Standardize typing and 0.13.2 releasenotes (#1646)

* 0.13.2 releasenotes

* Pin `openff-units=0.2.0`

* fix ff.get_partial_charges return type

* clean up type annotations so they don't have import paths

* fix unnecessary imports identified by flake8

---------

Co-authored-by: Matthew W. Thompson <mattwthompson@protonmail.com>

devtools/conda-envs/beta_rc_env.yaml

@@ -18,7 +18,7 @@ dependencies:
   - openmm >=7.6
   - openff-forcefields >=2023.05.1
   - smirnoff99Frosst
-  - openff-units >=0.2
+  - openff-units =0.2.0
   - openff-utilities >=0.1.5
   - openff-interchange-base >=0.2
   - openff-nagl >=0.2.2

devtools/conda-envs/openeye-examples.yaml

@@ -17,7 +17,7 @@ dependencies:
   - openff-forcefields >=2023.05.1
   - smirnoff99Frosst
   - openff-amber-ff-ports >=0.0.3
-  - openff-units >=0.2
+  - openff-units =0.2.0
   - openff-utilities >=0.1.5
   - openff-interchange-base >=0.3.3
   - openff-nagl >=0.2.2

devtools/conda-envs/openeye.yaml

@@ -16,7 +16,7 @@ dependencies:
   - openmm >=7.6
   - openff-forcefields >=2023.05.1
   - smirnoff99Frosst
-  - openff-units >=0.2
+  - openff-units =0.2.0
   - openff-utilities >=0.1.5
   - openff-interchange-base >=0.3.3
   - openff-nagl >=0.2.2

devtools/conda-envs/rdkit-examples.yaml

@@ -16,7 +16,7 @@ dependencies:
   - openff-forcefields >=2023.05.1
   - smirnoff99Frosst
   - openff-amber-ff-ports >=0.0.3
-  - openff-units >=0.2
+  - openff-units =0.2.0
   - openff-utilities >=0.1.5
   - openff-interchange-base >=0.3.3
   - openff-nagl >=0.2.2

devtools/conda-envs/rdkit.yaml

@@ -15,7 +15,7 @@ dependencies:
   - openmm >=7.6
   - openff-forcefields >=2023.05.1
   - smirnoff99Frosst
-  - openff-units >=0.2
+  - openff-units =0.2.0
   - openff-utilities >=0.1.5
   - openff-interchange-base >=0.3.3
   - openff-nagl >=0.2.2

devtools/conda-envs/test_env.yaml

@@ -16,7 +16,7 @@ dependencies:
   - openmm >=7.6
   - openff-forcefields >=2023.05.1
   - smirnoff99Frosst
-  - openff-units >=0.2
+  - openff-units =0.2.0
   - openff-utilities >=0.1.5
   - openff-interchange-base >=0.3.3
   - openff-nagl >=0.2.2

docs/releasehistory.md

@@ -6,21 +6,15 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 * `minor` increments add features but do not break API compatibility
 * `micro` increments represent bugfix releases or improvements in documentation
 
-## Current development
-
-### Behavior changes
+## 0.13.2
 
 ### Bugfixes
 
 - [PR #1640](https://github.com/openforcefield/openff-toolkit/pull/1640): Fixes issue [#1633](https://github.com/openforcefield/openff-toolkit/issues/1633) in which some force field attributes were erroneously parsed as `Quantity` objects and  issue [#1635](https://github.com/openforcefield/openff-toolkit/issues/1635) in which OpenFF 2.1.0 ("Sage") could not be loaded with Pint 0.22.
 
-### New features
 
 ### Improved documentation and warnings
-- [PR #1636](https://github.com/openforcefield/openff-toolkit/pull/1636): Make the Molecule Cookbook only pull down QCF records with fully defined stereo.
-
-
-### Examples updates
+- [PR #1636](https://github.com/openforcefield/openff-toolkit/pull/1636) and [PR #1643](https://github.com/openforcefield/openff-toolkit/pull/1643): Make the Molecule Cookbook and `Molecule.from_qcschema` docstring only pull down QCF records with fully defined stereo.
 
 
 ## 0.13.1

openff/toolkit/tests/mocking.py

@@ -1,14 +1,14 @@
 import numpy
-from openff.units import unit
+from openff.units import Quantity, unit
 
 from openff.toolkit.topology import Molecule
 from openff.toolkit.typing.engines.smirnoff import VirtualSiteHandler
 
 
 class VirtualSiteMocking:
     @staticmethod
-    def sp1_conformer() -> unit.Quantity:
-        return unit.Quantity(
+    def sp1_conformer() -> Quantity:
+        return Quantity(
             numpy.array(
                 [
                     [-2.0, +0.0, +0.0],
@@ -21,8 +21,8 @@ def sp1_conformer() -> unit.Quantity:
         )
 
     @staticmethod
-    def sp2_conformer() -> unit.Quantity:
-        return unit.Quantity(
+    def sp2_conformer() -> Quantity:
+        return Quantity(
             numpy.array(
                 [
                     [+1.0, +0.0, +0.0],
@@ -35,12 +35,12 @@ def sp2_conformer() -> unit.Quantity:
         )
 
     @staticmethod
-    def sp3_conformer() -> unit.Quantity:
+    def sp3_conformer() -> Quantity:
         """Returns the conformer of a dummy tetrahedral molecule with the
         first atom positioned at (0, 1, 0), the second atom at (0, 0, 0) and
         the remaining atoms at the corners of the tetrahedron.
         """
-        return unit.Quantity(
+        return Quantity(
             numpy.array(
                 [
                     [+0.0, +1.0, +0.0],
@@ -61,7 +61,7 @@ def bond_charge_parameter(
             type="BondCharge",
             smirks=smirks,
             name=name,
-            charge_increment=unit.Quantity(
+            charge_increment=Quantity(
                 [0.1 * param_multiple, 0.2 * param_multiple],
                 unit.elementary_charge,
             ),
@@ -93,7 +93,7 @@ def divalent_parameter(
         smirks: str,
         match: str,
         name: str = "EP",
-        angle: unit.Quantity = 0.0 * unit.degree,
+        angle: Quantity = 0.0 * unit.degree,
     ) -> VirtualSiteHandler.VirtualSiteType:
         return VirtualSiteHandler.VirtualSiteType(
             type="DivalentLonePair",

openff/toolkit/tests/test_toolkit_io.py

@@ -12,7 +12,7 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-from openff.units import unit
+from openff.units import Quantity, unit
 
 from openff.toolkit.tests import create_molecules
 from openff.toolkit.tests.utils import requires_openeye, requires_rdkit
@@ -72,7 +72,7 @@
 $$$$
 """
 
-CAFFEINE_2D_COORDS = unit.Quantity(
+CAFFEINE_2D_COORDS = Quantity(
     np.array(
         [
             (-1.1875, -9.6542, 0.0000),
@@ -277,7 +277,7 @@
 $$$$
 """
 
-CAFFEINE_3D_COORDS = unit.Quantity(
+CAFFEINE_3D_COORDS = Quantity(
     np.array(
         [
             (0.4700, 2.5688, 0.0006),

openff/toolkit/tests/test_toolkits.py

@@ -12,7 +12,7 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_almost_equal
-from openff.units import unit
+from openff.units import Quantity, unit
 
 from openff.toolkit.tests.create_molecules import (
     create_acetaldehyde,
@@ -261,9 +261,9 @@ def formic_acid_molecule() -> Molecule:
 
 
 @pytest.fixture()
-def formic_acid_conformers() -> Dict[str, unit.Quantity]:
+def formic_acid_conformers() -> Dict[str, Quantity]:
     return {
-        "cis": unit.Quantity(
+        "cis": Quantity(
             np.array(
                 [
                     [-0.95927322, -0.91789997, 0.36333418],
@@ -275,7 +275,7 @@ def formic_acid_conformers() -> Dict[str, unit.Quantity]:
             ),
             unit.angstrom,
         ),
-        "trans": unit.Quantity(
+        "trans": Quantity(
             np.array(
                 [
                     [-0.95927322, -0.91789997, 0.36333418],
@@ -382,7 +382,7 @@ def test_to_from_openeye_core_props_filled(self):
 
         # Populate core molecule property fields
         molecule.name = "Alice"
-        partial_charges = unit.Quantity(
+        partial_charges = Quantity(
             np.array(
                 [
                     -0.9,
@@ -408,7 +408,7 @@ def test_to_from_openeye_core_props_filled(self):
             unit.elementary_charge,
         )
         molecule.partial_charges = partial_charges
-        coords = unit.Quantity(
+        coords = Quantity(
             np.array(
                 [
                     ["0.0", "1.0", "2.0"],
@@ -584,7 +584,7 @@ def test_to_from_openeye_none_partial_charges(self):
 
     def test_to_openeye_typed_partial_charges(self):
         ethanol = create_ethanol()
-        ethanol.partial_charges = unit.Quantity(
+        ethanol.partial_charges = Quantity(
             np.zeros(ethanol.n_atoms, dtype=int), unit.elementary_charge
         )
         oemol = ethanol.to_openeye()
@@ -973,7 +973,7 @@ def test_write_pdb_preserving_atom_order(self):
         water.add_bond(0, 1, 1, False)
         water.add_bond(1, 2, 1, False)
         water.add_conformer(
-            unit.Quantity(
+            Quantity(
                 np.array([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]),
                 unit.angstrom,
             )
@@ -1150,7 +1150,7 @@ def test_write_multiconformer_mol_as_sdf(self):
         toolkit_wrapper = OpenEyeToolkitWrapper()
         filename = get_data_file_path("molecules/ethanol.sdf")
         ethanol = Molecule.from_file(filename, toolkit_registry=toolkit_wrapper)
-        ethanol.partial_charges = unit.Quantity(
+        ethanol.partial_charges = Quantity(
             np.array([-4.0, -3.0, -2.0, -1.0, 0.0, 1.0, 2.0, 3.0, 4.0]),
             unit.elementary_charge,
         )
@@ -1217,7 +1217,7 @@ def test_get_mol2_charges(self):
         molecule = Molecule.from_file(filename, toolkit_registry=toolkit_wrapper)
         assert len(molecule.conformers) == 1
         assert molecule.conformers[0].shape == (15, 3)
-        target_charges = unit.Quantity(
+        target_charges = Quantity(
             np.array(
                 [
                     -0.1342,
@@ -1349,7 +1349,7 @@ def test_apply_elf_conformer_selection(self):
 
         initial_conformers = [
             # Add a conformer with an internal H-bond.
-            unit.Quantity(
+            Quantity(
                 np.array(
                     [
                         [0.5477, 0.3297, -0.0621],
@@ -1366,7 +1366,7 @@ def test_apply_elf_conformer_selection(self):
                 unit.angstrom,
             ),
             # Add a conformer without an internal H-bond.
-            unit.Quantity(
+            Quantity(
                 np.array(
                     [
                         [0.5477, 0.3297, -0.0621],
@@ -2271,7 +2271,7 @@ def test_to_from_rdkit_core_props_filled(self):
 
         # Populate core molecule property fields
         molecule.name = "Alice"
-        partial_charges = unit.Quantity(
+        partial_charges = Quantity(
             np.array(
                 [
                     -0.9,
@@ -2297,7 +2297,7 @@ def test_to_from_rdkit_core_props_filled(self):
             unit.elementary_charge,
         )
         molecule.partial_charges = partial_charges
-        coords = unit.Quantity(
+        coords = Quantity(
             np.array(
                 [
                     ["0.0", "1.0", "2.0"],
@@ -2749,7 +2749,7 @@ def test_write_multiconformer_mol_as_sdf(self):
         toolkit_wrapper = RDKitToolkitWrapper()
         filename = get_data_file_path("molecules/ethanol.sdf")
         ethanol = Molecule.from_file(filename, toolkit_registry=toolkit_wrapper)
-        ethanol.partial_charges = unit.Quantity(
+        ethanol.partial_charges = Quantity(
             np.array([-4.0, -3.0, -2.0, -1.0, 0.0, 1.0, 2.0, 3.0, 4.0]),
             unit.elementary_charge,
         )
@@ -3042,7 +3042,7 @@ def test_elf_select_diverse_conformers(
         self,
         formic_acid_molecule: Molecule,
         expected_conformer_map: Dict[int, int],
-        rms_tolerance: unit.Quantity,
+        rms_tolerance: Quantity,
     ):
         """Test the greedy selection of 'diverse' ELF conformers."""
 
@@ -3077,7 +3077,7 @@ def test_apply_elf_conformer_selection(self):
 
         initial_conformers = [
             # Add a conformer with an internal H-bond.
-            unit.Quantity(
+            Quantity(
                 np.array(
                     [
                         [0.5477, 0.3297, -0.0621],
@@ -3094,7 +3094,7 @@ def test_apply_elf_conformer_selection(self):
                 unit.angstrom,
             ),
             # Add a conformer without an internal H-bond.
-            unit.Quantity(
+            Quantity(
                 np.array(
                     [
                         [0.5477, 0.3297, -0.0621],