Update CI, fix compatibility with OpenMM 7.7 (#249)

* 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

* Update src/openmmio.py

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

* 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

* Unpin OpenMM

* Allow old pip

* Fix syntax in version constraints

* Install dataclasses backport for networkx

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

.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 +1,11 @@
-name: test
+name: forcebalance-test
 channels:
   - conda-forge
-  - omnia
-  - ambermd
+  - bioconda
 dependencies:
     # Base depends
   - python
   - pip
-
     # Testing
   - pytest
   - pytest-cov
@@ -22,9 +20,7 @@ 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

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())