Merge branch 'master' into stable_fixes

.codecov.yml

@@ -0,0 +1,7 @@
+coverage:
+  precision: 1
+  round: down
+  range: "70...100"
+ignore:
+  - /usr/include/
+  - src/tests/

.gitignore

@@ -2,7 +2,6 @@
 csg_*.man
 csg_*.t2t
 csg_*.help
-libvotca*.pc
 libvotca*.a
 libvotca*.so
 libvotca*.so.*
@@ -37,6 +36,7 @@ src/tools/csg_density
 src/tools/csg_reupdate
 src/tools/csg_dlptopol
 share/scripts/inverse/*.pyc
+__pycache__/
 
 src/libcsg/gitversion.h
 src/libcsg/votca_config.h

.gitlab-ci.yml

@@ -37,15 +37,16 @@ stages:
     - mkdir -p build
     - pushd build
     - cmake .. -DENABLE_TESTING=ON -DBUILD_CSGAPPS=ON -DBUILD_XTP=ON -DBUILD_CTP=ON -DBUILD_CTP_MANUAL=ON -DBUILD_CSG_MANUAL=ON -DBUILD_XTP_MANUAL=ON
-      -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DBUILD_OWN_GROMACS=${BUILD_GROMACS}
+      -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DBUILD_OWN_GROMACS=${BUILD_GROMACS} -DENABLE_REGRESSION_TESTING=${REGRESSION_TESTING:-ON}
       -DMODULE_BUILD=${MODULE_BUILD} ${MODULE_BUILD:+-DCMAKE_INSTALL_PREFIX=/home/votca/votca.install}
       ${MINIMAL:+-DCMAKE_DISABLE_FIND_PACKAGE_HDF5=ON -DWITH_FFTW=OFF -DWITH_GSL=OFF -DCMAKE_DISABLE_FIND_PACKAGE_GSL=ON
       -DWITH_MKL=OFF -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON -DBUILD_MANPAGES=OFF -DWITH_GMX=OFF -DWITH_SQLITE3=OFF
-      -DCMAKE_DISABLE_FIND_PACKAGE_SQLITE3=ON -DBUILD_XTP=OFF -DBUILD_CTP=OFF}
+      -DCMAKE_DISABLE_FIND_PACKAGE_SQLITE3=ON -DBUILD_XTP=OFF -DBUILD_CTP=OFF -DENABLE_REGRESSION_TESTING=OFF}
     - make -O -k -j${j} -l${j} VERBOSE=1
     - make test CTEST_OUTPUT_ON_FAILURE=1
     - test -z "${MODULE_BUILD}" && make install DESTDIR=${PWD}/install && rm -rf ${PWD}/install/usr && rmdir ${PWD}/install
     - sudo make install
+    - if [[ ${CLANG_FORMAT} ]]; then make format && git -C ${CI_PROJECT_DIR}/votca/${CI_PROJECT_NAME} diff --exit-code; fi
     - ccache -s
 
 Debug GCC:
@@ -54,6 +55,7 @@ Debug GCC:
     CC: "gcc"
     CXX: "g++"
     CMAKE_BUILD_TYPE: "Debug"
+    CLANG_FORMAT: "yes"
   extends: .build
 
 None GCC:
@@ -123,6 +125,42 @@ Release Clang Ubuntu:
     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 Minimal:
   variables:
     CC: "gcc"
@@ -251,6 +289,7 @@ Release GCC GMX9999:
     CXX: "g++"
     CMAKE_BUILD_TYPE: "Release"
     DISTRO: "fedora_gmx9999"
+    REGRESSION_TESTING: "OFF"
   extends: .build
   allow_failure: true
 
@@ -260,6 +299,7 @@ Release Clang GMX9999:
     CXX: "clang++"
     CMAKE_BUILD_TYPE: "Release"
     DISTRO: "fedora_gmx9999"
+    REGRESSION_TESTING: "OFF"
   extends: .build
   allow_failure: true
 
@@ -269,6 +309,7 @@ Release GCC GMX9999D:
     CXX: "g++"
     CMAKE_BUILD_TYPE: "Release"
     DISTRO: "fedora_gmx9999_d"
+    REGRESSION_TESTING: "OFF"
   extends: .build
   allow_failure: true
 
@@ -278,6 +319,7 @@ Release Clang GMX9999D:
     CXX: "clang++"
     CMAKE_BUILD_TYPE: "Release"
     DISTRO: "fedora_gmx9999_d"
+    REGRESSION_TESTING: "OFF"
   extends: .build
   allow_failure: true
 
@@ -286,6 +328,7 @@ Release GCC OWN GMX:
     CC: "gcc"
     CXX: "g++"
     CMAKE_BUILD_TYPE: "Release"
+    DISTRO: "fedora_nogmx"
     CXXFLAGS: "-Wall"
     BUILD_GROMACS: "yes"
   extends: .build

.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
@@ -43,7 +59,7 @@ 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} ${TRAVIS_TAG:-origin/${TRAVIS_BRANCH}} && git -C ${HOME}/docker/votca submodule update --recursive --init;
      fi;
@@ -53,21 +69,15 @@ before_script:
      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 &&
@@ -76,13 +86,14 @@ 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 *;

CHANGELOG.md

@@ -1,20 +1,27 @@
-For more detailed information about the changes see the history of the [repository](https://github.com/votca/csg/commits/master).
+For more detailed information about the changes see the history of the
+[repository](https://github.com/votca/csg/commits/master).
+
+## Version 1.6-dev
 
 ## Version 1.5 _SuperVictor_ (released 31.01.19)
- * enable gitlab CI
+
+* enable gitlab CI
 
 ## Version 1.5_rc3 (released 19.01.19)
- * travis: fixed bug in building tags
- * cmake: only run csg_dump test if bash was found
+
+* travis: fixed bug in building tags
+* cmake: only run csg_dump test if bash was found
 
 ## Version 1.5_rc2 (released 16.01.19)
+
 * added REGRESSIONTEST_TOLERANCE cmake option
 * added bug fix for memory leak in bead class
 * added topology unit test
 
 ## Version 1.5_rc1 (released 28.12.18)
+
 * added support for 3 body distribution
-* allow usage of _ in gmx options
+* allow usage of \_ in gmx options
 * support espresso-4.0
 * added LAMMPS data topology reader
 * added LAMMPS dump writer
@@ -29,6 +36,7 @@ For more detailed information about the changes see the history of the [reposito
 * added unit and regression tests
 
 ## Version 1.4.1 (released 02.09.17)
+
 * fix pkg-config files
 * fix build with gmx-2017
 * added CSG_MDRUN_OPTS to run_gromacs.sh
@@ -38,41 +46,45 @@ For more detailed information about the changes see the history of the [reposito
 * tools: fix parallel build with mkl
 
 ## Version 1.4 _SuperKurt_ (released 29.10.16)
+
 * added cibi tutorial and manual section
 * install mkl headers if mkl is enabled
 * updated copyright
-* xmltopologyparser: tokenize on \n and \t as well (#195)
+* xmltopologyparser: tokenize on \\n and \\t as well (#195)
 * tools: added support for boost-1.62
 
 ## Version 1.4_rc1 (released 26.09.16)
- * switch to c++-11
- * dihedral support in csg_fmatch
- * support for tabulated bond in >=gmx-5
- * added full featured XMLTopologyReader
- * added regularization for IMC
- * changed neighborlist from std::list to std::vector
- * added cibi method
- * tools: added support for mkl as gsl replacement
- * lots of reader bug fixes
- * dropped support for gromacs-4 and clean up
- * dropped multi_g_rdf script
- * dropped thermforce iteration method
- * moved h5md reader to hdf5 without c++ api
+
+* switch to c++-11
+* dihedral support in csg_fmatch
+* support for tabulated bond in >=gmx-5
+* added full featured XMLTopologyReader
+* added regularization for IMC
+* changed neighborlist from std::list to std::vector
+* added cibi method
+* tools: added support for mkl as gsl replacement
+* lots of reader bug fixes
+* dropped support for gromacs-4 and clean up
+* dropped multi_g_rdf script
+* dropped thermforce iteration method
+* moved h5md reader to hdf5 without c++ api
 
 ## Version 1.3.1 (released 19.08.16)
+
 * histogram: use floor() on bin value
 * calculator: fixed namespace
 * VOTCARC: added shebang
 * fixed gromacs detection with >=cmake-3.4
 
 ## Version 1.3 _SuperUzma_ (released 15.01.16)
+
 * re-implemented csg_boltzmann --excl
 * added support for upcoming gromacs 2016
 
 ## Version 1.3_rc1 (released 23.09.15)
 
 * added new iterative methods: relative entropy, simplex optimization
-* added support for using hoomd-blue, lammps, ESPResSo, ESPResSo++ and dl_poly for iterative methods
+* added support for using the following with iterative methods: hoomd-blue, lammps, ESPResSo, ESPResSo++, dl_poly 
 * added pre-simulation feature for GROMACS (e.g. for minimization)
 * added rudimentary support for IBI with bonded interaction
 * made pdb reader work with libgmx
@@ -128,7 +140,7 @@ For more detailed information about the changes see the history of the [reposito
 * added thermforce iteration method
 * added csg_density
 * a lot of framework clean up
-* added type selector name:*
+* added type selector name:\*
 * allow long and restart of simulations
 * added database class through sqlite3
 
@@ -152,8 +164,8 @@ For more detailed information about the changes see the history of the [reposito
 * added man pages, man7 and man1 for all bins
 * csg_inverse: renamed ibm to ibi
 * csg_inverse: many internal improvements
-* csg_stat: added thread support, read exclusions from tpr file, uses grid search by default
-* csg_inverse: added convergence check, postadd plot, better logging and weaker die
+* csg_stat: added: thread support, read exclusions from tpr file, uses grid search by default
+* csg_inverse: added: convergence check, postadd plot, better logging, weaker die
 * csg_resample: added boundary conditions option and akima spline support
 * csg_stat or csg_fmatch give an error if trj not given (issue 29)
 * csg_get_interaction_property knows about defaults
@@ -180,16 +192,16 @@ For more detailed information about the changes see the history of the [reposito
 ## Version 1.0 (released 30.09.10)
 
 * added postupdate script for scaling the update
-* added options to perform analysis without giving a mapping file (--no-map). No need for dummy mapping file in IMC and csg_stat anymore.
+* imc and csg_stat: no longer require dummy mapping file (--no-map) option
 * allow comments in tables
 * fixed bug in pressure correction when p is negative
 * added support for gromacs devel version
 * fixed a bug when compiling with gcc-4.4
 * fixed a bug that pot.cur was change at every step
 * added application class for easy implementation of analysis programs
 * fixed bug if initial potential was given and not used
-* restart points in iterative procedure are not anymore deleted after step finished
-* preliminary reader for ESPResSo Blockfiles and ESPResSo as Simulation program for csg_inverse
+* restart points are no longer deleted after step finished
+* csg_inverse: preliminary reader for ESPResSo Blockfiles and ESPResSo 
 * preliminary reader for LAMMPS dump files (very limited features)
 * allow compling without gromacs
 * a lot new xml optionsfull support for gromacs 4.5
@@ -217,7 +229,7 @@ For more detailed information about the changes see the history of the [reposito
 
 ## Version 1.0_rc4 (released 08.02.10)
 
-* using libtool to build shared libs\
+* using libtool to build shared libs\\
 * fixed a bug in error calculation of multi_g_rdf
 
 ## Version 1.0_rc3 (released 29.01.10)
@@ -241,4 +253,3 @@ For more detailed information about the changes see the history of the [reposito
 ## Version 1.0_rc1 (released 11.12.09)
 
 * initial version
-