Debug RDKit-based examples workflow

.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
 
@@ -63,6 +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: >-

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
+  # nomkl
+  - 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 >=2024
     # Test-only/optional/dev/typing/examples
-  - pytest =8
+  - pytest >=8
   - pytest-xdist
   - pytest-rerunfailures
   - pyyaml
@@ -42,5 +41,10 @@ dependencies:
   - nbval
   - mdtraj
   - pdbfixer
-  - openmmforcefields >=0.11.2
-  - gromacs >=2023.3
+  - 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

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/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"
    ]

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",

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\")"
    ]
   },
   {

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"
    ]
   },

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",

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)"
    ]
   },
   {