Merge branch 'feature-sphinx_doc' into 'develop'

Feature sphinx doc

See merge request !26

.gitlab-ci.yml

@@ -2,7 +2,7 @@ stages:
   - docker_login
   - ci
   - deploy
-  - clean
+  - docker_logout
 
 docker_login:
   stage: docker_login
@@ -19,7 +19,7 @@ docker_login:
 ci:ubuntu_trusty:
   stage: ci
   script:
-    - docker build --force-rm --build-arg MDANSE_GIT_COMMIT=${CI_COMMIT_SHA} --build-arg MDANSE_GIT_BRANCH_NAME=${CI_COMMIT_REF_NAME} -t ci_mdanse_trusty -f ${CI_PROJECT_DIR}/BuildServer/Docker/Builder/Ubuntu-trusty/Dockerfile_build .
+    - docker build --force-rm --build-arg MDANSE_GIT_COMMIT=${CI_COMMIT_SHA} -t ci_mdanse_trusty -f ${CI_PROJECT_DIR}/BuildServer/Docker/Builder/Ubuntu-trusty/Dockerfile_build .
   allow_failure: false
   tags:
     - docker
@@ -29,7 +29,7 @@ ci:ubuntu_trusty:
 deploy:ubuntu_trusty:
   stage: deploy
   script:
-    - docker build --force-rm --build-arg MDANSE_GIT_BRANCH_NAME=${CI_COMMIT_REF_NAME} -t deploy_mdanse_trusty -f ${CI_PROJECT_DIR}/BuildServer/Docker/Builder/Ubuntu-trusty/Dockerfile_deploy .
+    - 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
     - ${CI_PROJECT_DIR}/BuildServer/Docker/upload_artefacts.sh trusty
   dependencies:
@@ -57,7 +57,7 @@ deploy:ubuntu_trusty:
 ci:ubuntu_xenial:
   stage: ci
   script:
-    - docker build --force-rm --build-arg MDANSE_GIT_COMMIT=${CI_COMMIT_SHA} --build-arg MDANSE_GIT_BRANCH_NAME=${CI_COMMIT_REF_NAME} -t ci_mdanse_xenial -f ${CI_PROJECT_DIR}/BuildServer/Docker/Builder/Ubuntu-xenial/Dockerfile_build .
+    - docker build --force-rm --build-arg MDANSE_GIT_COMMIT=${CI_COMMIT_SHA} -t ci_mdanse_xenial -f ${CI_PROJECT_DIR}/BuildServer/Docker/Builder/Ubuntu-xenial/Dockerfile_build .
   allow_failure: false
   tags:
     - docker
@@ -67,7 +67,7 @@ ci:ubuntu_xenial:
 deploy:ubuntu_xenial:
   stage: deploy
   script:
-    - docker build --force-rm --build-arg MDANSE_GIT_BRANCH_NAME=${CI_COMMIT_REF_NAME} -t deploy_mdanse_xenial -f ${CI_PROJECT_DIR}/BuildServer/Docker/Builder/Ubuntu-xenial/Dockerfile_deploy .
+    - 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
     - ${CI_PROJECT_DIR}/BuildServer/Docker/upload_artefacts.sh xenial
   dependencies:
@@ -95,7 +95,7 @@ deploy:ubuntu_xenial:
 ci:ubuntu_bionic:
   stage: ci
   script:
-    - docker build --force-rm --build-arg MDANSE_GIT_COMMIT=${CI_COMMIT_SHA} --build-arg MDANSE_GIT_BRANCH_NAME=${CI_COMMIT_REF_NAME} -t ci_mdanse_bionic -f ${CI_PROJECT_DIR}/BuildServer/Docker/Builder/Ubuntu-bionic/Dockerfile_build .
+    - docker build --force-rm --build-arg MDANSE_GIT_COMMIT=${CI_COMMIT_SHA} -t ci_mdanse_bionic -f ${CI_PROJECT_DIR}/BuildServer/Docker/Builder/Ubuntu-bionic/Dockerfile_build .
   allow_failure: false
   tags:
     - docker
@@ -105,7 +105,7 @@ ci:ubuntu_bionic:
 deploy:ubuntu_bionic:
   stage: deploy
   script:
-    - docker build --force-rm --build-arg MDANSE_GIT_BRANCH_NAME=${CI_COMMIT_REF_NAME} -t deploy_mdanse_bionic -f ${CI_PROJECT_DIR}/BuildServer/Docker/Builder/Ubuntu-bionic/Dockerfile_deploy .
+    - 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:
@@ -133,14 +133,15 @@ deploy:ubuntu_bionic:
 ci:osx:
   stage: ci
   script:
-    - source ${CI_PROJECT_DIR}/BuildServer/Unix/definitions_macos.sh
-    - source ${CI_PROJECT_DIR}/BuildServer/Unix/version.sh
+    - source ${CI_PROJECT_DIR}/BuildServer/Unix/MacOS/definitions.sh
+    - source ${CI_PROJECT_DIR}/BuildServer/Unix/setup_ci.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
+    - ${CI_PROJECT_DIR}/build
+    - ${CI_PROJECT_DIR}/temp
     expire_in: 1 hrs
   tags:
     - sci
@@ -149,9 +150,9 @@ ci:osx:
 deploy:osx:
   stage: deploy
   script:
-    - 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
+    - source ${CI_PROJECT_DIR}/BuildServer/Unix/MacOS/definitions.sh
+    - source ${CI_PROJECT_DIR}/BuildServer/Unix/setup_ci.sh
+    - ${CI_PROJECT_DIR}/BuildServer/Unix/MacOS/deploy.sh
   dependencies:
     - ci:osx
   allow_failure: false
@@ -178,13 +179,15 @@ ci:windows:
   stage: ci
   script:
     - call "%CI_PROJECT_DIR%\\BuildServer\\Windows\\definitions.bat"
-    - call "%CI_PROJECT_DIR%\\BuildServer\\Windows\\version.bat"
+    - call "%CI_PROJECT_DIR%\\BuildServer\\Windows\\setup_ci.bat"
     - call "%CI_PROJECT_DIR%\\BuildServer\\Windows\\build.bat"
     - call "%CI_PROJECT_DIR%\\BuildServer\\Windows\\tests.bat"
   allow_failure: false
   artifacts:
     paths:
     - "%CI_PROJECT_DIR%\\BuildServer\\Windows\\Build"
+    - "%CI_PROJECT_DIR%\\build"
+    - "%CI_PROJECT_DIR%\\Extensions"
     expire_in: 1 hrs
   tags:
     - sci
@@ -194,7 +197,7 @@ deploy:windows:
   stage: deploy
   script:
     - call "%CI_PROJECT_DIR%\\BuildServer\\Windows\\definitions.bat"
-    - call "%CI_PROJECT_DIR%\\BuildServer\\Windows\\version.bat"
+    - call "%CI_PROJECT_DIR%\\BuildServer\\Windows\\setup_ci.bat"
     - call "%CI_PROJECT_DIR%\\BuildServer\\Windows\\deploy.bat"
   dependencies:
     - ci:windows
@@ -214,35 +217,13 @@ deploy:windows:
     - sci
     - windows-10
 
-clean:docker:
-  stage: clean
+docker_logout:
+  stage: docker_logout
   when: always
   script:
-    - chmod 755 ${CI_PROJECT_DIR}/BuildServer/Docker/clean.sh
-    - ${CI_PROJECT_DIR}/BuildServer/Docker/clean.sh
-  after_script:
     - docker logout
   tags:
     - 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/Docker/Builder/Ubuntu-bionic/Dockerfile_build

@@ -4,15 +4,13 @@ SHELL ["/bin/bash", "-c"]
 
 ARG MDANSE_GIT_COMMIT
 
-ARG MDANSE_GIT_BRANCH_NAME
-
 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/definitions_debian.sh ${MDANSE_GIT_BRANCH_NAME}; source ./BuildServer/Unix/version.sh ; ./BuildServer/Unix/build.sh
+RUN source ./BuildServer/Unix/Debian/definitions.sh; source ./BuildServer/Unix/setup_ci.sh ; ./BuildServer/Unix/build.sh
 
-RUN source ./BuildServer/Unix/definitions_debian.sh ${MDANSE_GIT_BRANCH_NAME}; source ./BuildServer/Unix/version.sh ; ./BuildServer/Unix/tests.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

@@ -2,10 +2,8 @@ FROM ci_mdanse_bionic
 
 SHELL ["/bin/bash", "-c"]
 
-ARG MDANSE_GIT_BRANCH_NAME
-
 VOLUME builds
 
-RUN source ./BuildServer/Unix/definitions_debian.sh ${MDANSE_GIT_BRANCH_NAME}; source ./BuildServer/Unix/version.sh ; ./BuildServer/Unix/deploy_debian.sh
+RUN source ./BuildServer/Unix/Debian/definitions.sh; source ./BuildServer/Unix/setup_ci.sh ; ./BuildServer/Unix/Debian/deploy.sh
 
 

BuildServer/Docker/Builder/Ubuntu-trusty/Dockerfile_build

@@ -4,15 +4,13 @@ SHELL ["/bin/bash", "-c"]
 
 ARG MDANSE_GIT_COMMIT
 
-ARG MDANSE_GIT_BRANCH_NAME
-
 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/definitions_debian.sh ${MDANSE_GIT_BRANCH_NAME}; source ./BuildServer/Unix/version.sh ; ./BuildServer/Unix/build.sh
+RUN source ./BuildServer/Unix/Debian/definitions.sh; source ./BuildServer/Unix/setup_ci.sh ; ./BuildServer/Unix/build.sh
 
-RUN source ./BuildServer/Unix/definitions_debian.sh ${MDANSE_GIT_BRANCH_NAME}; source ./BuildServer/Unix/version.sh ; ./BuildServer/Unix/tests.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

@@ -2,10 +2,8 @@ FROM ci_mdanse_trusty
 
 SHELL ["/bin/bash", "-c"]
 
-ARG MDANSE_GIT_BRANCH_NAME
-
 VOLUME builds
 
-RUN source ./BuildServer/Unix/definitions_debian.sh ${MDANSE_GIT_BRANCH_NAME}; source ./BuildServer/Unix/version.sh ; ./BuildServer/Unix/deploy_debian.sh
+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

@@ -4,15 +4,13 @@ SHELL ["/bin/bash", "-c"]
 
 ARG MDANSE_GIT_COMMIT
 
-ARG MDANSE_GIT_BRANCH_NAME
-
 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/definitions_debian.sh ${MDANSE_GIT_BRANCH_NAME}; source ./BuildServer/Unix/version.sh ; ./BuildServer/Unix/build.sh
+RUN source ./BuildServer/Unix/Debian/definitions.sh; source ./BuildServer/Unix/setup_ci.sh ; ./BuildServer/Unix/build.sh
 
-RUN source ./BuildServer/Unix/definitions_debian.sh ${MDANSE_GIT_BRANCH_NAME}; source ./BuildServer/Unix/version.sh ; ./BuildServer/Unix/tests.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

@@ -2,10 +2,8 @@ FROM ci_mdanse_xenial
 
 SHELL ["/bin/bash", "-c"]
 
-ARG MDANSE_GIT_BRANCH_NAME
-
 VOLUME builds
 
-RUN source ./BuildServer/Unix/definitions_debian.sh ${MDANSE_GIT_BRANCH_NAME}; source ./BuildServer/Unix/version.sh ; ./BuildServer/Unix/deploy_debian.sh
+RUN source ./BuildServer/Unix/Debian/definitions.sh; source ./BuildServer/Unix/setup_ci.sh ; ./BuildServer/Unix/Debian/deploy.sh
 
 

BuildServer/Unix/Debian/definitions.sh

+export ARCH=amd64
+
+export DISTRO=$(lsb_release -c | cut -f2)
+
+export PYTHONEXE=/usr/bin/python
+
+export SED_I_COMMAND=(sed -i)
+

BuildServer/Unix/deploy_debian.sh → BuildServer/Unix/Debian/deploy.sh

@@ -9,58 +9,70 @@ export DISTUTILS_DEBUG=0
 #############################
 # PREPARATION
 #############################
-cd ${MDANSE_SOURCE_DIR}
-DEBIAN_ROOT_DIR=${MDANSE_SOURCE_DIR}/BuildServer/Build_Debian
+
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+DEBIAN_ROOT_DIR=${CI_TEMP_DIR}/dist
+
 rm -rf ${DEBIAN_ROOT_DIR}
-mkdir ${DEBIAN_ROOT_DIR}
+mkdir -p ${DEBIAN_ROOT_DIR}
 
 #############################
 # PACKAGING
 #############################
 echo -e "${BLUE}""Build debian tree""${NORMAL}"
 
-# Set automatically the good version number for the Debian control file
-sed -i "s/Version:.*/Version: ${VERSION_NAME}/g" BuildServer/Unix/Debian_resources/DEBIAN/control
-
 # Copy all the debian files (e.g. control, copyright, md5sum ...) into DEBIAN directory
-cp -r BuildServer/Unix/Debian_resources/DEBIAN ${DEBIAN_ROOT_DIR}/
+cp -r ${SCRIPT_DIR}/Resources/DEBIAN ${DEBIAN_ROOT_DIR}/
+# Set automatically the good version number for the Debian control file
+sed -i "s/Version:.*/Version: ${VERSION_NAME}/g" ${DEBIAN_ROOT_DIR}/DEBIAN/control
 chmod -R 755 ${DEBIAN_ROOT_DIR}/DEBIAN
 
 # Build the /usr/share/applications directory inside the debian root directory and copy the mdanse desktop file inside
 DEBIAN_APP_DIR=${DEBIAN_ROOT_DIR}/usr/share/applications
 mkdir -p ${DEBIAN_APP_DIR}
-cp BuildServer/Unix/Debian_resources/MDANSE.desktop ${DEBIAN_APP_DIR}/
+cp ${SCRIPT_DIR}/Resources/MDANSE.desktop ${DEBIAN_APP_DIR}/
 
 # Build the /usr/share/pixmaps directory inside the debian root directory and copy the mdanse icon file inside
 DEBIAN_PIXMAPS_DIR=${DEBIAN_ROOT_DIR}/usr/share/pixmaps
 mkdir -p ${DEBIAN_PIXMAPS_DIR}
-cp MDANSE/GUI/Icons/mdanse.png ${DEBIAN_PIXMAPS_DIR}/
+cp ${CI_PROJECT_DIR}/MDANSE/GUI/Icons/mdanse.png ${DEBIAN_PIXMAPS_DIR}/
 
 # Build the /usr/local/bin directory inside the debian root directory and copy the mdanse scripts inside
 DEBIAN_BIN_DIR=${DEBIAN_ROOT_DIR}/usr/local/bin
 mkdir -p ${DEBIAN_BIN_DIR}
-cp Scripts/* ${DEBIAN_BIN_DIR}/
+cp ${CI_PROJECT_DIR}/Scripts/* ${DEBIAN_BIN_DIR}/
 dos2unix ${DEBIAN_BIN_DIR}/mdanse_*
 
 # Build the usr/local/lib/python2.7/dist-packages directory inside the debian root directory and copy the MDANSE package inside
 DEBIAN_DIST_DIR=${DEBIAN_ROOT_DIR}/usr/local/lib/python2.7/dist-packages
 mkdir -p ${DEBIAN_DIST_DIR}
 
+cd ${CI_PROJECT_DIR}
+
+# Build API
+${PYTHONEXE} setup.py build_api build_help install --prefix=${CI_TEMP_INSTALL_DIR}
+
+status=$?
+if [ $status -ne 0 ]; then
+	echo -e "${RED}" "Failed to build MDANSE Documentation""${NORMAL}"
+	exit $status
+fi
+
 # Copy the localy installed ScientificPython, MMTK and MDANSE
-cp -r ${MDANSE_TEMPORARY_INSTALLATION_DIR}/lib/python2.7/site-packages/Scientific ${DEBIAN_DIST_DIR}
-cp -r ${MDANSE_TEMPORARY_INSTALLATION_DIR}/lib/python2.7/site-packages/MMTK ${DEBIAN_DIST_DIR}
-cp -r ${MDANSE_TEMPORARY_INSTALLATION_DIR}/lib/python2.7/site-packages/MDANSE ${DEBIAN_DIST_DIR}
+cp -r ${CI_TEMP_INSTALL_DIR}/lib/python2.7/site-packages/Scientific ${DEBIAN_DIST_DIR}
+cp -r ${CI_TEMP_INSTALL_DIR}/lib/python2.7/site-packages/MMTK ${DEBIAN_DIST_DIR}
+cp -r ${CI_TEMP_INSTALL_DIR}/lib/python2.7/site-packages/MDANSE ${DEBIAN_DIST_DIR}
 
 # Compute the Installed-Size field for the debian package
 instSize=$(du ${DEBIAN_ROOT_DIR} -b -s | cut -f1)
 sed -i "s/Installed-Size:.*/Installed-Size: $((1+(instSize/1024)))/g" ${DEBIAN_ROOT_DIR}/DEBIAN/control
 
 export TMPDIR=.
-fakeroot dpkg-deb -b ${DEBIAN_ROOT_DIR} ${MDANSE_SOURCE_DIR}/MDANSE-${VERSION_NAME}-${DISTRO}-${ARCH}.deb
+fakeroot dpkg-deb -b ${DEBIAN_ROOT_DIR} ${CI_PROJECT_DIR}/MDANSE-${VERSION_NAME}-${DISTRO}-${ARCH}.deb
 status=$?
 if [ $status -ne 0 ]; then
 	echo -e "${RED}" "Cannot build app.""${NORMAL}"
 	exit $status
 fi
 
-rm -rf ${MDANSE_TEMPORARY_INSTALLATION_DIR}
\ No newline at end of file