Import vendored openff.models from gufe

devtools/installer/construct.yaml

@@ -21,7 +21,7 @@ specs:
   - pytest-xdist
   # python needs to match https://github.com/googlecolab/backend-info/blob/main/os-info.txt
   # until colab pushes a fix
-  - python 3.11.11
+  - python 3.11.12
 
 # Not building an .exe for windows or a .pkg for macOS
 installer_type: sh

news/numpy2.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* Added compatibility for Numpy 2
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

openfe/protocols/openmm_rfe/equil_rfe_settings.py

@@ -10,7 +10,7 @@
 
 from typing import Literal
 from openff.units import unit
-from openff.models.types import FloatQuantity
+from gufe.vendor.openff.models.types import FloatQuantity
 
 from gufe.settings import (
     Settings,
@@ -36,8 +36,8 @@ class Config:
         arbitrary_types_allowed = True
 
     """Lambda schedule settings.
-    
-    Settings controlling the lambda schedule, these include the switching 
+
+    Settings controlling the lambda schedule, these include the switching
     function type, and the number of windows.
     """
     lambda_functions = 'default'
@@ -73,7 +73,7 @@ class Config:
     """
     softcore_LJ: Literal['gapsys', 'beutler']
     """
-    Whether to use the LJ softcore function as defined by Gapsys et al. 
+    Whether to use the LJ softcore function as defined by Gapsys et al.
     JCTC 2012, or the one by Beutler et al. Chem. Phys. Lett. 1994.
     Default 'gapsys'.
     """
@@ -82,7 +82,7 @@ class Config:
     turn_off_core_unique_exceptions = False
     """
     Whether to turn off interactions for new exceptions (not just 1,4s)
-    at lambda 0 and old exceptions at lambda 1 between unique atoms and core 
+    at lambda 0 and old exceptions at lambda 1 between unique atoms and core
     atoms. If False they are present in the nonbonded force. Default False.
     """
     explicit_charge_correction = False
@@ -108,9 +108,9 @@ class Config:
 class RelativeHybridTopologyProtocolSettings(Settings):
     protocol_repeats: int
     """
-    The number of completely independent repeats of the entire sampling 
-    process. The mean of the repeats defines the final estimate of FE 
-    difference, while the variance between repeats is used as the uncertainty.  
+    The number of completely independent repeats of the entire sampling
+    process. The mean of the repeats defines the final estimate of FE
+    difference, while the variance between repeats is used as the uncertainty.
     """
 
     @validator('protocol_repeats')

openfe/protocols/openmm_utils/omm_settings.py

@@ -11,7 +11,7 @@
 
 from typing import Optional, Literal
 from openff.units import unit
-from openff.models.types import FloatQuantity, ArrayQuantity
+from gufe.vendor.openff.models.types import FloatQuantity, ArrayQuantity
 from openff.interchange.components._packmol import _box_vectors_are_in_reduced_form
 
 from gufe.settings import (
@@ -571,15 +571,15 @@ class Config:
     Must be a multiple of ``OutputSettings.checkpoint_interval``
 
     Default `250`.
-    
+
     """
     early_termination_target_error: Optional[FloatQuantity['kilocalorie_per_mole']] = 0.0 * unit.kilocalorie_per_mole
     # todo: have default ``None`` or ``0.0 * unit.kilocalorie_per_mole``
     #  (later would give an example of unit).
     """
-    Target error for the real time analysis measured in kcal/mol. Once the MBAR 
-    error of the free energy is at or below this value, the simulation will be 
-    considered complete. 
+    Target error for the real time analysis measured in kcal/mol. Once the MBAR
+    error of the free energy is at or below this value, the simulation will be
+    considered complete.
     A suggested value of 0.12 * `unit.kilocalorie_per_mole` has
     shown to be effective in both hydration and binding free energy benchmarks.
     Default ``None``, i.e. no early termination will occur.
@@ -588,8 +588,8 @@ class Config:
     # todo: Add validators in the protocol
     """
     Simulation time which must pass before real time analysis is
-    carried out. 
-    
+    carried out.
+
     Default 500 * unit.picosecond.
     """
 
@@ -653,7 +653,7 @@ class Config:
 
     equilibration_length_nvt: Optional[FloatQuantity['nanosecond']]
     """
-    Length of the equilibration phase in the NVT ensemble in units of time. 
+    Length of the equilibration phase in the NVT ensemble in units of time.
     The total number of steps from this equilibration length
     (i.e. ``equilibration_length_nvt`` / :class:`IntegratorSettings.timestep`).
     If None, no NVT equilibration will be performed.
@@ -673,16 +673,16 @@ class Config:
     Frequency to write the xtc file. Default 5000 * unit.timestep.
     """
     preminimized_structure: Optional[str] = 'system.pdb'
-    """Path to the pdb file of the full pre-minimized system. 
+    """Path to the pdb file of the full pre-minimized system.
     Default 'system.pdb'."""
     minimized_structure: Optional[str] = 'minimized.pdb'
-    """Path to the pdb file of the system after minimization. 
+    """Path to the pdb file of the system after minimization.
     Only the specified atom subset is saved. Default 'minimized.pdb'."""
     equil_nvt_structure: Optional[str] = 'equil_nvt.pdb'
-    """Path to the pdb file of the system after NVT equilibration. 
+    """Path to the pdb file of the system after NVT equilibration.
     Only the specified atom subset is saved. Default 'equil_nvt.pdb'."""
     equil_npt_structure: Optional[str] = 'equil_npt.pdb'
-    """Path to the pdb file of the system after NPT equilibration. 
+    """Path to the pdb file of the system after NPT equilibration.
     Only the specified atom subset is saved. Default 'equil_npt.pdb'."""
     log_output: Optional[str] = 'simulation.log'
     """

openfe/setup/atom_mapping/perses_mapper.py

@@ -7,7 +7,7 @@
 """
 
 from openfe.utils import requires_package
-from openff.models.types import FloatQuantity
+from gufe.vendor.openff.models.types import FloatQuantity
 from openff.units import unit
 from openff.units.openmm import to_openmm