From e94db439d35683c8ca772e6b15c242584f7a98e0 Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Thu, 14 May 2026 15:52:05 -0500
Subject: [PATCH 1/9] Debug RDKit-based examples workflow

---
 .github/workflows/examples.yml          |  6 ++----
 devtools/conda-envs/rdkit-examples.yaml | 17 ++++++++---------
 2 files changed, 10 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/examples.yml b/.github/workflows/examples.yml
index 0943458e7..125661dd5 100644
--- a/.github/workflows/examples.yml
+++ b/.github/workflows/examples.yml
@@ -21,18 +21,16 @@ jobs:
     name: ${{ matrix.os }}, Python ${{ matrix.python-version }}, RDKit=${{ matrix.rdkit }}, OpenEye=${{ matrix.openeye }}, NAGL=${{ matrix.nagl }}
     runs-on: ${{ matrix.os }}
     strategy:
-      fail-fast: false
+      fail-fast: true
       matrix:
         os: [ubuntu-latest, macos-latest]
         python-version: [ "3.12"]
         rdkit: [true, false]
-        openeye: [true, false]
+        openeye: [false]
         nagl: [true, false]
         exclude:
           - rdkit: false
             openeye: false
-          - rdkit: true
-            openeye: true
           - rdkit: false
             nagl: true
 
diff --git a/devtools/conda-envs/rdkit-examples.yaml b/devtools/conda-envs/rdkit-examples.yaml
index dbb60133e..6c583f6bf 100644
--- a/devtools/conda-envs/rdkit-examples.yaml
+++ b/devtools/conda-envs/rdkit-examples.yaml
@@ -6,30 +6,29 @@ dependencies:
   - python
   - versioningit
   - packaging
-  - numpy <2.3
+  - numpy
   - networkx
   - cachetools
   # https://github.com/openforcefield/openff-toolkit/issues/2150
   - xmltodict <=1.0.2
   - python-constraint
-  - openmm >=7.6
-  - openff-forcefields >=2023.11
+  - openmm >=8.4
+  - openff-forcefields
   - openff-amber-ff-ports >=0.0.3
   - openff-units
   - openff-utilities >=0.1.5
   - openff-interchange-base >=0.5
   # No idea why this is necessary, see https://github.com/openforcefield/openff-toolkit/pull/1821
   - nomkl
-  - openff-nagl-base >=0.4.0
-  - openff-nagl-models >=0.3.0
+  - openff-nagl-base >=0.5.5
+  - openff-nagl-models >=2025.09
   - typing_extensions
   - nglview
     # Toolkit-specific
-  - ambertools
-    # https://github.com/rdkit/rdkit/issues/7221 and https://github.com/rdkit/rdkit/issues/7583
-  - rdkit =2024
+  - ambertools =24.8
+  - rdkit
     # Test-only/optional/dev/typing/examples
-  - pytest =8
+  - pytest >=8
   - pytest-xdist
   - pytest-rerunfailures
   - pyyaml

From a05dec4a6b82086c74cb25e5628c90444bf03ab3 Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Fri, 15 May 2026 11:35:47 -0500
Subject: [PATCH 2/9] Skip CI for now

---
 .github/workflows/CI.yml | 175 ---------------------------------------
 1 file changed, 175 deletions(-)
 delete mode 100644 .github/workflows/CI.yml

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
deleted file mode 100644
index 98db567a4..000000000
--- a/.github/workflows/CI.yml
+++ /dev/null
@@ -1,175 +0,0 @@
-name: CI
-
-on:
-  push:
-    branches:
-      - "main"
-  pull_request:
-    branches:
-      - "main"
-  schedule:
-    - cron: "21 0 * * *"
-  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: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, RDKit=${{ matrix.rdkit }}, 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
-      PYTEST_ARGS: -r fE --tb=short -nauto
-      COV: --cov=openff/toolkit/ --cov-append --cov-report=xml
-
-    steps:
-      - uses: actions/checkout@v6
-        with:
-          fetch-depth: 0
-
-      - name: Set environment variables
-        run: |
-          if [[ ${{ matrix.openeye }} == true && ${{ matrix.rdkit }} == 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 "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 "JOBNAME=RDKit" >> $GITHUB_ENV
-              echo "TOOLKIT_CHECKS=RDKIT" >> $GITHUB_ENV
-              echo "PACKAGES_TO_REMOVE=openeye-toolkits" >> $GITHUB_ENV
-          fi
-
-      - name: Install environment with ${{ env.JOBNAME }}
-        uses: mamba-org/setup-micromamba@v3
-        with:
-          environment-file: devtools/conda-envs/${{ env.ENVFILE }}.yaml
-          create-args: >-
-            python=${{ matrix.python-version }}
-
-      - name: Make oe_license.txt file from GH org secret "OE_LICENSE"
-        env:
-          OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
-        run: echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
-
-      - name: Install package
-        run: |
-          # While Interchange is being installed with pip, there is no need to
-          # force uninstall openff-toolkit-base since it's only pulled in when
-          # Interchange is installed with conda. Un-comment this when testing
-          # against a conda build of Interchange. (It may also be pulled down
-          # by `openmmforcefields` and should be removed in that case a well.)
-          micromamba remove --force openff-toolkit openff-toolkit-base
-          python -m pip install .
-
-      - name: Install test plugins
-        run: python -m pip install utilities/test_plugins
-
-      - name: Remove undesired toolkits
-        run: |
-          if [ ! -z "${{ 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: Optionally remove OpenFF NAGL
-        if: ${{ matrix.nagl == false }}
-        run: micromamba remove openff-nagl-base openff-nagl-models
-
-      - 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: Environment Information
-        run: |
-          micromamba info
-          micromamba list
-          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 }}
-        run: mypy -p "openff.toolkit"
-
-      - name: Run unit tests
-        run: |
-          PYTEST_ARGS+=" --ignore=openff/toolkit/_tests/test_examples.py"
-          PYTEST_ARGS+=" --ignore=openff/toolkit/_tests/test_links.py"
-
-          # TODO: Flip back to schedule condition before merge
-          PYTEST_ARGS+=" --runslow"
-
-          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 }}
-        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 }}
-        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 }}
-        run: |
-          pytest openff \
-            -v -x -n logical --no-cov --doctest-modules \
-            --ignore-glob='openff/toolkit/_tests*' \
-            --ignore=openff/toolkit/data/ \
-            --ignore=openff/toolkit/utils/utils.py
-
-      - name: Codecov
-        uses: codecov/codecov-action@v6
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          files: ./coverage.xml
-          disable_search: true
-          fail_ci_if_error: true
-
-      - name: Check links
-        if: ${{ matrix.rdkit == true && matrix.openeye == true }}
-        run: pytest -r fE --tb=short openff/toolkit/_tests/test_links.py

From fb769ab570835986894fad0a0883f53124601976 Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Fri, 15 May 2026 11:36:59 -0500
Subject: [PATCH 3/9] Add 10 minute timeout to virtual environment setup

---
 .github/workflows/examples.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/examples.yml b/.github/workflows/examples.yml
index 125661dd5..35ab07d74 100644
--- a/.github/workflows/examples.yml
+++ b/.github/workflows/examples.yml
@@ -61,6 +61,7 @@ jobs:
 
       - name: Install conda environment with ${{ env.ENVFILE }}
         uses: mamba-org/setup-micromamba@v3
+        timeout-minutes: 10
         with:
           environment-file: devtools/conda-envs/${{env.ENVFILE}}-examples.yaml
           create-args: >-

From 717847e01038d74d32a6787153aefd32711875a7 Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Fri, 15 May 2026 11:48:21 -0500
Subject: [PATCH 4/9] Help solver out a little bit

---
 devtools/conda-envs/rdkit-examples.yaml | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/devtools/conda-envs/rdkit-examples.yaml b/devtools/conda-envs/rdkit-examples.yaml
index 6c583f6bf..65f462c2d 100644
--- a/devtools/conda-envs/rdkit-examples.yaml
+++ b/devtools/conda-envs/rdkit-examples.yaml
@@ -26,7 +26,7 @@ dependencies:
   - nglview
     # Toolkit-specific
   - ambertools =24.8
-  - rdkit
+  - rdkit >=2024
     # Test-only/optional/dev/typing/examples
   - pytest >=8
   - pytest-xdist
@@ -42,4 +42,9 @@ dependencies:
   - mdtraj
   - pdbfixer
   - openmmforcefields >=0.11.2
-  - gromacs >=2023.3
+    # older versions okay, just constrain to help solver
+  - gromacs >=2025
+
+  # this is just to help the solver, and is a consequence of AmberTools not being re-built for
+  # any recent versions of Boot
+  - icu =75
\ No newline at end of file

From 3a3d7badc2d4dd43e37b2f6e646e5799dea930ec Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Fri, 15 May 2026 13:47:25 -0500
Subject: [PATCH 5/9] Try no `nomkl`

---
 devtools/conda-envs/rdkit-examples.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/devtools/conda-envs/rdkit-examples.yaml b/devtools/conda-envs/rdkit-examples.yaml
index 65f462c2d..b87fdcbeb 100644
--- a/devtools/conda-envs/rdkit-examples.yaml
+++ b/devtools/conda-envs/rdkit-examples.yaml
@@ -19,7 +19,7 @@ dependencies:
   - openff-utilities >=0.1.5
   - openff-interchange-base >=0.5
   # No idea why this is necessary, see https://github.com/openforcefield/openff-toolkit/pull/1821
-  - nomkl
+  # nomkl
   - openff-nagl-base >=0.5.5
   - openff-nagl-models >=2025.09
   - typing_extensions
@@ -41,10 +41,10 @@ dependencies:
   - nbval
   - mdtraj
   - pdbfixer
-  - openmmforcefields >=0.11.2
+  - openmmforcefields >=0.16.0
     # older versions okay, just constrain to help solver
   - gromacs >=2025
 
   # this is just to help the solver, and is a consequence of AmberTools not being re-built for
   # any recent versions of Boot
-  - icu =75
\ No newline at end of file
+  - icu =75

From 0acc0574e4450312ff4fde1667621878f6b04f4f Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Fri, 15 May 2026 14:37:58 -0500
Subject: [PATCH 6/9] Revert "Skip CI for now"

This reverts commit a05dec4a6b82086c74cb25e5628c90444bf03ab3.
---
 .github/workflows/CI.yml | 175 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 175 insertions(+)
 create mode 100644 .github/workflows/CI.yml

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
new file mode 100644
index 000000000..98db567a4
--- /dev/null
+++ b/.github/workflows/CI.yml
@@ -0,0 +1,175 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - "main"
+  pull_request:
+    branches:
+      - "main"
+  schedule:
+    - cron: "21 0 * * *"
+  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: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, RDKit=${{ matrix.rdkit }}, 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
+      PYTEST_ARGS: -r fE --tb=short -nauto
+      COV: --cov=openff/toolkit/ --cov-append --cov-report=xml
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: Set environment variables
+        run: |
+          if [[ ${{ matrix.openeye }} == true && ${{ matrix.rdkit }} == 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 "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 "JOBNAME=RDKit" >> $GITHUB_ENV
+              echo "TOOLKIT_CHECKS=RDKIT" >> $GITHUB_ENV
+              echo "PACKAGES_TO_REMOVE=openeye-toolkits" >> $GITHUB_ENV
+          fi
+
+      - name: Install environment with ${{ env.JOBNAME }}
+        uses: mamba-org/setup-micromamba@v3
+        with:
+          environment-file: devtools/conda-envs/${{ env.ENVFILE }}.yaml
+          create-args: >-
+            python=${{ matrix.python-version }}
+
+      - name: Make oe_license.txt file from GH org secret "OE_LICENSE"
+        env:
+          OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
+        run: echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
+
+      - name: Install package
+        run: |
+          # While Interchange is being installed with pip, there is no need to
+          # force uninstall openff-toolkit-base since it's only pulled in when
+          # Interchange is installed with conda. Un-comment this when testing
+          # against a conda build of Interchange. (It may also be pulled down
+          # by `openmmforcefields` and should be removed in that case a well.)
+          micromamba remove --force openff-toolkit openff-toolkit-base
+          python -m pip install .
+
+      - name: Install test plugins
+        run: python -m pip install utilities/test_plugins
+
+      - name: Remove undesired toolkits
+        run: |
+          if [ ! -z "${{ 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: Optionally remove OpenFF NAGL
+        if: ${{ matrix.nagl == false }}
+        run: micromamba remove openff-nagl-base openff-nagl-models
+
+      - 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: Environment Information
+        run: |
+          micromamba info
+          micromamba list
+          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 }}
+        run: mypy -p "openff.toolkit"
+
+      - name: Run unit tests
+        run: |
+          PYTEST_ARGS+=" --ignore=openff/toolkit/_tests/test_examples.py"
+          PYTEST_ARGS+=" --ignore=openff/toolkit/_tests/test_links.py"
+
+          # TODO: Flip back to schedule condition before merge
+          PYTEST_ARGS+=" --runslow"
+
+          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 }}
+        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 }}
+        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 }}
+        run: |
+          pytest openff \
+            -v -x -n logical --no-cov --doctest-modules \
+            --ignore-glob='openff/toolkit/_tests*' \
+            --ignore=openff/toolkit/data/ \
+            --ignore=openff/toolkit/utils/utils.py
+
+      - name: Codecov
+        uses: codecov/codecov-action@v6
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          disable_search: true
+          fail_ci_if_error: true
+
+      - name: Check links
+        if: ${{ matrix.rdkit == true && matrix.openeye == true }}
+        run: pytest -r fE --tb=short openff/toolkit/_tests/test_links.py

From 4a2a4cd5b1504cd111bfb19e1dee6ee1b319146d Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Fri, 15 May 2026 16:06:26 -0500
Subject: [PATCH 7/9] Bump Sage version

---
 examples/SMIRNOFF_simulation/run_simulation.ipynb             | 2 +-
 .../forcefield_modification/forcefield_modification.ipynb     | 4 ++--
 .../inspect_assigned_parameters.ipynb                         | 2 +-
 examples/toolkit_showcase/toolkit_showcase.ipynb              | 2 +-
 .../export_with_interchange.ipynb                             | 4 ++--
 .../BRD4_inhibitor_benchmark.ipynb                            | 2 +-
 examples/virtual_sites/vsite_showcase.ipynb                   | 4 ++--
 7 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/examples/SMIRNOFF_simulation/run_simulation.ipynb b/examples/SMIRNOFF_simulation/run_simulation.ipynb
index 020688f3d..1d21748fd 100644
--- a/examples/SMIRNOFF_simulation/run_simulation.ipynb
+++ b/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)"
diff --git a/examples/forcefield_modification/forcefield_modification.ipynb b/examples/forcefield_modification/forcefield_modification.ipynb
index 80b65b830..8e59b8857 100644
--- a/examples/forcefield_modification/forcefield_modification.ipynb
+++ b/examples/forcefield_modification/forcefield_modification.ipynb
@@ -96,7 +96,7 @@
     "ligand_smiles = \"CC(C)(C)c1c(O)c(O)c2c(c1O)[C@H]1OCCC[C@H]1[C@H](c1cc(O)c(O)c(F)c1)N2\"\n",
     "ligand = Molecule.from_smiles(ligand_smiles)\n",
     "ligand.generate_conformers(n_conformers=1)\n",
-    "force_field = ForceField(\"openff-2.2.0.offxml\")"
+    "force_field = ForceField(\"openff-2.3.0.offxml\")"
    ]
   },
   {
@@ -1862,7 +1862,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "force_field = ForceField(\"openff-2.1.0.offxml\")\n",
+    "force_field = ForceField(\"openff-2.3.0.offxml\")\n",
     "cyclic_nitrogen_angle = force_field[\"Angles\"].parameters[cyclic_nitrogen_smirks]\n",
     "cyclic_nitrogen_angle.angle = 179 * unit.degree"
    ]
diff --git a/examples/inspect_assigned_parameters/inspect_assigned_parameters.ipynb b/examples/inspect_assigned_parameters/inspect_assigned_parameters.ipynb
index b947e0ea8..4f0fe04f3 100644
--- a/examples/inspect_assigned_parameters/inspect_assigned_parameters.ipynb
+++ b/examples/inspect_assigned_parameters/inspect_assigned_parameters.ipynb
@@ -125,7 +125,7 @@
     "topology = Topology.from_molecules([molecule])\n",
     "\n",
     "# Let's label using the Sage force field\n",
-    "forcefield = ForceField(\"openff-2.2.0.offxml\")\n",
+    "forcefield = ForceField(\"openff-2.3.0.offxml\")\n",
     "\n",
     "# Run the molecule labeling\n",
     "molecule_force_list = forcefield.label_molecules(topology)\n",
diff --git a/examples/toolkit_showcase/toolkit_showcase.ipynb b/examples/toolkit_showcase/toolkit_showcase.ipynb
index 7eef9b1a8..cfb1c17aa 100644
--- a/examples/toolkit_showcase/toolkit_showcase.ipynb
+++ b/examples/toolkit_showcase/toolkit_showcase.ipynb
@@ -520,7 +520,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sage_ff14sb = ForceField(\"openff-2.2.0.offxml\", \"ff14sb_off_impropers_0.0.4.offxml\")"
+    "sage_ff14sb = ForceField(\"openff-2.3.0.offxml\", \"ff14sb_off_impropers_0.0.4.offxml\")"
    ]
   },
   {
diff --git a/examples/using_smirnoff_in_amber_or_gromacs/export_with_interchange.ipynb b/examples/using_smirnoff_in_amber_or_gromacs/export_with_interchange.ipynb
index ae5ca5995..442f816b8 100644
--- a/examples/using_smirnoff_in_amber_or_gromacs/export_with_interchange.ipynb
+++ b/examples/using_smirnoff_in_amber_or_gromacs/export_with_interchange.ipynb
@@ -92,7 +92,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -107,7 +107,7 @@
     }
    ],
    "source": [
-    "forcefield = ForceField(\"openff-2.2.0.offxml\")\n",
+    "forcefield = ForceField(\"openff-2.3.0.offxml\")\n",
     "forcefield"
    ]
   },
diff --git a/examples/using_smirnoff_with_amber_protein_forcefield/BRD4_inhibitor_benchmark.ipynb b/examples/using_smirnoff_with_amber_protein_forcefield/BRD4_inhibitor_benchmark.ipynb
index 4b7df39c6..b52e9eaed 100644
--- a/examples/using_smirnoff_with_amber_protein_forcefield/BRD4_inhibitor_benchmark.ipynb
+++ b/examples/using_smirnoff_with_amber_protein_forcefield/BRD4_inhibitor_benchmark.ipynb
@@ -80,7 +80,7 @@
    "source": [
     "ligand_molecule = Molecule.from_file(\"ligand.sdf\")\n",
     "\n",
-    "sage = ForceField(\"openff-2.2.0.offxml\")\n",
+    "sage = ForceField(\"openff-2.3.0.offxml\")\n",
     "\n",
     "ligand_system = sage.create_interchange(topology=ligand_molecule.to_topology())\n",
     "\n",
diff --git a/examples/virtual_sites/vsite_showcase.ipynb b/examples/virtual_sites/vsite_showcase.ipynb
index bb7b63cea..8ba8a369b 100644
--- a/examples/virtual_sites/vsite_showcase.ipynb
+++ b/examples/virtual_sites/vsite_showcase.ipynb
@@ -133,7 +133,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {
     "pycharm": {
      "name": "#%%\n"
@@ -184,7 +184,7 @@
     "\"\"\"\n",
     "\n",
     "# Load Sage and append our virtual sites\n",
-    "force_field = ForceField(\"openff-2.2.0.offxml\", vsite_offxml)"
+    "force_field = ForceField(\"openff-2.3.0.offxml\", vsite_offxml)"
    ]
   },
   {

From 31cee46093a2205c02ba768b4bf40cc58e686cc7 Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Fri, 15 May 2026 16:11:31 -0500
Subject: [PATCH 8/9] Reapply "Skip CI for now"

This reverts commit 0acc0574e4450312ff4fde1667621878f6b04f4f.
---
 .github/workflows/CI.yml | 175 ---------------------------------------
 1 file changed, 175 deletions(-)
 delete mode 100644 .github/workflows/CI.yml

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
deleted file mode 100644
index 98db567a4..000000000
--- a/.github/workflows/CI.yml
+++ /dev/null
@@ -1,175 +0,0 @@
-name: CI
-
-on:
-  push:
-    branches:
-      - "main"
-  pull_request:
-    branches:
-      - "main"
-  schedule:
-    - cron: "21 0 * * *"
-  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: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, RDKit=${{ matrix.rdkit }}, 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
-      PYTEST_ARGS: -r fE --tb=short -nauto
-      COV: --cov=openff/toolkit/ --cov-append --cov-report=xml
-
-    steps:
-      - uses: actions/checkout@v6
-        with:
-          fetch-depth: 0
-
-      - name: Set environment variables
-        run: |
-          if [[ ${{ matrix.openeye }} == true && ${{ matrix.rdkit }} == 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 "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 "JOBNAME=RDKit" >> $GITHUB_ENV
-              echo "TOOLKIT_CHECKS=RDKIT" >> $GITHUB_ENV
-              echo "PACKAGES_TO_REMOVE=openeye-toolkits" >> $GITHUB_ENV
-          fi
-
-      - name: Install environment with ${{ env.JOBNAME }}
-        uses: mamba-org/setup-micromamba@v3
-        with:
-          environment-file: devtools/conda-envs/${{ env.ENVFILE }}.yaml
-          create-args: >-
-            python=${{ matrix.python-version }}
-
-      - name: Make oe_license.txt file from GH org secret "OE_LICENSE"
-        env:
-          OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
-        run: echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
-
-      - name: Install package
-        run: |
-          # While Interchange is being installed with pip, there is no need to
-          # force uninstall openff-toolkit-base since it's only pulled in when
-          # Interchange is installed with conda. Un-comment this when testing
-          # against a conda build of Interchange. (It may also be pulled down
-          # by `openmmforcefields` and should be removed in that case a well.)
-          micromamba remove --force openff-toolkit openff-toolkit-base
-          python -m pip install .
-
-      - name: Install test plugins
-        run: python -m pip install utilities/test_plugins
-
-      - name: Remove undesired toolkits
-        run: |
-          if [ ! -z "${{ 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: Optionally remove OpenFF NAGL
-        if: ${{ matrix.nagl == false }}
-        run: micromamba remove openff-nagl-base openff-nagl-models
-
-      - 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: Environment Information
-        run: |
-          micromamba info
-          micromamba list
-          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 }}
-        run: mypy -p "openff.toolkit"
-
-      - name: Run unit tests
-        run: |
-          PYTEST_ARGS+=" --ignore=openff/toolkit/_tests/test_examples.py"
-          PYTEST_ARGS+=" --ignore=openff/toolkit/_tests/test_links.py"
-
-          # TODO: Flip back to schedule condition before merge
-          PYTEST_ARGS+=" --runslow"
-
-          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 }}
-        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 }}
-        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 }}
-        run: |
-          pytest openff \
-            -v -x -n logical --no-cov --doctest-modules \
-            --ignore-glob='openff/toolkit/_tests*' \
-            --ignore=openff/toolkit/data/ \
-            --ignore=openff/toolkit/utils/utils.py
-
-      - name: Codecov
-        uses: codecov/codecov-action@v6
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          files: ./coverage.xml
-          disable_search: true
-          fail_ci_if_error: true
-
-      - name: Check links
-        if: ${{ matrix.rdkit == true && matrix.openeye == true }}
-        run: pytest -r fE --tb=short openff/toolkit/_tests/test_links.py

From f0c8d76fd1667a1ed346af30e5f97784c32adbb5 Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Tue, 19 May 2026 10:47:09 -0500
Subject: [PATCH 9/9] Always use NAGL

---
 .github/workflows/examples.yml | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/.github/workflows/examples.yml b/.github/workflows/examples.yml
index 35ab07d74..cb386444b 100644
--- a/.github/workflows/examples.yml
+++ b/.github/workflows/examples.yml
@@ -18,7 +18,7 @@ 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 ${{ matrix.python-version }}, RDKit=${{ matrix.rdkit }}, OpenEye=${{ matrix.openeye }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: true
@@ -27,12 +27,9 @@ jobs:
         python-version: [ "3.12"]
         rdkit: [true, false]
         openeye: [false]
-        nagl: [true, false]
         exclude:
           - rdkit: false
             openeye: false
-          - rdkit: false
-            nagl: true
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
@@ -72,10 +69,6 @@ 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 .