pint typing fixes

src/alhambra_mixes/abbreviated.py

@@ -39,11 +39,11 @@
 Mix = Mix
 Exp = Experiment
 
-µM = ureg("µM")
-uM = ureg("uM")
-nM = ureg("nM")
-mM = ureg("mM")
-nL = ureg("nL")
-µL = ureg("µL")
-uL = ureg("uL")
-mL = ureg("mL")
+µM = ureg.Unit("µM")
+uM = ureg.Unit("uM")
+nM = ureg.Unit("nM")
+mM = ureg.Unit("mM")
+nL = ureg.Unit("nL")
+µL = ureg.Unit("µL")
+uL = ureg.Unit("uL")
+mL = ureg.Unit("mL")

src/alhambra_mixes/actions.py

@@ -44,9 +44,9 @@ def name(self) -> str:  # pragma: no cover
 
     def tx_volume(
         self,
-        mix_vol: Quantity[Decimal] = Q_(DNAN, uL),
+        mix_vol: DecimalQuantity = Q_(DNAN, uL),
         actions: Sequence[AbstractAction] = tuple(),
-    ) -> Quantity[Decimal]:  # pragma: no cover
+    ) -> DecimalQuantity:  # pragma: no cover
         """The total volume transferred by the action to the sample.  May depend on the total mix volume.
 
         Parameters
@@ -61,14 +61,14 @@ def tx_volume(
     def _mixlines(
         self,
         tablefmt: str | TableFormat,
-        mix_vol: Quantity[Decimal],
+        mix_vol: DecimalQuantity,
         actions: Sequence[AbstractAction] = tuple(),
     ) -> Sequence[MixLine]:  # pragma: no cover
         ...
 
     @abstractmethod
     def all_components(
-        self, mix_vol: Quantity[Decimal], actions: Sequence[AbstractAction] = tuple()
+        self, mix_vol: DecimalQuantity, actions: Sequence[AbstractAction] = tuple()
     ) -> pd.DataFrame:  # pragma: no cover
         """A dataframe containing all base components added by the action.
 
@@ -95,8 +95,8 @@ def with_reference(
         ...
 
     def dest_concentration(
-        self, mix_vol: Quantity[Decimal], actions: Sequence[AbstractAction] = tuple()
-    ) -> Quantity[Decimal]:
+        self, mix_vol: DecimalQuantity, actions: Sequence[AbstractAction] = tuple()
+    ) -> DecimalQuantity:
         """The destination concentration added to the mix by the action.
 
         Raises
@@ -109,8 +109,8 @@ def dest_concentration(
         raise ValueError("Single destination concentration not defined.")
 
     def dest_concentrations(
-        self, mix_vol: Quantity[Decimal], actions: Sequence[AbstractAction] = tuple()
-    ) -> Sequence[Quantity[Decimal]]:
+        self, mix_vol: DecimalQuantity, actions: Sequence[AbstractAction] = tuple()
+    ) -> Sequence[DecimalQuantity]:
         raise ValueError
 
     @property
@@ -121,9 +121,9 @@ def components(self) -> list[AbstractComponent]:
     @abstractmethod
     def each_volumes(
         self,
-        total_volume: Quantity[Decimal],
+        total_volume: DecimalQuantity,
         actions: Sequence[AbstractAction] = tuple(),
-    ) -> list[Quantity[Decimal]]:
+    ) -> list[DecimalQuantity]:
         ...
 
     @classmethod
@@ -200,7 +200,7 @@ def with_reference(
             )
 
     @property
-    def source_concentrations(self) -> list[Quantity[Decimal]]:
+    def source_concentrations(self) -> list[DecimalQuantity]:
         concs = [c.concentration for c in self.components]
         return concs
 
@@ -242,7 +242,7 @@ def _structure(
         return cls(**d)
 
     def all_components(
-        self, mix_vol: Quantity[Decimal], actions: Sequence[AbstractAction] = tuple()
+        self, mix_vol: DecimalQuantity, actions: Sequence[AbstractAction] = tuple()
     ) -> pd.DataFrame:
         newdf = _empty_components()
 
@@ -267,8 +267,8 @@ def all_components(
     def _compactstrs(
         self,
         tablefmt: str | TableFormat,
-        dconcs: Sequence[Quantity[Decimal]],
-        eavols: Sequence[Quantity[Decimal]],
+        dconcs: Sequence[DecimalQuantity],
+        eavols: Sequence[DecimalQuantity],
     ) -> Sequence[MixLine]:
         # locs = [(c.name,) + c.location for c in self.components]
         # names = [c.name for c in self.components]
@@ -296,18 +296,18 @@ def _compactstrs(
         )
 
         names: list[list[str]] = []
-        source_concs: list[Quantity[Decimal]] = []
-        dest_concs: list[Quantity[Decimal]] = []
+        source_concs: list[DecimalQuantity] = []
+        dest_concs: list[DecimalQuantity] = []
         numbers: list[int] = []
-        ea_vols: list[Quantity[Decimal]] = []
-        tot_vols: list[Quantity[Decimal]] = []
+        ea_vols: list[DecimalQuantity] = []
+        tot_vols: list[DecimalQuantity] = []
         plates: list[str] = []
         wells_list: list[list[WellPos]] = []
 
         for plate, plate_comps in locdf.groupby("plate"):  # type: str, pd.DataFrame
             for vol, plate_vol_comps in plate_comps.groupby(
                 "ea_vols"
-            ):  # type: Quantity[Decimal], pd.DataFrame
+            ):  # type: DecimalQuantity, pd.DataFrame
                 if pd.isna(plate_vol_comps["well"].iloc[0]):
                     if not pd.isna(plate_vol_comps["well"]).all():
                         raise ValueError
@@ -410,7 +410,7 @@ class FixedVolume(ActionWithComponents):
     | c1, c2, c3 | 200.00 nM | 66.67 nM  |   3 | 5.00 µl     | 15.00 µl     |       |        |
     """
 
-    fixed_volume: Quantity[Decimal] = attrs.field(
+    fixed_volume: DecimalQuantity = attrs.field(
         converter=_parse_vol_required, on_setattr=attrs.setters.convert
     )
     set_name: str | None = None
@@ -431,9 +431,9 @@ def __new__(cls, *args, **kwargs):
 
     def dest_concentrations(
         self,
-        mix_vol: Quantity[Decimal] = Q_(DNAN, uL),
+        mix_vol: DecimalQuantity = Q_(DNAN, uL),
         actions: Sequence[AbstractAction] = tuple(),
-    ) -> list[Quantity[Decimal]]:
+    ) -> list[DecimalQuantity]:
         return [
             x * y
             for x, y in zip(
@@ -443,10 +443,10 @@ def dest_concentrations(
 
     def each_volumes(
         self,
-        mix_vol: Quantity[Decimal] = Q_(DNAN, uL),
+        mix_vol: DecimalQuantity = Q_(DNAN, uL),
         actions: Sequence[AbstractAction] = tuple(),
-    ) -> list[Quantity[Decimal]]:
-        return [self.fixed_volume.to(uL)] * len(self.components)
+    ) -> list[DecimalQuantity]:
+        return [cast(DecimalQuantity, self.fixed_volume.to(uL))] * len(self.components)
 
     @property
     def name(self) -> str:
@@ -458,7 +458,7 @@ def name(self) -> str:
     def _mixlines(
         self,
         tablefmt: str | TableFormat,
-        mix_vol: Quantity[Decimal],
+        mix_vol: DecimalQuantity,
         actions: Sequence[AbstractAction] = tuple(),
     ) -> list[MixLine]:
         dconcs = self.dest_concentrations(mix_vol)
@@ -551,7 +551,7 @@ class EqualConcentration(FixedVolume):
     def __init__(
         self,
         components: Sequence[AbstractComponent | str] | AbstractComponent | str,
-        fixed_volume: str | Quantity[Decimal],
+        fixed_volume: str | DecimalQuantity,
         set_name: str | None = None,
         compact_display: bool = True,
         method: Literal["max_volume", "min_volume", "check"]
@@ -577,17 +577,17 @@ def __init__(
     ] = "min_volume"
 
     @property
-    def source_concentrations(self) -> List[Quantity[Decimal]]:
+    def source_concentrations(self) -> List[DecimalQuantity]:
         concs = super().source_concentrations
         if any(x != concs[0] for x in concs) and (self.method == "check"):
             raise ValueError("Not all components have equal concentration.")
         return concs
 
     def each_volumes(
         self,
-        mix_vol: Quantity[Decimal] = Q_(DNAN, uL),
+        mix_vol: DecimalQuantity = Q_(DNAN, uL),
         actions: Sequence[AbstractAction] = tuple(),
-    ) -> list[Quantity[Decimal]]:
+    ) -> list[DecimalQuantity]:
         # match self.equal_conc:
         if self.method == "min_volume":
             sc = self.source_concentrations
@@ -603,22 +603,22 @@ def each_volumes(
             sc = self.source_concentrations
             if any(x != sc[0] for x in sc):
                 raise ValueError("Concentrations")
-            return [self.fixed_volume.to(uL)] * len(self.components)
+            return [cast(DecimalQuantity, self.fixed_volume.to(uL))] * len(self.components)
         raise ValueError(f"equal_conc={repr(self.method)} not understood")
 
     def tx_volume(
         self,
-        mix_vol: Quantity[Decimal] = Q_(DNAN, uL),
+        mix_vol: DecimalQuantity = Q_(DNAN, uL),
         actions: Sequence[AbstractAction] = tuple(),
-    ) -> Quantity[Decimal]:
+    ) -> DecimalQuantity:
         if isinstance(self.method, Sequence) and (self.method[0] == "max_fill"):
             return self.fixed_volume * len(self.components)
         return sum(self.each_volumes(mix_vol), ureg("0.0 uL"))
 
     def _mixlines(
         self,
         tablefmt: str | TableFormat,
-        mix_vol: Quantity[Decimal],
+        mix_vol: DecimalQuantity,
         actions: Sequence[AbstractAction] = tuple(),
     ) -> list[MixLine]:
         ml = super()._mixlines(tablefmt, mix_vol)
@@ -683,29 +683,29 @@ class FixedConcentration(ActionWithComponents):
     | *Total:*   |           | 40.00 nM  |     |             | 25.00 µl     |       |        |
     """
 
-    fixed_concentration: Quantity[Decimal] = attrs.field(
+    fixed_concentration: DecimalQuantity = attrs.field(
         converter=_parse_conc_required, on_setattr=attrs.setters.convert
     )
     set_name: str | None = None
     compact_display: bool = True
-    min_volume: Quantity[Decimal] = attrs.field(
+    min_volume: DecimalQuantity = attrs.field(
         converter=_parse_vol_optional_none_zero,
         default=ZERO_VOL,
         on_setattr=attrs.setters.convert,
     )
 
     def dest_concentrations(
         self,
-        mix_vol: Quantity[Decimal] = Q_(DNAN, uL),
+        mix_vol: DecimalQuantity = Q_(DNAN, uL),
         actions: Sequence[AbstractAction] = tuple(),
-    ) -> list[Quantity[Decimal]]:
+    ) -> list[DecimalQuantity]:
         return [self.fixed_concentration] * len(self.components)
 
     def each_volumes(
         self,
-        mix_vol: Quantity[Decimal] = Q_(DNAN, uL),
+        mix_vol: DecimalQuantity = Q_(DNAN, uL),
         actions: Sequence[AbstractAction] = tuple(),
-    ) -> list[Quantity[Decimal]]:
+    ) -> list[DecimalQuantity]:
         ea_vols = [
             mix_vol * r
             for r in _ratio(self.fixed_concentration, self.source_concentrations)
@@ -727,7 +727,7 @@ def each_volumes(
     def _mixlines(
         self,
         tablefmt: str | TableFormat,
-        mix_vol: Quantity[Decimal],
+        mix_vol: DecimalQuantity,
         actions: Sequence[AbstractAction] = tuple(),
     ) -> list[MixLine]:
         dconcs = self.dest_concentrations(mix_vol)
@@ -772,18 +772,18 @@ class ToConcentration(ActionWithComponents):
     takes into account other contents of the mix, and only adds enough to reach a particular final
     concentration."""
 
-    fixed_concentration: Quantity[Decimal] = attrs.field(
+    fixed_concentration: DecimalQuantity = attrs.field(
         converter=_parse_conc_required, on_setattr=attrs.setters.convert
     )
     compact_display: bool = True
-    min_volume: Quantity[Decimal] = attrs.field(
+    min_volume: DecimalQuantity = attrs.field(
         converter=_parse_vol_optional,
         default=Q_(DNAN, uL),
         on_setattr=attrs.setters.convert,
     )
 
     def _othercomps(
-        self, mix_vol: Quantity[Decimal], actions: Sequence[AbstractAction] = tuple()
+        self, mix_vol: DecimalQuantity, actions: Sequence[AbstractAction] = tuple()
     ):
         cps = _empty_components()
 
@@ -820,10 +820,10 @@ def _othercomps(
 
     def dest_concentrations(
         self,
-        mix_vol: Quantity[Decimal],
+        mix_vol: DecimalQuantity,
         actions: Sequence[AbstractAction] = tuple(),
         _othercomps: pd.DataFrame | None = None,
-    ) -> Sequence[Quantity[Decimal]]:
+    ) -> Sequence[DecimalQuantity]:
         if _othercomps is None and actions:
             _othercomps = self._othercomps(mix_vol, actions)
         if _othercomps is not None:
@@ -839,10 +839,10 @@ def dest_concentrations(
 
     def each_volumes(
         self,
-        mix_vol: Quantity[Decimal] = Q_(DNAN, uL),
+        mix_vol: DecimalQuantity = Q_(DNAN, uL),
         actions: Sequence[AbstractAction] = tuple(),
         _othercomps: pd.DataFrame | None = None,
-    ) -> list[Quantity[Decimal]]:
+    ) -> list[DecimalQuantity]:
         ea_vols = [
             mix_vol * r
             for r in _ratio(
@@ -867,7 +867,7 @@ def each_volumes(
     def _mixlines(
         self,
         tablefmt: str | TableFormat,
-        mix_vol: Quantity[Decimal],
+        mix_vol: DecimalQuantity,
         actions: Sequence[AbstractAction] = tuple(),
     ) -> list[MixLine]:
         othercomps = self._othercomps(mix_vol, actions)

src/alhambra_mixes/components.py

@@ -113,9 +113,9 @@ def printed_name(self, tablefmt: str | TableFormat) -> str:
 
     def _update_volumes(
         self,
-        consumed_volumes: Dict[str, Quantity[Decimal]] = {},
-        made_volumes: Dict[str, Quantity[Decimal]] = {},
-    ) -> Tuple[Dict[str, Quantity[Decimal]], Dict[str, Quantity[Decimal]]]:
+        consumed_volumes: Dict[str, DecimalQuantity] = {},
+        made_volumes: Dict[str, DecimalQuantity] = {},
+    ) -> Tuple[Dict[str, DecimalQuantity], Dict[str, DecimalQuantity]]:
         """
         Given a
         """

src/alhambra_mixes/experiments.py

@@ -20,7 +20,7 @@
 import attrs
 
 from .dictstructure import _structure, _unstructure
-from .units import DNAN, Q_, ZERO_VOL, Decimal, uL, Quantity
+from .units import DNAN, Q_, ZERO_VOL, Decimal, uL, Quantity, DecimalQuantity
 from .mixes import Mix
 from .mixes import VolumeError
 
@@ -102,10 +102,10 @@ def add_mix(
         name: str = "",
         test_tube_name: str | None = None,
         *,
-        fixed_total_volume: Quantity[Decimal] | str = Q_(DNAN, uL),
-        fixed_concentration: str | Quantity[Decimal] | None = None,
+        fixed_total_volume: DecimalQuantity | str = Q_(DNAN, uL),
+        fixed_concentration: str | DecimalQuantity | None = None,
         buffer_name: str = "Buffer",
-        min_volume: Quantity[Decimal] | str = Q_("0.5", uL),
+        min_volume: DecimalQuantity | str = Q_("0.5", uL),
         check_volumes: bool | None = None,
         apply_reference: bool = True,
         check_existing: bool | Literal["equal"] = "equal",
@@ -199,9 +199,9 @@ def __iter__(self) -> Iterator[AbstractComponent]:
 
     def consumed_and_produced_volumes(
         self,
-    ) -> Mapping[str, Tuple[Quantity[Decimal], Quantity[Decimal]]]:
-        consumed_volume: Dict[str, Quantity[Decimal]] = {}
-        produced_volume: Dict[str, Quantity[Decimal]] = {}
+    ) -> Mapping[str, Tuple[DecimalQuantity, DecimalQuantity]]:
+        consumed_volume: Dict[str, DecimalQuantity] = {}
+        produced_volume: Dict[str, DecimalQuantity] = {}
         for component in self.components.values():
             component._update_volumes(consumed_volume, produced_volume)
         return {