Merge branch 'main' into fix/system_template_generator

openmm · Jul 19, 2023 · 0724acf · 0724acf
2 parents c198793 + 8660a1a
commit 0724acf
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Showing 8 changed files with 387 additions and 272 deletions.
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -20,16 +20,15 @@ concurrency:
 
 jobs:
   test:
-    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, Latest openff-toolkit ${{ matrix.latest-openff-toolkit }}
+    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.8", "3.9", "3.10"]
-        latest-openff-toolkit: [true, false]
+        python-version: ["3.9", "3.10"]  # Add 3.11 in with AmberTools 23
         exclude:
           - python-version: "3.10"
             os: macos-latest
@@ -38,10 +37,10 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Setup Conda Environment
-      uses: mamba-org/provision-with-micromamba@main
+      uses: mamba-org/setup-micromamba@v1
       with:
         environment-file: devtools/conda-envs/test_env.yaml
-        extra-specs: |
+        create-args: >-
           python=${{ matrix.python-version }}
 
     - name: License OpenEye
@@ -52,16 +51,6 @@ jobs:
       env:
         SECRET_OE_LICENSE: ${{ secrets.OE_LICENSE }}
 
-    - name: "Install openff-toolkit >= 0.11 API changes"
-      if: ${{ matrix.latest-openff-toolkit == true }}
-      run: |
-        micromamba update -y -c conda-forge "openff-toolkit >=0.11.3"
-
-    - name: "Install openff-toolkit <  0.11 API changes"
-      if: ${{ matrix.latest-openff-toolkit == false }}
-      run: |
-        micromamba install -y -c conda-forge "openff-toolkit==0.10.6" "openff-toolkit-base==0.10.6"
-
     - name: Install Package
       run: |
         pip list
@@ -77,10 +66,11 @@ jobs:
 
     - name: Test Installed Package
       run: |
-        pytest -v -x --log-cli-level $LOGLEVEL $COV_ARGS --durations=20 \
+        pytest -v --log-cli-level $LOGLEVEL $COV_ARGS --durations=20 \
           openmmforcefields/tests/test_amber_import.py \
           openmmforcefields/tests/test_template_generators.py \
-          openmmforcefields/tests/test_system_generator.py
+          openmmforcefields/tests/test_system_generator.py \
+          -k "not TestEspalomaTemplateGenerator"
       env:
         COV_ARGS: --cov=openmmforcefields --cov-config=setup.cfg --cov-append --cov-report=xml
         LOGLEVEL: "INFO"
@@ -106,7 +96,6 @@ jobs:
       working-directory: ./charmm
 
     - name: Run docstrings
-      if: ${{ matrix.latest-openff-toolkit == true }}
       continue-on-error: True
       run: |
         pytest --doctest-modules openmmforcefields --ignore=openmmforcefields/tests

diff --git a/.github/workflows/espaloma_ci.yaml b/.github/workflows/espaloma_ci.yaml
@@ -0,0 +1,66 @@
+name: EspalomaCI
+
+on:
+  push:
+    branches:
+      - "main"
+  pull_request:
+    branches:
+      - "main"
+  schedule:
+    - cron: "0 0 * * *"
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, Latest openff-toolkit ${{ matrix.latest-openff-toolkit }}
+    runs-on: ${{ matrix.os }}
+    env:
+      OE_LICENSE: ${{ github.workspace }}/oe_license.txt
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.9", "3.10"]  # Add 3.11 in with AmberTools 23
+        exclude:
+          - python-version: "3.10"
+            os: macos-latest
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Setup Conda Environment
+      uses: mamba-org/setup-micromamba@v1
+      with:
+        environment-file: devtools/conda-envs/test_env.yaml
+        create-args: >-
+          python=${{ matrix.python-version }}
+
+    - name: Install Package
+      run: |
+        pip list
+        micromamba list
+        micromamba remove --force openmmforcefields
+        python -m pip install .
+
+    - name: Conda Environment Information
+      run: |
+        micromamba info
+        micromamba list
+        python -c "from openmmforcefields import __version__, __file__; print(__version__, __file__)"
+
+    - name: Test Installed Package
+      run: |
+        pytest -v --log-cli-level $LOGLEVEL $COV_ARGS --durations=20 \
+          -m "espaloma" openmmforcefields/tests --runespaloma
+      env:
+        COV_ARGS: --cov=openmmforcefields --cov-config=setup.cfg --cov-append --cov-report=xml
+        LOGLEVEL: "INFO"
+        KMP_DUPLICATE_LIB_OK: "True"
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -14,17 +14,17 @@ dependencies:
     # Testing
   - pytest
   - pytest-cov
-  - codecov
+  - pytest-xdist
+  - pytest-randomly
 
     # Requirements for converted force field installer
   - openmm >=7.6.0
 
-  - openff-units >=0.1.8
-  - openff-amber-ff-ports >=0.0.3
+  - openff-toolkit >=0.11
 
     # Requirements for conversion tools
   - pyyaml
-  - ambertools >=18.0 # contains sufficiently recent ParmEd
+  - ambertools =22
   - lxml
   - networkx
 
@@ -41,6 +41,6 @@ dependencies:
     # TODO: Rework this once espaloma is on conda-forge
     #
   - pytorch >=1.8.0
-  - dgl
+  - dgl <1
   - qcportal >=0.15.0
   - espaloma
diff --git a/openmmforcefields/ffxml/amber/opc3.xml b/openmmforcefields/ffxml/amber/opc3.xml
@@ -17,7 +17,7 @@
   </Residue>
  </Residues>
  <HarmonicBondForce>
-  <Bond class1="OW" class2="HW" length="0.978882" k="502416.0"/>
+  <Bond class1="OW" class2="HW" length="0.0978882" k="502416.0"/>
  </HarmonicBondForce>
  <HarmonicAngleForce>
   <!-- angle = arccos(1 - (1.598507**2 / (2*0.978882**2))) -->

diff --git a/openmmforcefields/generators/template_generators.py b/openmmforcefields/generators/template_generators.py
@@ -1280,7 +1280,7 @@ def __init__(self, molecules=None, cache=None, forcefield=None, **kwargs):
             self._smirnoff_forcefield = openff.toolkit.typing.engines.smirnoff.ForceField(filename)
         except Exception as e:
             _logger.error(e)
-            raise ValueError(f"Can't find specified SMIRNOFF force field ({forcefield}) in install paths")
+            raise ValueError(f"Can't find specified SMIRNOFF force field ({forcefield}) in install paths") from e
 
         # Delete constraints, if present
         if 'Constraints' in self._smirnoff_forcefield._parameter_handlers:

diff --git a/openmmforcefields/tests/conftest.py b/openmmforcefields/tests/conftest.py
@@ -0,0 +1,21 @@
+"""Default configuration and objects for tests"""
+
+import pytest
+
+def pytest_addoption(parser):
+    parser.addoption(
+        "--runespaloma", action="store_true", default=False, help="run espaloma tests"
+    )
+
+
+def pytest_configure(config):
+    config.addinivalue_line("markers", "espaloma: mark test as slow to run")
+
+
+def pytest_collection_modifyitems(config, items):
+    skip_slow = pytest.mark.skip(reason="need --runespaloma option to run")
+
+    if not config.getoption("--runespaloma"):
+        for item in items:
+            if "espaloma" in item.keywords:
+                item.add_marker(skip_slow)