Codebase list votca-xtp / upstream/1.6.2
New upstream version 1.6.2 Nicholas Breen 3 years ago
19 changed file(s) with 411 addition(s) and 530 deletion(s). Raw diff Collapse all Expand all
+40
-0
.github/workflows/changelog.yml less more
0 name: Changelog
1 on:
2 issue_comment:
3 types: [created]
4 jobs:
5 edit:
6 name: add entry
7 if: ${{ startsWith(github.event.comment.body, '@votca-bot changelog:') }}
8 runs-on: ubuntu-latest
9 steps:
10 - name: Check if message comes from PR
11 uses: octokit/request-action@v2.x
12 id: issue_info
13 with:
14 route: GET /repos/:repository/issues/:pull_number
15 repository: ${{ github.repository }}
16 pull_number: ${{ github.event.issue.number }}
17 GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
18 - name: Get PR info
19 if: ${{ fromJSON(steps.issue_info.outputs.data).pull_request }}
20 uses: octokit/request-action@v2.x
21 id: pr_info
22 with:
23 route: GET /repos/:repository/pulls/:pull_number
24 repository: ${{ github.repository }}
25 pull_number: ${{ github.event.issue.number }}
26 GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
27 - name: Checkout head branch from PR
28 if: ${{ fromJSON(steps.issue_info.outputs.data).pull_request }}
29 uses: actions/checkout@v2.2.0
30 with:
31 repository: ${{ fromJSON(steps.pr_info.outputs.data).head.repo.full_name }}
32 ref: ${{ fromJSON(steps.pr_info.outputs.data).head.ref }}
33 token: ${{ secrets.VOTCA_BOT_TOKEN }}
34 - name: Create and commit changelog entry
35 if: ${{ fromJSON(steps.issue_info.outputs.data).pull_request }}
36 uses: votca/actions/changelog@master
37 with:
38 message: ${{ github.event.comment.body }}
39 pr_number: ${{ github.event.issue.number }}
+75
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.github/workflows/continuous-integration-workflow.yml less more
0 name: CI
1 on:
2 pull_request:
3 branches:
4 - master
5 - stable
6
7 jobs:
8 CI:
9 continue-on-error: ${{ matrix.distro == 'ubuntu_devel' || matrix.distro == 'fedora_rawhide' || matrix.continue-on-error == true }}
10 strategy:
11 matrix:
12 distro: [latest, fedora_rawhide, opensuse, ubuntu, ubuntu_devel, ubuntu_rolling, ubuntu_18.04, intel]
13 toolchain: [gnu, clang]
14 cmake_build_type: [Release, Debug]
15 minimal: [false]
16 own_gmx: [false]
17 module_build: [false]
18 coverage: [false]
19 no_regression_testing: [true]
20 include:
21 - distro: latest
22 toolchain: gnu
23 cmake_build_type: Release
24 module_build: true
25 no_regression_testing: true
26 runs-on: ubuntu-latest
27 container: votca/buildenv:${{ matrix.distro }}
28 steps:
29 - uses: actions/checkout@v2.2.0
30 with:
31 fetch-depth: 0
32 - name: Run Votca Setup
33 id: setup
34 uses: votca/actions/setup@master
35 with:
36 distro: ${{ matrix.distro }}
37 toolchain: ${{ matrix.toolchain }}
38 minimal: ${{ matrix.minimal == true }}
39 module: ${{ matrix.module_build == true }}
40 own_gmx: ${{ matrix.own_gmx == true }}
41 regression_testing: ${{ matrix.no_regression_testing != true }}
42 coverage: ${{ matrix.coverage }}
43 cmake_build_type: ${{ matrix.cmake_build_type }}
44 ctest_args: ${{ matrix.ctest_args }}
45 cmake_args: ${{ matrix.cmake_args }}
46 - uses: actions/cache@v2
47 with:
48 path: ~/.ccache
49 key: ${{ steps.setup.outputs.cache_key }}
50 restore-keys: ${{ steps.setup.outputs.cache_restore_key }}
51 - name: CMake
52 run: mkdir builddir && cd builddir && cmake ${{ steps.setup.outputs.cmake_args }} ../votca
53 - name: Build
54 run: |
55 ccache -z
56 cmake --build builddir -- -j ${{ steps.setup.outputs.jobs }}
57 ccache -s
58 - name: Tests
59 run: ctest --output-on-failure ${{ steps.setup.outputs.ctest_args }}
60 working-directory: builddir
61 - name: Doxygen
62 if: ${{ ! matrix.module_build }}
63 run: cmake --build builddir --target doxygen
64 - name: Build Sphinx
65 if: ${{ steps.setup.outputs.build_sphinx == 'true' }}
66 run: cmake --build builddir --target doc
67 - name: Test DESTDIR Install
68 if: ${{ ! matrix.module_build }}
69 run: DESTDIR=${PWD}/install cmake --build builddir --target install && rm -rf ${PWD}/install/usr && rmdir ${PWD}/install
70 - name: Install
71 run: sudo cmake --build builddir --target install
72 - name: Check Formatting
73 if: ${{ steps.setup.outputs.check_format == 'true' }}
74 run: cmake --build builddir --target format && git -C votca/${{ steps.setup.outputs.module }} diff --exit-code
+37
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.github/workflows/create-pr.yml less more
0 name: Create PR
1 on:
2 push:
3 branches:
4 - stable
5
6 jobs:
7 PR:
8 name: Create
9 if: github.repository_owner == 'votca'
10 runs-on: ubuntu-latest
11 steps:
12 - name: Checkout code
13 uses: actions/checkout@master
14 with:
15 ref: ${{ github.event.ref }}
16 fetch-depth: 0
17 token: ${{ secrets.VOTCA_BOT_TOKEN }}
18 - name: Try to merge master branch
19 run: |
20 git config --global user.name "Votca Bot"
21 git config --global user.email "github@votca.org"
22 git checkout -b stable_fixes
23 git merge origin/master || true
24 git push origin stable_fixes
25 - name: Create Pull Request
26 uses: actions/github-script@0.3.0
27 with:
28 github-token: ${{ secrets.VOTCA_BOT_TOKEN }}
29 script: |
30 github.pulls.create({
31 owner: 'votca',
32 repo: 'xtp',
33 title: 'Fixes from stable',
34 head: 'stable_fixes',
35 base: 'master'
36 })
+28
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.github/workflows/create-release.yml less more
0 name: Make Release
1 on:
2 push:
3 tags:
4 - 'v[1-9]*'
5
6 jobs:
7 release:
8 name: Make Release
9 if: github.repository_owner == 'votca'
10 runs-on: ubuntu-latest
11 steps:
12 - name: Checkout code
13 uses: actions/checkout@v2
14 - name: Create Changlog
15 uses: votca/actions/release_changelog@master
16 with:
17 version: ${{ github.ref }}
18 changelog: 'release_changelog.md'
19 - name: Create Release
20 uses: actions/create-release@v1
21 env:
22 GITHUB_TOKEN: ${{ secrets.VOTCA_BOT_TOKEN }}
23 with:
24 tag_name: ${{ github.ref }}
25 release_name: ${{ github.ref }}
26 prerelease: ${{ contains(github.ref, 'rc') }}
27 body_path: 'release_changelog.md'
+46
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.github/workflows/format.yml less more
0 name: Format
1 on:
2 issue_comment:
3 types: [created]
4 jobs:
5 edit:
6 name: clang-format
7 if: ${{ github.event.comment.body == '@votca-bot format' }}
8 runs-on: ubuntu-latest
9 container: votca/buildenv:format
10 steps:
11 - name: Check if message comes from PR
12 uses: octokit/request-action@v2.x
13 id: issue_info
14 with:
15 route: GET /repos/:repository/issues/:pull_number
16 repository: ${{ github.repository }}
17 pull_number: ${{ github.event.issue.number }}
18 GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
19 - name: Get PR info
20 if: ${{ fromJSON(steps.issue_info.outputs.data).pull_request }}
21 uses: octokit/request-action@v2.x
22 id: pr_info
23 with:
24 route: GET /repos/:repository/pulls/:pull_number
25 repository: ${{ github.repository }}
26 pull_number: ${{ github.event.issue.number }}
27 GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
28 - name: Checkout head branch from PR
29 if: ${{ fromJSON(steps.issue_info.outputs.data).pull_request }}
30 uses: actions/checkout@master
31 with:
32 repository: ${{ fromJSON(steps.pr_info.outputs.data).head.repo.full_name }}
33 ref: ${{ fromJSON(steps.pr_info.outputs.data).head.ref }}
34 token: ${{ secrets.VOTCA_BOT_TOKEN }}
35 - name: Run clang-format
36 if: ${{ fromJSON(steps.issue_info.outputs.data).pull_request }}
37 run: find . -type f -regex ".*\.\(c\|h\|cc\|cpp\|hpp\)" -print0 | xargs -0 clang-format -i -style=file
38 - name: Commit and push
39 if: ${{ fromJSON(steps.issue_info.outputs.data).pull_request }}
40 run: |
41 git config --global user.name "Votca Bot"
42 git config --global user.email "github@votca.org"
43 git add -u
44 git commit -m "Format code using $(clang-format --version)" || true
45 git push
+18
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.github/workflows/forward-to-votca.yml less more
0 name: Forward
1 on:
2 push:
3 branches:
4 - master
5 - stable
6
7 jobs:
8 VOTCA:
9 if: github.repository_owner == 'votca'
10 runs-on: ubuntu-latest
11 steps:
12 - name: Update submodule
13 uses: votca/actions/forward@master
14 with:
15 module: ${{ github.repository }}
16 token: ${{ secrets.VOTCA_BOT_TOKEN }}
17
+5
-127
.gitlab-ci.yml less more
00 stages:
1 - canary
21 - build
32
43 .build_script:
3433 - pushd build
3534 - cmake .. -DCMAKE_VERBOSE_MAKEFILE=ON -DENABLE_TESTING=ON -DBUILD_XTP=ON -DENABLE_WERROR=ON
3635 -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
36 ${CMAKE_GENERATOR:+-G${CMAKE_GENERATOR}}
3737 -DMODULE_BUILD=${MODULE_BUILD} ${MODULE_BUILD:+-DCMAKE_INSTALL_PREFIX=/home/votca/votca.install}
38 -DWITH_MKL=${WITH_MKL} -DCMAKE_DISABLE_FIND_PACKAGE_MKL=${DISABLE_MKL}
38 -DCMAKE_DISABLE_FIND_PACKAGE_MKL=${DISABLE_MKL}
3939 -DUSE_CUDA=${USE_CUDA}
40 - cmake --build . -- -j2
40 - cmake --build . --parallel 2
4141 - ctest --output-on-failure
42 - test -z "${MODULE_BUILD}" && DESTDIR=${PWD}/install cmake --build . --target install && rm -rf ${PWD}/install/usr && rmdir ${PWD}/install
43 - sudo cmake --build . --target install
42 - test -z "${MODULE_BUILD}" && DESTDIR=${PWD}/install cmake --install . && rm -rf ${PWD}/install/usr && rmdir ${PWD}/install
43 - sudo cmake --install .
4444 - if [[ ${CLANG_FORMAT} ]]; then cmake --build . --target format && git -C ${CI_PROJECT_DIR}/votca/${CI_PROJECT_NAME} diff --exit-code; fi
4545 - ccache -s
4646
5050 image: votca/buildenv:${DISTRO}
5151 extends: .build_script
5252
53 Debug GCC:
54 stage: canary
55 variables:
56 CC: "gcc"
57 CXX: "g++"
58 CMAKE_BUILD_TYPE: "Debug"
59 CLANG_FORMAT: "yes"
60 extends: .build
61
62 None GCC:
63 variables:
64 CC: "gcc"
65 CXX: "g++"
66 CMAKE_BUILD_TYPE: ""
67 extends: .build
68
69 None Clang:
70 variables:
71 CC: "clang"
72 CXX: "clang++"
73 CMAKE_BUILD_TYPE: ""
74 extends: .build
75
76 Debug Clang:
77 variables:
78 CC: "clang"
79 CXX: "clang++"
80 CMAKE_BUILD_TYPE: "Debug"
81 extends: .build
82
83 Release GCC:
84 variables:
85 CC: "gcc"
86 CXX: "g++"
87 CMAKE_BUILD_TYPE: "Release"
88 extends: .build
89
90 Release Clang:
91 variables:
92 CC: "clang"
93 CXX: "clang++"
94 CMAKE_BUILD_TYPE: "Release"
95 extends: .build
96
97 Debug GCC Ubuntu:
98 variables:
99 CC: "gcc"
100 CXX: "g++"
101 CMAKE_BUILD_TYPE: "Debug"
102 DISTRO: "ubuntu"
103 extends: .build
104
105 Debug Clang Ubuntu:
106 variables:
107 CC: "clang"
108 CXX: "clang++"
109 CMAKE_BUILD_TYPE: "Debug"
110 DISTRO: "ubuntu"
111 extends: .build
112
113 Release GCC Ubuntu:
114 variables:
115 CC: "gcc"
116 CXX: "g++"
117 CMAKE_BUILD_TYPE: "Release"
118 DISTRO: "ubuntu"
119 extends: .build
120
121 Release Clang Ubuntu:
122 variables:
123 CC: "clang"
124 CXX: "clang++"
125 CMAKE_BUILD_TYPE: "Release"
126 DISTRO: "ubuntu"
127 extends: .build
128
129 Debug GCC Rawhide:
130 variables:
131 CC: "gcc"
132 CXX: "g++"
133 CMAKE_BUILD_TYPE: "Debug"
134 DISTRO: "fedora_rawhide"
135 extends: .build
136 allow_failure: true
137
138 Debug Clang Rawhide:
139 variables:
140 CC: "clang"
141 CXX: "clang++"
142 CMAKE_BUILD_TYPE: "Debug"
143 DISTRO: "fedora_rawhide"
144 extends: .build
145 allow_failure: true
146
147 Release GCC Rawhide:
148 variables:
149 CC: "gcc"
150 CXX: "g++"
151 CMAKE_BUILD_TYPE: "Release"
152 DISTRO: "fedora_rawhide"
153 extends: .build
154 allow_failure: true
155
156 Release Clang Rawhide:
157 variables:
158 CC: "clang"
159 CXX: "clang++"
160 CMAKE_BUILD_TYPE: "Release"
161 DISTRO: "fedora_rawhide"
162 extends: .build
163 allow_failure: true
164
165 Release GCC Module:
166 variables:
167 CC: "gcc"
168 CXX: "g++"
169 CMAKE_BUILD_TYPE: "Release"
170 MODULE_BUILD: "yes"
171 extends: .build
172
17353 Debug GPU Ubuntu:
17454 variables:
17555 CC: "gcc"
17656 CXX: "g++"
17757 CMAKE_BUILD_TYPE: "Debug"
17858 USE_CUDA: "yes"
179 WITH_MKL: "no"
18059 DISABLE_MKL: "yes"
181 NO_INSTALL: "yes"
18260 before_script:
18361 - source /opt/gromacs-2019/bin/GMXRC.bash
18462 extends: .build_script
+0
-136
.travis.yml less more
0 # the original source of this file can be found in votca/votca repository
1 # add changes there!
2 # To update:
3 # wget -O .travis.yml https://raw.githubusercontent.com/votca/votca/master/.travis.yml
4 language: cpp
5
6 sudo: required
7
8 services:
9 - docker
10
11 git:
12 quiet: true
13
14 stages:
15 - canary
16 - test
17 - deploy
18
19 jobs:
20 include:
21 - stage: canary
22 env: ENV=3
23 - stage: deploy
24 if: repo = votca/votca AND type != pull_request
25 env: ENV=1
26
27 env:
28 matrix:
29 - ENV=1
30 - ENV=2
31 - ENV=3
32 - ENV=4
33 - ENV=5
34 - ENV=6
35 - ENV=7
36 - ENV=8
37 - ENV=9
38 - ENV=10
39 - ENV=11
40 - ENV=12
41 - ENV=13
42 - ENV=14
43 - ENV=15
44 - ENV=16
45 - ENV=17
46 - ENV=18
47 - ENV=19
48 - ENV=20
49
50 before_script:
51 - git checkout -b current_commit
52 - cd ../../
53 - if [[ ${TRAVIS_REPO_SLUG} = */votca ]]; then
54 if [[ ${TRAVIS_BRANCH} = next ]]; then
55 git -C ${TRAVIS_REPO_SLUG} submodule foreach git checkout master;
56 git -C ${TRAVIS_REPO_SLUG} submodule foreach git pull;
57 fi;
58 cp -vr ${TRAVIS_REPO_SLUG}/docker ${HOME};
59 mv -v ${TRAVIS_REPO_SLUG} $HOME/docker;
60 else
61 git clone -q --recursive https://github.com/votca/votca.git $HOME/docker/votca;
62 if [[ ${TRAVIS_BRANCH} != master ]]; then
63 git -C ${HOME}/docker/votca checkout -b ${TRAVIS_BRANCH} ${TRAVIS_TAG:-origin/${TRAVIS_BRANCH}} && git -C ${HOME}/docker/votca submodule update --recursive --init;
64 fi;
65 git -C ${HOME}/docker/votca/${TRAVIS_REPO_SLUG#*/} fetch ${PWD}/${TRAVIS_REPO_SLUG} current_commit;
66 git -C ${HOME}/docker/votca/${TRAVIS_REPO_SLUG#*/} checkout -f FETCH_HEAD;
67 cp -vr ${HOME}/docker/votca/docker/* ${HOME}/docker;
68 if [[ -d ${TRAVIS_REPO_SLUG}/docker ]]; then cp -vr ${TRAVIS_REPO_SLUG}/docker/* ${HOME}/docker; fi;
69 fi
70 - source ${HOME}/docker/set_env.sh
71 - test -n "${SKIP}" || cp -r $HOME/.ccache ${HOME}/docker/ccache
72 - sed -i "1s/latest/${DISTRO:-latest}/" ${HOME}/docker/Dockerfile
73 - if [[ ! ${SKIP} ]]; then
74 travis_retry timeout 540 docker pull $(sed -n '1s/FROM //p' ${HOME}/docker/Dockerfile) | cat;
75 fi
76
77 script:
78 - if [[ ! ${SKIP} ]]; then
79 travis_retry docker build "${docker_opts[@]}"
80 ${TRAVIS_TAG:+-t votca/votca:${TRAVIS_TAG}}
81 -t votca/votca:latest -t votca/votca:${TRAVIS_BRANCH} ${HOME}/docker/ &&
82 rm -rf $HOME/.ccache &&
83 CON=$(docker run -d votca/votca:${TRAVIS_BRANCH} /bin/bash) &&
84 docker cp ${CON}:/home/votca/.ccache ${HOME}/;
85 fi
86
87 after_success:
88 - if [[ ${TRAVIS_REPO_SLUG} != votca/votca || ${TRAVIS_BUILD_STAGE_NAME} != "Deploy" || ${SKIP} ]]; then travis_terminate 0; fi
89 - shopt -s extglob && [[ ${TRAVIS_BRANCH} = @(master|stable|v1.*) ]] && DEPLOY=yes
90 - if [[ ${TRAVIS_BRANCH} = master ]]; then DOCKER_TAG=latest; else DOCKER_TAG="${TRAVIS_BRANCH}"; fi
91 - if [[ ${DOCKER_USERNAME} && ${DOCKER_PASSWORD} && ${TRAVIS_PULL_REQUEST} == false && ${DEPLOY} ]]; then
92 docker login -u="$DOCKER_USERNAME" -p="$DOCKER_PASSWORD";
93 docker push "${TRAVIS_REPO_SLUG}:${DOCKER_TAG}";
94 fi
95 - if true; then
96 git clone --depth=1 https://github.com/votca/doxygen.git "$HOME/devdoc";
97 cd $HOME/devdoc;
98 rm -f *;
99 git checkout -- CNAME;
100 docker cp ${CON}:/home/votca/votca/build/share/doc/html . ;
101 mv html/* .; rmdir html;
102 docker cp ${CON}:/home/votca/votca/build/csg-manual/manual.pdf . ;
103 docker cp ${CON}:/home/votca/votca/build/xtp/manual/xtp-manual.pdf . ;
104 git add --all .;
105 if [[ ${TRAVIS_BRANCH} = master && ${encrypted_7abbb71c3ba6_key} && ${encrypted_7abbb71c3ba6_iv} && ${TRAVIS_PULL_REQUEST} == false ]]; then
106 git config --global user.name "Automatic Deployment (Travis CI)";
107 git config --global user.email "votca-commits@googlegroups.com";
108 git commit -m "Documentation Update";
109 openssl aes-256-cbc -K $encrypted_7abbb71c3ba6_key -iv $encrypted_7abbb71c3ba6_iv -in keys/deploy3.enc -out ~/.ssh/id_rsa -d;
110 chmod 600 ~/.ssh/id_rsa;
111 git push git@github.com:votca/doxygen.git gh-pages;
112 else
113 git status;
114 git diff --cached --no-color | head -c 1k;
115 fi;
116 fi
117
118 branches:
119 only:
120 - master
121 - development
122 - stable
123 - next
124 - /^v\d+\.\d+(\.\d+|_rc\d+)?$/
125
126 cache:
127 - ccache
128
129 compiler:
130 - gcc
131 - clang
132
133 notifications:
134 email:
135 - votca-commits@googlegroups.com
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CHANGELOG.md less more
00 For more detailed information about the changes see the history of the
11 [repository](https://github.com/votca/xtp/commits/master).
2
3 ## Version 1.6.2 (released 22.08.20)
4 * move CI to GitHub Actions (#512, #514, #516, #519)
5 * add more checks to the dft_parse_part (#521)
6 * make unit tests work in parallel (#530)
27
38 ## Version 1.6.1 (released 21.06.20)
49 * fix warnings on Ubuntu 20.04 (#438, #460)
+1
-1
CMakeLists.txt less more
11 project(votca-xtp)
22
33
4 set(PROJECT_VERSION "1.6.1")
4 set(PROJECT_VERSION "1.6.2")
55 set(PROJECT_CONTACT "bugs@votca.org")
66 string(REGEX REPLACE "^[1-9]+\\.([1-9]+).*$" "\\1" SOVERSION "${PROJECT_VERSION}")
77 if (NOT ${SOVERSION} MATCHES "[1-9]+")
+1
-1
src/libxtp/jobcalculators/eqm.cc less more
227227 WriteLoggerToFile(work_dir + "/dft.log", dft_logger);
228228 }
229229
230 if (!_do_dft_parse) {
230 if (!_do_dft_parse && (_do_gwbse || _do_esp)) {
231231 // load the DFT data from serialized orbitals object
232232 std::string ORB_FILE =
233233 eqm_work_dir + "/molecules/" + frame_dir + "/" + orb_file;
+2
-1
src/tests/CMakeLists.txt less more
8787 add_executable(unit_${PROG} ${PROG}.cc)
8888 target_link_libraries(unit_${PROG} votca_xtp Boost::unit_test_framework)
8989 target_compile_definitions(unit_${PROG} PRIVATE BOOST_TEST_DYN_LINK)
90 add_test(unit_${PROG} unit_${PROG})
90 file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/Run_unit_${PROG})
91 add_test(NAME unit_${PROG} COMMAND $<TARGET_FILE:unit_${PROG}> WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/Run_unit_${PROG})
9192 # run tests for xtp (for coverage) as well
9293 set_tests_properties(unit_${PROG} PROPERTIES LABELS "xtp;votca;unit")
9394 endforeach(PROG)
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tutorials/.github/workflows/continuous-integration-workflow.yml less more
0 name: CI
1 on:
2 pull_request:
3 branches:
4 - master
5 - stable
6
7 jobs:
8 CI:
9 continue-on-error: ${{ matrix.distro == 'ubuntu_devel' || matrix.distro == 'fedora_rawhide' || matrix.continue-on-error == true }}
10 strategy:
11 matrix:
12 distro: [latest, fedora_rawhide, opensuse, ubuntu, ubuntu_devel, ubuntu_rolling, ubuntu_18.04]
13 toolchain: [gnu]
14 cmake_build_type: [Release]
15 minimal: [false]
16 own_gmx: [false]
17 module_build: [false]
18 coverage: [false]
19 no_regression_testing: [true]
20 include:
21 - distro: latest
22 toolchain: gnu
23 cmake_build_type: Release
24 module_build: true
25 no_regression_testing: true
26 runs-on: ubuntu-latest
27 container: votca/buildenv:${{ matrix.distro }}
28 steps:
29 - uses: actions/checkout@v2.2.0
30 with:
31 fetch-depth: 0
32 - name: Run Votca Setup
33 id: setup
34 uses: votca/actions/setup@master
35 with:
36 distro: ${{ matrix.distro }}
37 toolchain: ${{ matrix.toolchain }}
38 minimal: ${{ matrix.minimal == true }}
39 module: ${{ matrix.module_build == true }}
40 own_gmx: ${{ matrix.own_gmx == true }}
41 regression_testing: ${{ matrix.no_regression_testing != true }}
42 coverage: ${{ matrix.coverage }}
43 cmake_build_type: ${{ matrix.cmake_build_type }}
44 ctest_args: ${{ matrix.ctest_args }}
45 cmake_args: ${{ matrix.cmake_args }}
46 - uses: actions/cache@v2
47 with:
48 path: ~/.ccache
49 key: ${{ steps.setup.outputs.cache_key }}
50 restore-keys: ${{ steps.setup.outputs.cache_restore_key }}
51 - name: CMake
52 run: mkdir builddir && cd builddir && cmake ${{ steps.setup.outputs.cmake_args }} ../votca
53 - name: Build
54 run: |
55 ccache -z
56 cmake --build builddir -- -j ${{ steps.setup.outputs.jobs }}
57 ccache -s
58 - name: Tests
59 run: ctest --output-on-failure ${{ steps.setup.outputs.ctest_args }}
60 working-directory: builddir
61 - name: Build Sphinx
62 if: ${{ steps.setup.outputs.build_sphinx == 'true' }}
63 run: cmake --build builddir --target doc
64 - name: Test DESTDIR Install
65 if: ${{ ! matrix.module_build }}
66 run: DESTDIR=${PWD}/install cmake --build builddir --target install && rm -rf ${PWD}/install/usr && rmdir ${PWD}/install
67 - name: Install
68 run: sudo cmake --build builddir --target install
69 - name: Check for untracked files
70 run: git status --porcelain && git status --porcelain | sed Q1
71 working-directory: votca/${{ steps.setup.outputs.module }}
+37
-0
tutorials/.github/workflows/create-pr.yml less more
0 name: Create PR
1 on:
2 push:
3 branches:
4 - stable
5
6 jobs:
7 PR:
8 name: Create
9 if: github.repository_owner == 'votca'
10 runs-on: ubuntu-latest
11 steps:
12 - name: Checkout code
13 uses: actions/checkout@master
14 with:
15 ref: ${{ github.event.ref }}
16 fetch-depth: 0
17 token: ${{ secrets.VOTCA_BOT_TOKEN }}
18 - name: Try to merge master branch
19 run: |
20 git config --global user.name "Votca Bot"
21 git config --global user.email "github@votca.org"
22 git checkout -b stable_fixes
23 git merge origin/master || true
24 git push origin stable_fixes
25 - name: Create Pull Request
26 uses: actions/github-script@0.3.0
27 with:
28 github-token: ${{ secrets.VOTCA_BOT_TOKEN }}
29 script: |
30 github.pulls.create({
31 owner: 'votca',
32 repo: 'xtp-tutorials',
33 title: 'Fixes from stable',
34 head: 'stable_fixes',
35 base: 'master'
36 })
+20
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tutorials/.github/workflows/create-release.yml less more
0 name: Make Release
1 on:
2 push:
3 tags:
4 - 'v[1-9]*'
5
6 jobs:
7 release:
8 name: Make Release
9 if: github.repository_owner == 'votca'
10 runs-on: ubuntu-latest
11 steps:
12 - name: Create Release
13 uses: actions/create-release@v1
14 env:
15 GITHUB_TOKEN: ${{ secrets.VOTCA_BOT_TOKEN }}
16 with:
17 tag_name: ${{ github.ref }}
18 release_name: ${{ github.ref }}
19 prerelease: ${{ contains(github.ref, 'rc') }}
+18
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tutorials/.github/workflows/forward-to-votca.yml less more
0 name: Forward
1 on:
2 push:
3 branches:
4 - master
5 - stable
6
7 jobs:
8 VOTCA:
9 if: github.repository_owner == 'votca'
10 runs-on: ubuntu-latest
11 steps:
12 - name: Update submodule
13 uses: votca/actions/forward@master
14 with:
15 module: ${{ github.repository }}
16 token: ${{ secrets.VOTCA_BOT_TOKEN }}
17
+5
-127
tutorials/.gitlab-ci.yml less more
00 stages:
1 - canary
21 - build
32
43 .build_script:
3433 - pushd build
3534 - cmake .. -DCMAKE_VERBOSE_MAKEFILE=ON -DENABLE_TESTING=ON -DBUILD_XTP=ON -DENABLE_WERROR=ON
3635 -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
36 ${CMAKE_GENERATOR:+-G${CMAKE_GENERATOR}}
3737 -DMODULE_BUILD=${MODULE_BUILD} ${MODULE_BUILD:+-DCMAKE_INSTALL_PREFIX=/home/votca/votca.install}
38 -DWITH_MKL=${WITH_MKL} -DCMAKE_DISABLE_FIND_PACKAGE_MKL=${DISABLE_MKL}
38 -DCMAKE_DISABLE_FIND_PACKAGE_MKL=${DISABLE_MKL}
3939 -DUSE_CUDA=${USE_CUDA}
40 - cmake --build . -- -j2
40 - cmake --build . --parallel 2
4141 - ctest --output-on-failure
42 - test -z "${MODULE_BUILD}" && DESTDIR=${PWD}/install cmake --build . --target install && rm -rf ${PWD}/install/usr && rmdir ${PWD}/install
43 - sudo cmake --build . --target install
42 - test -z "${MODULE_BUILD}" && DESTDIR=${PWD}/install cmake --install . && rm -rf ${PWD}/install/usr && rmdir ${PWD}/install
43 - sudo cmake --install .
4444 - if [[ ${CLANG_FORMAT} ]]; then cmake --build . --target format && git -C ${CI_PROJECT_DIR}/votca/${CI_PROJECT_NAME} diff --exit-code; fi
4545 - ccache -s
4646
5050 image: votca/buildenv:${DISTRO}
5151 extends: .build_script
5252
53 Debug GCC:
54 stage: canary
55 variables:
56 CC: "gcc"
57 CXX: "g++"
58 CMAKE_BUILD_TYPE: "Debug"
59 CLANG_FORMAT: "yes"
60 extends: .build
61
62 None GCC:
63 variables:
64 CC: "gcc"
65 CXX: "g++"
66 CMAKE_BUILD_TYPE: ""
67 extends: .build
68
69 None Clang:
70 variables:
71 CC: "clang"
72 CXX: "clang++"
73 CMAKE_BUILD_TYPE: ""
74 extends: .build
75
76 Debug Clang:
77 variables:
78 CC: "clang"
79 CXX: "clang++"
80 CMAKE_BUILD_TYPE: "Debug"
81 extends: .build
82
83 Release GCC:
84 variables:
85 CC: "gcc"
86 CXX: "g++"
87 CMAKE_BUILD_TYPE: "Release"
88 extends: .build
89
90 Release Clang:
91 variables:
92 CC: "clang"
93 CXX: "clang++"
94 CMAKE_BUILD_TYPE: "Release"
95 extends: .build
96
97 Debug GCC Ubuntu:
98 variables:
99 CC: "gcc"
100 CXX: "g++"
101 CMAKE_BUILD_TYPE: "Debug"
102 DISTRO: "ubuntu"
103 extends: .build
104
105 Debug Clang Ubuntu:
106 variables:
107 CC: "clang"
108 CXX: "clang++"
109 CMAKE_BUILD_TYPE: "Debug"
110 DISTRO: "ubuntu"
111 extends: .build
112
113 Release GCC Ubuntu:
114 variables:
115 CC: "gcc"
116 CXX: "g++"
117 CMAKE_BUILD_TYPE: "Release"
118 DISTRO: "ubuntu"
119 extends: .build
120
121 Release Clang Ubuntu:
122 variables:
123 CC: "clang"
124 CXX: "clang++"
125 CMAKE_BUILD_TYPE: "Release"
126 DISTRO: "ubuntu"
127 extends: .build
128
129 Debug GCC Rawhide:
130 variables:
131 CC: "gcc"
132 CXX: "g++"
133 CMAKE_BUILD_TYPE: "Debug"
134 DISTRO: "fedora_rawhide"
135 extends: .build
136 allow_failure: true
137
138 Debug Clang Rawhide:
139 variables:
140 CC: "clang"
141 CXX: "clang++"
142 CMAKE_BUILD_TYPE: "Debug"
143 DISTRO: "fedora_rawhide"
144 extends: .build
145 allow_failure: true
146
147 Release GCC Rawhide:
148 variables:
149 CC: "gcc"
150 CXX: "g++"
151 CMAKE_BUILD_TYPE: "Release"
152 DISTRO: "fedora_rawhide"
153 extends: .build
154 allow_failure: true
155
156 Release Clang Rawhide:
157 variables:
158 CC: "clang"
159 CXX: "clang++"
160 CMAKE_BUILD_TYPE: "Release"
161 DISTRO: "fedora_rawhide"
162 extends: .build
163 allow_failure: true
164
165 Release GCC Module:
166 variables:
167 CC: "gcc"
168 CXX: "g++"
169 CMAKE_BUILD_TYPE: "Release"
170 MODULE_BUILD: "yes"
171 extends: .build
172
17353 Debug GPU Ubuntu:
17454 variables:
17555 CC: "gcc"
17656 CXX: "g++"
17757 CMAKE_BUILD_TYPE: "Debug"
17858 USE_CUDA: "yes"
179 WITH_MKL: "no"
18059 DISABLE_MKL: "yes"
181 NO_INSTALL: "yes"
18260 before_script:
18361 - source /opt/gromacs-2019/bin/GMXRC.bash
18462 extends: .build_script
+0
-136
tutorials/.travis.yml less more
0 # the original source of this file can be found in votca/votca repository
1 # add changes there!
2 # To update:
3 # wget -O .travis.yml https://raw.githubusercontent.com/votca/votca/master/.travis.yml
4 language: cpp
5
6 sudo: required
7
8 services:
9 - docker
10
11 git:
12 quiet: true
13
14 stages:
15 - canary
16 - test
17 - deploy
18
19 jobs:
20 include:
21 - stage: canary
22 env: ENV=3
23 - stage: deploy
24 if: repo = votca/votca AND type != pull_request
25 env: ENV=1
26
27 env:
28 matrix:
29 - ENV=1
30 - ENV=2
31 - ENV=3
32 - ENV=4
33 - ENV=5
34 - ENV=6
35 - ENV=7
36 - ENV=8
37 - ENV=9
38 - ENV=10
39 - ENV=11
40 - ENV=12
41 - ENV=13
42 - ENV=14
43 - ENV=15
44 - ENV=16
45 - ENV=17
46 - ENV=18
47 - ENV=19
48 - ENV=20
49
50 before_script:
51 - git checkout -b current_commit
52 - cd ../../
53 - if [[ ${TRAVIS_REPO_SLUG} = */votca ]]; then
54 if [[ ${TRAVIS_BRANCH} = next ]]; then
55 git -C ${TRAVIS_REPO_SLUG} submodule foreach git checkout master;
56 git -C ${TRAVIS_REPO_SLUG} submodule foreach git pull;
57 fi;
58 cp -vr ${TRAVIS_REPO_SLUG}/docker ${HOME};
59 mv -v ${TRAVIS_REPO_SLUG} $HOME/docker;
60 else
61 git clone -q --recursive https://github.com/votca/votca.git $HOME/docker/votca;
62 if [[ ${TRAVIS_BRANCH} != master ]]; then
63 git -C ${HOME}/docker/votca checkout -b ${TRAVIS_BRANCH} ${TRAVIS_TAG:-origin/${TRAVIS_BRANCH}} && git -C ${HOME}/docker/votca submodule update --recursive --init;
64 fi;
65 git -C ${HOME}/docker/votca/${TRAVIS_REPO_SLUG#*/} fetch ${PWD}/${TRAVIS_REPO_SLUG} current_commit;
66 git -C ${HOME}/docker/votca/${TRAVIS_REPO_SLUG#*/} checkout -f FETCH_HEAD;
67 cp -vr ${HOME}/docker/votca/docker/* ${HOME}/docker;
68 if [[ -d ${TRAVIS_REPO_SLUG}/docker ]]; then cp -vr ${TRAVIS_REPO_SLUG}/docker/* ${HOME}/docker; fi;
69 fi
70 - source ${HOME}/docker/set_env.sh
71 - test -n "${SKIP}" || cp -r $HOME/.ccache ${HOME}/docker/ccache
72 - sed -i "1s/latest/${DISTRO:-latest}/" ${HOME}/docker/Dockerfile
73 - if [[ ! ${SKIP} ]]; then
74 travis_retry timeout 540 docker pull $(sed -n '1s/FROM //p' ${HOME}/docker/Dockerfile) | cat;
75 fi
76
77 script:
78 - if [[ ! ${SKIP} ]]; then
79 travis_retry docker build "${docker_opts[@]}"
80 ${TRAVIS_TAG:+-t votca/votca:${TRAVIS_TAG}}
81 -t votca/votca:latest -t votca/votca:${TRAVIS_BRANCH} ${HOME}/docker/ &&
82 rm -rf $HOME/.ccache &&
83 CON=$(docker run -d votca/votca:${TRAVIS_BRANCH} /bin/bash) &&
84 docker cp ${CON}:/home/votca/.ccache ${HOME}/;
85 fi
86
87 after_success:
88 - if [[ ${TRAVIS_REPO_SLUG} != votca/votca || ${TRAVIS_BUILD_STAGE_NAME} != "Deploy" || ${SKIP} ]]; then travis_terminate 0; fi
89 - shopt -s extglob && [[ ${TRAVIS_BRANCH} = @(master|stable|v1.*) ]] && DEPLOY=yes
90 - if [[ ${TRAVIS_BRANCH} = master ]]; then DOCKER_TAG=latest; else DOCKER_TAG="${TRAVIS_BRANCH}"; fi
91 - if [[ ${DOCKER_USERNAME} && ${DOCKER_PASSWORD} && ${TRAVIS_PULL_REQUEST} == false && ${DEPLOY} ]]; then
92 docker login -u="$DOCKER_USERNAME" -p="$DOCKER_PASSWORD";
93 docker push "${TRAVIS_REPO_SLUG}:${DOCKER_TAG}";
94 fi
95 - if true; then
96 git clone --depth=1 https://github.com/votca/doxygen.git "$HOME/devdoc";
97 cd $HOME/devdoc;
98 rm -f *;
99 git checkout -- CNAME;
100 docker cp ${CON}:/home/votca/votca/build/share/doc/html . ;
101 mv html/* .; rmdir html;
102 docker cp ${CON}:/home/votca/votca/build/csg-manual/manual.pdf . ;
103 docker cp ${CON}:/home/votca/votca/build/xtp/manual/xtp-manual.pdf . ;
104 git add --all .;
105 if [[ ${TRAVIS_BRANCH} = master && ${encrypted_7abbb71c3ba6_key} && ${encrypted_7abbb71c3ba6_iv} && ${TRAVIS_PULL_REQUEST} == false ]]; then
106 git config --global user.name "Automatic Deployment (Travis CI)";
107 git config --global user.email "votca-commits@googlegroups.com";
108 git commit -m "Documentation Update";
109 openssl aes-256-cbc -K $encrypted_7abbb71c3ba6_key -iv $encrypted_7abbb71c3ba6_iv -in keys/deploy3.enc -out ~/.ssh/id_rsa -d;
110 chmod 600 ~/.ssh/id_rsa;
111 git push git@github.com:votca/doxygen.git gh-pages;
112 else
113 git status;
114 git diff --cached --no-color | head -c 1k;
115 fi;
116 fi
117
118 branches:
119 only:
120 - master
121 - development
122 - stable
123 - next
124 - /^v\d+\.\d+(\.\d+|_rc\d+)?$/
125
126 cache:
127 - ccache
128
129 compiler:
130 - gcc
131 - clang
132
133 notifications:
134 email:
135 - votca-commits@googlegroups.com
+1
-1
tutorials/CMakeLists.txt less more
11
22 project(xtp-tutorials)
33
4 set(PROJECT_VERSION "1.6.1")
4 set(PROJECT_VERSION "1.6.2")
55
66 set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules)
77 include(GNUInstallDirs)