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Only test against OpenFF Toolkit 0.10.3 and on Python 3.7+
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Tinker with CI

Update Python versions

Try `--use-pep517`

Pin to Openmm 7.6

Debug: Turn off switching function in ALL cases

Attempt to isolate CustomNonbondedForce.setUseSwitchingFunction

Isolate mmopts

Debug

Focus tests more on old failures

Drop tinker stuff

Fix typo

Remove some debug code

Revert debug state

Fix syntax, add back Python 3.6

Allow a version of the toolkit compatible with Python 3.6

Versions 0.10.1 and 0.10.2 are broken but not yet off of conda-forge, so
the pinning here MUST ensure that old builds are 0.10.0 or OLDER

Update src/openmmio.py

Co-authored-by: Jeff Wagner <[email protected]>

Unpin OpenMM

Allow old pip

Fix syntax in version constraints

Install dataclasses backport for networkx

Install OpenFF Evaluator and Recharge in CI

Install `openff-evaluator-base` to avoid installing Yank

Install (unlicensed) OpenEye Toolkits
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mattwthompson committed Mar 8, 2022
1 parent a8659b2 commit 770ba0c
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Showing 3 changed files with 42 additions and 37 deletions.
50 changes: 22 additions & 28 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,10 @@ on:
branches:
- "master"

defaults:
run:
shell: bash -l {0}

jobs:
test:
runs-on: ${{ matrix.os }}
Expand All @@ -18,9 +22,11 @@ jobs:
- macOS-latest
- ubuntu-latest
python-version:
- 3.6
- 3.7
- 3.8
- "3.6"
- "3.7"
- "3.8"
- "3.9"

env:
CI_OS: ${{ matrix.os }}
PYVER: ${{ matrix.python-version }}
Expand All @@ -30,11 +36,12 @@ jobs:
- name: Checkout
uses: actions/checkout@v2

- uses: conda-incubator/[email protected]
- name: Install dependencies with Minicondna
uses: conda-incubator/[email protected]
with:
python-version: ${{ matrix.python-version }}
activate-environment: test
channel-priority: true
mamba-version: "*"
activate-environment: forcebalance-test
environment-file: devtools/conda-envs/test_env.yaml
auto-activate-base: false

Expand All @@ -46,33 +53,19 @@ jobs:
ulimit -a
- name: Environment Information
shell: bash -l {0}
run: |
conda info --all
conda list
- name: Install OpenFF stack and OpenEye on Python 3.6+
if: ${{ matrix.python-version != 2.7}}
shell: bash -l {0}
run: |
conda install openff-toolkit -c conda-forge -y
# Need to replace ndcctools with this block
# - name: Install Work Queue
# shell: bash -l {0}
# run: |
# wget https://raw.githubusercontent.com/leeping/forcebalance/master/tools/install-cctools.sh
# bash install-cctools.sh
# echo "Checking for Work Queue import; if successful, no message will be printed"
# python -c "import work_queue"
# export PATH="$GITHUB_WORKSPACE/opt/cctools/current/bin:$PATH"

- name: Install GROMACS
shell: bash -l {0}
run: |
# This will not install double precision, needs to be replaced with a fresh build
conda install gromacs=2019.1 -c bioconda -c conda-forge -y
- name: Install Tinker
run: |
if [[ "$CI_OS" == 'ubuntu-latest' ]]; then
Expand Down Expand Up @@ -101,26 +94,27 @@ jobs:
tar xvjf targets.tar.bz2
cd ../../
- name: Install backport of dataclasses
if: ${{ matrix.python-version == 3.6}}
run: |
pip install dataclasses
- name: Install package
shell: bash -l {0}
run: |
# python setup.py install
python -m pip install --no-deps .
python -c "import forcebalance; print(forcebalance.__version__)"
- name: Run tests
run: |
pytest -v --cov=forcebalance --cov-config=setup.cfg --durations=0 --cov-report=xml
- name: Run water study
shell: bash -l {0}
run: |
cd studies/001_water_tutorial
tar xvjf targets.tar.bz2
ForceBalance very_simple.in
cd ../../
- name: Run tests
shell: bash -l {0}
run: |
pytest -v --cov=forcebalance --cov-config=setup.cfg --durations=0 --cov-report=xml
- name: Codecov
uses: codecov/[email protected]
with:
Expand Down
16 changes: 8 additions & 8 deletions devtools/conda-envs/test_env.yaml
Original file line number Diff line number Diff line change
@@ -1,13 +1,12 @@
name: test
name: forcebalance-test
channels:
- conda-forge
- omnia
- ambermd
- bioconda
- openeye
dependencies:
# Base depends
- python
- pip

# Testing
- pytest
- pytest-cov
Expand All @@ -22,9 +21,10 @@ dependencies:
- pymbar
- openmm
- ambertools
# The following two are not compatible with python 2.7 and 3.5, so they are conditionally installed in .travis.yml
#- openforcefield
#- openeye-toolkits

- ndcctools
- geometric
- gromacs =2019.1
- openff-toolkit >=0.10.3|<=0.10.0
- openff-evaluator-base
- openff-recharge
- openeye-toolkits
13 changes: 12 additions & 1 deletion src/openmmio.py
Original file line number Diff line number Diff line change
Expand Up @@ -980,7 +980,18 @@ def update_simulation(self, **kwargs):
#printcool_dictionary(self.mmopts, title="Creating/updating simulation in engine %s with system settings:" % (self.name))
# for b in list(self.mod.topology.bonds()):
# print b[0].index, b[1].index
self.system = self.forcefield.createSystem(self.mod.topology, **self.mmopts)
try:
self.system = self.forcefield.createSystem(self.mod.topology, **self.mmopts)
# This try/except block catches a failure case introduced by the release of openmm 7.7
# where a ValueError would be raised if createSystem was given an unused kwarg.
# Now, when that error occurs, we remove the unused kwargs from mmopts.
# More info at https://github.com/leeping/forcebalance/issues/246
except ValueError as e:
if 'useSwitchingFunction' not in str(e):
raise e
self.mmopts.pop('useSwitchingFunction')
self.mmopts.pop('switchingDistance')
self.system = self.forcefield.createSystem(self.mod.topology, **self.mmopts)
self.vsinfo = PrepareVirtualSites(self.system)
self.nbcharges = np.zeros(self.system.getNumParticles())

Expand Down

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