Only test against OpenFF Toolkit 0.10.3 and on Python 3.7+

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

.github/workflows/ci.yml

@@ -8,6 +8,10 @@ on:
     branches:
       - "master"
 
+defaults:
+  run:
+    shell: bash -l {0}
+
 jobs:
   test:
     runs-on: ${{ matrix.os }}
@@ -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 }}
@@ -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
 
@@ -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
@@ -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:

devtools/conda-envs/test_env.yaml

@@ -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
@@ -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

src/openmmio.py

@@ -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())