documentation updates and diagram aesthetic improvements

biosteam/_preferences.py

@@ -54,7 +54,7 @@ class DisplayPreferences:
                  'label_color', 'label_color', 'depth_colors', 'stream_width',
                  'unit_color', 'unit_label_color', 'unit_periphery_color',
                  'fill_cluster', 'graphviz_format', 'tooltips_full_results',
-                 'graphviz_html_height')
+                 'graphviz_html_height', 'show_all_streams')
 
     def __init__(self):
         #: Whether to label the ID of streams with sources and sinks in process 
@@ -118,6 +118,9 @@ def __init__(self):
             'unit': ('225px', '400px'),
         }
 
+        #: Whether to show all streams, including empty feeds and products.
+        self.show_all_streams = True
+
     def temporary(self):
         """Return a TemporaryPreferences object that will revert back to original
         preferences after context management."""
@@ -236,7 +239,7 @@ def dark_mode(self, stream='#98a2ad', label='#e5e5e5', bg='transparent',
                        unit_periphery_color, fill_cluster, save)
 
     def light_mode(self, stream='#4e4e4e', label='#4e4e4e', bg='#ffffffff',
-                   cluster=['#7ac0832f', '#ffffff9f'], unit_color='white:#CDCDCD', 
+                   cluster=['#d5edf02f', '#ffffffdf'], unit_color='white:#CDCDCD', 
                    unit_label_color='black', unit_periphery_color='#4e4e4e',
                    fill_cluster=True, save=False):
         """Set diagram display colors to light mode."""

biosteam/_system.py

@@ -3023,7 +3023,7 @@ def results(self, with_units=True):
             return series
 
     # Report summary
-    def save_report(self, file: Optional[str]='report.xlsx', dpi: Optional[str]='300', **stream_properties): 
+    def save_report(self, file: Optional[str]='report.xlsx', dpi: Optional[str]='900', **stream_properties): 
         """
         Save a system report as an xlsx file.
         

biosteam/_unit.py

@@ -336,7 +336,7 @@ def __init_subclass__(cls,
                         "must implement a '_run' method unless the "
                         "'isabstract' keyword argument is True"
                     )
-        if '__init__' in dct:
+        if '__init__' in dct or '_init' in dct:
             init = dct['__init__']
             annotations = init.__annotations__
             for i in ('ins', 'outs'):

biosteam/digraph/digraph.py

@@ -267,7 +267,7 @@ def update_digraph_from_path(f, path, recycle, depth, unit_names,
     streams = [i for i in all_streams if (not i.sink or i.sink in units) and (not i.source or i.source in units)]
     other_streams.update(all_streams.difference(streams))
     connections = get_all_connections(recycles, excluded_connections)
-    add_connections(f, connections, unit_names, color='#f98f60', fontcolor='#f98f60')
+    add_connections(f, connections, unit_names, color='#f1777f', fontcolor='#f1777f')
     connections = get_all_connections(streams, excluded_connections)
     add_connections(f, connections, unit_names)
     depth += 1
@@ -395,6 +395,7 @@ def add_connection(f: Digraph, connection, unit_names, pen_width=None, **edge_op
         # Make stream nodes / unit-stream edges / unit-unit edges
         if has_sink and not has_source:
             # Feed stream case
+            if not preferences.show_all_streams and stream.isempty(): return
             f.node(ref,
                    width='0.15', 
                    height='0.15',
@@ -408,6 +409,7 @@ def add_connection(f: Digraph, connection, unit_names, pen_width=None, **edge_op
             f.edge(ref, unit_names[sink], labeltooltip=tooltip)
         elif has_source and not has_sink:
             # Product stream case
+            if not preferences.show_all_streams and stream.isempty(): return
             f.node(ref, 
                    width='0.15', 
                    height='0.2',
@@ -428,8 +430,6 @@ def add_connection(f: Digraph, connection, unit_names, pen_width=None, **edge_op
                    **inlet_options, penwidth=penwidth, **outlet_options)
             label = ID if preferences.label_streams else ''
             f.edge(unit_names[source], unit_names[sink], label=label, labeltooltip=tooltip)
-        else:
-            f.node(ID)
     elif has_sink and has_source:
         # Missing process stream case
         inlet_options = sink._graphics.get_inlet_options(sink, sink_index)

biosteam/facilities/_boiler_turbogenerator.py

@@ -37,25 +37,16 @@ class BoilerTurbogenerator(bst.Facility):
     Parameters
     ----------
     ins : 
-        [0] Liquid/solid feed that will be burned.
-        
-        [1] Gas feed that will be burned.
-        
-        [2] Make-up water. 
-        
-        [3] Natural gas to satisfy steam and power requirement.
-        
-        [4] Lime for flue gas desulfurization.
-        
-        [5] Boiler chemicals.
-        
+        * [0] Liquid/solid feed that will be burned.
+        * [1] Gas feed that will be burned.
+        * [2] Make-up water. 
+        * [3] Natural gas to satisfy steam and power requirement.
+        * [4] Lime for flue gas desulfurization.
+        * [5] Boiler chemicals.
     outs : 
-        [0] Total emissions produced.
-        
-        [1] Blowdown water.
-        
-        [2] Ash disposal.
-        
+        * [0] Total emissions produced.
+        * [1] Blowdown water.
+        * [2] Ash disposal.
     boiler_efficiency : float, optional
         Fraction of heat transferred to steam. Defaults to 0.8.
     turbo_generator_efficiency : float, optional
@@ -74,13 +65,12 @@ class BoilerTurbogenerator(bst.Facility):
         Whether to purchase natural gas to satisfy system electricity demand
         if there is not enough heat from process feeds (i.e., inlets 0 and 1).
         If True, natural gas is purchased to satisfy system heat and electricity demand
-        (even if there is not enough heat from the feed wastes and gas);
-        if False, natural gas is only purchased to satisfy system heat demand
-        (i.e., electricity will be purchased from the grid if there is not
-         enough heat from the feeds).
+        when there is not enough heat from the feed and gas.
+        If False, natural gas is only purchased to satisfy system heat demand
+        and electricity will be purchased from the grid if there is not
+        enough heat from the feeds.
         In either case, if there is excess heat from the process feeds,
-        electricity will still be produced
-        (i.e., this argument only affects the calculation of natural gas flow).
+        electricity will still be produced.
     boiler_efficiency_basis : str, optional
         Basis of boiler efficiency. Defaults to 'LHV' (i.e., lower heating value).
         'HHV' (i.e., higher heating value) is also a valid basis. 

biosteam/units/distillation.py

@@ -12,7 +12,7 @@
 .. autoclass:: biosteam.units.distillation.BinaryDistillation 
 .. autoclass:: biosteam.units.distillation.ShortcutColumn
 .. autoclass:: biosteam.units.distillation.MESHDistillation
-.. autocalss:: biosteam.units.distillation.AdiabaticMultiStageVLEColumn
+.. autoclass:: biosteam.units.distillation.AdiabaticMultiStageVLEColumn
 
 References
 ----------
@@ -2158,26 +2158,6 @@ class MESHDistillation(MultiStageEquilibrium, new_graphics=False):
     Create a distillation column that rigorously converges MESH 
     (Mass, Equilibrium, Summation, and Enthalpy) equations. 
     
-    The convergence algorithm decouples the equilibrium relationships, 
-    mass balances, and energy balances using a custom version of the Wang-Henke 
-    bubble point method. This algorithm is authored by Yoel Cortes-Pena, but is 
-    not yet peer reviewed. The main difference is that the tridiagonal matrix of 
-    mass balances across stages is used to solve for flow rates instead of mass 
-    fractions and an internal loop is added to converge phase fractions based 
-    on the energy balance. 
-    
-    The initialization algorithm first converges a "collapsed" column without 
-    adiabatic stages which have no feeds or side draws. This collapsed column 
-    is initialized by solving for liquid and vapor flow rates assuming no phase 
-    change across adiabatic stages and unity partition coefficients at 
-    reboilers/condensers (in which case the stripping factor is equal to the 
-    boil-up ratio).
-    
-    The Murphree efficiency (i.e. stage efficiency) is based on the 
-    modified O'Connell correlation [2]_. The diameter is based on tray 
-    separation and flooding velocity [1]_ [3]_. Purchase costs are based on 
-    correlations compiled by Warren et. al. [4]_.
-
     Parameters
     ----------
     ins : 
@@ -2235,8 +2215,9 @@ class MESHDistillation(MultiStageEquilibrium, new_graphics=False):
 
     Examples
     --------
-    # Simulate distillation column with 5 stages, a 0.673 reflux ratio, 
-    # 2.57 boilup ratio, and feed at stage 2:
+    Simulate distillation column with 5 stages, a 0.673 reflux ratio, 
+    2.57 boilup ratio, and feed at stage 2:
+    
     >>> import biosteam as bst
     >>> bst.settings.set_thermo(['Water', 'Ethanol'], cache=True)
     >>> feed = bst.Stream('feed', Ethanol=80, Water=100, T=80.215 + 273.15)
@@ -2280,6 +2261,28 @@ class MESHDistillation(MultiStageEquilibrium, new_graphics=False):
     Total purchase cost                                          USD  1.24e+05
     Utility cost                                              USD/hr      48.1
     
+    Notes
+    -----
+    The convergence algorithm decouples the equilibrium relationships, 
+    mass balances, and energy balances using a custom version of the Wang-Henke 
+    bubble point method. This algorithm is authored by Yoel Cortes-Pena, but is 
+    not yet peer reviewed. The main difference is that the tridiagonal matrix of 
+    mass balances across stages is used to solve for flow rates instead of mass 
+    fractions and an internal loop is added to converge phase fractions based 
+    on the energy balance. 
+    
+    The initialization algorithm first converges a "collapsed" column without 
+    adiabatic stages which have no feeds or side draws. This collapsed column 
+    is initialized by solving for liquid and vapor flow rates assuming no phase 
+    change across adiabatic stages and unity partition coefficients at 
+    reboilers/condensers (in which case the stripping factor is equal to the 
+    boil-up ratio).
+    
+    The Murphree efficiency (i.e. stage efficiency) is based on the 
+    modified O'Connell correlation [2]_. The diameter is based on tray 
+    separation and flooding velocity [1]_ [3]_. Purchase costs are based on 
+    correlations compiled by Warren et. al. [4]_.
+    
     """
 
     auxiliary_unit_names = (

biosteam/units/splitting.py

@@ -10,7 +10,6 @@
 
 .. contents:: :local:
     
-.. autoclass:: biosteam.units.splitting.Splitter
 .. autoclass:: biosteam.units.splitting.Splitter
 .. autoclass:: biosteam.units.splitting.PhaseSplitter 
 .. autoclass:: biosteam.units.splitting.MockSplitter

biosteam/utils/piping.py

@@ -834,7 +834,9 @@ def superposition(parent, port):
 
 
 @superposition(Stream, 'sink')
-class SuperpositionInlet(Stream): # Both parent and auxiliary unit inlet.
+class SuperpositionInlet(Stream): 
+    """Create a SuperpositionInlet that references an inlet from another 
+    unit operation."""
     __slots__ = ()
 
     def __init__(self, port, sink=None):
@@ -843,7 +845,9 @@ def __init__(self, port, sink=None):
 
 
 @superposition(Stream, 'source')
-class SuperpositionOutlet(Stream): # Both parent and auxiliary unit outlet.
+class SuperpositionOutlet(Stream):
+    """Create a SuperpositionOutlet that references an outlet from another 
+    unit operation."""
     __slots__ = ()
 
     def __init__(self, port, source=None):

biosteam/wastewater/high_rate/polishing_filter.py

@@ -55,8 +55,8 @@ class PolishingFilter(bst.Unit):
     HLR : float
         Hydraulic loading rate of influent, [m3/m2/hr].
     X_decomp : float
-        Fraction of the influent COD converted to biogas (`filter_type`=="anaerobic")
-        or CO2 (`filter_type`=="aerobic").
+        Fraction of the influent COD converted to biogas (`filter_type` == "anaerobic")
+        or CO2 (`filter_type` == "aerobic").
     X_growth : float
         Fraction of the influent COD converted to biomass growth.
     split : dict