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Test against openff-interchange-0.4.0beta1 #1930

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Test against openff-interchange-0.4.0beta1 #1930

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4c132f6
Test against `openff-interchange-0.4.0beta1`
mattwthompson Aug 29, 2024
591820d
Merge remote-tracking branch 'upstream/main' into test-interchange-0.…
mattwthompson Sep 30, 2024
bbbf2d8
Test against branch
mattwthompson Sep 30, 2024
9d86ba4
Undo change
mattwthompson Sep 30, 2024
e1d9491
Revert some changes for simpler diff
mattwthompson Oct 1, 2024
94bac50
Another simplification
mattwthompson Oct 1, 2024
6775636
Test against `openff-interchange-0.4.0beta1`
mattwthompson Aug 29, 2024
adbee90
Test against branch
mattwthompson Sep 30, 2024
0e60594
Undo change
mattwthompson Sep 30, 2024
3b06e51
Revert some changes for simpler diff
mattwthompson Oct 1, 2024
684e2c9
Another simplification
mattwthompson Oct 1, 2024
62b3676
Simplify
mattwthompson Oct 1, 2024
6e52d22
Merge remote-tracking branch 'upstream/test-interchange-0.4.0beta1' i…
mattwthompson Oct 1, 2024
0647c44
Merge remote-tracking branch 'upstream/main' into test-interchange-0.…
mattwthompson Oct 1, 2024
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1 change: 1 addition & 0 deletions devtools/conda-envs/conda.yaml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
name: latest-deployment
channels:
- conda-forge/label/openff-interchange_rc
- conda-forge
dependencies:
# Base depends
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1 change: 1 addition & 0 deletions devtools/conda-envs/conda_oe.yaml
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@@ -1,5 +1,6 @@
name: latest-deployment
channels:
- conda-forge/label/openff-interchange_rc
- conda-forge
- openeye
dependencies:
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1 change: 1 addition & 0 deletions devtools/conda-envs/installer.yaml
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@@ -1,6 +1,7 @@
name: constructor

channels:
- conda-forge/label/openff-interchange_rc
- defaults
- conda-forge

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7 changes: 5 additions & 2 deletions devtools/conda-envs/openeye-examples.yaml
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@@ -1,11 +1,12 @@
name: openeye-examples
channels:
- conda-forge/label/openff-interchange_rc
- openeye
- conda-forge
dependencies:
# Base depends
- python
- pydantic =1
- pydantic
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For both packaging and testing yamls, should we set this to pydantic >2? Or is it redundant since it will be impossible to install this with a pydantic-1-compatible Interchange?

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  • I think pydantic >2/pydantic >=2 would be unwise since that bets on current builds being compatible with Pydantic v3+ out of the box, which I don't trust. pydantic =2 should be fine, if a little redundant since the toolkit itself has no direct opinions on Pydantic compatibility
  • Yes, installing v1 (install-time/packaging level) will be impossible with Interchange 0.4

- packaging
- numpy
- networkx
Expand All @@ -19,7 +20,7 @@ dependencies:
- openff-amber-ff-ports >=0.0.3
- openff-units =0.2.0
- openff-utilities >=0.1.5
- openff-interchange-base >=0.3.19
- openff-interchange-base >=0.4.0beta1
- openff-nagl-base ~=0.4.0
- openff-nagl-models ==0.3.0
- typing_extensions
Expand All @@ -43,3 +44,5 @@ dependencies:
- pdbfixer
- openmmforcefields >=0.11.2
- gromacs >=2023.3
- pip:
- git+https://github.com/openforcefield/openff-interchange.git@fix-1052
7 changes: 5 additions & 2 deletions devtools/conda-envs/openeye.yaml
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Original file line number Diff line number Diff line change
@@ -1,11 +1,12 @@
name: openff-toolkit-test-openeye
channels:
- conda-forge/label/openff-interchange_rc
- openeye
- conda-forge
dependencies:
# Base depends
- python
- pydantic =1
- pydantic
- packaging
- numpy
- networkx
Expand All @@ -19,7 +20,7 @@ dependencies:
- openff-units =0.2.0
- openff-amber-ff-ports
- openff-utilities >=0.1.5
- openff-interchange-base >=0.3.19
- openff-interchange-base >=0.4.0beta1
- openff-nagl-base ~=0.4.0
- openff-nagl-models ==0.3.0
- typing_extensions
Expand All @@ -40,3 +41,5 @@ dependencies:
- mdtraj
- nglview
- parmed =3
- pip:
- git+https://github.com/openforcefield/openff-interchange.git@fix-1052
7 changes: 5 additions & 2 deletions devtools/conda-envs/rdkit-examples.yaml
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@@ -1,10 +1,11 @@
name: rdkit-examples
channels:
- conda-forge/label/openff-interchange_rc
- conda-forge
dependencies:
# Base depends
- python
- pydantic =1
- pydantic
- packaging
- numpy
- networkx
Expand All @@ -18,7 +19,7 @@ dependencies:
- openff-amber-ff-ports >=0.0.3
- openff-units =0.2.0
- openff-utilities >=0.1.5
- openff-interchange-base >=0.3.19
- openff-interchange-base >=0.4.0beta1
- openff-nagl-base ~=0.4.0
- openff-nagl-models ==0.3.0
- typing_extensions
Expand All @@ -45,3 +46,5 @@ dependencies:
- pdbfixer
- openmmforcefields >=0.11.2
- gromacs >=2023.3
- pip:
- git+https://github.com/openforcefield/openff-interchange.git@fix-1052
7 changes: 5 additions & 2 deletions devtools/conda-envs/rdkit.yaml
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Original file line number Diff line number Diff line change
@@ -1,10 +1,11 @@
name: openff-toolkit-test-rdkit
channels:
- conda-forge/label/openff-interchange_rc
- conda-forge
dependencies:
# Base depends
- python
- pydantic =1
- pydantic
- packaging
- numpy
- networkx
Expand All @@ -18,7 +19,7 @@ dependencies:
- openff-units =0.2.0
- openff-amber-ff-ports
- openff-utilities >=0.1.5
- openff-interchange-base >=0.3.19
- openff-interchange-base >=0.4.0beta1
- openff-nagl-base ~=0.4.0
- openff-nagl-models ==0.3.0
- typing_extensions
Expand All @@ -39,3 +40,5 @@ dependencies:
- qcportal >=0.50
- qcengine
- nglview
- pip:
- git+https://github.com/openforcefield/openff-interchange.git@fix-1052
1 change: 1 addition & 0 deletions devtools/conda-envs/release-build.yaml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
name: release-build
channels:
- conda-forge/label/openff-interchange_rc
- conda-forge

dependencies:
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6 changes: 4 additions & 2 deletions devtools/conda-envs/test_env.yaml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
name: openff-toolkit-test
channels:
- conda-forge/label/openff-interchange_rc
- openeye
- conda-forge
dependencies:
Expand All @@ -19,7 +20,7 @@ dependencies:
- openff-units =0.2.0
- openff-amber-ff-ports
- openff-utilities >=0.1.5
- openff-interchange-base >=0.3.19
- openff-interchange-base >=0.4.0beta1
- openff-nagl-base ~=0.4.0
- openff-nagl-models ==0.3.0
# Toolkit-specific
Expand Down Expand Up @@ -47,7 +48,7 @@ dependencies:
- nomkl
- mypy
- typing_extensions
- pydantic =1
- pydantic
- pip:
- types-setuptools
- types-toml
Expand All @@ -56,3 +57,4 @@ dependencies:
- types-xmltodict
- types-cachetools
- mongo-types
- git+https://github.com/openforcefield/openff-interchange.git@fix-1052
12 changes: 3 additions & 9 deletions openff/toolkit/_tests/test_forcefield.py
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Expand Up @@ -4015,6 +4015,8 @@ def test_fractional_bondorder_invalid_interpolation_method(self):
Ensure that requesting an invalid interpolation method leads to a
FractionalBondOrderInterpolationMethodUnsupportedError
"""
from pydantic import ValidationError

mol = create_ethanol()

forcefield = ForceField(
Expand All @@ -4025,18 +4027,10 @@ def test_fractional_bondorder_invalid_interpolation_method(self):
)._fractional_bondorder_interpolation = "invalid method name"
topology = Topology.from_molecules([mol])

# This error will be either from v1 of the package (if v1 is installed)
# or the faked v1 API (if v2 is installed). Ensure the v1 error or a
# mimick of it is imported
try:
from pydantic.v1 import ValidationError
except ImportError:
from pydantic import ValidationError

# If important, this can be a custom exception instead of a verbose ValidationError
with pytest.raises(
ValidationError,
match="given=invalid method name",
match="Input should be 'linear'.*input_value='invalid method name'",
):
forcefield.create_openmm_system(
topology,
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6 changes: 2 additions & 4 deletions openff/toolkit/typing/engines/smirnoff/forcefield.py
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Expand Up @@ -1383,8 +1383,6 @@ def get_partial_charges(self, molecule: "Molecule", **kwargs: Any) -> Quantity:
charge calculation to be cached.

"""
from openff.interchange import Interchange

from openff.toolkit import Molecule, unit

if not isinstance(molecule, Molecule):
Expand All @@ -1396,8 +1394,8 @@ def get_partial_charges(self, molecule: "Molecule", **kwargs: Any) -> Quantity:
return Quantity(
[
c.m
for c in Interchange.from_smirnoff(
force_field=self, topology=[molecule], **kwargs
for c in self.create_interchange(
topology=molecule.to_topology(), **kwargs,
)["Electrostatics"].charges.values()
],
unit.elementary_charge,
Expand Down
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