openforcefield · mattwthompson · Aug 4, 2023 · Aug 4, 2023 · Aug 4, 2023 · Aug 4, 2023
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -22,13 +22,14 @@ defaults:
 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 }}
+    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, RDKit=${{ matrix.rdkit }}, OpenEye=${{ matrix.openeye }}, Pydantic v${{ matrix.pydantic-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
         python-version: ["3.9", "3.10", "3.11"]
+        pydantic-version: ["1", "2"]
         rdkit: [true, false]
         openeye: [true, false]
         exclude:
@@ -79,6 +80,7 @@ jobs:
           environment-file: devtools/conda-envs/${{ env.ENVFILE }}.yaml
           create-args: >-
             python=${{ matrix.python-version }}
+            pydantic=${{ matrix.pydantic-version }}
 
       - name: Additional info about the build
         run: |
@@ -106,6 +108,10 @@ jobs:
         run: |
           python -m pip install utilities/test_plugins
 
+      - name: Install QCPortal
+        if: ${{ matrix.pydantic-version == 1 }}
+        run: micromamba install qcelemental "qcportal ==0.15.8" -c conda-forge
+
       - name: Remove undesired toolkits
         run: |
           if [ ! -z "${{ env.PACKAGES_TO_REMOVE }}" ]; then
@@ -162,12 +168,12 @@ jobs:
           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 }}
+        if: ${{ matrix.rdkit == true && matrix.openeye == true && matrix.pydantic-version == 1 }}
         run: |
           pytest -v --no-cov --durations=5 --nbval --ignore docs/_build/ docs/
 
       - name: Run examples in docstrings
-        if: ${{ matrix.rdkit == true && matrix.openeye == true }}
+        if: ${{ matrix.rdkit == true && matrix.openeye == true && matrix.pydantic-version == 1 }}
         run: |
           pytest openff \
             -v -x -n logical --no-cov --doctest-modules \

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,6 +2,11 @@ ci:
   autoupdate_schedule: "quarterly"
 files: ^openff|(^examples/((?!deprecated).)*$)|^docs
 repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+  - id: end-of-file-fixer
+    exclude: '\.(json|pdb)$'
 - repo: https://github.com/psf/black
   rev: 24.1.1
   hooks:

diff --git a/devtools/conda-envs/beta_rc_env.yaml b/devtools/conda-envs/beta_rc_env.yaml
@@ -43,8 +43,6 @@ dependencies:
   - mdtraj
   - nbval
   - mypy
-  - typing_extensions
-  - pydantic =1
   - pip:
     - types-setuptools
     - types-toml

diff --git a/devtools/conda-envs/openeye-examples.yaml b/devtools/conda-envs/openeye-examples.yaml
@@ -5,7 +5,6 @@ channels:
 dependencies:
     # Base depends
   - python
-  - pydantic =1
   - packaging
   - numpy
   - networkx

diff --git a/devtools/conda-envs/openeye.yaml b/devtools/conda-envs/openeye.yaml
@@ -5,7 +5,6 @@ channels:
 dependencies:
     # Base depends
   - python
-  - pydantic =1
   - packaging
   - numpy
   - networkx
@@ -39,4 +38,4 @@ dependencies:
   - qcengine
   - mdtraj
   - nglview
-  - parmed =3
+  - parmed =3
diff --git a/devtools/conda-envs/rdkit-examples.yaml b/devtools/conda-envs/rdkit-examples.yaml
@@ -4,7 +4,6 @@ channels:
 dependencies:
     # Base depends
   - python
-  - pydantic =1
   - packaging
   - numpy
   - networkx

diff --git a/devtools/conda-envs/rdkit.yaml b/devtools/conda-envs/rdkit.yaml
@@ -4,7 +4,6 @@ channels:
 dependencies:
     # Base depends
   - python
-  - pydantic =1
   - packaging
   - numpy
   - networkx

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -45,9 +45,8 @@ dependencies:
   - nomkl
   - mypy
   - typing_extensions
-  - pydantic =1
   - pip:
     - types-setuptools
     - types-toml
     - types-PyYAML
-    - mongo-types
+    - mongo-types
diff --git a/docs/_static/images/favicon.svg b/docs/_static/images/favicon.svg
diff --git a/docs/_templates/autosummary/base.rst b/docs/_templates/autosummary/base.rst
@@ -17,4 +17,4 @@ but free functions do not.
 
 .. currentmodule:: {{ module }}
 
-.. auto{{ objtype }}:: {{ objname }}
+.. auto{{ objtype }}:: {{ objname }}
diff --git a/docs/topology.md b/docs/topology.md
@@ -38,4 +38,3 @@ including offering serialization to a variety of standard formats (including [XM
     HierarchyScheme
     HierarchyElement
 ```
-
diff --git a/docs/users/figures/vsite_examples.svg b/docs/users/figures/vsite_examples.svg
diff --git a/docs/users/figures/vsite_matches.svg b/docs/users/figures/vsite_matches.svg
diff --git a/docs/users/figures/vsite_matches_name.svg b/docs/users/figures/vsite_matches_name.svg
diff --git a/docs/users/figures/vsite_smirks_to_particle.svg b/docs/users/figures/vsite_smirks_to_particle.svg
diff --git a/docs/users/smirnoff.md b/docs/users/smirnoff.md
@@ -89,4 +89,4 @@ general or as specific as needed.
 :::{hint} 
 This page is not the SMIRNOFF spec; it has been moved to the
 [standards repository].
-:::
+:::
diff --git a/docs/utils.rst b/docs/utils.rst
@@ -162,4 +162,3 @@ Exceptions raised by the Toolkit.
     :toctree: api/generated/
 
     exceptions
-
diff --git a/examples/conformer_energies/.gitignore b/examples/conformer_energies/.gitignore
@@ -1,2 +1,2 @@
 ruxolitinib.csv
-ruxolitinib_conf*_minimized.sdf
+ruxolitinib_conf*_minimized.sdf
diff --git a/examples/external/swap_amber_parameters/README.md b/examples/external/swap_amber_parameters/README.md
@@ -5,4 +5,3 @@ This example illustrates how the [ParmEd](http://parmed.github.io/ParmEd/html/in
 ### BRD4:inhibitor complex
 
 * [`swap_existing_ligand_parameters.ipynb`](swap_existing_ligand_parameters.ipynb) contains an example illustrating taking a fully parameterized BRD4 protein-ligand system, with an AMBER protein force field and GAFF ligand parameters, and replacing the ligand parameters with OpenFF parameters from SMIRNOFF format. The BRD4:inhibitor complex is taken from the [free energy benchmark systems living review](https://www.annualreviews.org/doi/abs/10.1146/annurev-biophys-070816-033654) [GitHub repo](https://github.com/MobleyLab/benchmarksets/tree/master/input_files/BRD4).
-
diff --git a/examples/external/using_smirnoff_with_amber_protein_forcefield/.gitignore b/examples/external/using_smirnoff_with_amber_protein_forcefield/.gitignore
@@ -1,3 +1,3 @@
 complex.*
 receptor.*
-ligand.*
+ligand.*
diff --git a/examples/external/using_smirnoff_with_amber_protein_forcefield/README.md b/examples/external/using_smirnoff_with_amber_protein_forcefield/README.md
@@ -3,4 +3,3 @@
 ### BRD4:inhibitor complex
 
 [`BRD4_inhibitor_benchmark.ipynb`](BRD4_inhibitor_benchmark.ipynb) contains an example illustrating applying Sage and ff14SB parameters to a BRD4:inhibitor complex taken from the [free energy benchmark systems living review](https://www.annualreviews.org/doi/abs/10.1146/annurev-biophys-070816-033654) [GitHub repo](https://github.com/MobleyLab/benchmarksets/tree/master/input_files/BRD4).
-
diff --git a/examples/toolkit_showcase/sim.mdp b/examples/toolkit_showcase/sim.mdp
@@ -60,4 +60,3 @@ constraint-algorithm   = LINCS ; Use fast and stable LINCS constraint algorithm
 continuation           = no ; Apply constraints to the initial configuration (important since energy minimisation was unconstrained)
 lincs-order            = 4 ; Increase if you get LINCS errors
 lincs-iter             = 1 ; Increase if you get LINCS errors
-
diff --git a/openff/toolkit/_tests/test_molecule.py b/openff/toolkit/_tests/test_molecule.py
@@ -3417,8 +3417,8 @@ def test_qcschema_molecule_record_round_trip_from_to_from(self):
             Molecule.from_qcschema(mol_dict)
 
 
+@requires_pkg("IPython")
 class TestMoleculeVisualization:
-    @requires_pkg("IPython")
     @requires_rdkit
     def test_visualize_rdkit(self):
         """
@@ -3476,8 +3476,15 @@ def test_visualize_openeye(self):
     )
     def test_ipython_repr_no_nglview(self):
         """Test that the default Molecule repr does not break when nglview is not installed"""
+        from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE, RDKIT_AVAILABLE
+
         molecule = Molecule().from_smiles("CCO")
-        molecule._ipython_display_()
+
+        if RDKIT_AVAILABLE:
+            # the default is `backend="rdkit"`
+            molecule.visualize()
+        elif OPENEYE_AVAILABLE:
+            molecule.visualize(backend="openeye")
 
     def test_get_coordinates(self):
         from openff.toolkit.utils._viz import MoleculeNGLViewTrajectory

diff --git a/openff/toolkit/_tests/utils.py b/openff/toolkit/_tests/utils.py
@@ -6,7 +6,6 @@
 import collections
 import copy
 import functools
-import importlib
 import itertools
 import os
 import pprint
@@ -17,6 +16,7 @@
 import openmm
 import pytest
 from openff.units.openmm import to_openmm
+from openff.utilities import has_package, skip_if_missing
 from openmm import unit as openmm_unit
 
 from openff.toolkit import unit
@@ -45,59 +45,9 @@
 )
 
 
-def has_pkg(pkg_name):
-    """
-    Helper function to generically check if a package is installed. Intended
-    to be used to check for optional dependencies.
-
-    Parameters
-    ----------
-    pkg_name : str
-        The name of the package to check the availability of
-
-    Returns
-    -------
-    pkg_available : bool
-        Boolean indicator if the package is available or not
+has_pkg = has_package
 
-    Examples
-    --------
-    >>> has_numpy = has_pkg('numpy')
-    >>> has_numpy
-    True
-    >>> has_foo = has_pkg('other_non_installed_pkg')
-    >>> has_foo
-    False
-    """
-    try:
-        importlib.import_module(pkg_name)
-    except ModuleNotFoundError:
-        return False
-    return True
-
-
-def requires_pkg(pkg_name, reason=None):
-    """
-    Helper function to generate a pytest.mark.skipif decorator
-    for any package. This allows tests to be skipped if some
-    optional dependency is not found.
-
-    Parameters
-    ----------
-    pkg_name : str
-        The name of the package that is required for a test(s)
-    reason : str, optional
-        Explanation of why the skipped it to be tested
-
-    Returns
-    -------
-    requires_pkg : _pytest.mark.structures.MarkDecorator
-        A pytest decorator that will skip tests if the package is not available
-    """
-    if not reason:
-        reason = f"Package {pkg_name} is required, but was not found."
-    requires_pkg = pytest.mark.skipif(not has_pkg(pkg_name), reason=reason)
-    return requires_pkg
+requires_pkg = skip_if_missing
 
 
 @contextmanager

diff --git a/openff/toolkit/data/molecules/README.md b/openff/toolkit/data/molecules/README.md
@@ -18,4 +18,3 @@ contains all the molecules in `AlkEthOH_tripos.tar.gz/AlkEthOH_test_filt1`.
 **For all molecule sets**
         - `*` = `ff` for parm@frosst atom types
         - `*` = `tripos` for tripos atom types
-
diff --git a/openff/toolkit/data/molecules/z_3_hydroxy_propenal.sdf b/openff/toolkit/data/molecules/z_3_hydroxy_propenal.sdf
@@ -20,4 +20,4 @@
   3  8  1  0  0  0  0
   4  9  1  0  0  0  0
 M  END
-$$$$
+$$$$
diff --git a/openff/toolkit/data/reference_energies/README.md b/openff/toolkit/data/reference_energies/README.md
@@ -3,4 +3,4 @@
 - `reference_after_802.json` - generated by `openff/toolkit/tests/test_energies.py` with conda environment reference_after_802.txt, corresponds to commit 02dba85c51dcff3ee3426d2a407811ac9bac1749 in PR #802, between 0.9.0 and 0.9.1
 - `reference_after_1007.json` - generated by `openff/toolkit/tests/test_energies.py` with conda environment reference_after_1007.txt, corresponds to commit 6ac06efb7d0e91a960325cfc45874500af52274c in PR #948, between 0.9.2 and 0.9.3. 
   This change tracks the effect of partial charge normalization on the reference energies of the test set.
-  Note that that PR #948 was superseded by #1007, since it #948 gained an irreconcilably large merge conflict with master during its development.  
+  Note that that PR #948 was superseded by #1007, since it #948 gained an irreconcilably large merge conflict with master during its development.  
diff --git a/openff/toolkit/data/reference_energies/reference_after_1007.json.txt b/openff/toolkit/data/reference_energies/reference_after_1007.json.txt
@@ -347,4 +347,4 @@ dependencies:
     - pytraj==2.0.5
     - sander==16.0
     - z3-solver==4.8.10.0
-prefix: /Users/jeffreywagner/miniconda3/envs/off-tk-dev
+prefix: /Users/jeffreywagner/miniconda3/envs/off-tk-dev
diff --git a/openff/toolkit/data/test_forcefields/README.md b/openff/toolkit/data/test_forcefields/README.md
@@ -20,4 +20,3 @@
 - `GBSA_HCT-1.0.offxml`: An experimental force field used in validation tests against OpenMM's implementation of the [Hawkins-Cramer-Truhlar](http://docs.openmm.org/latest/userguide/zbibliography.html#hawkins1995) GBSA model (corresponding to igb=1 in AMBER) 
 - `GBSA_OBC1-1.0.offxml`: An experimental force field used in validation tests against OpenMM's implementation of the [Onufriev-Bashford-Case](http://docs.openmm.org/latest/userguide/zbibliography.html#onufriev2004) using the GB(OBC)I model (corresponding to igb=2 in AMBER) 
 - `GBSA_OBC2-1.0.offxml`: An experimental force field used in validation tests against OpenMM's implementation of the [Onufriev-Bashford-Case](http://docs.openmm.org/latest/userguide/zbibliography.html#onufriev2004) using the GB(OBC)II model (corresponding to igb=5 in AMBER) 
-
diff --git a/openff/toolkit/data/test_forcefields/frcmod.Frosst_AlkEthOH_withIDs b/openff/toolkit/data/test_forcefields/frcmod.Frosst_AlkEthOH_withIDs
@@ -82,4 +82,3 @@ MOD4      RE
   CT          1.9080  0.1094  PrmIdVdw008    Spellmeyer
 
 END
-
diff --git a/openff/toolkit/data/test_forcefields/old/test_ff_0_0_2_spec_0_3.offxml b/openff/toolkit/data/test_forcefields/old/test_ff_0_0_2_spec_0_3.offxml
@@ -326,4 +326,4 @@
 		<Atom smirks="[#35:1]" epsilon="0.32 * mole**-1 * kilocalorie" id="n26" rmin_half="2.22 * angstrom"></Atom>
 		<Atom smirks="[#53:1]" epsilon="0.4 * mole**-1 * kilocalorie" id="n27" rmin_half="2.35 * angstrom"></Atom>
 	</vdW>
-</SMIRNOFF>
+</SMIRNOFF>
diff --git a/openff/toolkit/data/test_forcefields/old/test_ff_0_0_4_fixed_spec_0_3.offxml b/openff/toolkit/data/test_forcefields/old/test_ff_0_0_4_fixed_spec_0_3.offxml
@@ -334,4 +334,4 @@
 		<Atom smirks="[#35X0-1:1]" epsilon="0.0586554 * mole**-1 * kilocalorie" id="n34" rmin_half="2.608 * angstrom"></Atom>
 		<Atom smirks="[#53X0-1:1]" epsilon="0.0536816 * mole**-1 * kilocalorie" id="n35" rmin_half="2.86 * angstrom"></Atom>
 	</vdW>
-</SMIRNOFF>
+</SMIRNOFF>
diff --git a/openff/toolkit/data/test_forcefields/old/test_ff_0_0_4_spec_0_3.offxml b/openff/toolkit/data/test_forcefields/old/test_ff_0_0_4_spec_0_3.offxml
@@ -334,4 +334,4 @@
 		<Atom smirks="[#35X0-1:1]" epsilon="0.0586554 * mole**-1 * kilocalorie" id="n34" rmin_half="2.608 * angstrom"></Atom>
 		<Atom smirks="[#53X0-1:1]" epsilon="0.0536816 * mole**-1 * kilocalorie" id="n35" rmin_half="2.86 * angstrom"></Atom>
 	</vdW>
-</SMIRNOFF>
+</SMIRNOFF>
diff --git a/openff/toolkit/utils/utils.py b/openff/toolkit/utils/utils.py
@@ -101,6 +101,7 @@ def get_data_file_path(relative_path: str) -> str:
 
     _DATA_ROOT = files("openff.toolkit") / "data"
 
+    # mypy unhappy because this might not return a path, might be fixed with 3.10+
     file_path = _DATA_ROOT / relative_path
 
     if not file_path.exists():  # type: ignore[attr-defined]