Merge pull request #9 from votca/for/stable/merge_master

junghans · web-flow · commit eeb3d87cb529 · 2020-02-11T12:19:33.000-07:00
Merge over master changes
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -0,0 +1,188 @@
+stages:
+  - canary
+  - build
+
+.build_script:
+  retry:
+    max: 2
+  variables:
+    CCACHE_DIR: "${CI_PROJECT_DIR}/ccache"
+  stage: build
+  artifacts:
+    paths:
+      - ${CI_PROJECT_DIR}/votca
+    when: always
+  dependencies: []
+  cache:
+    paths:
+      - ccache/
+  script:
+    - ccache -z
+    - j="$(grep -c processor /proc/cpuinfo 2>/dev/null)" || j=0; ((j++))
+    - git branch commit_of_build_${CI_BUILD_ID} ${CI_COMMIT_SHA}
+    - git clone https://github.com/votca/votca
+    - pushd votca
+    - if [[ ${CI_COMMIT_TAG} = v[12].[0-9]* ]]; then
+        git checkout -b ${CI_COMMIT_TAG} ${CI_COMMIT_TAG};
+      elif [[ ( ${CI_COMMIT_REF_NAME} =~ ^for/([^/]*)/.* || ${CI_COMMIT_REF_NAME} =~ ^(stable)$ ) && ${BASH_REMATCH[1]} != master ]]; then
+        git checkout -b ${BASH_REMATCH[1]} origin/${BASH_REMATCH[1]};
+      fi
+    - git submodule update --recursive --init
+    - git -C ${CI_PROJECT_NAME} fetch ${CI_PROJECT_DIR} commit_of_build_${CI_BUILD_ID}
+    - git -C ${CI_PROJECT_DIR} branch -d commit_of_build_${CI_BUILD_ID}
+    - git -C ${CI_PROJECT_NAME} checkout -f ${CI_COMMIT_SHA}
+    - mkdir -p build
+    - pushd build
+    - cmake .. -DCMAKE_VERBOSE_MAKEFILE=ON -DENABLE_TESTING=ON -DBUILD_XTP=ON -DENABLE_WERROR=ON
+      -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+      -DMODULE_BUILD=${MODULE_BUILD} ${MODULE_BUILD:+-DCMAKE_INSTALL_PREFIX=/home/votca/votca.install}
+      -DWITH_MKL=${WITH_MKL} -DCMAKE_DISABLE_FIND_PACKAGE_MKL=${DISABLE_MKL}
+      -DUSE_CUDA=${USE_CUDA}      
+    - cmake --build . -- -j2
+    - ctest --output-on-failure
+    - test -z "${MODULE_BUILD}" && DESTDIR=${PWD}/install cmake --build . --target install && rm -rf ${PWD}/install/usr && rmdir ${PWD}/install
+    - sudo cmake --build . --target install
+    - if [[ ${CLANG_FORMAT} ]]; then cmake --build . --target format && git -C ${CI_PROJECT_DIR}/votca/${CI_PROJECT_NAME} diff --exit-code; fi
+    - ccache -s
+
+.build:
+  variables:
+    DISTRO: "latest"
+  image: votca/buildenv:${DISTRO}
+  extends: .build_script
+    
+Debug GCC:
+  stage: canary
+  variables:
+    CC: "gcc"
+    CXX: "g++"
+    CMAKE_BUILD_TYPE: "Debug"
+    CLANG_FORMAT: "yes"
+  extends: .build
+
+None GCC:
+  variables:
+    CC: "gcc"
+    CXX: "g++"
+    CMAKE_BUILD_TYPE: ""
+  extends: .build
+
+None Clang:
+  variables:
+    CC: "clang"
+    CXX: "clang++"
+    CMAKE_BUILD_TYPE: ""
+  extends: .build
+
+Debug Clang:
+  variables:
+    CC: "clang"
+    CXX: "clang++"
+    CMAKE_BUILD_TYPE: "Debug"
+  extends: .build
+
+Release GCC:
+  variables:
+    CC: "gcc"
+    CXX: "g++"
+    CMAKE_BUILD_TYPE: "Release"
+  extends: .build
+
+Release Clang:
+  variables:
+    CC: "clang"
+    CXX: "clang++"
+    CMAKE_BUILD_TYPE: "Release"
+  extends: .build
+
+Debug GCC Ubuntu:
+  variables:
+    CC: "gcc"
+    CXX: "g++"
+    CMAKE_BUILD_TYPE: "Debug"
+    DISTRO: "ubuntu"
+  extends: .build
+
+Debug Clang Ubuntu:
+  variables:
+    CC: "clang"
+    CXX: "clang++"
+    CMAKE_BUILD_TYPE: "Debug"
+    DISTRO: "ubuntu"
+  extends: .build
+
+Release GCC Ubuntu:
+  variables:
+    CC: "gcc"
+    CXX: "g++"
+    CMAKE_BUILD_TYPE: "Release"
+    DISTRO: "ubuntu"
+  extends: .build
+
+Release Clang Ubuntu:
+  variables:
+    CC: "clang"
+    CXX: "clang++"
+    CMAKE_BUILD_TYPE: "Release"
+    DISTRO: "ubuntu"
+  extends: .build
+
+Debug GCC Rawhide:
+  variables:
+    CC: "gcc"
+    CXX: "g++"
+    CMAKE_BUILD_TYPE: "Debug"
+    DISTRO: "fedora_rawhide"
+  extends: .build
+  allow_failure: true
+
+Debug Clang Rawhide:
+  variables:
+    CC: "clang"
+    CXX: "clang++"
+    CMAKE_BUILD_TYPE: "Debug"
+    DISTRO: "fedora_rawhide"
+  extends: .build
+  allow_failure: true
+
+Release GCC Rawhide:
+  variables:
+    CC: "gcc"
+    CXX: "g++"
+    CMAKE_BUILD_TYPE: "Release"
+    DISTRO: "fedora_rawhide"
+  extends: .build
+  allow_failure: true
+
+Release Clang Rawhide:
+  variables:
+    CC: "clang"
+    CXX: "clang++"
+    CMAKE_BUILD_TYPE: "Release"
+    DISTRO: "fedora_rawhide"
+  extends: .build
+  allow_failure: true
+
+Release GCC Module:
+  variables:
+    CC: "gcc"
+    CXX: "g++"
+    CMAKE_BUILD_TYPE: "Release"
+    MODULE_BUILD: "yes"
+  extends: .build
+
+Debug GPU Ubuntu:
+  variables:
+    CC: "gcc"
+    CXX: "g++"
+    CMAKE_BUILD_TYPE: "Debug"
+    USE_CUDA: "yes"
+    WITH_MKL: "no"
+    DISABLE_MKL: "yes"
+    NO_INSTALL: "yes"
+  before_script:
+    - source /opt/gromacs-2019/bin/GMXRC.bash
+  extends: .build_script
+  allow_failure: true
+  tags:
+    - gpu
diff --git a/.travis.yml b/.travis.yml
@@ -9,6 +9,22 @@ sudo: required
 services:
 - docker
 
+git:
+  quiet: true
+
+stages:
+  - canary
+  - test
+  - deploy
+
+jobs:
+  include:
+    - stage: canary
+      env: ENV=3
+    - stage: deploy
+      if: repo = votca/votca AND type != pull_request
+      env: ENV=1
+
 env:
   matrix:
     - ENV=1
@@ -43,31 +59,25 @@ before_script:
      cp -vr ${TRAVIS_REPO_SLUG}/docker ${HOME};
      mv -v ${TRAVIS_REPO_SLUG} $HOME/docker;
    else
-     git clone --recursive https://github.com/votca/votca.git $HOME/docker/votca;
+     git clone -q --recursive https://github.com/votca/votca.git $HOME/docker/votca;
      if [[ ${TRAVIS_BRANCH} != master ]]; then
-       git -C ${HOME}/docker/votca checkout -b ${TRAVIS_BRANCH} origin/${TRAVIS_BRANCH} && git -C ${HOME}/docker/votca submodule update --recursive --init;
+       git -C ${HOME}/docker/votca checkout -b ${TRAVIS_BRANCH} ${TRAVIS_TAG:-origin/${TRAVIS_BRANCH}} && git -C ${HOME}/docker/votca submodule update --recursive --init;
      fi;
      git -C ${HOME}/docker/votca/${TRAVIS_REPO_SLUG#*/} fetch ${PWD}/${TRAVIS_REPO_SLUG} current_commit;
      git -C ${HOME}/docker/votca/${TRAVIS_REPO_SLUG#*/} checkout -f FETCH_HEAD;
      cp -vr ${HOME}/docker/votca/docker/* ${HOME}/docker;
      if [[ -d ${TRAVIS_REPO_SLUG}/docker ]]; then cp -vr ${TRAVIS_REPO_SLUG}/docker/* ${HOME}/docker; fi;
    fi
  - source ${HOME}/docker/set_env.sh
- - cp -r $HOME/.ccache ${HOME}/docker/ccache
+ - test -n "${SKIP}" || cp -r $HOME/.ccache ${HOME}/docker/ccache
  - sed -i "1s/latest/${DISTRO:-latest}/" ${HOME}/docker/Dockerfile
  - if [[ ! ${SKIP} ]]; then 
-     travis_retry timeout 540 docker pull $(sed -n '1s/FROM //p' ${HOME}/docker/Dockerfile);
+     travis_retry timeout 540 docker pull $(sed -n '1s/FROM //p' ${HOME}/docker/Dockerfile) | cat;
    fi
 
 script:
  - if [[ ! ${SKIP} ]]; then
      travis_retry docker build "${docker_opts[@]}"
-                 --build-arg CC=${CC} --build-arg CXX=${CXX} --build-arg CXXFLAGS="-Wall ${WERROR:+-Werror}"
-                 --build-arg CI=${CI} --build-arg TRAVIS=${TRAVIS} --build-arg TRAVIS_OS_NAME=${DISTRO:-fedora}
-                 --build-arg TRAVIS_BRANCH=${TRAVIS_BRANCH} --build-arg TRAVIS_JOB_NUMBER=${TRAVIS_JOB_NUMBER}
-                 --build-arg TRAVIS_PULL_REQUEST=${TRAVIS_PULL_REQUEST} --build-arg TRAVIS_JOB_ID=${TRAVIS_JOB_ID}
-                 --build-arg TRAVIS_TAG=${TRAVIS_TAG} --build-arg TRAVIS_REPO_SLUG=${TRAVIS_REPO_SLUG}
-                 --build-arg TRAVIS_COMMIT=${TRAVIS_COMMIT}
                  ${TRAVIS_TAG:+-t votca/votca:${TRAVIS_TAG}}
                  -t votca/votca:latest -t votca/votca:${TRAVIS_BRANCH} ${HOME}/docker/ &&
      rm -rf $HOME/.ccache &&
@@ -76,21 +86,21 @@ script:
    fi
 
 after_success:
-  - shopt -s extglob && [[ ${TRAVIS_BRANCH} = @(master|stable|v1.*) && ${CC} = *gcc* && ${DOCKERHUB} = yes && ! ${SKIP} ]] && DEPLOY=yes
+  - if [[ ${TRAVIS_REPO_SLUG} != votca/votca || ${TRAVIS_BUILD_STAGE_NAME} != "Deploy" || ${SKIP} ]]; then travis_terminate 0; fi
+  - shopt -s extglob && [[ ${TRAVIS_BRANCH} = @(master|stable|v1.*) ]] && DEPLOY=yes
   - if [[ ${TRAVIS_BRANCH} = master ]]; then DOCKER_TAG=latest; else DOCKER_TAG="${TRAVIS_BRANCH}"; fi
   - if [[ ${DOCKER_USERNAME} && ${DOCKER_PASSWORD} && ${TRAVIS_PULL_REQUEST} == false && ${DEPLOY} ]]; then
         docker login -u="$DOCKER_USERNAME" -p="$DOCKER_PASSWORD";
         docker push "${TRAVIS_REPO_SLUG}:${DOCKER_TAG}";
     fi
-  - if [[ ${DOXYGEN} = yes && ! ${SKIP} ]]; then
+  - if true; then
       git clone --depth=1 https://github.com/votca/doxygen.git "$HOME/devdoc";
       cd $HOME/devdoc;
       rm -f *;
       git checkout -- CNAME;
       docker cp ${CON}:/home/votca/votca/build/share/doc/html . ;
       mv html/* .; rmdir html;
       docker cp ${CON}:/home/votca/votca/build/csg-manual/manual.pdf . ;
-      docker cp ${CON}:/home/votca/votca/build/ctp/manual/ctp-manual.pdf . ;
       docker cp ${CON}:/home/votca/votca/build/xtp/manual/xtp-manual.pdf . ;
       git add --all .;
       if [[ ${TRAVIS_BRANCH} = master && ${encrypted_7abbb71c3ba6_key} && ${encrypted_7abbb71c3ba6_iv} && ${TRAVIS_PULL_REQUEST} == false ]]; then
@@ -106,6 +116,14 @@ after_success:
       fi;
     fi
 
+branches:
+  only:
+  - master
+  - development
+  - stable
+  - next
+  - /^v\d+\.\d+(\.\d+|_rc\d+)?$/
+
 cache:
   - ccache
 
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -4,3 +4,25 @@ project(xtp-tutorials)
 
 set(PROJECT_VERSION "1.6_rc2")
 
+set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules)
+include(GNUInstallDirs)
+
+install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/ DESTINATION ${CMAKE_INSTALL_DATADIR}/votca/xtp-tutorials
+	PATTERN ".git*" EXCLUDE
+	PATTERN "CMake*" EXCLUDE PATTERN "cmake_install.cmake" EXCLUDE
+	PATTERN "install_manifest.txt" EXCLUDE PATTERN "*~" EXCLUDE)
+
+configure_file(${CMAKE_MODULE_PATH}/cmake_uninstall.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake IMMEDIATE @ONLY)
+option(ENABLE_TESTING "Test if cmake worked" OFF)
+if(ENABLE_TESTING)
+  enable_testing()
+  add_test(regression_xtp-tutorial_UninstallExists ${CMAKE_COMMAND} -DFileToCheck=${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake
+           -P ${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FileExists.cmake)
+
+  set_tests_properties(regression_xtp-tutorial_UninstallExists PROPERTIES LABELS "xtp-tutorials")
+endif(ENABLE_TESTING)
+add_custom_target(uninstall-xtp-tutorials COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake)
+if(NOT TARGET uninstall)
+  add_custom_target(uninstall)
+endif()
+add_dependencies(uninstall uninstall-xtp-tutorials)
diff --git a/CMakeModules/FileExists.cmake b/CMakeModules/FileExists.cmake
@@ -0,0 +1,5 @@
+if(EXISTS ${FileToCheck})
+  message("${FileToCheck} exists.")
+else()
+  message(FATAL_ERROR "${FileToCheck} doesn't exist.")
+endif()
diff --git a/CMakeModules/cmake_uninstall.cmake.in b/CMakeModules/cmake_uninstall.cmake.in
@@ -0,0 +1,22 @@
+IF(NOT EXISTS "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt")
+  MESSAGE(FATAL_ERROR "Cannot find install manifest: \"@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt\"")
+ENDIF(NOT EXISTS "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt")
+
+FILE(READ "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt" files)
+STRING(REGEX REPLACE "\n" ";" files "${files}")
+FOREACH(file ${files})
+  MESSAGE(STATUS "Uninstalling \"$ENV{DESTDIR}${file}\"")
+  IF(EXISTS "$ENV{DESTDIR}${file}")
+    EXEC_PROGRAM(
+      "@CMAKE_COMMAND@" ARGS "-E remove \"$ENV{DESTDIR}${file}\""
+      OUTPUT_VARIABLE rm_out
+      RETURN_VALUE rm_retval
+      )
+    IF(NOT "${rm_retval}" STREQUAL 0)
+      MESSAGE(FATAL_ERROR "Problem when removing \"$ENV{DESTDIR}${file}\"")
+    ENDIF(NOT "${rm_retval}" STREQUAL 0)
+  ELSE(EXISTS "$ENV{DESTDIR}${file}")
+    MESSAGE(STATUS "File \"$ENV{DESTDIR}${file}\" does not exist.")
+  ENDIF(EXISTS "$ENV{DESTDIR}${file}")
+ENDFOREACH(file)
+
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 This is a tutorial for the VOTCA-XTP package
 
-How to approach the tutorial? [Click here](https://github.com/votca/xtp-tutorials/blob/electrostatics/guide/TUTORIAL.md).
+How to approach the tutorial? [Click here](https://github.com/votca/xtp-tutorials/blob/master/guide/TUTORIAL.md).
 
 Installation instructions and developer information can be found
 [here](https://github.com/votca/votca/blob/master/share/doc/INSTALL.md)
@@ -11,18 +11,22 @@ http://www.votca.org
 The development of VOTCA is mainly funded by academic research grants. If you
 use this package, please cite the VOTCA papers:
 
-* Electronic Excitations in Complex Molecular Environments: Many-Body Green’s
-  Functions Theory in VOTCA-XTP Jens Wehner, Lothar Brombacher, Joshua Brown,
-  Christoph Junghans, Onur Caylak, Yuriy Khalak, Pranav Madhikar, Gianluca
-  Tirimbo, Björn Baumeier J. Chem. Theory Comput. 14, 6353 (2018).
+*   Excited-State Electronic Structure of Molecules Using Many-Body Green’s Functions: Quasiparticles and Electron-Hole Excitations with VOTCA-XTP,
+    G. Tirimbo, V. Sundaram, O. Caylak, W. Scharpach, J. Sijen, C. Junghans, J. Brown, F. Zapata Ruiz, N. Renaud, J. Wehner, and B. Baumeier,
+    ChemRxiv:11477895 (2020).
 
-* Microscopic simulations of charge transport in disordered organic semiconductors
-  V. Ruehle, A. Lukyanov, F. May, M. Schrader, T. Vehoff, J. Kirkpatrick, B. Baumeier and D. Andrienko
-  J. Chem. Theo. Comp. 7, 3335-3345 (2011) 
+*   Electronic Excitations in Complex Molecular Environments: Many-Body Green’s
+    Functions Theory in VOTCA-XTP Jens Wehner, Lothar Brombacher, Joshua Brown,
+    Christoph Junghans, Onur Caylak, Yuriy Khalak, Pranav Madhikar, Gianluca
+    Tirimbo, Björn Baumeier J. Chem. Theory Comput. 14, 6353 (2018).
 
-* Versatile Object-oriented Toolkit for Coarse-graining Applications,
-  V.Ruehle, C. Junghans, A. Lukyanov, K. Kremer, D. Andrienko,
-  J. Chem. Theo. Comp. 5 (12), 3211 (2009) 
+*   Microscopic simulations of charge transport in disordered organic semiconductors
+    V. Ruehle, A. Lukyanov, F. May, M. Schrader, T. Vehoff, J. Kirkpatrick, B. Baumeier and D. Andrienko
+    J. Chem. Theo. Comp. 7, 3335-3345 (2011) 
+
+*   Versatile Object-oriented Toolkit for Coarse-graining Applications,
+    V.Ruehle, C. Junghans, A. Lukyanov, K. Kremer, D. Andrienko,
+    J. Chem. Theo. Comp. 5 (12), 3211 (2009) 
 
 In case of questions, please post them in the google discussion group
 for votca at [here](https://groups.google.com/forum/#!forum/votca)
