Add support for QCSchema v2 and test on Python 3.14

.github/workflows/CI.yml

@@ -23,7 +23,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.12", "3.13"]
+        python-version: ["3.12", "3.13", "3.14"]
         openeye: [true, false]
         nagl: [true, false]
         exclude:

.github/workflows/examples.yml

@@ -24,7 +24,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: [ "3.12"]
+        python-version: [ "3.12", "3.14" ]
 
     env:
       PYTEST_ARGS: -r fE -v -x --tb=short -nauto --durations=10

devtools/conda-envs/examples.yaml

@@ -20,8 +20,7 @@ dependencies:
   - openff-nagl-models >=2025
   - nglview
     # Toolkit-specific
-    # https://github.com/rdkit/rdkit/issues/7221 and https://github.com/rdkit/rdkit/issues/7583
-  - rdkit =2024
+  - rdkit
     # Test-only/optional/dev/typing/examples
   - pytest =8
   - pytest-xdist

devtools/conda-envs/test_env.yaml

@@ -20,9 +20,7 @@ dependencies:
   - openff-nagl-models >=0.3.0
     # Toolkit-specific
   - ambertools >=22
-    # rdkit 2024.03.6 and 2024.09.1 packages fail when run natively on osx-arm64 macs
-    # https://github.com/rdkit/rdkit/issues/7583
-  - rdkit !=2024.03.6,!=2024.09.1
+  - rdkit >=2025
 
   - openeye::openeye-toolkits
     # Test-only/optional/dev/typing

devtools/conda-envs/test_env_no_openeye.yaml

@@ -20,8 +20,7 @@ dependencies:
   - openff-nagl-models >=0.3.0
     # Toolkit-specific
   - ambertools >=22
-    # https://github.com/rdkit/rdkit/issues/7221 and https://github.com/rdkit/rdkit/issues/7583
-  - rdkit !=2024.03.6,!=2024.03.5
+  - rdkit >=2025
     # Test-only/optional/dev/typing
   - pytest =8
   - pytest-cov

docs/releasehistory.md

@@ -12,12 +12,16 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 
 ### Behavior changes
 
+- [PR #2238](https://github.com/openforcefield/openff-toolkit/pull/2238): Adds support for QCSchema V2 in `Molecule.to_qcschema`, which now only returns QCSchema V2 models.
+
 ### Bugfixes
 
 - [PR #2234](https://github.com/openforcefield/openff-toolkit/pull/2234): Fixes some deprecation warnings thrown by using deprecated Pydantic V1 methods in tests.
 - [PR #2236](https://github.com/openforcefield/openff-toolkit/pull/2236): Fixes a rare case in which force field files with similar names were incorrectly loaded.
 
-### New features
+### Tests updated
+
+- [PR #2238](https://github.com/openforcefield/openff-toolkit/pull/2238): Run tests on Python 3.14.
 
 ### Improved documentation and warnings
 

examples/QCArchive_interface/QCarchive_interface.ipynb

@@ -16,19 +16,19 @@
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-     "shell.execute_reply": "2026-05-25T19:46:21.503399Z",
-     "shell.execute_reply.started": "2026-05-25T19:46:15.496407Z"
+     "iopub.execute_input": "2026-09-18T18:11:52.229678Z",
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+     "iopub.status.idle": "2026-09-18T18:11:56.853976Z",
+     "shell.execute_reply": "2026-09-18T18:11:56.853311Z",
+     "shell.execute_reply.started": "2026-09-18T18:11:52.229671Z"
     },
     "scrolled": true
    },
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "678eea5ba7b04d1892b4a5e800deea61",
+       "model_id": "d80f270f7f8345599434d07c7a6f7a2d",
        "version_major": 2,
        "version_minor": 0
       },
@@ -42,7 +42,7 @@
      "output_type": "stream",
      "text": [
       "  id  type                record_count  name\n",
-      "----  ----------------  --------------  ---------------------------------------------------------------------------------------\n",
+      "----  ----------------  --------------  ----------------------------------------------------------------------------------------\n",
       "  35  torsiondrive                 454  OpenFF Fragmenter Phenyl Benchmark\n",
       "  36  torsiondrive                 820  OpenFF Group1 Torsions\n",
       "  41  optimization                 937  OpenFF Optimization Set 1\n",
@@ -240,7 +240,7 @@
       " 463  singlepoint               158905  tmQM xtb Dataset T=100K low-mw high-coordinate mult=5 v0.0\n",
       " 464  singlepoint               206240  tmQM xtb Dataset T=100K low-mw high-coordinate mult=3 v0.0\n",
       " 465  singlepoint                  968  OpenFF TMC Atom Energies v0.0\n",
-      " 467  optimization                1968  TM Benchmark Optimization Dataset Step 2 v0.0\n",
+      " 467  optimization                2624  TM Benchmark Optimization Dataset Step 2 v0.0\n",
       " 468  singlepoint                68794  tmQM xtb Dataset T=100K low-mw high-coordinate geom-mult=3 v0.0\n",
       " 469  singlepoint               102338  tmQM xtb Dataset T=100K low-mw high-coordinate geom-mult=1 v0.0\n",
       " 470  torsiondrive                1371  OpenFF SMIRNOFF Sage 2.3.0\n",
@@ -250,8 +250,12 @@
       " 474  optimization                6780  OpenFF NSP Optimization Set 1 Nitrogen v4.0\n",
       " 475  optimization                7940  OpenFF NSP Optimization Set 1 Sulfur v4.0\n",
       " 476  torsiondrive                  27  OpenFF Lipid Torsion Drives v4.1\n",
-      " 477  optimization               80972  OpenFF Organometallic Complexes Architector Minimum Energy Structures v0.0\n",
-      " 478  optimization                2350  OpenFF SPICE2 Subset Optimization Dataset v4.0\n"
+      " 477  optimization              161944  OpenFF Organometallic Complexes Architector Minimum Energy Structures v0.0\n",
+      " 478  optimization                2350  OpenFF SPICE2 Subset Optimization Dataset v4.0\n",
+      " 479  torsiondrive                  50  OpenFF PEG Ether Fragments TorsionDrives v4.0\n",
+      " 480  optimization              389480  OpenFF Architector Methyl-Capped Metal Complexes Optimization Dataset v0.0\n",
+      " 481  optimization              389480  OpenFF Architector Unconstrained Methyl-Capped Metal Complexes Optimization Dataset v0.0\n",
+      " 482  optimization              142198  tmQM Charge Multiplicity Variant Optimization Dataset v0.0\n"
      ]
     }
    ],
@@ -277,11 +281,11 @@
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-     "shell.execute_reply": "2026-05-25T19:46:21.588122Z",
-     "shell.execute_reply.started": "2026-05-25T19:46:21.504701Z"
+     "iopub.execute_input": "2026-09-18T18:11:56.854869Z",
+     "iopub.status.busy": "2026-09-18T18:11:56.854594Z",
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+     "shell.execute_reply": "2026-09-18T18:11:56.896318Z",
+     "shell.execute_reply.started": "2026-09-18T18:11:56.854858Z"
     }
    },
    "outputs": [],
@@ -304,11 +308,11 @@
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-     "shell.execute_reply": "2026-05-25T19:46:21.912544Z",
-     "shell.execute_reply.started": "2026-05-25T19:46:21.589223Z"
+     "iopub.execute_input": "2026-09-18T18:11:56.897664Z",
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+     "iopub.status.idle": "2026-09-18T18:11:57.098351Z",
+     "shell.execute_reply": "2026-09-18T18:11:57.097211Z",
+     "shell.execute_reply.started": "2026-09-18T18:11:56.897636Z"
     }
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    "outputs": [],
@@ -328,11 +332,11 @@
    "execution_count": 4,
    "metadata": {
     "execution": {
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-     "shell.execute_reply": "2026-05-25T19:46:21.921956Z",
-     "shell.execute_reply.started": "2026-05-25T19:46:21.913678Z"
+     "iopub.execute_input": "2026-09-18T18:11:57.098938Z",
+     "iopub.status.busy": "2026-09-18T18:11:57.098830Z",
+     "iopub.status.idle": "2026-09-18T18:11:57.123227Z",
+     "shell.execute_reply": "2026-09-18T18:11:57.122574Z",
+     "shell.execute_reply.started": "2026-09-18T18:11:57.098927Z"
     }
    },
    "outputs": [
@@ -417,7 +421,18 @@
        "         [ 3.28745938e+00, -6.00243631e+00, -9.86032950e+00]]),\n",
        "  'name': 'C29ClFH26N4O4S',\n",
        "  'identifiers': {'molecule_hash': '58aaa33a5e7d9445e4276a015de257c3d6bde558',\n",
-       "   'molecular_formula': 'C29ClFH26N4O4S'},\n",
+       "   'molecular_formula': 'C29ClFH26N4O4S',\n",
+       "   'smiles': None,\n",
+       "   'inchi': None,\n",
+       "   'inchikey': None,\n",
+       "   'canonical_explicit_hydrogen_smiles': None,\n",
+       "   'canonical_isomeric_explicit_hydrogen_mapped_smiles': None,\n",
+       "   'canonical_isomeric_explicit_hydrogen_smiles': None,\n",
+       "   'canonical_isomeric_smiles': None,\n",
+       "   'canonical_smiles': None,\n",
+       "   'pubchem_cid': None,\n",
+       "   'pubchem_sid': None,\n",
+       "   'pubchem_conformerid': None},\n",
        "  'molecular_charge': 0.0,\n",
        "  'molecular_multiplicity': 1,\n",
        "  'masses': array([12.        , 12.        , 12.        , 12.        , 12.        ,\n",
@@ -577,11 +592,11 @@
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    "outputs": [],
@@ -602,11 +617,11 @@
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-     "shell.execute_reply.started": "2026-05-25T19:46:22.099144Z"
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     "scrolled": true
    },
@@ -615,7 +630,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "<class 'qcelemental.models.v1.molecule.Molecule'>\n",
+      "<class 'qcelemental.models._v1v2.molecule.Molecule'>\n",
       "6 6\n",
       "6 6\n",
       "6 6\n",
@@ -713,11 +728,11 @@
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@@ -765,18 +780,18 @@
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     {
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+       "model_id": "893433354cf84b14bed5634e4528aa57",
        "version_major": 2,
        "version_minor": 0
       },
@@ -798,18 +813,18 @@
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+     "shell.execute_reply.started": "2026-09-18T18:11:57.362293Z"
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    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "5d9fa5b8107c433e8d66f75114ea60a0",
+       "model_id": "17c03a78ef5d40efaaabe63f568bbe57",
        "version_major": 2,
        "version_minor": 0
       },
@@ -844,11 +859,11 @@
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+     "shell.execute_reply.started": "2026-09-18T18:11:57.383219Z"
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    "outputs": [],
@@ -857,11 +872,14 @@
     "\n",
     "# set up the RDKit task\n",
     "rdkit_task = {\n",
-    "    \"schema_name\": \"qcschema_input\",\n",
+    "    \"schema_name\": \"qcschema_atomic_input\",\n",
+    "    \"schema_version\": 2,\n",
     "    \"molecule\": qc_molecule,\n",
-    "    \"driver\": \"energy\",\n",
-    "    \"model\": {\"method\": \"uff\", \"basis\": None},\n",
-    "    \"keywords\": {\"scf_type\": \"df\"},\n",
+    "    \"specification\": {\n",
+    "        \"driver\": \"energy\",\n",
+    "        \"model\": {\"method\": \"uff\", \"basis\": None},\n",
+    "        \"keywords\": {\"scf_type\": \"df\"},\n",
+    "    },\n",
     "}\n",
     "\n",
     "# now lets compute the energy using qcengine and RDKit and print the result\n",
@@ -873,11 +891,11 @@
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    "metadata": {
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+     "iopub.execute_input": "2026-09-18T18:11:57.606313Z",
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     "tags": []
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@@ -912,7 +930,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.13.13"
+   "version": "3.13.15"
   },
   "widgets": {
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openff/toolkit/_tests/test_parameters.py

@@ -819,7 +819,7 @@ def test_index(self):
             parameters.index("[#2:1]")
 
         p4 = ParameterType(smirks="[#2:1]")
-        with pytest.raises(ValueError, match="is not in list"):
+        with pytest.raises(ValueError, match=" not in list"):
             parameters.index(p4)
 
         with pytest.raises(TypeError, match="non-None values for start"):

openff/toolkit/topology/molecule.py

@@ -4451,7 +4451,7 @@ def to_qcschema(self, multiplicity=1, conformer=0, extras=None):
 
         Returns
         ---------
-        qcelemental.models.Molecule
+        qcelemental.models.v2.Molecule
             A validated QCElemental Molecule.
 
         Examples
@@ -4504,7 +4504,7 @@ def to_qcschema(self, multiplicity=1, conformer=0, extras=None):
             "identifiers": identifiers,
         }
 
-        return qcel.models.Molecule.from_data(schema_dict, validate=True)
+        return qcel.models.v2.Molecule.from_data(schema_dict, validate=True)
 
     @classmethod
     def from_mapped_smiles(