Require RDKit

.github/workflows/CI.yml

@@ -18,22 +18,17 @@ defaults:
 jobs:
   test:
     if: (github.event_name == 'schedule' && github.repository == 'openforcefield/openff-toolkit') || (github.event_name != 'schedule')
-    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, RDKit=${{ matrix.rdkit }}, OpenEye=${{ matrix.openeye }}, NAGL=${{ matrix.nagl }}
+    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, OpenEye=${{ matrix.openeye }}, NAGL=${{ matrix.nagl }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
         python-version: ["3.12", "3.13"]
-        rdkit: [true, false]
         openeye: [true, false]
         nagl: [true, false]
         exclude:
-          - rdkit: false
-            openeye: false
           - openeye: true
             python-version: "3.13"
-          - rdkit: false
-            nagl: true
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
@@ -47,24 +42,17 @@ jobs:
 
       - name: Set environment variables
         run: |
-          if [[ ${{ matrix.openeye }} == true && ${{ matrix.rdkit }} == true ]]; then
+          if [[ ${{ matrix.openeye }} == true ]]; then
               echo "ENVFILE=test_env" >> $GITHUB_ENV
-              echo "JOBNAME=RDKit and OpenEye" >> $GITHUB_ENV
-              echo "TOOLKIT_CHECKS=RDKIT OPENEYE" >> $GITHUB_ENV
-              echo "PACKAGES_TO_REMOVE=" >> $GITHUB_ENV
-          fi
-
-          if [[ ${{ matrix.openeye }} == true && ${{ matrix.rdkit }} == false ]]; then
-              echo "ENVFILE=openeye" >> $GITHUB_ENV
-              echo "JOBNAME=OpenEye" >> $GITHUB_ENV
+              echo "JOBNAME=With OpenEye" >> $GITHUB_ENV
               echo "TOOLKIT_CHECKS=OPENEYE" >> $GITHUB_ENV
-              echo "PACKAGES_TO_REMOVE=ambertools rdkit" >> $GITHUB_ENV
+              echo "PACKAGES_TO_REMOVE=" >> $GITHUB_ENV
           fi
 
-          if [[ ${{ matrix.openeye }} == false && ${{ matrix.rdkit }} == true ]]; then
-              echo "ENVFILE=rdkit" >> $GITHUB_ENV
-              echo "JOBNAME=RDKit" >> $GITHUB_ENV
-              echo "TOOLKIT_CHECKS=RDKIT" >> $GITHUB_ENV
+          if [[ ${{ matrix.openeye }} == false ]]; then
+              echo "ENVFILE=no-openeye" >> $GITHUB_ENV
+              echo "JOBNAME=No OpenEye" >> $GITHUB_ENV
+              echo "TOOLKIT_CHECKS=" >> $GITHUB_ENV
               echo "PACKAGES_TO_REMOVE=openeye-toolkits" >> $GITHUB_ENV
           fi
 
@@ -127,12 +115,7 @@ jobs:
           pip list
 
       - name: Run mypy
-        # When possible re-enable this with OE+RDK=True, but for now rdkit builds often have bugs
-        # in stubs and there are other subtleties (in the source code and builds) that reduce the number
-        # of available builds.
-        # See ex https://github.com/rdkit/rdkit/issues/7221
-        # and https://github.com/rdkit/rdkit/issues/7583
-        if: ${{ matrix.rdkit == false && matrix.openeye == true }}
+        if: ${{ matrix.openeye == true }}
         run: mypy -p "openff.toolkit"
 
       - name: Run unit tests
@@ -146,15 +129,15 @@ jobs:
           python -m pytest -x --durations=20 $PYTEST_ARGS $COV openff/toolkit/_tests
 
       - name: Run code snippets in docs
-        if: ${{ matrix.rdkit == true && matrix.openeye == true && matrix.nagl == true }}
+        if: ${{ matrix.openeye == true && matrix.nagl == true }}
         run: pytest -v --no-cov --doctest-glob="docs/*.rst" --doctest-glob="docs/*.md" docs/
 
       - name: Run notebooks in docs
-        if: ${{ matrix.rdkit == true && matrix.openeye == true }}
+        if: ${{ matrix.openeye == true }}
         run: python -m pytest -v --durations=10 --no-cov --nbval-lax docs/
 
       - name: Run examples in docstrings
-        if: ${{ matrix.rdkit == true && matrix.openeye == true && matrix.nagl == true }}
+        if: ${{ matrix.openeye == true && matrix.nagl == true }}
         run: |
           pytest openff \
             -v -x -n logical --no-cov --doctest-modules \
@@ -171,5 +154,5 @@ jobs:
           fail_ci_if_error: true
 
       - name: Check links
-        if: ${{ matrix.rdkit == true && matrix.openeye == true }}
+        if: ${{ matrix.openeye == true }}
         run: pytest -r fE --tb=short openff/toolkit/_tests/test_links.py

devtools/conda-envs/rdkit-examples.yaml → devtools/conda-envs/no-openeye-examples.yaml

@@ -1,4 +1,4 @@
-name: rdkit-examples
+name: no-openeye-examples
 channels:
   - conda-forge
 dependencies:
@@ -27,7 +27,7 @@ dependencies:
     # Toolkit-specific
   - ambertools
     # https://github.com/rdkit/rdkit/issues/7221 and https://github.com/rdkit/rdkit/issues/7583
-  - rdkit =2024
+  - rdkit =2024  # Bump me!
     # Test-only/optional/dev/typing/examples
   - pytest =8
   - pytest-xdist

devtools/conda-envs/rdkit.yaml → devtools/conda-envs/no-openeye.yaml

@@ -1,4 +1,4 @@
-name: openff-toolkit-test-rdkit
+name: openff-toolkit-test-no-openeye
 channels:
   - conda-forge
 dependencies:

devtools/conda-envs/test_env.yaml

@@ -48,3 +48,5 @@ dependencies:
   - nbval
   # No idea why this is necessary, see https://github.com/openforcefield/openff-toolkit/pull/1821
   - nomkl
+  - mypy =1.18
+  - typing_extensions