riverine.experiments ==================== .. py:module:: riverine.experiments Classes ------- .. autoapisummary:: riverine.experiments.AbstractLocationType riverine.experiments.LocationInfo riverine.experiments.LocationDict riverine.experiments.Experiment Functions --------- .. autoapisummary:: riverine.experiments._exp_attr_set_reference Module Contents --------------- .. py:function:: _exp_attr_set_reference(self, attribute: Any, reference: riverine.references.Reference | None) -> riverine.references.Reference | None .. py:class:: AbstractLocationType .. py:attribute:: __slots__ :value: () .. py:property:: name :abstractmethod: .. py:property:: is_echo_source_compatible :type: bool :abstractmethod: .. py:class:: LocationInfo .. py:attribute:: echo_source_type :type: str | None :value: None .. py:attribute:: echo_dest_type :type: str | None :value: None .. py:attribute:: full_location :type: tuple[str, Ellipsis] :value: () .. py:attribute:: info :type: dict[str, Any] .. py:method:: from_obj(obj) -> LocationInfo :classmethod: .. py:class:: LocationDict(locs: dict[str, LocationInfo | Any]) .. py:attribute:: _locs :type: dict[str, LocationInfo] .. py:method:: from_obj(obj) -> LocationDict :classmethod: .. py:method:: __getitem__(key: str) -> LocationInfo .. py:method:: __setitem__(key: str, value: LocationInfo | Any) -> None .. py:method:: __delitem__(key: str) -> None .. py:method:: __contains__(key: str) -> bool .. py:method:: __iter__() -> Iterator[str] .. py:method:: __len__() -> int .. py:method:: keys() -> collections.abc.KeysView[str] .. py:method:: values() -> collections.abc.ValuesView[LocationInfo] .. py:method:: items() -> collections.abc.ItemsView[str, LocationInfo] .. py:method:: __repr__() -> str .. py:method:: __str__() -> str .. py:method:: __eq__(other) -> bool .. py:method:: get(key: str, default: Any | None = None) -> LocationInfo | None .. py:class:: Experiment A class collecting many related mixes and components, allowing methods to be run that consider all of them together. Components can be referenced, and set, by name with [], and can be iterated through. .. py:attribute:: __hash__ .. py:attribute:: components :type: dict[str, riverine.components.AbstractComponent] .. py:attribute:: volume_checks :type: bool :value: True .. py:attribute:: reference :type: riverine.references.Reference | None .. py:attribute:: locations :type: LocationDict .. py:method:: generate_picklist(_cache_key=None) -> Experiment.generate_picklist.PickList .. py:method:: add(component: riverine.components.AbstractComponent, *, check_volumes: bool | None = None, apply_reference: bool = True, check_existing: bool | Literal['equal'] = 'equal') -> Experiment .. py:method:: add_mix(mix_or_actions: riverine.mixes.Mix | Sequence[riverine.actions.AbstractAction] | riverine.actions.AbstractAction, name: str = '', test_tube_name: str | None = None, *, fixed_total_volume: riverine.units.DecimalQuantity | str | None = None, fixed_concentration: str | riverine.units.DecimalQuantity | None = None, buffer_name: str = 'Buffer', min_volume: riverine.units.DecimalQuantity | str = Q_('0.5', uL), check_volumes: bool | None = None, apply_reference: bool = True, check_existing: bool | Literal['equal'] = 'equal') -> Experiment Add a mix to the experiment, either as a Mix object, or by creating a new Mix. Either the first argument should be a Mix, or arguments should be passed as for initializing a Mix. If check_volumes is True (by default), the mix will be added to the experiment, and volumes checked. If the mix causes a volume usage problem, it will not be added to the Experiment, and a VolumeError will be raised. If check_existing is True (by default), then a exception is raised if the experiment already contains a mix with the name `name`. Otherwise, the existing mix is replaced with the new mix. .. py:method:: __setitem__(name: str, mix: riverine.components.AbstractComponent) -> None .. py:method:: get(key: str, default=None) .. py:method:: __getitem__(name: str) -> riverine.components.AbstractComponent .. py:method:: __delitem__(name: str) -> None .. py:method:: __contains__(name: str) -> bool .. py:method:: remove_mix(name: str) -> None Remove a mix from the experiment, referenced by name, .. py:method:: remove(name: str) -> None Remove a mix from the experiment, referenced by name, .. py:method:: __len__() -> int .. py:method:: __iter__() -> Iterator[riverine.components.AbstractComponent] .. py:method:: consumed_and_produced_volumes() -> Mapping[str, Tuple[riverine.units.DecimalQuantity, riverine.units.DecimalQuantity]] .. py:method:: check_volumes(showall: bool = False, display: bool = True, raise_error: bool = False) -> str | None Check to ensure that consumed volumes are less than made volumes. .. py:method:: _unstructure() -> dict[str, Any] Create a dict representation of the Experiment. .. py:method:: _structure(d: dict[str, Any]) -> Experiment :classmethod: Create an Experiment from a dict representation. .. py:method:: load(filename_or_stream: str | os.PathLike | TextIO) -> Experiment :classmethod: Load an experiment from a JSON-formatted file created by Experiment.save. .. py:method:: resolve_components() -> None Resolve string/blank-component components in mixes, searching through the mixes in the experiment. FIXME Add used mixes to the experiment if they are not already there. .. py:method:: save(filename_or_stream: str | os.PathLike | TextIO) -> None Save an experiment to a JSON-formatted file. Tries to store each component/mix only once, with other mixes referencing those components. .. py:method:: use_reference(reference: riverine.references.Reference) -> Experiment Apply a Reference, in place, to all components in the Experiment.