Update examples dependencies

.github/workflows/examples.yml

@@ -18,51 +18,28 @@ defaults:
 jobs:
   test:
     if: (github.event_name == 'schedule' && github.repository == 'openforcefield/openff-toolkit') || (github.event_name != 'schedule')
-    name: ${{ matrix.os }}, Python ${{ matrix.python-version }}, RDKit=${{ matrix.rdkit }}, OpenEye=${{ matrix.openeye }}, NAGL=${{ matrix.nagl }}
+    name: ${{ matrix.os }}, Python ${{ matrix.python-version }}, OpenEye=${{ matrix.openeye }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
         python-version: [ "3.12"]
-        rdkit: [true, false]
         openeye: [true, false]
-        nagl: [true, false]
-        exclude:
-          - rdkit: false
-            openeye: false
-          - rdkit: true
-            openeye: true
-          - rdkit: false
-            nagl: true
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
       PACKAGE: openff
-      PYTEST_ARGS: -r fE -v -x --tb=short -nauto --durations=10
+      PYTEST_ARGS: -r fE -v -x --tb=auto -nauto --durations=10
       NB_ARGS: --nbval-lax --dist loadscope --ignore=examples/deprecated
 
     steps:
       - uses: actions/checkout@v7
 
-      - 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 ${{ env.ENVFILE }}
+      - name: Set up conda environment
         uses: mamba-org/setup-micromamba@v3
         with:
-          environment-file: devtools/conda-envs/${{env.ENVFILE}}-examples.yaml
+          environment-file: devtools/conda-envs/examples.yaml
           create-args: >-
             python=${{ matrix.python-version }}
 
@@ -71,38 +48,12 @@ jobs:
           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
-        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
-
-      - name: Check uninstalled toolkits
-        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
+      - name: Install OpenEye Toolkits
+        if: ${{ matrix.openeye == 'true' }}
+        run: micromamba install -c openeye openeye-toolkits -y
 
       - name: Environment Information
         run: |
@@ -112,28 +63,8 @@ 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/"
-          fi
-
           python -m pytest $PYTEST_ARGS $NB_ARGS examples

devtools/conda-envs/openeye-examples.yaml → devtools/conda-envs/examples.yaml

@@ -1,6 +1,5 @@
-name: openeye-examples
+name: openff-toolkit-examples
 channels:
-  - openeye
   - conda-forge
 dependencies:
     # Base depends
@@ -12,31 +11,32 @@ dependencies:
   # https://github.com/openforcefield/openff-toolkit/issues/2150
   - xmltodict <=1.0.2
   - python-constraint
-  - openmm >=7.6
-  - openff-forcefields >=2023.11
+  - openmm
+  - openff-forcefields >=2025
   - openff-amber-ff-ports >=0.0.3
   - openff-units
   - openff-utilities >=0.1.5
   - openff-interchange-base >=0.5
-  - openff-nagl-base >=0.4.0
-  - openff-nagl-models >=0.3.0
+  - openff-nagl-base >=0.5.2
+  - openff-nagl-models >=2025
   - typing_extensions
   - nglview
     # Toolkit-specific
-  - openeye-toolkits
+  - rdkit >=2024
     # Test-only/optional/dev/typing/examples
-  - pytest =8
+  - pytest
   - pytest-xdist
   - pytest-rerunfailures
+  - pytest-timeout
   - pyyaml
   - toml
   - bson
   - msgpack-python
   - qcelemental
   - qcportal >=0.50
   - qcengine
-  - mdtraj
   - nbval
+  - mdtraj
   - pdbfixer
-  - openmmforcefields >=0.11.2
-  - gromacs >=2023.3
+  - gromacs >=2026
+  - pyedr