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Fix vsite fits #475

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Fix vsite fits

Fix vsite fits #475

Workflow file for this run

.github/workflows/ci.yml at 0c637fd
name: ci
on:
push:
branches:
- "master"
pull_request:
branches:
- "master"
defaults:
run:
shell: bash -l {0}
jobs:
test:
name: Test on ${{ matrix.os }} (py=${{ matrix.python-version }}, gmx=${{ matrix.gmx-version }})
runs-on: ${{ matrix.os }}
timeout-minutes: 120
strategy:
fail-fast: false
matrix:
os:
- macOS-latest
- ubuntu-latest
python-version:
- "3.9"
- "3.10"
- "3.11"
- "3.12"
# pymbar 3 does not support Python 3.13
# - "3.13"
gmx-version:
- "5"
- "2019"
- "2024"
- "2025"
exclude:
# a 2022 build doesn't seem to exist for mac
- os: macOS-latest
gmx-version: "2022"
include:
# just to test warnings
- os: ubuntu-latest
python-version: "3.11"
gmx-version: "4"
- os: ubuntu-latest
python-version: "3.11"
gmx-version: "2022"
- os: ubuntu-latest
python-version: "3.11"
gmx-version: "2023"
- os: ubuntu-latest
python-version: "3.11"
gmx-version: "2024.3"
env:
CI_OS: ${{ matrix.os }}
PYVER: ${{ matrix.python-version }}
GMXVER: ${{ matrix.gmx-version }}
PACKAGE: forcebalance
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Set up conda environment with gromacs
if: (matrix.gmx-version != '5' && matrix.gmx-version != '4' && matrix.gmx-version != '2022' && matrix.gmx-version != '2023') && (matrix.python-version == '3.9' || matrix.python-version == '3.10')
uses: mamba-org/setup-micromamba@v1
with:
# Use a reduced legacy environment for Python 3.9/3.10 builds.
environment-file: devtools/conda-envs/test_env_py39.yaml
create-args: >- # beware the >- instead of |, we don't split on newlines but on spaces
python=${{ matrix.python-version }}
- name: Set up conda environment for Python 3.11 or higher
uses: mamba-org/setup-micromamba@v1
if: (matrix.python-version != '3.9' && matrix.python-version != '3.10') && (matrix.gmx-version != '5' && matrix.gmx-version != '4' && matrix.gmx-version != '2022' && matrix.gmx-version != '2023')
with:
environment-file: devtools/conda-envs/test_env.yaml
create-args: >- # beware the >- instead of |, we don't split on newlines but on spaces
python=${{ matrix.python-version }} gromacs=${{ matrix.gmx-version }}.*=nompi_dblprec*
- name: Set up conda environment without gromacs
if: matrix.gmx-version == '5' || matrix.gmx-version == '4'
uses: mamba-org/setup-micromamba@v1
with:
# Use the legacy env for Python 3.9/3.10, full env otherwise.
environment-file: ${{ (matrix.python-version == '3.9' || matrix.python-version == '3.10') && 'devtools/conda-envs/test_env_py39.yaml' || 'devtools/conda-envs/test_env.yaml' }}
create-args: >- # beware the >- instead of |, we don't split on newlines but on spaces
python=${{ matrix.python-version }}
- name: Set up conda environment with single-precision gromacs (rejected versions)
if: matrix.gmx-version == '2022' || matrix.gmx-version == '2023'
uses: mamba-org/setup-micromamba@v1
with:
# dblprec conda-forge builds don't exist for 2022/2023; single-precision is sufficient
# for the version-rejection test.
# Use the legacy env for Python 3.9/3.10, full env otherwise.
environment-file: ${{ (matrix.python-version == '3.9' || matrix.python-version == '3.10') && 'devtools/conda-envs/test_env_py39.yaml' || 'devtools/conda-envs/test_env.yaml' }}
create-args: >-
python=${{ matrix.python-version }} gromacs=${{ matrix.gmx-version }}
- name: Pin setuptools for Python <= 3.10
if: matrix.python-version == '3.9' || matrix.python-version == '3.10'
shell: bash -l {0}
run: pip install "setuptools<82"
- name: Additional info about the build
shell: bash
run: |
uname -a
df -h
ulimit -a
- name: Environment Information
run: |
micromamba info
micromamba list
# Need to replace ndcctools with this block
# - name: Install Work Queue
# run: |
# wget https://raw.githubusercontent.com/leeping/forcebalance/master/tools/install-cctools.sh
# bash install-cctools.sh
# echo "Checking for Work Queue import; if successful, no message will be printed"
# python -c "import work_queue"
# export PATH="$GITHUB_WORKSPACE/opt/cctools/current/bin:$PATH"
- name: Install Tinker
run: |
if [[ "$CI_OS" == 'ubuntu-latest' ]]; then
wget https://dasher.wustl.edu/tinker/downloads/bin-linux-8.8.3.tar.gz -O tinker.tar.gz
fi
if [[ "$CI_OS" == 'macOS-latest' ]]; then
wget https://dasher.wustl.edu/tinker/downloads/bin-macos-8.8.3.tar.gz -O tinker.tar.gz
fi
tar xvzf tinker.tar.gz &> untar.log
mkdir -p $GITHUB_WORKSPACE/opt/tinker/8.8.3
if [[ "$CI_OS" == 'ubuntu-latest' ]]; then
mv bin-linux $GITHUB_WORKSPACE/opt/tinker/8.8.3/bin
fi
if [[ "$CI_OS" == 'macOS-latest' ]]; then
mv bin-macos $GITHUB_WORKSPACE/opt/tinker/8.8.3/bin
fi
echo "$GITHUB_WORKSPACE/opt/tinker/8.8.3/bin" >> $GITHUB_PATH
- name: Install Gromacs
if: matrix.gmx-version == '5'
run: |
wget http://ftp.gromacs.org/pub/gromacs/gromacs-5.1.5.tar.gz
tar xvzf gromacs-5.1.5.tar.gz
cd gromacs-5.1.5
cp -r cmake cmake_s
cd cmake
cmake -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/opt/gromacs/5.1.5 -DGMX_DOUBLE=ON -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_POLICY_VERSION_MINIMUM=3.5 -DGMX_USE_RDTSCP=OFF -DGMX_SIMD=None ..
# replace http:/w with https://w
sed -i.bak 's|http:/w|https://w|g' CMakeCache.txt && rm -f CMakeCache.txt.bak
make -j 8 && make install
cd ../cmake_s
cmake -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/opt/gromacs/5.1.5 -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_POLICY_VERSION_MINIMUM=3.5 -DGMX_USE_RDTSCP=OFF -DGMX_SIMD=None ..
sed -i.bak 's|http:/w|https://w|g' CMakeCache.txt && rm -f CMakeCache.txt.bak
make -j 8 && make install
cd ..
. $GITHUB_WORKSPACE/opt/gromacs/5.1.5/bin/GMXRC.bash
echo "$GITHUB_WORKSPACE/opt/gromacs/5.1.5/bin" >> $GITHUB_PATH
which gmx
which gmx_d
gmx help
gmx dump -h
- name: Install Gromacs
if: matrix.gmx-version == '4'
run: |
wget http://ftp.gromacs.org/pub/gromacs/gromacs-4.6.7.tar.gz
tar xvzf gromacs-4.6.7.tar.gz
cd gromacs-4.6.7
cp -r cmake cmake_s
cd cmake
cmake -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/opt/gromacs/4.6.7 -DGMX_DOUBLE=ON -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_POLICY_VERSION_MINIMUM=3.5 -DGMX_USE_RDTSCP=OFF -DGMX_SIMD=None ..
# replace http:/w with https://w
sed -i.bak 's|http:/w|https://w|g' CMakeCache.txt && rm -f CMakeCache.txt.bak
make -j 8 && make install
cd ../cmake_s
cmake -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/opt/gromacs/4.6.7 -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_POLICY_VERSION_MINIMUM=3.5 -DGMX_USE_RDTSCP=OFF -DGMX_SIMD=None ..
sed -i.bak 's|http:/w|https://w|g' CMakeCache.txt && rm -f CMakeCache.txt.bak
make -j 8 && make install
cd ..
. $GITHUB_WORKSPACE/opt/gromacs/4.6.7/bin/GMXRC.bash
echo "$GITHUB_WORKSPACE/opt/gromacs/4.6.7/bin" >> $GITHUB_PATH
which mdrun
- name: Extract data archives
run: |
cd studies/001_water_tutorial
tar xvjf targets.tar.bz2
cd ../../
- name: Install package
run: |
python -m pip install --no-deps .
python -c "import forcebalance; print(forcebalance.__version__)"
- name: Run version-rejection test
if: matrix.gmx-version == '4' || matrix.gmx-version == '2022' || matrix.gmx-version == '2023' || matrix.gmx-version == '2024.3'
run: |
pytest -v --run-gmx-rejected -k test_gmx_version_rejected src/tests/test_gmxio.py
- name: Run tests
if: matrix.gmx-version != '4' && matrix.gmx-version != '2022' && matrix.gmx-version != '2023' && matrix.gmx-version != '2024.3'
run: |
pytest -v --cov=forcebalance --cov-config=setup.cfg --durations=0 --cov-report=xml --timeout=2000 src/tests/
- name: Run water study
if: matrix.gmx-version != '4' && matrix.gmx-version != '2022' && matrix.gmx-version != '2023' && matrix.gmx-version != '2024.3'
run: |
cd studies/001_water_tutorial
tar xvjf targets.tar.bz2
ForceBalance very_simple.in
cd ../../
- name: Codecov
if: matrix.gmx-version != '4' && matrix.gmx-version != '2022' && matrix.gmx-version != '2023' && matrix.gmx-version != '2024.3'
uses: codecov/codecov-action@v3
with:
file: ./coverage.xml
fail_ci_if_error: false