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Modified config.yml for CircleCI to troubleshoot
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wehs7661 committed May 28, 2024
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73 changes: 1 addition & 72 deletions .circleci/config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -8,75 +8,4 @@ jobs:
environment:
PYTHON_VERSION: "3.8"
steps:
- checkout

- run:
name: Show the system information and resource limits
command: |
uname -a
df -h
ulimit -a
- run:
name: Installing dependencies for GROMACS
command: |
sudo apt-get update
sudo apt install build-essential
sudo apt-get install ccache libblas-dev libfftw3-dev liblapack-dev libmpich-dev libxml2-dev mpich ninja-build
wget -O - https://apt.kitware.com/keys/kitware-archive-latest.asc 2>/dev/null | gpg --dearmor - | sudo tee /etc/apt/trusted.gpg.d/kitware.gpg >/dev/null
sudo apt-add-repository 'deb https://apt.kitware.com/ubuntu/ focal main' -y
sudo apt install cmake && cmake --version
- run:
name: Install the latest version of GROMACS
command: |
gcc --version
g++ --version
export CC=`which gcc`
export CXX=`which g++`
cd $HOME && mkdir pkgs
git clone https://gitlab.com/gromacs/gromacs.git
cd gromacs && mkdir build && cd build
cmake .. -DCMAKE_CXX_COMPILER=$CXX -DCMAKE_C_COMPILER=$CC -DCMAKE_INSTALL_PREFIX=$HOME/pkgs
make install
source $HOME/pkgs/bin/GMXRC
gmx --version
- run:
name: Install the ensemble_md package
command: |
python3 -m pip install --upgrade pip
python3 -m pip install .
- run:
name: Run unit tests
command: |
source $HOME/pkgs/bin/GMXRC
pip3 install pytest
pip3 install pytest-mpi
pip3 install pytest-cov
coverage run -m pytest -vv --disable-pytest-warnings --color=yes ensemble_md/tests
mpirun -np 4 coverage run --rcfile setup.cfg -m pytest ensemble_md/tests/test_mpi_func.py --with-mpi -vv --disable-pytest-warnings --color=yes # this will generate multiple .coverage* files that can be combined
coverage combine # This will combine multiple .coverage* files into a single .coverage file that will be uploaded and reported.
# Below are some old commands:
# pytest -vv --disable-pytest-warnings --cov=ensemble_md --cov-report=xml --color=yes ensemble_md/tests/
# COVERAGE_FILE=.coverage_1 pytest -vv --disable-pytest-warnings --cov=ensemble_md --cov-report=xml --color=yes ensemble_md/tests/
# COVERAGE_FILE=.coverage_2 mpirun -np 4 pytest -vv --disable-pytest-warnings --cov=ensemble_md --cov-report=xml --color=yes ensemble_md/tests/test_mpi_func.py --with-mpi
- run:
name: CodeCov
command: |
bash <(curl -s https://codecov.io/bash)
- store_test_results:
path: test-results

workflows:
continuous-integration:
jobs:
- test


- run: echo hello

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