Add replacements for pint dynamic classes. (#341)

Author: SimonBoothroyd

devtools/conda-envs/test_env.yaml

@@ -19,7 +19,7 @@ dependencies:
   - pandas
   - openmm
   - networkx
-  - pint >=0.10.1,<0.15
+  - pint >=0.16.1
   - packmol
   - pymbar >=3.0.5
   - mdtraj >=1.9.3

docs/layers/workflowlayer.rst

@@ -26,7 +26,7 @@
 
 .. |parameter_gradient_key|       replace:: :py:class:`~openff.evaluator.forcefield.ParameterGradientKey`
 
-.. |quantity|                     replace:: :py:class:`~pint.Quantity`
+.. |quantity|                     replace:: :py:class:`~openff.evaluator.utils.units.Quantity`
 
 Workflow Layers
 ===============

docs/observables/observables.rst

@@ -11,8 +11,8 @@
 .. |parameter_gradient|      replace:: :py:class:`~openff.evaluator.forcefield.ParameterGradient`
 .. |parameter_gradient_key|  replace:: :py:class:`~openff.evaluator.forcefield.ParameterGradientKey`
 
-.. |quantity|                replace:: :py:class:`~pint.Quantity`
-.. |measurement|             replace:: :py:class:`~pint.Measurement`
+.. |quantity|                replace:: :py:class:`~openff.evaluator.utils.units.Quantity`
+.. |measurement|             replace:: :py:class:`~openff.evaluator.utils.units.Measurement`
 
 .. |float|                   replace:: :py:class:`~float`
 .. |int|                     replace:: :py:class:`~int`
@@ -57,17 +57,17 @@ Supported Operations
 
 .. rst-class:: spaced-list
 
-    - **+ and -**: |observable| objects can be summed with and subtracted from other |observable| objects, pint
+    - **+ and -**: |observable| objects can be summed with and subtracted from other |observable| objects,
       |quantity| objects, floats or integers. When two |observable| objects are summed / subtracted, their gradients are
       combined by summing / subtracting also. When an |observable| is summed / subtracted with a |quantity|,
       |float| or |int| object it is assumed that these objects do not depend on any force field parameters.
 
-    - **\***: |observable| objects may be multiplied by other |observable| objects, pint |quantity| objects, and |float|
+    - **\***: |observable| objects may be multiplied by other |observable| objects, |quantity| objects, and |float|
       or |int| objects. When two |observable| objects are multiplied their gradients are propagated using the product
       rule. When an |observable| is multiplied by a |quantity|, |float| or |int| object it is assumed that these
       objects do not depend on any force field parameters.
 
-    - **/**: |observable| objects may be divided by other |observable| objects, pint |quantity| objects, and |float| or
+    - **/**: |observable| objects may be divided by other |observable| objects, |quantity| objects, and |float| or
       |int| objects. Gradients are propagated through the division using the quotient rule. When an |observable| is
       divided by a |quantity|, |float| or |int| object (or when these objects are divided by an |observable| object)
       it is assumed that these objects do not depend on any force field parameters.

docs/workflows/protocols.rst

@@ -69,7 +69,7 @@ The inputs and outputs of a protocol are defined using the custom |input_attribu
         # once it is executed.
         result = OutputAttribute(
             docstring="The sum of the values.",
-            type_hint=typing.Union[int, float, pint.Measurement, pint.Quantity],
+            type_hint=typing.Union[int, float, unit.Measurement, unit.Quantity],
         )
 
         def _execute(self, directory, available_resources):
@@ -193,7 +193,7 @@ just wish to take the larger / smaller of the two inputs::
 
     timestep = InputAttribute(
         docstring="The timestep to evolve the system by at each step.",
-        type_hint=pint.Quantity,
+        type_hint=unit.Quantity,
         merge_behavior=InequalityMergeBehaviour.SmallestValue,
         default_value=2.0 * unit.femtosecond,
     )

docs/workflows/replicators.rst

@@ -33,7 +33,7 @@
 .. |replicator_value|             replace:: :py:class:`~openff.evaluator.workflow.utils.ReplicatorValue`
 .. |placeholder_id|               replace:: :py:attr:`~openff.evaluator.workflow.schemas.ProtocolReplicator.placeholder_id`
 
-.. |quantity|                     replace:: :py:class:`~pint.Quantity`
+.. |quantity|                     replace:: :py:class:`~openff.evaluator.utils.units.Quantity`
 
 Replicators
 ===========

openff/evaluator/__init__.py

@@ -3,20 +3,11 @@
 A physical property evaluation toolkit from the Open Forcefield Consortium.
 """
 
-import warnings
-
-import pint
-
 from ._version import get_versions
 from .plugins import register_default_plugins, register_external_plugins
+from .utils.units import DEFAULT_UNIT_REGISTRY
 
-unit = pint.UnitRegistry()
-unit.default_format = "~"
-pint.set_application_registry(unit)
-
-with warnings.catch_warnings():
-    warnings.simplefilter("ignore")
-    pint.Quantity([])
+unit = DEFAULT_UNIT_REGISTRY
 
 # Load the default plugins
 register_default_plugins()

openff/evaluator/attributes/attributes.py

@@ -7,8 +7,6 @@
 from collections.abc import Iterable, Mapping
 from enum import Enum, IntEnum, IntFlag
 
-import pint
-
 from openff.evaluator import unit
 from openff.evaluator.attributes.typing import is_instance_of_type, is_supported_type
 from openff.evaluator.utils.serialization import TypedBaseModel
@@ -94,7 +92,7 @@ def validate(self, attribute_type=None):
                 )
 
             elif isinstance(attribute_value, Iterable) and not isinstance(
-                attribute_value, pint.Quantity
+                attribute_value, (unit.Quantity, unit.Measurement)
             ):
 
                 iterable_values = (
@@ -188,8 +186,6 @@ def __getstate__(self):
 
     def __setstate__(self, state):
 
-        import pint
-
         attribute_names = self.get_attributes()
 
         for name in attribute_names:
@@ -205,22 +201,6 @@ def __setstate__(self, state):
             elif attribute.optional and name not in state:
                 state[name] = UNDEFINED
 
-            if isinstance(state[name], pint.Measurement) and not isinstance(
-                state[name], unit.Measurement
-            ):
-
-                state[name] = unit.Measurement.__new__(
-                    unit.Measurement, state[name].value, state[name].error
-                )
-
-            elif isinstance(state[name], pint.Quantity) and not isinstance(
-                state[name], unit.Quantity
-            ):
-
-                state[name] = unit.Quantity.__new__(
-                    unit.Quantity, state[name].magnitude, state[name].units
-                )
-
             self._set_value(name, state[name])
 
 
@@ -276,14 +256,7 @@ def __init__(
             )
 
         if hasattr(type_hint, "__qualname__"):
-
-            if type_hint.__qualname__ == "build_quantity_class.<locals>.Quantity":
-                docstring = f"Quantity: {docstring}"
-            elif type_hint.__qualname__ == "build_quantity_class.<locals>.Unit":
-                docstring = f"Unit: {docstring}"
-            else:
-                docstring = f"{type_hint.__qualname__}: {docstring}"
-
+            docstring = f"{type_hint.__qualname__}: {docstring}"
         elif hasattr(type_hint, "__name__"):
             docstring = f"{type_hint.__name__}: {docstring}"
         else:
@@ -293,7 +266,7 @@ def __init__(
         self._default_value = default_value
 
         if isinstance(
-            default_value, (int, float, str, pint.Quantity, pint.Measurement, Enum)
+            default_value, (int, float, str, unit.Quantity, unit.Measurement, Enum)
         ) or (
             isinstance(default_value, (list, tuple, set, frozenset))
             and len(default_value) <= 4

openff/evaluator/backends/backends.py

@@ -5,8 +5,6 @@
 import re
 from enum import Enum
 
-import pint
-
 from openff.evaluator import unit
 
 
@@ -157,7 +155,7 @@ def __init__(
         assert self._per_thread_memory_limit is not None
 
         assert (
-            isinstance(self._per_thread_memory_limit, pint.Quantity)
+            isinstance(self._per_thread_memory_limit, unit.Quantity)
             and unit.get_base_units(unit.byte)[-1]
             == unit.get_base_units(self._per_thread_memory_limit.units)[-1]
         )

openff/evaluator/data/units/__init__.py

@@ -0,0 +1,44 @@
+# Based on the default Pint constants definition file (0.16.1)
+#   https://github.com/hgrecco/pint/tree/master/pint
+#
+# Based on the International System of Units
+# Language: english
+# Source: https://physics.nist.gov/cuu/Constants/
+#         https://physics.nist.gov/PhysRefData/XrayTrans/Html/search.html
+# :copyright: 2013,2019 by Pint Authors, see https://github.com/hgrecco/pint/blob/0.16.1/AUTHORS for more details.
+
+#### MATHEMATICAL CONSTANTS ####
+# As computed by Maxima with fpprec:50
+
+pi     = 3.1415926535897932384626433832795028841971693993751 = π  # pi
+
+#### DEFINED EXACT CONSTANTS ####
+# Recommended CODATA-2018 values
+
+speed_of_light = 299792458 m/s = c = c_0                      # since 1983
+planck_constant = 6.62607015e-34 J s = h                      # since May 2019
+elementary_charge = 1.602176634e-19 C = e                     # since May 2019
+avogadro_number = 6.02214076e23                               # since May 2019
+boltzmann_constant = 1.380649e-23 J K^-1 = k = k_B            # since May 2019
+standard_atmosphere = 1.01325e5 Pa = atm = atmosphere         # since 1954
+
+#### DERIVED EXACT CONSTANTS ####
+# Floating-point conversion may introduce inaccuracies
+
+zeta = c / (cm/s) = ζ
+dirac_constant = h / (2 * π) = ħ = hbar = atomic_unit_of_action = a_u_action
+avogadro_constant = avogadro_number * mol^-1 = N_A
+molar_gas_constant = k * N_A = R
+
+#### MEASURED CONSTANTS ####
+# Recommended CODATA-2018 values
+
+rydberg_constant = 1.0973731568160e7 * m^-1 = R_∞ = R_inf                                  # (21)
+atomic_mass_constant = 1.66053906660e-27 kg = m_u                                          # (50)
+electron_mass = 9.1093837015e-31 kg = m_e = atomic_unit_of_mass = a_u_mass                 # (28)
+
+#### DERIVED CONSTANTS ####
+
+fine_structure_constant = (2 * h * R_inf / (m_e * c)) ** 0.5 = α = alpha
+vacuum_permeability = 2 * α * h / (e ** 2 * c) = µ_0 = mu_0 = mu0 = magnetic_constant
+vacuum_permittivity = e ** 2 / (2 * α * h * c) = ε_0 = epsilon_0 = eps_0 = eps0 = electric_constant