Do not use AmberTools in examples

.github/workflows/examples.yml

@@ -25,16 +25,9 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-latest]
         python-version: [ "3.12"]
-        rdkit: [true, false]
+        rdkit: [true]
         openeye: [true, false]
-        nagl: [true, false]
-        exclude:
-          - rdkit: false
-            openeye: false
-          - rdkit: true
-            openeye: true
-          - rdkit: false
-            nagl: true
+        nagl: [true]
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
@@ -47,64 +40,35 @@ jobs:
         with:
           fetch-depth: 0
 
-      - name: Set environment variables
-        run: |
-          if [[ ${{ matrix.openeye }} == true && ${{ matrix.rdkit }} == false ]]; then
-              echo "ENVFILE=openeye" >> $GITHUB_ENV
-              echo "TOOLKIT_CHECKS=OPENEYE" >> $GITHUB_ENV
-              echo "PACKAGES_TO_REMOVE=ambertools rdkit" >> $GITHUB_ENV
-          fi
-
-          if [[ ${{ matrix.openeye }} == false && ${{ matrix.rdkit }} == true ]]; then
-              echo "ENVFILE=rdkit" >> $GITHUB_ENV
-              echo "TOOLKIT_CHECKS=RDKIT" >> $GITHUB_ENV
-              echo "PACKAGES_TO_REMOVE=openeye-toolkits" >> $GITHUB_ENV
-          fi
-
-      - name: Install conda environment with ${{ env.ENVFILE }}
+      - name: Install base conda environment
         uses: mamba-org/setup-micromamba@v3
         with:
-          environment-file: devtools/conda-envs/${{env.ENVFILE}}-examples.yaml
+          environment-file: devtools/conda-envs/base-examples.yaml
           create-args: >-
             python=${{ matrix.python-version }}
 
+      - name: Install OpenEye toolkits
+        if: ${{ matrix.openeye == true }}
+        run: micromamba install -c openeye "openeye-toolkits >=2024" -y
+
       - name: Make oe_license.txt file from GH org secret "OE_LICENSE"
+        if: ${{ matrix.openeye == true }}
         env:
           OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
         run: echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
 
-      - name: Optionally remove OpenFF NAGL
-        if: ${{ matrix.nagl == false }}
-        run: micromamba remove openff-nagl-base openff-nagl-models --force
-
       - name: Install package
         run: python -m pip install .
 
-      - name: Remove undesired toolkits
+      - name: Check OpenEye installed
+        if: ${{ matrix.openeye == true }}
         run: |
-          # If openmmforcefields is included in either environment file,
-          # remove RDKit and AmberTools brought in by it. Currently it's not included,
-          # so don't remove it.
-          if [ ! -z "${{ env.PACKAGES_TO_REMOVE }}" ]; then
-            for cpkg in ${{ env.PACKAGES_TO_REMOVE }}; do
-              if [[ $(micromamba list | grep $cpkg) ]]; then micromamba remove --force $cpkg --yes ; fi
-            done
-          fi
-
-      - name: Check installed toolkits
-        run: |
-          for tk in ${{ env.TOOLKIT_CHECKS }}; do
-            python -c "from openff.toolkit.utils.toolkits import ${tk}_AVAILABLE; assert ${tk}_AVAILABLE, '${tk} unavailable'"
-          done
+          python -c "from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE; assert OPENEYE_AVAILABLE, 'OpenEye unavailable'"
 
-      - name: Check uninstalled toolkits
+      - name: Check OpenEye NOT installed
+        if: ${{ matrix.openeye == false }}
         run: |
-          if [ ! -z "${{ env.PACKAGES_TO_REMOVE }}" ]; then
-            for tk in ${{ env.PACKAGES_TO_REMOVE }}; do
-              TK=$(echo ${tk%-*} | tr 'a-z' 'A-Z')
-              python -c "from openff.toolkit.utils.toolkits import ${TK}_AVAILABLE; assert not ${TK}_AVAILABLE, '${TK} available'"
-            done
-          fi
+          python -c "from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE; assert not OPENEYE_AVAILABLE, 'OpenEye available but shouldn\'t be'"
 
       - name: Environment Information
         run: |
@@ -114,25 +78,10 @@ jobs:
 
       - name: Run example scripts
         run: |
-          if [[ ${{ matrix.rdkit }} == false ]]; then
-            PYTEST_ARGS+=" --ignore=examples/check_dataset_parameter_coverage"
-            PYTEST_ARGS+=" --ignore=examples/QCArchive_interface"
-          fi
           pytest $PYTEST_ARGS openff/toolkit/_tests/test_examples.py
 
       - name: Run example notebooks
         run: |
-          if [[ ${{ matrix.rdkit }} == false ]]; then
-            NB_ARGS+=" --ignore=examples/QCArchive_interface"
-            NB_ARGS+=" --ignore=examples/visualization"
-            NB_ARGS+=" --ignore=examples/check_dataset_parameter_coverage"
-            NB_ARGS+=" --ignore=examples/conformer_energies"
-            NB_ARGS+=" --ignore=examples/using_smirnoff_in_amber_or_gromacs"
-            NB_ARGS+=" --ignore=examples/using_smirnoff_with_amber_protein_forcefield"
-            NB_ARGS+=" --ignore=examples/SMIRNOFF_simulation"
-            NB_ARGS+=" --ignore=examples/toolkit_showcase"
-          fi
-
           # GROMACS builds are not stable on macOS + GHA
           if [[ ${{ matrix.os }} == macos-latest ]]; then
             NB_ARGS+=" --ignore=examples/using_smirnoff_in_amber_or_gromacs/"

devtools/conda-envs/rdkit-examples.yaml → devtools/conda-envs/base-examples.yaml

@@ -1,4 +1,4 @@
-name: rdkit-examples
+name: base-examples
 channels:
   - conda-forge
 dependencies:
@@ -24,10 +24,8 @@ dependencies:
   - openff-nagl-models >=0.3.0
   - typing_extensions
   - nglview
-    # Toolkit-specific
-  - ambertools
     # https://github.com/rdkit/rdkit/issues/7221 and https://github.com/rdkit/rdkit/issues/7583
-  - rdkit =2024
+  - rdkit >=2024
     # Test-only/optional/dev/typing/examples
   - pytest =8
   - pytest-xdist
@@ -42,5 +40,5 @@ dependencies:
   - nbval
   - mdtraj
   - pdbfixer
-  - openmmforcefields >=0.11.2
+  # openmmforcefields >=0.15
   - gromacs >=2023.3

devtools/conda-envs/rdkit.yaml

@@ -21,8 +21,6 @@ dependencies:
   - openff-nagl-base >=0.4.0
   - openff-nagl-models >=0.3.0
   - typing_extensions
-    # Toolkit-specific
-  - ambertools >=22
     # https://github.com/rdkit/rdkit/issues/7221 and https://github.com/rdkit/rdkit/issues/7583
   - rdkit !=2024.03.6,!=2024.03.5
     # Test-only/optional/dev/typing

examples/SMIRNOFF_simulation/run_simulation.ipynb

@@ -114,7 +114,7 @@
     ")\n",
     "\n",
     "# Load the OpenFF \"Sage\" force field.\n",
-    "forcefield = ForceField(\"openff-2.2.0.offxml\")\n",
+    "forcefield = ForceField(\"openff-2.3.0.offxml\")\n",
     "\n",
     "# Parametrize the topology and create an Interchange object.\n",
     "interchange = forcefield.create_interchange(topology)"

examples/conformer_energies/conformer_energies.py

@@ -41,8 +41,8 @@ def compute_conformer_energies_from_file(filename):
         + f" ({molecule.name})"
     )
 
-    # Load the openff-2.2.1 force field appropriate for vacuum calculations (without constraints)
-    forcefield = ForceField("openff_unconstrained-2.2.1.offxml")
+    # Load the openff-2.3.0 force field appropriate for vacuum calculations (without constraints)
+    forcefield = ForceField("openff_unconstrained-2.3.0.offxml")
     # Create an Interchange object, which stores the result of parametrizing with this force field
     print(f"Parametrizing {molecule.name} (may take a moment to calculate charges)...")
     interchange = forcefield.create_interchange(molecule.to_topology())