python
-/usr/local/bin/python setup.py build >> BuildServer/Darwin/Scripts/build_log.txt 2>&1
-/usr/local/bin/python setup.py install >> BuildServer/Darwin/Scripts/build_log.txt 2>&1

BuildServer/Darwin/Scripts/run_deploy.sh

-#!/bin/bash
-
-# This script is to package the MDANSE package for Mac OS X
-
-#############################
-# CONFIGURATION
-#############################
-
-## Add some colors
-ROUGE="\\033[1;31m"
-BLEU="\\033[1;34m"
-
-COMMIT_ID=$(git rev-parse --short HEAD)
-VERSION_NAME=`sed -n 's/__version__.*=.*\"\(.*\)\"/\1/p' MDANSE/__pkginfo__.py`
-
-if [[ ${CI_BUILD_REF_NAME} =~ develop ]]
-then
-    if [ -n "${WEEKLY_BUILD}" ]
-    then
-        VERSION_NAME=${VERSION_NAME}-"weekly-"`date +%Y-%m-%d`
-    fi
-    VERSION_NAME=${VERSION_NAME}-${COMMIT_ID}
-fi
-
-export VERSION_NAME
-
-##Select the build target
-BUILD_TARGET=darwin
-
-echo -e "$BLEU""Packaging MDANSE" "$NORMAL"
-rm -rf BuildServer/Darwin/Build
-mkdir BuildServer/Darwin/Build
-
-# debug option for py2app, if needed
-export DISTUTILS_DEBUG=0
-
-cd BuildServer/Darwin/Scripts
-
-/usr/local/bin/python build.py py2app >> build_log.txt 2>&1
-
-rc=$?
-if [[ $rc != 0 ]]; then
-	echo -e "$ROUGE""Cannot build app." "$NORMAL"
-	exit 1
-fi
-
-cd ../Build
-
-# Do some manual cleanup, e.g.
-# matplotlib/tests ==> 45.2 Mb
-rm -rf dist/MDANSE.app/Contents/Resources/lib/python2.7/matplotlib/tests
-rm -rf dist/MDANSE.app/Contents/Resources/mpl-data/sample_data
-
-MDANSE_DMG=MDANSE-${VERSION_NAME}-${BUILD_TARGET}.dmg
-
-#Add MDANSE version file (should read the version from the bundle with pyobjc, but will figure that out later)
-echo "${VERSION_NAME}" > dist/MDANSE.app/Contents/Resources/version
-
-rm -f ./${MDANSE_DMG}
-rm -f ./rw.${MDANSE_DMG}
-
-hdiutil unmount /Volumes/MDANSE -force -quiet
-
-sleep 5
-
-../Tools/create-dmg/create-dmg --background "../Resources/background.jpg" --volname "MDANSE" --window-pos 200 120 --window-size 800 400 --icon MDANSE.app 200 190 --hide-extension MDANSE.app --app-drop-link 600 185 "${MDANSE_DMG}" ./dist
-
-exit

BuildServer/Darwin/Scripts/run_tests.sh

-#!/bin/bash
-
-ROUGE="\\033[1;31m"
-
-# Performs the unit tests
-cd Tests/UnitTests
-nosetests --verbosity=3 -P .
-# Exit now if unable to run tests
-if [ $? -ne 0 ]; then
-	status = $?
-	echo -e "$ROUGE""One or several unit tests failed"
-	exit status
-fi
-cd ../..
-
-cd Tests/FunctionalTests/Jobs
-python BuildJobTests.py
-nosetests --verbosity=3 --exe -P .
-if [ $? -ne 0 ]; then
-	status=$?
-	echo -e "$ROUGE""One or several functional tests failed"
-	exit status
-fi
-cd ../../..

BuildServer/Darwin/Tools/create-dmg/.gitignore

-.svn

BuildServer/Debian/run_build.sh

-#!/bin/bash
-
-export ARCH=$1
-export DISTRO=$2
-
-#############################
-# CONFIGURATION
-#############################
-
-## Add some colors
-BLEU="\\033[1;34m"
-
-cd
-cd $CI_PROJECT_DIR
-
-# Update the __pkginfo__ file with the current commit 
-COMMIT_ID=$(git rev-parse --short HEAD)
-sed -i "s/.*__commit__.*/__commit__ = \"${COMMIT_ID}\"/" MDANSE/__pkginfo__.py
-
-# Get revision number from git (without trailing newline)
-echo -e "$BLEU""Commit id = ${COMMIT_ID}<--" "$NORMAL"
-
-# Now build last version
-echo "$BLEU""Building MDANSE" "$NORMAL"
-python setup.py build
-

BuildServer/Debian/run_tests.sh

-#!/bin/bash
-
-ROUGE="\\033[1;31m"
-
-cd $CI_PROJECT_DIR
-
-export PYTHONPATH=${CI_PROJECT_DIR}/build/lib.linux-x86_64-2.7
-
-# Performs the unit tests
-cd Tests/UnitTests
-nosetests --verbosity=3 -P .
-# Exit now if unable to run tests
-if [ $? -ne 0 ]; then
-	status = $?
-	echo -e "$ROUGE""One or several unit tests failed"
-	exit status
-fi
-cd ../..
-
-# Performs the functional tests
-cd Tests/FunctionalTests/Jobs
-python BuildJobTests.py
-nosetests --verbosity=3 --exe -P .
-if [ $? -ne 0 ]; then
-	status=$?
-	echo -e "$ROUGE""One or several functional tests failed"
-	exit status
-fi
-

BuildServer/Docker/Builder/Ubuntu-bionic/Dockerfile_build

+FROM docker.ill.fr/scientific-software/mdanse:ubuntu-bionic
+
+SHELL ["/bin/bash", "-c"]
+
+ARG MDANSE_GIT_COMMIT
+