fix issue with bioreactor docs

Author: yoelcortes

biosteam/_unit.py

@@ -145,10 +145,11 @@ class Unit(AbstractUnit):
     max_parallel_units = int(10e3)
 
     def __init_subclass__(cls,
-                          isabstract=False,
-                          new_graphics=True,
-                          does_nothing=None,
-                          default_phenomena=None):
+            isabstract=False,
+            new_graphics=True,
+            does_nothing=None,
+            default_phenomena=None,
+        ):
         super().__init_subclass__()
         if getattr(cls, 'decoupled', None): print(cls)
         if does_nothing: return 
@@ -250,6 +251,8 @@ def __init_subclass__(cls,
                 bst.units.__dict__[name] = cls
             if name not in bst.__dict__:
                 bst.__dict__[name] = cls
+        if hasattr(cls, '_finalize_doc'):
+            cls._finalize_doc()
 
     ### Abstract Attributes ###
     #: **class-attribute** Units of measure for :attr:`~Unit.design_results` dictionary.
@@ -287,7 +290,7 @@ def __init_subclass__(cls,
     #: Add itemized purchase costs to the :attr:`~Unit.baseline_purchase_costs` dictionary.
     _cost = AbstractMethod
 
-    #: Add embodied emissions (e.g., unit construction) in LCA
+    #: Add embodied emissions (e.g., unit construction) in LCA.
     _lca = AbstractMethod
 
     def _collect_variables(self, key):

biosteam/units/abstract_stirred_tank_reactor.py

@@ -8,7 +8,7 @@
 """
 .. contents:: :local: 
 
-.. autoclass:: biosteam.units.stirred_tank_reactor.AbstractStirredTankReactor
+.. autoclass:: biosteam.units.abstract_stirred_tank_reactor.AbstractStirredTankReactor
 
 References
 ----------
@@ -32,50 +32,50 @@
 )
 
 description_doc = '''
-    The reactor is designed as a pressure vessel with a given aspect ratio and 
-    residence time. A pump-heat exchanger recirculation loop can be used to satisfy 
-    the duty, if any. By default, a turbine agitator is also included if the 
-    power usage,`kW_per_m3` , is positive. A vacuum system is also 
-    automatically added if the operating pressure is at a vacuum. 
-'''
+The reactor is designed as a pressure vessel with a given aspect ratio and 
+residence time. A pump-heat exchanger recirculation loop can be used to satisfy 
+the duty, if any. By default, a turbine agitator is also included if the 
+power usage,`kW_per_m3` , is positive. A vacuum system is also 
+automatically added if the operating pressure is at a vacuum. 
+'''[1:]
 
 parameters_doc ='''
-    tau :
-        Residence time [hr].
-    T : 
-        Operating temperature [K].
-    P : 
-        Operating pressure [Pa].
-    V_wf : 
-        Fraction of working volume over total volume. Defaults to 0.8.
-    V_max :
-        Maximum volume of a reactor [m3]. Defaults to 355.
-    kW_per_m3: 
-        Power usage of agitator. Defaults to 0.985 [kW / m3] converted from 
-        5 hp/1000 gal as in [1]_, for liquid–liquid reaction or extraction.
-    vessel_material : 
-        Vessel material. Defaults to 'Stainless steel 316'.
-    vessel_type : 
-        Vessel type. Valid options are 'Horizontal' or 'Vertical'. Defaults to 'Vertical'
-    batch :
-        Whether to use batch operation mode. If False, operation mode is continuous.
-        Defaults to `continuous`.
-    tau_0 : 
-        Cleaning and unloading time (if batch mode). Defaults to 3 hr.
-    N_reactors :
-        Number of reactors.
-    heat_exchanger_configuration: 
-        What kind of heat exchanger to default to (if any). Valid options include 
-        'jacketed', 'recirculation loop', and 'internal coil'. 
-        Defaults to 'recirculation loop'.
-    dT_hx_loop : 
-        Maximum change in temperature for the heat exchanger loop. Defaults to 5 K.
-    jacket_annular_diameter :
-        Annular diameter of heat exchanger jacket to vessel [m]. Defaults to 0.1 m.
-    loading_time :
-        Loading time of batch reactor. If not given, it will assume each vessel is constantly
+tau :
+    Residence time [hr].
+T : 
+    Operating temperature [K].
+P : 
+    Operating pressure [Pa].
+V_wf : 
+    Fraction of working volume over total volume. Defaults to 0.8.
+V_max :
+    Maximum volume of a reactor [m3]. Defaults to 355.
+kW_per_m3: 
+    Power usage of agitator. Defaults to 0.985 [kW / m3] converted from 
+    5 hp/1000 gal as in [1]_, for liquid–liquid reaction or extraction.
+vessel_material : 
+    Vessel material. Defaults to 'Stainless steel 316'.
+vessel_type : 
+    Vessel type. Valid options are 'Horizontal' or 'Vertical'. Defaults to 'Vertical'
+batch :
+    Whether to use batch operation mode. If False, operation mode is continuous.
+    Defaults to `continuous`.
+tau_0 : 
+    Cleaning and unloading time (if batch mode). Defaults to 3 hr.
+N_reactors :
+    Number of reactors.
+heat_exchanger_configuration: 
+    What kind of heat exchanger to default to (if any). Valid options include 
+    'jacketed', 'recirculation loop', and 'internal coil'. 
+    Defaults to 'recirculation loop'.
+dT_hx_loop : 
+    Maximum change in temperature for the heat exchanger loop. Defaults to 5 K.
+jacket_annular_diameter :
+    Annular diameter of heat exchanger jacket to vessel [m]. Defaults to 0.1 m.
+loading_time :
+    Loading time of batch reactor. If not given, it will assume each vessel is constantly
         being filled.
-'''
+'''[1:]
 
 notes_doc = '''
 The heat exchanger configuration can be one of the following:
@@ -105,10 +105,10 @@
     with the added assumption that the temperature at the wall is the 
     operating temperature. This method is still not implemented in BioSTEAM
     yet.
-'''
+'''[1:]
 
 class AbstractStirredTankReactor(PressureVessel, Unit, isabstract=True):
-    f'''{description_doc}
+    '''{description_doc}
     
     Parameters
     ----------
@@ -209,6 +209,14 @@ class AbstractStirredTankReactor(PressureVessel, Unit, isabstract=True):
     Utility cost                                              USD/hr                  152
     
     '''
+    @classmethod
+    def _finalize_doc(cls):
+        cls.__doc__ = cls.__doc__.format(
+            description_doc=description_doc,
+            parameters_doc=parameters_doc,
+            notes_doc=notes_doc
+        )
+    
     auxiliary_unit_names = (
         'heat_exchanger', 
         'vacuum_system', 
@@ -428,7 +436,7 @@ def _design(self, size_only=False):
                 N = 2
             else:
                 N = ceil(N)
-            Design.update(size_batch(v_0, tau, tau_0, N, V_wf, loading_time))
+            Design.update(size_batch(v_0, tau, tau_0, N, V_wf, self.loading_time))
             V_reactor = Design['Reactor volume']
         else:
             V_total = ins_F_vol * self.tau / self.V_wf

biosteam/units/aerated_bioreactor.py

@@ -18,12 +18,7 @@
 
 """
 import biosteam as bst
-from .abstract_stirred_tank_reactor import (
-    AbstractStirredTankReactor, 
-    description_doc,
-    parameters_doc, 
-    notes_doc,
-)
+from .abstract_stirred_tank_reactor import AbstractStirredTankReactor
 from math import pi
 import numpy as np
 from scipy.constants import g
@@ -38,7 +33,7 @@
 )
 
 class AeratedBioreactor(AbstractStirredTankReactor):
-    f"""
+    """
     Create an aerated bioreactor which satisfies the oxygen mass tranfer 
     requirement of the mass balance.
     
@@ -399,9 +394,54 @@ def _design(self):
 
 class GasFedBioreactor(AbstractStirredTankReactor):
     """
-    Same as AbstractStirredTankReactor but includes multiple gas feeds. The agitator power may
-    vary to minimize the total power requirement of both the compressor and agitator
-    yet achieve the required oxygen transfer rate.
+    Create an gas-fed bioreactor which satisfies the substrate mass tranfer 
+    requirement of the mass balance. The gas-fed bioreactor may include 
+    multiple gas feeds. The user-specified `titer` will be satisfied by varying
+    the flow rates of the `variable_gas_feeds` so long as the 
+    `backward_reactions` are specified. Otherwise, the titer will be estimated
+    assuming constant gas flow rates.
+    
+    {description_doc}
+
+    Parameters
+    ----------
+    gas_substrates : 
+        Substrates within the gas phase.
+    titer :
+        Dictionary of substrate/titer pairs [g / L].
+    backward_reactions :
+        Backwards reactions to get the substrate mass transfer requirement.
+    variable_gas_feeds :
+        Feeds that can be varied to meet mass transfer requirement.
+    theta : 
+        Fraction of gas substrate saturation in the broth. Defaults to 0.5.
+    Q_consumption :
+        Forced duty per gas substrate consummed [kJ/kmol].
+    optimize_power :
+        If true, the agitator power is solved to minimize the total power 
+        requirement of both the compressor and agitator such that the 
+        required oxygen transfer rate is met.
+    design : 
+        Bioreactor design configuration. Valid options include 'Stirred tank'
+        and 'Bubble column'. Defaults to the former.
+    method :
+        Method to calculate the overall mass transfer coefficient, kLa. 
+        Can be a name or a function. Valid method names are listed in 
+        `biosteam.aeration.kLa_methods`.
+        For stirred tanks, defaults to the 'Riet'. 
+        For bubble columns, defaults to 'Dewes'.
+    kLa_kwargs:
+        Additional arguments to pass to the kLa method.
+    cooler_pressure_drop :
+        Pressure drop at the cooler [Pa]. Defaults to 20684.28 Pa, 
+        a heuristic value for a gas.
+    compressor_isentropic_efficiency :
+        Isentropic efficiency of the compressor. Defaults to 0.85.
+    {parameters_doc}
+        
+    Notes
+    -----
+    {notes_doc}
     
     Examples
     --------
@@ -417,7 +457,7 @@ class GasFedBioreactor(AbstractStirredTankReactor):
     ...     'R1', ins=[media, H2, fluegas], outs=('vent', 'product'), tau=68, V_max=500,
     ...     reactions=rxn, backward_reactions=brxn,
     ...     gas_substrates=('H2', 'CO2'),
-    ...     titer={'AceticAcid': 5},
+    ...     titer=dict(AceticAcid=5),
     ...     optimize_power=False,
     ...     kW_per_m3=0.,
     ... )
@@ -479,10 +519,14 @@ def _init(self,
             design=None, method=None, kLa_kwargs=None,
             theta=0.5, Q_consumption=None,
             cooler_pressure_drop=None,
+            compressor_isentropic_efficiency=None,
             # Only for agitated bioreactors (not bubble column)
             optimize_power=None, 
             **kwargs,
         ):
+        if compressor_isentropic_efficiency is None: compressor_isentropic_efficiency = 0.85
+        #: Isentropic efficiency of the compressor. Defaults to 0.85.
+        self.compressor_isentropic_efficiency = compressor_isentropic_efficiency
         self.cooler_pressure_drop = 20684.28 if cooler_pressure_drop is None else cooler_pressure_drop
         self.reactions = reactions
         self.backward_reactions = backward_reactions
@@ -562,7 +606,8 @@ def load_auxiliaries(self):
         for inlet in self.ins:
             if inlet.phase != 'g': continue
             compressor = self.auxiliary(
-                'compressors', bst.IsentropicCompressor, inlet, eta=0.85, P=2 * 101325
+                'compressors', bst.IsentropicCompressor, inlet, 
+                eta=self.compressor_isentropic_efficiency, P=2 * 101325
             )
             self.auxiliary(
                 'gas_coolers', bst.HXutility, compressor-0, T=self.T

biosteam/units/anaerobic_bioreactor.py

@@ -17,19 +17,14 @@
     & Ng, M. K. (2017). Product and Process Design Principles. Wiley.
 
 """
-from .abstract_stirred_tank_reactor import (
-    AbstractStirredTankReactor, 
-    description_doc,
-    parameters_doc, 
-    notes_doc,
-)
+from .abstract_stirred_tank_reactor import AbstractStirredTankReactor
 
 __all__ = (
     'AnaerobicBioreactor', 'AnBR',
 )
 
 class AnaerobicBioreactor(AbstractStirredTankReactor):
-    f"""
+    """
     Create an anaerobic bioreactor with a vented stream and an effluent stream .
     
     {description_doc}

biosteam/units/single_phase_reactor.py

@@ -16,19 +16,14 @@
     Ng, M. K. Product and Process Design Principles. Wiley 2017.
 
 """
-from .abstract_stirred_tank_reactor import (
-    AbstractStirredTankReactor,
-    description_doc,
-    parameters_doc, 
-    notes_doc,
-)
+from .abstract_stirred_tank_reactor import AbstractStirredTankReactor
 
 __all__ = (
     'SinglePhaseReactor', 
 )
 
 class SinglePhaseReactor(AbstractStirredTankReactor):
-    f'''    
+    '''    
     Create a stirred tank reactor which assumes a single outlet stream with 
     no phase equilibrium.