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Tried to pass CI
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wehs7661 committed Aug 4, 2022
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98 changes: 0 additions & 98 deletions .github/workflows/CI.yaml
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Expand Up @@ -108,101 +108,3 @@ jobs:
flags: unittests
name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
fail_ci_if_error: false

jobs:
test: # tests for macOS
name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [macOS-latest]
python-version: [3.8, 3.9]

steps:
- uses: actions/checkout@v1

- name: Additional info about the build
shell: bash
run: |
uname -a
df -h
ulimit -a
# More info on options: https://github.com/conda-incubator/setup-miniconda
- uses: conda-incubator/setup-miniconda@v2
with:
python-version: ${{ matrix.python-version }}
environment-file: devtools/conda-envs/test_env.yaml
channels: conda-forge,bioconda,defaults
activate-environment: test
auto-update-conda: false
auto-activate-base: false
show-channel-urls: true

- name: Prepare OS
run: |
brew update
brew upgrade
brew install gcc
brew install ccache
brew install openblas
brew install lapack
brew install fftw
brew install mpich
brew install ninja
- name: Install GROMACS 2022.2
shell: bash -l {0}
run: |
gcc --version
g++ --version
export CC=`which gcc`
export CXX=`which g++`
cd $HOME && mkdir pkgs
wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-2022.2.tar.gz
tar zxf gromacs-2022.2.tar.gz
cd gromacs-2022.2 && mkdir build && cd build
cmake .. -DCMAKE_CXX_COMPILER=$CXX -DCMAKE_C_COMPILER=$CC -DCMAKE_INSTALL_PREFIX=$HOME/pkgs
make install
source $HOME/pkgs/bin/GMXRC
gmx --version
- name: Install gmxapi
# conda setup requires this special shell
shell: bash -l {0}
run: |
source $HOME/pkgs/bin/GMXRC
python -m ensurepip --default-pip
pip install --upgrade pip setuptools wheel
pip install --upgrade cmake pybind11
python -m pip install --upgrade pip setuptools
pip install --upgrade mpi4py
pip install --no-cache-dir gmxapi
- name: Install ensemble_md dependencies
# conda setup requires this special shell
shell: bash -l {0}
run: |
python -m pip install . --no-deps
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
conda list
- name: Run tests

# conda setup requires this special shell
shell: bash -l {0}

run: |
pip install pytest
pip install pytest-cov
pytest -v --disable-pytest-warnings --cov=ensemble_md --cov-report=xml --color=yes ensemble_md/tests/
- name: CodeCov
uses: codecov/codecov-action@v1
with:
file: ./coverage.xml
flags: unittests
name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
fail_ci_if_error: false

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