Merge branch 'main' into dev

.github/workflows/build-only.yml

@@ -4,9 +4,9 @@ name: build-only
 
 on:
   push:
-    branches: [beta, dev]
+    branches: [beta, dev, trial]
   pull_request:
-    branches: [beta, dev]
+    branches: [beta, dev, trial]
 
 jobs:
   build:

docs/source/FAQ.rst

@@ -77,6 +77,26 @@ There are multiple possible reasons:
         Then when you open the Jupyter Notebook, select the ``<KERNEL NAME>`` kernel when you create a new notebook you can find more details in this post about `enabling multiple kernels in Jupyter Notebook <https://medium.com/@ace139/enable-multiple-kernels-in-jupyter-notebooks-6098c738fe72>`_.
 
 
+``underlying object has vanished``
+**********************************
+This error is related to ``numba`` caching, we haven't figured out the exact mechanism, but clearing cache will help resolve it. One/both of the following approaches should work:
+
+1. Clear cache. Remove all ``.pyc``, ``.nbc``, and ``.nbi`` files, you can do this in your CLI using (replace <DIR> with the directory to your ``thermosteam``, ``biosteam``, ``qsdsan``, and ``exposan`` directory):
+
+   .. code::
+
+       get-childitem . -recurse -include *.pyc, *.nbc, *.nbi | remove-item
+
+2. Uninstalling and reinstalling a different version of ``numba``. Suppose you now have 0.58.1 and the newest version is 0.60.0, you can do:
+
+   .. code::
+
+       pip uninstall numba
+       pip install --no-cache-dir numba==0.60.0
+
+The ``--no-cache-dir`` option is to do a fresh installation rather than using previously downloaded packages. Note that you need to exit out your editor/any other programs that are currently using numba. Otherwise the uninstallation is incomplete, you might be prompted to do a manual removal, or this won't work.
+
+
 ``UnicodeDecodeError``
 **********************
 When using non-English operating systems, you may run into errors similar to (cp949 is the case of Korean Windows):

docs/source/conf.py

@@ -31,7 +31,7 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.4.0'
+version = '1.4.1'
 # The full version, including alpha/beta/rc tags.
 release = version
 

qsdsan/__init__.py

@@ -45,7 +45,6 @@
 Flowsheet = _bst.Flowsheet
 main_flowsheet = _bst.main_flowsheet
 default_utilities = _bst.default_utilities
-CEPCI_by_year = _bst.units.design_tools.CEPCI_by_year
 
 # Global variables
 currency = 'USD'
@@ -54,6 +53,7 @@
 
 
 from . import utils
+CEPCI_by_year = utils.indices.tea_indices['CEPCI']
 from ._component import *
 from ._components import *
 from ._sanstream import *

qsdsan/_impact_item.py

@@ -822,7 +822,7 @@ def linked_stream(self, new_s):
                          f'is replaced with {self.ID}.')
                 else:
                     warn(f'The original `StreamImpactItem` linked to stream {new_s.ID} '
-                         f'is replaced with upon the creation of a new stream.')
+                         f'is replaced upon the creation of a new stream.')
             new_s._stream_impact_item = self
         self._linked_stream = new_s
 

qsdsan/_lca.py

@@ -175,6 +175,9 @@ class LCA:
     >>> # Retrieve impacts associated with a specific indicator
     >>> lca.get_total_impacts()[GWP.ID] # doctest: +ELLIPSIS
     349737809...
+    >>> # Annual results
+    >>> lca.get_total_impacts(annual=True)[GWP.ID] # doctest: +ELLIPSIS
+    34973780...
     >>> # Or breakdowns of the different category
     >>> lca.get_impact_table('Construction') # doctest: +SKIP
     >>> # Below is for testing purpose, you do not need it
@@ -637,12 +640,13 @@ def get_unit_impacts(
 
         return tot
 
-    def _append_cat_sum(self, cat_table, cat, tot):
+    def _append_cat_sum(self, cat_table, cat, tot, annual=False):
         num = len(cat_table)
         cat_table.loc[num] = '' # initiate a blank spot for value to be added later
-
+        suffix = '/yr' if annual else ''
+
         for i in self.indicators:
-            cat_table[f'{i.ID} [{i.unit}]'][num] = tot[i.ID]
+            cat_table[f'{i.ID} [{i.unit}{suffix}]'][num] = tot[i.ID]
             cat_table[f'Category {i.ID} Ratio'][num] = 1
 
         if cat in ('construction', 'transportation'):
@@ -662,17 +666,21 @@ def get_impact_table(self, category, annual=False):
         Parameters
         ----------
         category : str
-            Can be 'construction', 'transportation', 'stream', or 'other'.
+            Can be 'Construction', 'Transportation', 'Stream', or 'Other'.
         annual : bool
             If True, will return the annual impacts considering `uptime_ratio`
             instead of across the system lifetime.
         '''
         time = self.lifetime_hr
+        sys_yr = self.lifetime
         cat = category.lower()
         tot_f = getattr(self, f'get_{cat}_impacts')
-        kwargs = {'annual': annual} if cat != 'other' else {}
+        # kwargs = {'annual': annual} if cat != 'other' else {}
+        kwargs = {'annual': annual}
         tot = tot_f(**kwargs)
-
+        suffix = '/yr' if annual else''
+        _append_cat_sum = self._append_cat_sum
+
         if cat in ('construction', 'transportation'):
             units = sorted(getattr(self, f'_{cat}_units'),
                               key=(lambda su: su.ID))
@@ -684,31 +692,35 @@ def get_impact_table(self, category, annual=False):
             # Note that item_dct = dict.fromkeys([item.ID for item in items], []) won't work
             item_dct = dict.fromkeys([item.ID for item in items])
             for item_ID in item_dct.keys():
-                item_dct[item_ID] = dict(SanUnit=[], Quantity=[])
+                item_dct[item_ID] = {'SanUnit': [], f'Quantity{suffix}': []}
             for su in units:
                 if not isinstance(su, SanUnit):
                     continue
                 for i in getattr(su, cat):
                     item_dct[i.item.ID]['SanUnit'].append(su.ID)
                     if cat == 'transportation':
-                        item_dct[i.item.ID]['Quantity'].append(i.quantity*time/i.interval)
+                        quantity = i.quantity*time/i.interval
+                        quantity = quantity/sys_yr if annual else quantity
+                        item_dct[i.item.ID][f'Quantity{suffix}'].append(quantity)
                     else: # construction
                         lifetime = i.lifetime or su.lifetime or self.lifetime
                         if isinstance(lifetime, dict): # in the case the the equipment is not in the unit lifetime dict
                             lifetime = lifetime.get(i.item.ID) or self.lifetime
-                        constr_ratio = self.lifetime/lifetime if self.annualize_construction else ceil(self.lifetime/lifetime)
-                        item_dct[i.item.ID]['Quantity'].append(i.quantity*constr_ratio)
+                        constr_ratio = sys_yr/lifetime if self.annualize_construction else ceil(sys_yr/lifetime)
+                        quantity = i.quantity * constr_ratio
+                        quantity = quantity/sys_yr if annual else quantity
+                        item_dct[i.item.ID][f'Quantity{suffix}'].append(quantity)
 
             dfs = []
             for item in items:
                 dct = item_dct[item.ID]
                 dct['SanUnit'].append('Total')
-                dct['Quantity'] = np.append(dct['Quantity'], sum(dct['Quantity']))
-                if dct['Quantity'].sum() == 0.: dct['Item Ratio'] = 0
-                else: dct['Item Ratio'] = dct['Quantity']/dct['Quantity'].sum()*2
+                dct[f'Quantity{suffix}'] = np.append(dct[f'Quantity{suffix}'], sum(dct[f'Quantity{suffix}']))
+                if dct[f'Quantity{suffix}'].sum() == 0.: dct['Item Ratio'] = 0
+                else: dct['Item Ratio'] = dct[f'Quantity{suffix}']/dct[f'Quantity{suffix}'].sum()*2
                 for i in self.indicators:
                     if i.ID in item.CFs:
-                        dct[f'{i.ID} [{i.unit}]'] = impact = dct['Quantity']*item.CFs[i.ID]
+                        dct[f'{i.ID} [{i.unit}{suffix}]'] = impact = dct[f'Quantity{suffix}']*item.CFs[i.ID]
                         dct[f'Category {i.ID} Ratio'] = impact/tot[i.ID]
                     else:
                         dct[f'{i.ID} [{i.unit}]'] = dct[f'Category {i.ID} Ratio'] = 0
@@ -721,55 +733,57 @@ def get_impact_table(self, category, annual=False):
                 dfs.append(df)
 
             table = pd.concat(dfs)
-            return self._append_cat_sum(table, cat, tot)
+            return _append_cat_sum(table, cat, tot, annual=annual)
 
-        ind_head = sum(([f'{i.ID} [{i.unit}]',
+        ind_head = sum(([f'{i.ID} [{i.unit}{suffix}]',
                          f'Category {i.ID} Ratio'] for i in self.indicators), [])
 
         if cat in ('stream', 'streams'):
-            headings = ['Stream', 'Mass [kg]', *ind_head]
+            headings = ['Stream', f'Mass [kg]{suffix}', *ind_head]
             item_dct = dict.fromkeys(headings)
             for key in item_dct.keys():
                 item_dct[key] = []
             for ws_item in self.stream_inventory:
                 ws = ws_item.linked_stream
                 item_dct['Stream'].append(ws.ID)
                 mass = ws_item.flow_getter(ws) * time
-                item_dct['Mass [kg]'].append(mass)
+                mass = mass/sys_yr if annual else mass
+                item_dct[f'Mass [kg]{suffix}'].append(mass)
                 for ind in self.indicators:
                     if ind.ID in ws_item.CFs.keys():
                         impact = ws_item.CFs[ind.ID]*mass
-                        item_dct[f'{ind.ID} [{ind.unit}]'].append(impact)
+                        item_dct[f'{ind.ID} [{ind.unit}{suffix}]'].append(impact)
                         item_dct[f'Category {ind.ID} Ratio'].append(impact/tot[ind.ID])
                     else:
-                        item_dct[f'{ind.ID} [{ind.unit}]'].append(0)
+                        item_dct[f'{ind.ID} [{ind.unit}{suffix}]'].append(0)
                         item_dct[f'Category {ind.ID} Ratio'].append(0)
             table = pd.DataFrame.from_dict(item_dct)
             table.set_index(['Stream'], inplace=True)
-            return self._append_cat_sum(table, cat, tot)
+            return _append_cat_sum(table, cat, tot, annual=annual)
 
         elif cat == 'other':
-            headings = ['Other', 'Quantity', *ind_head]
+            headings = ['Other', f'Quantity{suffix}', *ind_head]
             item_dct = dict.fromkeys(headings)
             for key in item_dct.keys():
                 item_dct[key] = []
             for other_ID in self.other_items.keys():
                 other = self.other_items[other_ID]['item']
-                item_dct['Other'].append(f'{other_ID} [{other.functional_unit}]')
+                item_dct['Other'].append(f'{other_ID}')
                 quantity = self.other_items[other_ID]['quantity']
-                item_dct['Quantity'].append(quantity)
+                quantity = quantity/sys_yr if annual else quantity
+                item_dct[f'Quantity{suffix}'].append(quantity)
                 for ind in self.indicators:
                     if ind.ID in other.CFs.keys():
                         impact = other.CFs[ind.ID]*quantity
-                        item_dct[f'{ind.ID} [{ind.unit}]'].append(impact)
+                        item_dct[f'{ind.ID} [{ind.unit}{suffix}]'].append(impact)
                         item_dct[f'Category {ind.ID} Ratio'].append(impact/tot[ind.ID])
                     else:
-                        item_dct[f'{ind.ID} [{ind.unit}]'].append(0)
+                        item_dct[f'{ind.ID} [{ind.unit}{suffix}]'].append(0)
                         item_dct[f'Category {ind.ID} Ratio'].append(0)
 
             table = pd.DataFrame.from_dict(item_dct)
             table.set_index(['Other'], inplace=True)
-            return self._append_cat_sum(table, cat, tot)
+            return _append_cat_sum(table, cat, tot, annual=annual)
 
         raise ValueError(
             'category can only be "Construction", "Transportation", "Stream", or "Other", ' \

qsdsan/_sanstream.py

@@ -170,12 +170,13 @@ def copy_flow(self, other, IDs=..., *, remove=False, exclude=False):
         --------
         :func:`copy` for the differences between ``copy``, ``copy_like``, and ``copy_flow``.
         '''
+        stream_impact_item = self.stream_impact_item
         Stream.copy_flow(self, other=other, IDs=IDs, remove=remove, exclude=exclude)
 
         if not isinstance(other, SanStream):
             return
 
-        self._stream_impact_item = None
+        self._stream_impact_item = stream_impact_item
 
 
     def flow_proxy(self, ID=None):

qsdsan/_sanunit.py

@@ -217,6 +217,7 @@ def __init__(self, ID='', ins=None, outs=(), thermo=None, init_with='WasteStream
             self._assert_compatible_property_package()
 
         self._utility_cost = None
+        self._recycle_system = None
 
         ##### qsdsan-specific #####
         for i in (*construction, *transportation, *equipment):
@@ -631,10 +632,11 @@ def results(self, with_units=True, include_utilities=True,
                 include_total_cost=True, include_installed_cost=False,
                 include_zeros=True, external_utilities=(), key_hook=None):
 
+        if super().results is None: return super().results
         results = super().results(with_units, include_utilities,
                                   include_total_cost, include_installed_cost,
                                   include_zeros, external_utilities, key_hook)
-        if not self.add_OPEX: self.add_OPEX = {'Additional OPEX': 0}
+        if not hasattr(self, 'add_OPEX'): self.add_OPEX = {'Additional OPEX': 0}
         for k, v in self.add_OPEX.items():
             if not with_units:
                 results.loc[(k, '')] = v
@@ -647,7 +649,7 @@ def results(self, with_units=True, include_utilities=True,
                     results.insert(0, 'Units', '')
                     results.loc[(k, ''), :] = ('USD/hr', v)
                     results.columns.name = type(self).__name__
-        if with_units:
+        if with_units and results is not None:
             results.replace({'USD': f'{currency}', 'USD/hr': f'{currency}/hr'},
                             inplace=True)
         return results

qsdsan/_waste_stream.py

@@ -154,7 +154,11 @@ def __init__(self, dct, F_vol, MW, phase, phase_container):
     def output(self, index, value):
         '''Concentration flows, in mg/L (g/m3).'''
         f_mass = value * self.MW[index]
-        phase = self.phase or self.phase_container.phase
+        if self.phase:
+            phase = self.phase
+        else:
+            try: phase = self.phase_container._phase
+            except: phase = self.phase_container
         if phase != 'l':
             raise AttributeError('Concentration only valid for liquid phase.')
         V_sum = self.F_vol
@@ -186,7 +190,7 @@ def by_conc(self, TP):
         check_data=False,
         )
     return conc
-indexer.ChemicalMolarFlowIndexer.by_conc = by_conc
+ChemicalMolarFlowIndexer.by_conc = by_conc
 del by_conc
 
 

qsdsan/data/process_data/_pm2asm2d.tsv

@@ -0,0 +1,39 @@
+	X_CHL	X_ALG	X_CH	X_LI	S_CO2	S_A	S_F	S_O2	S_NH	S_NO	S_P	X_N_ALG	X_P_ALG	S_N2	S_ALK	S_I	X_I	X_S	X_H	X_AUT
+photoadaptation	1																			
+ammonium_uptake									-1			1								
+phosphorus_uptake											-1		1							
+growth_pho		1			?			1				?	?							
+carbohydrate_storage_pho			1		?			1												
+lipid_storage_pho				1	?			1												
+carbohydrate_growth_pho		1	(-Y_CH_PHO/Y_X_ALG_PHO)		?			?				?	?							
+lipid_growth_pho		1		(-Y_LI_PHO/Y_X_ALG_PHO)	?			?				?	?							
+carbohydrate_maintenance_pho			-1		?			-1												
+lipid_maintenance_pho				-1	?			-1												
+endogenous_respiration_pho		-1			?			-1				?	?							
+growth_ace		1			?	(-1)/Y_X_ALG_HET_ACE		?				?	?							
+carbohydrate_storage_ace			1		?	(-1)/Y_CH_ND_HET_ACE		?												
+lipid_storage_ace				1	?	(-1)/Y_LI_ND_HET_ACE		?												
+carbohydrate_growth_ace		1	(-Y_CH_NR_HET_ACE/Y_X_ALG_HET_ACE)		?			?				?	?							
+lipid_growth_ace		1		(-Y_LI_NR_HET_ACE/Y_X_ALG_HET_ACE)	?			?				?	?							
+carbohydrate_maintenance_ace			-1		?			-1												
+lipid_maintenance_ace				-1	?			-1												
+endogenous_respiration_ace		-1			?			-1				?	?							
+growth_glu		1			?		(-1)/Y_X_ALG_HET_GLU	?				?	?							
+carbohydrate_storage_glu			1		?		(-1)/Y_CH_ND_HET_GLU	?												
+lipid_storage_glu				1	?		(-1)/Y_LI_ND_HET_GLU	?												
+carbohydrate_growth_glu		1	(-Y_CH_NR_HET_GLU/Y_X_ALG_HET_GLU)		?			?				?	?							
+lipid_growth_glu		1		(-Y_LI_NR_HET_GLU/Y_X_ALG_HET_GLU)	?			?				?	?							
+carbohydrate_maintenance_glu			-1		?			-1												
+lipid_maintenance_glu				-1	?			-1												
+endogenous_respiration_glu		-1			?			-1				?	?							
+aero_hydrolysis							1-f_SI		?		?				?	f_SI		-1		
+anox_hydrolysis							1-f_SI		?		?				?	f_SI		-1		
+anae_hydrolysis							1-f_SI		?		?				?	f_SI		-1		
+hetero_growth_S_F							(-1)/Y_H	1-1/Y_H	?		?				?				1	
+hetero_growth_S_A						(-1)/Y_H		1-1/Y_H	?		?				?				1	
+denitri_S_F							(-1)/Y_H		?	(Y_H-1)/(20/7*Y_H)	?			(1-Y_H)/(20/7*Y_H)	?				1	
+denitri_S_A						(-1)/Y_H			?	(Y_H-1)/(20/7*Y_H)	?			(1-Y_H)/(20/7*Y_H)	?				1	
+ferment						1	-1		?		?				?					
+hetero_lysis									?		?				?		f_XI_H	1-f_XI_H	-1	
+auto_aero_growth								(Y_A-32/7)/Y_A	?	1/Y_A	?				?					1
+auto_lysis									?		?				?		f_XI_AUT	1-f_XI_AUT		-1

qsdsan/data/process_data/_pm2asm2d_1.tsv

@@ -0,0 +1,28 @@
+	X_CHL	X_ALG	X_CH	X_LI	S_CO2	S_A	S_F	S_O2	S_NH	S_NO	S_P	X_N_ALG	X_P_ALG	S_N2	S_ALK	S_I	X_I	X_S	X_H	X_AUT
+photoadaptation	1																			
+ammonium_uptake									-1			1								
+phosphorus_uptake											-1		1							
+growth_pho		1			?			1				?	?							
+carbohydrate_storage_pho			1		?			1												
+lipid_storage_pho				1	?			1												
+carbohydrate_growth_pho		1	(-Y_CH_PHO/Y_X_ALG_PHO)		?			?				?	?							
+lipid_growth_pho		1		(-Y_LI_PHO/Y_X_ALG_PHO)	?			?				?	?							
+carbohydrate_maintenance_pho			-1		?			-1												
+lipid_maintenance_pho				-1	?			-1												
+endogenous_respiration_pho		-1			?			-1				?	?							
+growth_ace		1			?	(-1)/Y_X_ALG_HET_ACE		?				?	?							
+carbohydrate_storage_ace			1		?	(-1)/Y_CH_ND_HET_ACE		?												
+lipid_storage_ace				1	?	(-1)/Y_LI_ND_HET_ACE		?												
+carbohydrate_growth_ace		1	(-Y_CH_NR_HET_ACE/Y_X_ALG_HET_ACE)		?			?				?	?							
+lipid_growth_ace		1		(-Y_LI_NR_HET_ACE/Y_X_ALG_HET_ACE)	?			?				?	?							
+carbohydrate_maintenance_ace			-1		?			-1												
+lipid_maintenance_ace				-1	?			-1												
+endogenous_respiration_ace		-1			?			-1				?	?							
+growth_glu		1			?		(-1)/Y_X_ALG_HET_GLU	?				?	?							
+carbohydrate_storage_glu			1		?		(-1)/Y_CH_ND_HET_GLU	?												
+lipid_storage_glu				1	?		(-1)/Y_LI_ND_HET_GLU	?												
+carbohydrate_growth_glu		1	(-Y_CH_NR_HET_GLU/Y_X_ALG_HET_GLU)		?			?				?	?							
+lipid_growth_glu		1		(-Y_LI_NR_HET_GLU/Y_X_ALG_HET_GLU)	?			?				?	?							
+carbohydrate_maintenance_glu			-1		?			-1												
+lipid_maintenance_glu				-1	?			-1												
+endogenous_respiration_glu		-1			?			-1				?	?							

qsdsan/data/process_data/_pm2asm2d_2.tsv

@@ -0,0 +1,12 @@
+	X_CHL	X_ALG	X_CH	X_LI	S_CO2	S_A	S_F	S_O2	S_NH	S_NO	S_P	X_N_ALG	X_P_ALG	S_N2	S_ALK	S_I	X_I	X_S	X_H	X_AUT
+aero_hydrolysis							1-f_SI		?		?				?	f_SI		-1		
+anox_hydrolysis							1-f_SI		?		?				?	f_SI		-1		
+anae_hydrolysis							1-f_SI		?		?				?	f_SI		-1		
+hetero_growth_S_F							(-1)/Y_H	1-1/Y_H	?		?				?				1	
+hetero_growth_S_A						(-1)/Y_H		1-1/Y_H	?		?				?				1	
+denitri_S_F							(-1)/Y_H		?	(Y_H-1)/(20/7*Y_H)	?			(1-Y_H)/(20/7*Y_H)	?				1	
+denitri_S_A						(-1)/Y_H			?	(Y_H-1)/(20/7*Y_H)	?			(1-Y_H)/(20/7*Y_H)	?				1	
+ferment						1	-1		?		?				?					
+hetero_lysis									?		?				?		f_XI_H	1-f_XI_H	-1	
+auto_aero_growth								(Y_A-32/7)/Y_A	?	1/Y_A	?				?					1
+auto_lysis									?		?				?		f_XI_AUT	1-f_XI_AUT		-1