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Prepare v1.0.1 (#357)
* Fix README * Fix zenodo contributor list * Add Singularity instruction to README * Copy Python frontend module to build dir always Fixes #317 * Fix NMR * Add NMR note in manual * Add doc strings for H_... interation operators * Add warning for complex NMR tensor eigenvalues * Fix typo * Check for NaN in NMR tensor * Handle missing MW guess orbitals, fixes #338 (#341) * Simplify GHA workflow * Create mrchem-gha.yml * Move code coverage job to GHA * Move Minazo linting to GHA * Install clang-format with APT * Clean up * Say bye to Travis * Danger lints * Simple * Remove Travis CI badge * Update DANGER_GITHUB_API_TOKEN * Scramble formatting to check Minazo works * Appease Minazo, the mighty bot * Fix runtime failure while reading basis set for SAD guess (#344) * Debug issue with the conda package * Perfect trimming of string * Token * Try with GITHUB_TOKEN * Refactor Danger action * Try to fix Minazo * Try to heal Minazo, part N * Update Gemfile.lock * Fix precision issue with chk initial guess (#347) * Change fetch-depth (#348) * Change fetch-depth See here: danger/danger#1103 (comment) * Check if GITHUB_TOKEN is necessary * Giggles * Which one do I need? * Tokens * Stupid tokens * Token in the wild * Don't know * Try something else * Remove conditional * back to pull_request * Make it stop * Revert * Clean up actions (#350) * Clean up actions * Fix YAML syntax * Fix MPI deadlock for shared-mem with bank * Update token in Minazo workflow * Use v1 of checkout action * Limit Eigen to single thread (#352) Threading lead to highly unpredictable results for large matrix-matrix multiplications. * Change clone command to https version (#353) * Change clone command to https version * Change clone command to https version * Misc fixes for v1.0.1 (#355) * Minor fixes in printed output - Print orbital norms regardless of MPI ownership. - Use proper absolute threshold for printed status of energy convergergence. * Fix README error in Singluarity command * Remove non-existing git version from tools/betzy.env * Force grid refinement on HydrogenFunction, closes #354 * Decommission Minazo (#356) * Bump version 1.0.1 Co-authored-by: Roberto Di Remigio <[email protected]> Co-authored-by: Roberto Di Remigio <[email protected]> Co-authored-by: Luca Frediani <[email protected]>
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‎.ci/Dangerfile

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‎.ci/Gemfile

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‎.ci/Gemfile.lock

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‎.github/mrchem-codecov.yml

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name: mrchem-codecov
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channels:
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- conda-forge
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dependencies:
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- cmake
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- cxx-compiler
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- eigen
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- lcov
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- mrcpp
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- ninja
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- nlohmann_json
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- xcfun

‎.github/mrchem-gha.yml

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name: mrchem-gha
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channels:
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- conda-forge
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dependencies:
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- cmake
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- cxx-compiler
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- eigen
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- mrcpp
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- ninja
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- nlohmann_json
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- xcfun

‎.github/workflows/build-test.yml

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steps:
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- uses: actions/checkout@v2
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- name: Set up Python 3.6
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uses: actions/setup-python@v2
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- name: Cache conda
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uses: actions/cache@v1
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env:
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CACHE_NUMBER: 0 # Increase this value to reset cache if .github/mrchem-gha.yml has not changed
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with:
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python-version: 3.6
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path: ~/conda_pkgs_dir
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key:
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${{ matrix.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('.github/mrchem-gha.yml') }}
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- uses: conda-incubator/setup-miniconda@v2
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with:
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auto-update-conda: true
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auto-activate-base: false
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activate-environment: mrchem-gha
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environment-file: .github/mrchem-gha.yml
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channel-priority: true
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python-version: 3.6
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use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
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- name: Install dependencies
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run: |
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sudo chown -R $USER $CONDA
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$CONDA/bin/conda create --name mrchem python=3.6 eigen mrcpp xcfun nlohmann_json ninja -c conda-forge
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- name: Configure
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shell: bash
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shell: bash -l {0}
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run: |
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source $CONDA/bin/activate mrchem
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python ./setup --type=$BUILD_TYPE --omp --arch-flags=false --generator=Ninja --prefix=$GITHUB_WORKSPACE/Software/MRChem build --cmake-options="-DCMAKE_PREFIX_PATH=$CONDA_PREFIX -DPYTHON_EXECUTABLE=$CONDA_PREFIX/bin/python"
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python ./setup --type=$BUILD_TYPE --omp --arch-flags=false --generator=Ninja --prefix=$GITHUB_WORKSPACE/Software/MRChem build
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- name: Build
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shell: bash
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shell: bash -l {0}
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run: |
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source $CONDA/bin/activate mrchem
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cmake --build build --config $BUILD_TYPE --target install -- -v -d stats
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- name: Test
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shell: bash
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shell: bash -l {0}
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run: |
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cd build
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source $CONDA/bin/activate mrchem
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ctest -C $BUILD_TYPE --output-on-failure --verbose

‎.github/workflows/code-coverage.yml

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name: Compute code coverage for MRChem
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on:
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push:
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branches:
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- master
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pull_request:
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branches:
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- master
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env:
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BUILD_TYPE: Debug
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Set up environment
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uses: conda-incubator/setup-miniconda@v2
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with:
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auto-update-conda: true
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auto-activate-base: false
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activate-environment: mrchem-codecov
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environment-file: .github/mrchem-codecov.yml
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channel-priority: true
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python-version: 3.6
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- name: Configure
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shell: bash -l {0}
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run: |
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python ./setup --type=$BUILD_TYPE --arch-flags=false --coverage --generator=Ninja --prefix=$GITHUB_WORKSPACE/Software/MRChem build
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- name: Build
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shell: bash -l {0}
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run: |
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cmake --build build --config $BUILD_TYPE --target install -- -v -d stats
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- name: Test MRChem and generate coverage report
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shell: bash -l {0}
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run: |
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cd build
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ctest -C $BUILD_TYPE --output-on-failure --verbose
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lcov --version
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lcov --directory . --capture --output-file coverage.info
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lcov --remove coverage.info '/usr/*' --output-file coverage.info
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lcov --remove coverage.info 'external/*' --output-file coverage.info
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lcov --remove coverage.info 'test/*' --output-file coverage.info
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lcov --list coverage.info
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v1

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