Merge branch 'main' into add/contributing

docs/conf.py

@@ -145,13 +145,9 @@ html_theme_options = {
     ],
     "accent_color": "cantina-purple",
     "navigation_with_keys": False,
-    "navbar_end": ["navbar-icon-links"],  # TODO: add "theme-switcher" to add back dark mode toggle
 }
 html_logo = "_static/OFE-color-icon.svg"
 html_favicon = '_static/OFE-color-icon.svg'
-html_context = {
-   "default_mode": "light"
-}
 # temporary fix, see https://github.com/pydata/pydata-sphinx-theme/issues/1662
 html_sidebars = {
     "installation": [],

docs/environment.yaml

@@ -27,7 +27,7 @@ dependencies:
 - tqdm
 - pip:
   - git+https://github.com/OpenFreeEnergy/gufe@main
-  - git+https://github.com/OpenFreeEnergy/ofe-sphinx-theme@v0.3.0
+  - git+https://github.com/OpenFreeEnergy/ofe-sphinx-theme@v0.3.1
   # pip install these so that conda-forge gufe doesn't pull in ambertools and cause a memory error
   - git+https://github.com/OpenFreeEnergy/kartograf@main
   - git+https://github.com/OpenFreeEnergy/konnektor@main

openfe/protocols/openmm_septop/equil_septop_method.py

@@ -710,7 +710,7 @@ class SepTopProtocolResult(gufe.ProtocolResult):
 
         return production_lengths
 
-    def restraint_geometries(self) -> tuple[list[dict[str, Any]], list[dict[str, Any]]]:
+    def restraint_geometries(self) -> tuple[list[BoreschRestraintGeometry], list[BoreschRestraintGeometry]]:
         """
         Get a list of the restraint geometries for the
         complex simulations. These define the atoms that have
@@ -726,11 +726,15 @@ class SepTopProtocolResult(gufe.ProtocolResult):
           in the system that are involved in the restraint of ligand B.
         """
         geometry_A = [
-            pus[0].outputs["restraint_geometry_A"]
+            BoreschRestraintGeometry.model_validate(
+                pus[0].outputs["restraint_geometry_A"]
+            )
             for pus in self.data["complex_setup"].values()
         ]
         geometry_B = [
-            pus[0].outputs["restraint_geometry_B"]
+            BoreschRestraintGeometry.model_validate(
+                pus[0].outputs["restraint_geometry_B"]
+            )
             for pus in self.data["complex_setup"].values()
         ]
 

openfe/tests/protocols/openmm_septop/test_septop_protocol.py

@@ -30,6 +30,7 @@ from openfe.protocols.openmm_septop.equil_septop_method import (
 )
 from openfe.protocols.openmm_septop.utils import deserialize
 from openfe.protocols.openmm_utils import system_validation
+from openfe.protocols.restraint_utils.geometry.boresch import BoreschRestraintGeometry
 from openfe.tests.protocols.conftest import compute_energy
 from openff.units import unit as offunit
 from openff.units.openmm import ensure_quantity, from_openmm
@@ -1434,7 +1435,12 @@ class TestProtocolResult:
         assert isinstance(geom, tuple)
         assert len(geom) == 2
         assert isinstance(geom[0], list)
-        assert isinstance(geom[0][0], dict)
-        assert list(geom[0][0].keys()) == [
-            'guest_atoms', 'host_atoms', 'r_aA0', 'theta_A0', 'theta_B0', 'phi_A0', 'phi_B0', 'phi_C0',
-        ]
+        assert isinstance(geom[0][0], BoreschRestraintGeometry)
+        assert geom[0][0].guest_atoms == [1779, 1778, 1777]
+        assert geom[0][0].host_atoms == [802, 801, 800]
+        assert pytest.approx(geom[0][0].r_aA0) == 0.774170 * offunit.nanometer
+        assert pytest.approx(geom[0][0].theta_A0) == 1.793181 * offunit.radian
+        assert pytest.approx(geom[0][0].theta_B0) == 1.501008 * offunit.radian
+        assert pytest.approx(geom[0][0].phi_A0) == 0.939174 * offunit.radian
+        assert pytest.approx(geom[0][0].phi_B0) == -1.504071 * offunit.radian
+        assert pytest.approx(geom[0][0].phi_C0) == -0.745093 * offunit.radian