Use Pixi to manage examples

.github/workflows/examples.yml

@@ -11,131 +11,53 @@ on:
     - cron: "0 4 * * *"
   workflow_dispatch:
 
-defaults:
-  run:
-    shell: bash -l {0}
-
 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: ${{ matrix.os }}, environment=${{ matrix.environment }}
     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
+        environment:
+          - examples-ambertools
+          - examples-openeye
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
-      PACKAGE: openff
-      PYTEST_ARGS: -r fE -v -x --tb=short -nauto --durations=10
-      NB_ARGS: --nbval-lax --dist loadscope --ignore=examples/deprecated
 
     steps:
       - uses: actions/checkout@v6
         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 ${{ env.ENVFILE }}
-        uses: mamba-org/setup-micromamba@v3
+      - name: Set up virtual environment
+        uses: prefix-dev/setup-pixi@v0.9.6
         with:
-          environment-file: devtools/conda-envs/${{env.ENVFILE}}-examples.yaml
-          create-args: >-
-            python=${{ matrix.python-version }}
+          pixi-version: v0.70.0
+          environments: ${{ matrix.environment }}
+          frozen: true
 
       - name: Make oe_license.txt file from GH org secret "OE_LICENSE"
+        if: contains(matrix.environment, 'openeye')
         env:
           OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
         run: echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
 
-      - name: Optionally remove OpenFF NAGL
-        if: ${{ matrix.nagl == false }}
-        run: micromamba remove openff-nagl-base openff-nagl-models --force
-
-      - name: Install package
-        run: python -m pip install .
-
-      - name: Remove undesired toolkits
-        run: |
-          # If openmmforcefields is included in either environment file,
-          # remove RDKit and AmberTools brought in by it. Currently it's not included,
-          # so don't remove it.
-          if [ ! -z "${{ 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
+      - name: Check OpenEye installed
+        if: contains(matrix.environment, 'openeye')
         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
+          pixi run -e examples-openeye python -c "from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE; assert OPENEYE_AVAILABLE, 'OpenEye unavailable'"
 
-      - name: Environment Information
+      - name: Check OpenEye NOT installed
+        if: ! contains(matrix.environment, 'openeye')
         run: |
-          micromamba info
-          micromamba list
-          pip list
+          pixi run -e examples-ambertools python -c "from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE; assert not OPENEYE_AVAILABLE, 'OpenEye available but shouldn\'t be'"
 
       - 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
+        run: pixi run -e ${{ matrix.environment }} run_scripts
 
       - 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
+        run: pixi run -e ${{ matrix.environment }} run_notebooks