Merge branch 'develop' of https://code.ill.fr/scientific-software/mdanse into develop

.gitlab-ci.yml

 stages:
-  - docker_login
+  - docker_pre_clean
   - ci
   - deploy
-  - docker_logout
+  - docker_post_clean
 
-docker_login:
-  stage: docker_login
+docker_pre_clean:
+  stage: docker_pre_clean
   script:
-    - docker login -u gitlab-ci-token -p ${CI_JOB_TOKEN} ${CI_REGISTRY}
+    - ${CI_PROJECT_DIR}/BuildServer/Docker/clean.sh
+  allow_failure: true
   tags:
     - docker
     - sci
     - ubuntu
-  
+
+docker_post_clean:
+  stage: docker_post_clean
+  script:
+    - ${CI_PROJECT_DIR}/BuildServer/Docker/clean.sh
+  allow_failure: true
+  when: always
+  tags:
+    - docker
+    - sci
+    - ubuntu
+
 ############################
-# ubuntu trusty  pipeline
+# ubuntu trusty pipeline
 ############################
 ci:ubuntu_trusty:
   stage: ci
   script:
-    - docker build --force-rm --build-arg MDANSE_GIT_COMMIT=${CI_COMMIT_SHA} -t ci_mdanse_trusty -f ${CI_PROJECT_DIR}/BuildServer/Docker/Builder/Ubuntu-trusty/Dockerfile_build .
+    - docker build --force-rm=true -t ci_mdanse_trusty -f ${CI_PROJECT_DIR}/BuildServer/Docker/Ubuntu-trusty/Dockerfile_setup .
+    - docker build --force-rm=true --build-arg CI_COMMIT_SHORT_SHA=${CI_COMMIT_SHORT_SHA} --build-arg CI_COMMIT_REF_NAME=${CI_COMMIT_REF_NAME} --no-cache -t ci_mdanse_trusty_build -f ${CI_PROJECT_DIR}/BuildServer/Docker/Ubuntu-trusty/Dockerfile_build .
+    - docker run -iv${PWD}:/artifacts/ ci_mdanse_trusty_build
   allow_failure: false
+  artifacts:
+    paths:
+    - ${CI_PROJECT_DIR}/build
+    - ${CI_PROJECT_DIR}/temp
+    expire_in: 1 hrs
   tags:
     - docker
     - sci
@@ -29,9 +48,9 @@ ci:ubuntu_trusty:
 deploy:ubuntu_trusty:
   stage: deploy
   script:
-    - 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
+    - docker build --force-rm=true -t ci_mdanse_trusty -f ${CI_PROJECT_DIR}/BuildServer/Docker/Ubuntu-trusty/Dockerfile_setup .
+    - docker build --force-rm=true --build-arg CI_COMMIT_SHORT_SHA=${CI_COMMIT_SHORT_SHA} --build-arg CI_COMMIT_REF_NAME=${CI_COMMIT_REF_NAME} --no-cache -t ci_mdanse_trusty_build -f ${CI_PROJECT_DIR}/BuildServer/Docker/Ubuntu-trusty/Dockerfile_deploy .
+    - docker run -iv${PWD}:/artifacts/ ci_mdanse_trusty_build
   dependencies:
     - ci:ubuntu_trusty
   allow_failure: false
@@ -46,20 +65,27 @@ deploy:ubuntu_trusty:
   when: on_success
   artifacts:
     paths:
-    - ./*.deb
+    - ${CI_PROJECT_DIR}/*.deb
   tags:
     - docker
     - sci
     - ubuntu
 
 ############################
-# ubuntu xenial  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 .
+    - docker build --force-rm=true -t ci_mdanse_xenial -f ${CI_PROJECT_DIR}/BuildServer/Docker/Ubuntu-xenial/Dockerfile_setup .
+    - docker build --force-rm=true --build-arg  CI_COMMIT_SHORT_SHA=${CI_COMMIT_SHORT_SHA} --build-arg CI_COMMIT_REF_NAME=${CI_COMMIT_REF_NAME} --no-cache -t ci_mdanse_xenial_build -f ${CI_PROJECT_DIR}/BuildServer/Docker/Ubuntu-xenial/Dockerfile_build .
+    - docker run -iv${PWD}:/artifacts/ ci_mdanse_xenial_build
   allow_failure: false
+  artifacts:
+    paths:
+    - ${CI_PROJECT_DIR}/build
+    - ${CI_PROJECT_DIR}/temp
+    expire_in: 1 hrs
   tags:
     - docker
     - sci
@@ -68,9 +94,9 @@ ci:ubuntu_xenial:
 deploy:ubuntu_xenial:
   stage: deploy
   script:
-    - 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
+    - docker build --force-rm=true -t ci_mdanse_xenial -f ${CI_PROJECT_DIR}/BuildServer/Docker/Ubuntu-xenial/Dockerfile_setup .
+    - docker build --force-rm=true --build-arg CI_COMMIT_SHORT_SHA=${CI_COMMIT_SHORT_SHA} --build-arg CI_COMMIT_REF_NAME=${CI_COMMIT_REF_NAME} --no-cache -t ci_mdanse_xenial_build -f ${CI_PROJECT_DIR}/BuildServer/Docker/Ubuntu-xenial/Dockerfile_deploy .
+    - docker run -iv${PWD}:/artifacts/ ci_mdanse_xenial_build
   dependencies:
     - ci:ubuntu_xenial
   allow_failure: false
@@ -85,7 +111,7 @@ deploy:ubuntu_xenial:
   when: on_success
   artifacts:
     paths:
-    - ./*.deb
+    - ${CI_PROJECT_DIR}/*.deb
   tags:
     - docker
     - sci
@@ -97,8 +123,15 @@ deploy:ubuntu_xenial:
 ci:ubuntu_bionic:
   stage: ci
   script:
-    - docker build --force-rm --build-arg MDANSE_GIT_COMMIT=${CI_COMMIT_SHA} -t ci_mdanse_bionic -f ${CI_PROJECT_DIR}/BuildServer/Docker/Builder/Ubuntu-bionic/Dockerfile_build .
+    - docker build --force-rm=true -t ci_mdanse_bionic -f ${CI_PROJECT_DIR}/BuildServer/Docker/Ubuntu-bionic/Dockerfile_setup .
+    - docker build --force-rm=true --build-arg CI_COMMIT_SHORT_SHA=${CI_COMMIT_SHORT_SHA} --build-arg CI_COMMIT_REF_NAME=${CI_COMMIT_REF_NAME} --build-arg CI_COMMIT_SHORT_SHA=${CI_COMMIT_SHORT_SHA} --build-arg CI_COMMIT_REF_NAME=${CI_COMMIT_REF_NAME} --no-cache -t ci_mdanse_bionic_build -f ${CI_PROJECT_DIR}/BuildServer/Docker/Ubuntu-bionic/Dockerfile_build .
+    - docker run -iv${PWD}:/artifacts/ ci_mdanse_bionic_build
   allow_failure: false
+  artifacts:
+    paths:
+    - ${CI_PROJECT_DIR}/build
+    - ${CI_PROJECT_DIR}/temp
+    expire_in: 1 hrs
   tags:
     - docker
     - sci
@@ -107,9 +140,9 @@ ci:ubuntu_bionic:
 deploy:ubuntu_bionic:
   stage: deploy
   script:
-    - 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
+    - docker build --force-rm=true -t ci_mdanse_bionic -f ${CI_PROJECT_DIR}/BuildServer/Docker/Ubuntu-bionic/Dockerfile_setup .
+    - docker build --force-rm=true --build-arg CI_COMMIT_SHORT_SHA=${CI_COMMIT_SHORT_SHA} --build-arg CI_COMMIT_REF_NAME=${CI_COMMIT_REF_NAME} --no-cache -t ci_mdanse_bionic_build -f ${CI_PROJECT_DIR}/BuildServer/Docker/Ubuntu-bionic/Dockerfile_deploy .
+    - docker run -iv${PWD}:/artifacts/ ci_mdanse_bionic_build
   dependencies:
     - ci:ubuntu_bionic
   allow_failure: false
@@ -221,14 +254,3 @@ deploy:windows:
   tags:
     - sci
     - windows-10
-
-docker_logout:
-  stage: docker_logout
-  when: always
-  script:
-    - docker logout
-  tags:
-    - docker
-    - sci
-    - ubuntu
-

BuildServer/Docker/Builder/Ubuntu-bionic/Dockerfile_build

-FROM docker.ill.fr/scientific-software/mdanse:ubuntu-bionic
-
-SHELL ["/bin/bash", "-c"]
-
-ARG MDANSE_GIT_COMMIT
-
-RUN GIT_SSL_NO_VERIFY=true git clone https://code.ill.fr/scientific-software/mdanse.git
-
-WORKDIR mdanse
-
-RUN git checkout ${MDANSE_GIT_COMMIT}
-
-RUN source ./BuildServer/Unix/Debian/definitions.sh; source ./BuildServer/Unix/setup_ci.sh ; ./BuildServer/Unix/build.sh
-
-RUN source ./BuildServer/Unix/Debian/definitions.sh; source ./BuildServer/Unix/setup_ci.sh ; ./BuildServer/Unix/tests.sh
-

BuildServer/Docker/Builder/Ubuntu-bionic/Dockerfile_deploy

-FROM ci_mdanse_bionic
-
-SHELL ["/bin/bash", "-c"]
-
-VOLUME builds
-
-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/Docker/Builder/Ubuntu-trusty/Dockerfile_build

-FROM docker.ill.fr/scientific-software/mdanse:ubuntu-trusty
-
-SHELL ["/bin/bash", "-c"]
-
-ARG MDANSE_GIT_COMMIT
-
-RUN GIT_SSL_NO_VERIFY=true git clone https://code.ill.fr/scientific-software/mdanse.git
-
-WORKDIR mdanse
-
-RUN git checkout ${MDANSE_GIT_COMMIT}
-
-RUN source ./BuildServer/Unix/Debian/definitions.sh; source ./BuildServer/Unix/setup_ci.sh ; ./BuildServer/Unix/build.sh
-
-RUN source ./BuildServer/Unix/Debian/definitions.sh; source ./BuildServer/Unix/setup_ci.sh ; ./BuildServer/Unix/tests.sh
-

BuildServer/Docker/Builder/Ubuntu-trusty/Dockerfile_deploy

-FROM ci_mdanse_trusty
-
-SHELL ["/bin/bash", "-c"]
-
-VOLUME builds
-
-RUN source ./BuildServer/Unix/Debian/definitions.sh; source ./BuildServer/Unix/setup_ci.sh ; ./BuildServer/Unix/Debian/deploy.sh
-
-

BuildServer/Docker/Builder/Ubuntu-xenial/Dockerfile_build

-FROM docker.ill.fr/scientific-software/mdanse:ubuntu-xenial
-
-SHELL ["/bin/bash", "-c"]
-
-ARG MDANSE_GIT_COMMIT
-
-RUN GIT_SSL_NO_VERIFY=true git clone https://code.ill.fr/scientific-software/mdanse.git
-
-WORKDIR mdanse
-
-RUN git checkout ${MDANSE_GIT_COMMIT}
-
-RUN source ./BuildServer/Unix/Debian/definitions.sh; source ./BuildServer/Unix/setup_ci.sh ; ./BuildServer/Unix/build.sh
-
-RUN source ./BuildServer/Unix/Debian/definitions.sh; source ./BuildServer/Unix/setup_ci.sh ; ./BuildServer/Unix/tests.sh
-

BuildServer/Docker/Builder/Ubuntu-xenial/Dockerfile_deploy

-FROM ci_mdanse_xenial
-
-SHELL ["/bin/bash", "-c"]
-
-VOLUME builds
-
-RUN source ./BuildServer/Unix/Debian/definitions.sh; source ./BuildServer/Unix/setup_ci.sh ; ./BuildServer/Unix/Debian/deploy.sh
-
-

BuildServer/Docker/Setup/build.sh

-#!/bin/bash
-
-docker build --force-rm -t docker.ill.fr/scientific-software/mdanse:$1 -f $2/Dockerfile .
-

BuildServer/Docker/Ubuntu-bionic/Dockerfile_build

+FROM ci_mdanse_bionic
+
+SHELL ["/bin/bash", "-c"]
+
+ARG CI_COMMIT_SHORT_SHA
+ARG CI_COMMIT_REF_NAME
+
+ENV CI_COMMIT_SHORT_SHA=${CI_COMMIT_SHORT_SHA}
+ENV CI_COMMIT_REF_NAME=${CI_COMMIT_REF_NAME}
+
+COPY ./ /app/
+WORKDIR /app
+
+CMD source ./BuildServer/Unix/Debian/definitions.sh;  source ./BuildServer/Unix/setup_ci.sh; ./BuildServer/Unix/build.sh; ./BuildServer/Unix/tests.sh; cp -a ${CI_PROJECT_DIR}/build /artifacts/; cp -a ${CI_PROJECT_DIR}/temp /artifacts/
\ No newline at end of file

BuildServer/Docker/Ubuntu-bionic/Dockerfile_deploy

+FROM ci_mdanse_bionic
+
+SHELL ["/bin/bash", "-c"]
+
+ARG CI_COMMIT_SHORT_SHA
+ARG CI_COMMIT_REF_NAME
+
+ENV CI_COMMIT_SHORT_SHA=${CI_COMMIT_SHORT_SHA}
+ENV CI_COMMIT_REF_NAME=${CI_COMMIT_REF_NAME}
+
+COPY ./ /app/
+WORKDIR /app
+
+CMD source ./BuildServer/Unix/Debian/definitions.sh;  source ./BuildServer/Unix/setup_ci.sh; source ./BuildServer/Unix/bionic_dependencies_modification.sh; ./BuildServer/Unix/Debian/deploy.sh; cp -a *.deb /artifacts/
\ No newline at end of file

BuildServer/Docker/Setup/Ubuntu-bionic/Dockerfile → BuildServer/Docker/Ubuntu-bionic/Dockerfile_setup

 FROM ubuntu:bionic
 
+ENV https_proxy http://proxy.ill.fr:8888
+ENV http_proxy http://proxy.ill.fr:8888
+
 RUN export DEBIAN_FRONTEND=noninteractive
 
 RUN apt-get update
@@ -25,6 +28,4 @@ RUN apt-get install -y --no-install-recommends python-nose
 RUN apt-get install -y --no-install-recommends python-sphinx
 RUN apt-get install -y --no-install-recommends pyro
 
-RUN apt-get install -y --no-install-recommends lsb-release
-
-
+RUN apt-get install -y --no-install-recommends lsb-release
\ No newline at end of file

BuildServer/Docker/Ubuntu-trusty/Dockerfile_build

+FROM ci_mdanse_trusty
+
+SHELL ["/bin/bash", "-c"]
+
+ARG CI_COMMIT_SHORT_SHA
+ARG CI_COMMIT_REF_NAME
+
+ENV CI_COMMIT_SHORT_SHA=${CI_COMMIT_SHORT_SHA}
+ENV CI_COMMIT_REF_NAME=${CI_COMMIT_REF_NAME}
+
+COPY ./ /app/
+WORKDIR /app
+
+CMD source ./BuildServer/Unix/Debian/definitions.sh;  source ./BuildServer/Unix/setup_ci.sh; ./BuildServer/Unix/build.sh; ./BuildServer/Unix/tests.sh; cp -a ${CI_PROJECT_DIR}/build /artifacts/; cp -a ${CI_PROJECT_DIR}/temp /artifacts/
\ No newline at end of file

BuildServer/Docker/Ubuntu-trusty/Dockerfile_deploy

+FROM ci_mdanse_trusty
+
+SHELL ["/bin/bash", "-c"]
+
+ARG CI_COMMIT_SHORT_SHA
+ARG CI_COMMIT_REF_NAME
+
+ENV CI_COMMIT_SHORT_SHA=${CI_COMMIT_SHORT_SHA}
+ENV CI_COMMIT_REF_NAME=${CI_COMMIT_REF_NAME}
+
+COPY ./ /app/
+WORKDIR /app
+
+CMD source ./BuildServer/Unix/Debian/definitions.sh;  source ./BuildServer/Unix/setup_ci.sh; ./BuildServer/Unix/Debian/deploy.sh; cp -a *.deb /artifacts/
\ No newline at end of file

BuildServer/Docker/Setup/Ubuntu-trusty/Dockerfile → BuildServer/Docker/Ubuntu-trusty/Dockerfile_setup

 FROM ubuntu:trusty
 
+ENV https_proxy http://proxy.ill.fr:8888
+ENV http_proxy http://proxy.ill.fr:8888
+
+RUN export DEBIAN_FRONTEND=noninteractive
+
 RUN apt-get update
 
 RUN apt-get install -y tzdata
@@ -23,5 +28,4 @@ RUN apt-get install -y --no-install-recommends python-nose
 RUN apt-get install -y --no-install-recommends python-sphinx
 RUN apt-get install -y --no-install-recommends pyro
 
-RUN apt-get install -y --no-install-recommends lsb-release
-
+RUN apt-get install -y --no-install-recommends lsb-release
\ No newline at end of file

BuildServer/Docker/Ubuntu-xenial/Dockerfile_build

+FROM ci_mdanse_xenial
+
+SHELL ["/bin/bash", "-c"]
+
+ARG CI_COMMIT_SHORT_SHA
+ARG CI_COMMIT_REF_NAME
+
+ENV CI_COMMIT_SHORT_SHA=${CI_COMMIT_SHORT_SHA}
+ENV CI_COMMIT_REF_NAME=${CI_COMMIT_REF_NAME}
+
+COPY ./ /app/
+WORKDIR /app
+
+CMD source ./BuildServer/Unix/Debian/definitions.sh;  source ./BuildServer/Unix/setup_ci.sh; ./BuildServer/Unix/build.sh; ./BuildServer/Unix/tests.sh; cp -a ${CI_PROJECT_DIR}/build /artifacts/; cp -a ${CI_PROJECT_DIR}/temp /artifacts/
\ No newline at end of file

BuildServer/Docker/Ubuntu-xenial/Dockerfile_deploy

+FROM ci_mdanse_xenial
+
+SHELL ["/bin/bash", "-c"]
+
+ARG CI_COMMIT_SHORT_SHA
+ARG CI_COMMIT_REF_NAME
+
+ENV CI_COMMIT_SHORT_SHA=${CI_COMMIT_SHORT_SHA}
+ENV CI_COMMIT_REF_NAME=${CI_COMMIT_REF_NAME}
+
+COPY ./ /app/
+WORKDIR /app
+
+CMD source ./BuildServer/Unix/Debian/definitions.sh;  source ./BuildServer/Unix/setup_ci.sh; ./BuildServer/Unix/Debian/deploy.sh; cp -a *.deb /artifacts/
\ No newline at end of file

BuildServer/Docker/Setup/Ubuntu-xenial/Dockerfile → BuildServer/Docker/Ubuntu-xenial/Dockerfile_setup

 FROM ubuntu:xenial
 
+ENV https_proxy http://proxy.ill.fr:8888
+ENV http_proxy http://proxy.ill.fr:8888
+
+RUN export DEBIAN_FRONTEND=noninteractive
+
 RUN apt-get update
 
 RUN apt-get install -y tzdata
@@ -23,5 +28,4 @@ RUN apt-get install -y --no-install-recommends python-nose
 RUN apt-get install -y --no-install-recommends python-sphinx
 RUN apt-get install -y --no-install-recommends pyro
 
-RUN apt-get install -y --no-install-recommends lsb-release
-
+RUN apt-get install -y --no-install-recommends lsb-release
\ No newline at end of file

BuildServer/Docker/clean.sh

 # Return the docker containers that are exited
 exited_containers=`docker ps -q -f "status=exited"`
-
 # If some have been found, remove them
 if [ -n "$exited_containers" ]
 then
     docker rm -f ${exited_containers}
 fi
 
-# Return the docker images corresponding to MDANSE
-images=`docker images -a --format "{{.Repository}}:{{.Tag}}" | grep _mdanse_` 
-
-# If some have been found, remove them
-if [ -n "$images" ]
-then
-    docker rmi -f ${images}
-fi
-
 # Return the docker images that are in dangling state
 images=`docker images -q -f "dangling=true"`
-
 # If some dangling images have been found, remove them
 if [ -n "$images" ]
 then
     docker rmi -f ${images}
 fi
-

BuildServer/Unix/MacOS/Resources/dmg/builder/create-dmg.builder

-SET	app_name	create-dmg
-
-VERSION	create-dmg.cur	create-dmg	heads/master
-
-NEWDIR	build.dir	temp	%-build	-
-
-NEWFILE	create-dmg.zip	featured	%.zip	%
-
-
-COPYTO	[build.dir]
-	INTO	create-dmg	[create-dmg.cur]/create-dmg
-	INTO	sample	[create-dmg.cur]/sample
-	INTO	support	[create-dmg.cur]/support
-	
-SUBSTVARS	[build.dir<alter>]/create-dmg	[[]]
-
-
-ZIP	[create-dmg.zip]
-	INTO	[build-files-prefix]	[build.dir]
-
-
-PUT	megabox-builds	create-dmg.zip
-PUT	megabox-builds	build.log
-
-PUT	s3-builds	create-dmg.zip
-PUT	s3-builds	build.log

BuildServer/Unix/MacOS/build.py

-# coding=utf-8
-
-import os
-import sys
-
-if sys.platform.startswith('darwin'):
-    from setuptools import setup
-
-    version = os.environ['VERSION_NAME']
-    project_dir = os.environ['CI_PROJECT_DIR']
-
-    APP = [os.path.join(project_dir,'Scripts','mdanse_gui')]
-
-    PLIST = {
-        u'CFBundleName': u'MDANSE',
-        u'CFBundleShortVersionString': version,
-        u'CFBundleVersion': version,
-        u'CFBundleIdentifier': u'eu.ill.MDANSE-'+version,
-        u'LSApplicationCategoryType': u'public.app-category.science'
-    }
-    OPTIONS = {
-        'argv_emulation': False,# has to be False otherwise triggers problems with wxPython which lose some events that are captured by OS
-        'iconfile': os.path.join(project_dir,'Src','GUI','Icons','mdanse.icns'),
-        'excludes': 'PyQt4',
-		'matplotlib_backends': '-',
-        'optimize': '1',
-        'plist': PLIST,
-        'bdist_base': os.environ['CI_TEMP_BUILD_DIR'],
-        'dist_dir': os.path.join(os.environ['CI_TEMP_DIR'],'dist'),
-        'graph': False,
-        'xref': False,
-        'packages' : ["MDANSE","MMTK","Scientific","matplotlib"]
-    }
-
-    setup(
-        name='MDANSE',
-        app=APP,
-        options={'py2app': OPTIONS},
-        setup_requires=['py2app']
-    )
-else:
-    print 'No build_app implementation for your system.'