Merge branch 'main' of https://github.com/QSD-Group/QSDsan into trial

QSD-Group · Dec 10, 2024 · 90c4f67 · 90c4f67
2 parents ceca243 + af5acab
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diff --git a/.github/workflows/build-dev.yml b/.github/workflows/build-dev.yml
@@ -0,0 +1,37 @@
+# This workflow will install Python dependencies, run tests with a variety of Python versions, and report coverage
+
+name: build-dev
+
+on:
+  push:
+    branches: [dev]
+  pull_request:
+    branches: [dev]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        # os: [ubuntu-latest, macos-latest, windows-latest] if want multiple os
+        python-version: ["3.9", "3.10"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install pytest nbval
+        pip install --no-cache-dir git+https://github.com/BioSTEAMDevelopmentGroup/thermosteam.git@qsdsan
+        pip install --no-cache-dir git+https://github.com/BioSTEAMDevelopmentGroup/biosteam.git@qsdsan
+        pip install --no-cache-dir git+https://github.com/QSD-Group/EXPOsan.git@bsm2
+        pip install --no-cache-dir -r requirements.txt
+    - name: Test with pytest
+      run: |
+        pytest
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -4,6 +4,32 @@ Change Log
 This document records notable changes to `QSDsan <https://github.com/QSD-Group/QSDsan>`_. We aim to follow `Semantic Versioning <https://semver.org/>`_.
 
 
+`1.4.0`_
+--------
+- A lot of the updates have been focused on the dynamic simulation, now the open-loop Benchmark Simulation Model No. 2 (`BSM2 <https://github.com/QSD-Group/EXPOsan/tree/main/exposan/bsm2>`_) configuration has been implemented with new process models and unit operation including
+
+	- :class:`qsdsan.processes.ADM1p`
+	- :class:`qsdsan.processes.ADM1_p_extension`
+	- :class:`qsdsan.processes.ModifiedADM1`
+	- :class:`qsdsan.processes.mASM2d`
+	- :class:`qsdsan.sanunits.IdealClarifier`
+	- :class:`qsdsan.sanunits.PrimaryClarifier`
+	- :class:`qsdsan.sanunits.PrimaryClarifierBSM2`
+	- :class:`qsdsan.sanunits.GasExtractionMembrane`
+	- :class:`qsdsan.sanunits.Thickener`
+	- :class:`qsdsan.sanunits.Centrifuge`
+	- :class:`qsdsan.sanunits.Incinerator`
+	- :class:`qsdsan.sanunits.BatchExperiment`
+	- :class:`qsdsan.sanunits.PFR`
+	- :class:`qsdsan.sanunits.BeltThickener`
+	- :class:`qsdsan.sanunits.SludgeCentrifuge`
+	- :class:`qsdsan.sanunits.SludgeThickener`
+
+- New publications
+
+	- Feng et al., *Environmental Science & Technology*, on the sustainability of `hydrothermal liquefaction (HTL) <https://doi.org/10.1021/acs.est.3c07394>`_ for resource recovery from a range of wet organic wastes.
+
+
 `1.3.0`_
 --------
 - Enhance and use QSDsan's capacity for dynamic simulation for emerging technologies and benchmark configurations (see EXPOsan METAB and PM2 (on the algae branch, still under development) modules).
@@ -185,6 +211,7 @@ Official release of ``QSDsan`` v1.0.0!
 .. _Trimmer et al.: https://doi.org/10.1021/acs.est.0c03296
 
 .. Commit links
+.. _1.4.0: https://github.com/QSD-Group/QSDsan/releases/tag/v1.4.0
 .. _1.3.0: https://github.com/QSD-Group/QSDsan/releases/tag/v1.3.0
 .. _1.2.0: https://github.com/QSD-Group/QSDsan/releases/tag/v1.2.0
 .. _1.1.0: https://github.com/QSD-Group/QSDsan/releases/tag/v1.1.0

diff --git a/docs/source/FAQ.rst b/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):

diff --git a/docs/source/Systems.rst b/docs/source/Systems.rst
@@ -63,7 +63,7 @@ A variety of other sanitation and resource recovery systems have been developed
 
 #. Modular encapsulated two-stage anaerobic biological (METAB) system
 
-    * Manuscript: Zhang et al., Sustainable design of a modular anaerobic system for distributed energy recovery from industrial wastewaters, In Prep.
+    * Publication: `Zhang <https://doi.org/10.1021/acs.est.4c05389>`_ et al., 2024.
     * `metab EXPOsan module <https://github.com/QSD-Group/EXPOsan/tree/main/exposan/metab>`_
 
 #. EcoRecover system: microalgae-based tertiary P recovery process

diff --git a/docs/source/api/processes/ADM1p.rst b/docs/source/api/processes/ADM1p.rst
@@ -0,0 +1,7 @@
+Anaerobic Digestion Model No.1 with P extension (ADM1 P/Extension)
+==================================================================
+.. autoclass:: qsdsan.processes.ADM1_p_extension
+   :members:
+
+.. autoclass:: qsdsan.processes.ADM1p
+   :members:
diff --git a/docs/source/api/processes/ASM2d.rst b/docs/source/api/processes/ASM2d.rst
@@ -1,4 +1,7 @@
 Activated Sludge Model No.2d (ASM2d)
 ====================================
 .. autoclass:: qsdsan.processes.ASM2d
+   :members:
+
+.. autoclass:: qsdsan.processes.mASM2d
    :members:
diff --git a/docs/source/api/processes/_index.rst b/docs/source/api/processes/_index.rst
@@ -11,12 +11,18 @@ List of Biological Kinetic Models
 | ADM1     | `adm`_           | `Batstone`_ et al., 2002    |
 |          |                  | `Rosen and Jeppsson`_, 2006 |
 +----------+------------------+-----------------------------+
+| ADM1p    | `bsm2`_          | `Alex`_ et al., 2008        |
++----------+------------------+-----------------------------+
+| mADM1    |                  |                             |
++----------+------------------+-----------------------------+
 | ASM1     | `asm`_ & `bsm1`_ | `Henze`_ et al., 2006       |
 +----------+------------------+-----------------------------+
 | ASM2d    | `asm`_ & `bsm1`_ | `Henze`_ et al., 2006       |
 +----------+------------------+-----------------------------+
-| PM2      | `pm2_ecorecover`_| N/A                         |
-|          | & `pm2_batch`_   |				    |
+| mASM2d   | `bsm2`_          | `Alex`_ et al., 2008        |
++----------+------------------+-----------------------------+
+| PM2      | `pm2_ecorecover`_|                             |
+|          | & `pm2_batch`_   |                             |
 +----------+------------------+-----------------------------+
 
 
@@ -41,10 +47,12 @@ List of Other Kinetic Modules
 .. _adm: https://github.com/QSD-Group/EXPOsan/tree/main/exposan/adm
 .. _asm: https://github.com/QSD-Group/EXPOsan/tree/main/exposan/asm
 .. _bsm1: https://github.com/QSD-Group/EXPOsan/tree/main/exposan/bsm1
+.. _bsm2: https://github.com/QSD-Group/EXPOsan/tree/main/exposan/bsm2
 .. _bwaise: https://github.com/QSD-Group/EXPOsan/tree/main/exposan/bwaise
 .. _pm2_batch: https://github.com/QSD-Group/EXPOsan/tree/main/exposan/pm2_batch
 .. _pm2_ecorecover: https://github.com/QSD-Group/EXPOsan/tree/main/exposan/pm2_ecorecover
 
+.. _Alex: http://iwa-mia.org/wp-content/uploads/2022/09/TR3_BSM_TG_Tech_Report_no_3_BSM2_General_Description.pdf
 .. _Batstone: https://iwaponline.com/ebooks/book/152/Anaerobic-Digestion-Model-No-1-ADM1
 .. _EPA design manual: https://nepis.epa.gov/Exe/ZyPURL.cgi?Dockey=3000464S.TXT
 .. _Henze: https://iwaponline.com/ebooks/book/96/
@@ -59,9 +67,11 @@ Links to docs
    :maxdepth: 1
 
    ADM1
+   ADM1p
    Aeration
    ASM1
    ASM2d
    Decay
    KineticReaction
+   mADM1
    PM2
diff --git a/docs/source/api/processes/mADM1.rst b/docs/source/api/processes/mADM1.rst
@@ -0,0 +1,4 @@
+Modified Anaerobic Digestion Model No.1 (MADM1)
+===============================================
+.. autoclass:: qsdsan.processes.ModifiedADM1
+   :members:
diff --git a/docs/source/api/sanunits/MembraneGasExtraction.rst b/docs/source/api/sanunits/MembraneGasExtraction.rst
@@ -0,0 +1,4 @@
+Membrane Gas Extraction
+=======================
+.. automodule:: qsdsan.sanunits._membrane_gas_extraction
+    :members:
diff --git a/docs/source/api/sanunits/_index.csv b/docs/source/api/sanunits/_index.csv
@@ -38,12 +38,15 @@ Lagoon,No,No,Completed
 LiquidTreatmentBed,No,No,Completed
 LumpedCost,No,No,Completed
 MembraneDistillation,No,No,Completed
+MembraneGasExtraction,No,No,Completed
 MixTank,No,No,Completed
 Mixer,Yes,Yes,Completed
 MURT (multi-unit reinvented toilet),No,No,Completed
+PFR (plug flow reactor),Yes,No,Under development
 PhaseChanger,No,Yes,Completed
 PitLatrine,No,No,Completed
 PolishingFilter,No,No,Completed
+PrimaryClarifier,Yes,No,Completed
 Pump,Yes,No,Completed
 Reactor,No,No,Completed
 ReversedSplitter,No,Yes,Completed

diff --git a/docs/source/api/sanunits/_index.rst b/docs/source/api/sanunits/_index.rst
@@ -39,6 +39,7 @@ Individual Unit Operations
    DynamicInfluent
    ElectrochemicalCell
    Excretion
+   facilities
    Flash
    heat_exchanging
    hydroprocessing
@@ -48,15 +49,17 @@ Individual Unit Operations
    Lagoon
    membrane_bioreactor
    MembraneDistillation
+   MembraneGasExtraction
    non_reactive
    PolishingFilter
    pumping
    Reactor
    Screening
    Sedimentation
    SepticTank
-   sludge_thickening
    SludgePasteurization
+   sludge_thickening
+   sludge_treatment   
    suspended_growth_bioreactor
    tank
    toilet

diff --git a/docs/source/api/sanunits/facilities.rst b/docs/source/api/sanunits/facilities.rst
@@ -0,0 +1,4 @@
+Distillation
+============
+.. automodule:: qsdsan.sanunits._facilities
+    :members:
diff --git a/docs/source/api/sanunits/sludge_treatment.rst b/docs/source/api/sanunits/sludge_treatment.rst
@@ -0,0 +1,4 @@
+Sludge Treatment
+================
+.. automodule:: qsdsan.sanunits._sludge_treatment
+    :members:
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -31,7 +31,7 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.3.1'
+version = '1.4.1'
 # The full version, including alpha/beta/rc tags.
 release = version
 

diff --git a/qsdsan/__init__.py b/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 *

diff --git a/qsdsan/_component.py b/qsdsan/_component.py
@@ -561,6 +561,8 @@ def i_NOD(self, i):
         if i == None:
             if self.degradability in ('Readily', 'Slowly') or self.formula in ('H3N', 'NH4', 'NH3', 'NH4+', 'H4N+'):
                 i = self.i_N * molecular_weight({'O':4}) / molecular_weight({'N':1})
+            elif self.formula == 'N2':
+                i = self.i_N * molecular_weight({'O':5}) / molecular_weight({'N':2})
             elif self.formula in ('NO2-', 'HNO2'):
                 i = self.i_N * molecular_weight({'O':1}) / molecular_weight({'N':1})
             else:

diff --git a/qsdsan/_components.py b/qsdsan/_components.py
@@ -154,8 +154,10 @@ def extend(self, components):
     def compile(self, skip_checks=False):
         '''Cast as a :class:`CompiledComponents` object.'''
         components = tuple(self)
+        tmo._chemicals.prepare(components, skip_checks)
         setattr(self, '__class__', CompiledComponents)
-        try: self._compile(components, skip_checks)
+
+        try: self._compile(components)
         except Exception as error:
             setattr(self, '__class__', Components)
             setattr(self, '__dict__', {i.ID: i for i in components})
@@ -614,11 +616,11 @@ def compile(self, skip_checks=False):
         pass
 
 
-    def _compile(self, components, skip_checks=False):
+    def _compile(self, components):
         dct = self.__dict__
         tuple_ = tuple # this speeds up the code
         components = tuple_(dct.values())
-        CompiledChemicals._compile(self, components, skip_checks)
+        CompiledChemicals._compile(self, components)
         for component in components:
             missing_properties = component.get_missing_properties(_key_component_properties)
             if not missing_properties: continue

diff --git a/qsdsan/_impact_item.py b/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