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Merged
mattwthompson merged 10 commits into from
Sep 28, 2026
Merged

Add support for QCSchema v2 and test on Python 3.14 #2238

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5865da7
Test on Python 3.14
mattwthompson Sep 18, 2026
834bfe9
Update RDKit constraint(s)
mattwthompson Sep 18, 2026
7065593
New-ish/old-ish QCSchema compatibility
mattwthompson Sep 18, 2026
43b8e18
Update test regex
mattwthompson Sep 18, 2026
63326aa
Update QCEngine call
mattwthompson Sep 18, 2026
4725db1
Update release history
mattwthompson Sep 18, 2026
c9d5184
fix releasenotes, reduce test matrix bloat
j-wags Sep 25, 2026
8394273
Only return QCSchema V2 molecules
mattwthompson Sep 25, 2026
72d7900
Merge remote-tracking branch 'upstream/test-py314' into test-py314
mattwthompson Sep 25, 2026
5794ab4
Update release notes
mattwthompson Sep 25, 2026
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5 changes: 1 addition & 4 deletions .github/workflows/CI.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -23,12 +23,9 @@ 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:
- openeye: true
python-version: "3.13"

env:
OE_LICENSE: ${{ github.workspace }}/oe_license.txt
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/examples.yml
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Expand Up @@ -24,7 +24,7 @@ jobs:
fail-fast: false
matrix:
os: [ubuntu-latest, macos-latest]
python-version: [ "3.12"]
python-version: [ "3.12", "3.13", "3.14" ]

env:
PYTEST_ARGS: -r fE -v -x --tb=short -nauto --durations=10
Expand Down
3 changes: 1 addition & 2 deletions devtools/conda-envs/examples.yaml
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Expand Up @@ -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
Expand Down
4 changes: 1 addition & 3 deletions devtools/conda-envs/test_env.yaml
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Expand Up @@ -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
Expand Down
3 changes: 1 addition & 2 deletions devtools/conda-envs/test_env_no_openeye.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
156 changes: 87 additions & 69 deletions examples/QCArchive_interface/QCarchive_interface.ipynb
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Expand Up @@ -16,19 +16,19 @@
"execution_count": 1,
"metadata": {
"execution": {
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"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "678eea5ba7b04d1892b4a5e800deea61",
"model_id": "d80f270f7f8345599434d07c7a6f7a2d",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -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",
Expand Down Expand Up @@ -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",
Expand All @@ -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"
]
}
],
Expand All @@ -277,11 +281,11 @@
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"outputs": [],
Expand All @@ -304,11 +308,11 @@
"execution_count": 3,
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"outputs": [],
Expand All @@ -328,11 +332,11 @@
"execution_count": 4,
"metadata": {
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"shell.execute_reply.started": "2026-09-18T18:11:57.098927Z"
}
},
"outputs": [
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -577,11 +592,11 @@
"execution_count": 5,
"metadata": {
"execution": {
"iopub.execute_input": "2026-05-25T19:46:21.923099Z",
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},
"outputs": [],
Expand All @@ -602,11 +617,11 @@
"execution_count": 6,
"metadata": {
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"iopub.execute_input": "2026-05-25T19:46:22.099156Z",
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"shell.execute_reply.started": "2026-09-18T18:11:57.266930Z"
},
"scrolled": true
},
Expand All @@ -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",
Expand Down Expand Up @@ -713,11 +728,11 @@
"execution_count": 7,
"metadata": {
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"outputs": [
Expand Down Expand Up @@ -765,18 +780,18 @@
"execution_count": 8,
"metadata": {
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{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "e792d4ffed78496f8c91ab5f78effb6e",
"model_id": "893433354cf84b14bed5634e4528aa57",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -798,18 +813,18 @@
"execution_count": 9,
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{
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "17c03a78ef5d40efaaabe63f568bbe57",
"version_major": 2,
"version_minor": 0
},
Expand Down Expand Up @@ -844,11 +859,11 @@
"execution_count": 10,
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},
"outputs": [],
Expand All @@ -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",
Expand All @@ -873,11 +891,11 @@
"execution_count": 11,
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"tags": []
},
Expand Down Expand Up @@ -912,7 +930,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.13.13"
"version": "3.13.15"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
Expand Down
2 changes: 1 addition & 1 deletion openff/toolkit/_tests/test_parameters.py
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Expand Up @@ -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"):
Expand Down
8 changes: 6 additions & 2 deletions openff/toolkit/topology/molecule.py
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Expand Up @@ -4451,7 +4451,7 @@ def to_qcschema(self, multiplicity=1, conformer=0, extras=None):

Returns
---------
qcelemental.models.Molecule
qcelemental.models.v2.Molecule
Comment thread
mattwthompson marked this conversation as resolved.
A validated QCElemental Molecule.

Examples
Expand Down Expand Up @@ -4504,7 +4504,11 @@ def to_qcschema(self, multiplicity=1, conformer=0, extras=None):
"identifiers": identifiers,
}

return qcel.models.Molecule.from_data(schema_dict, validate=True)
try:
return qcel.models.v2.Molecule.from_data(schema_dict, validate=True)
except AttributeError: # other errors to capture here?

@j-wags j-wags Sep 25, 2026

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This could be tightened up with something hasattr(qcel.models, "v2") instead.

# fallback for older QCElemental models (Pydantic V1 or V1/V2 compatibility)
return qcel.models.Molecule.from_data(schema_dict, validate=True)

@classmethod
def from_mapped_smiles(
Expand Down
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