Regarding the issue of the lactic acid article code

[zasddsgg]

@yalinli2 Hello, if I want to reproduce Figures 4 and 5 in the article (Sustainable Lactic Acid Production from Lignocellulosic Biomass), which code and data should I use? Thanks for your help.

[zasddsgg]

@yalinli2 Hello, The file seems to be unable to be opened (https://github.com/BioSTEAMDevelopmentGroup/Bioindustrial-Park/blob/f56692d3bc06527b57dc77ed7cb929a40b59bc4d/BioSTEAM%202.x.x/biorefineries/lactic/results/2-1_ferm_diluted.xlsx). Could I consult you where I can find the codes and data needed for Figures 4 and 5? Thanks for your help.

[yalinli2]

@zasddsgg I'm not sure why you couldn't open that file. GitHub doesn't should a preview of Excel files online, but you can just download and open it.

To produce Figure 4, you need to simulate the system at different yield and titer combinations (original codes); to product Figure 5, you need to simulate the system at different feedstock carbohydrate content and feedstock price combinations (original codes).

The original codes work for the specific commit as mentioned in the repo doc.

If you want to run the codes with current BioSTEAM, most likely you'll need to rewrite or update the codes so that they are compatible.

[zasddsgg]

Thank you for your answer. I downloaded the Excel file (https://github.com/BioSTEAMDevelopmentGroup/Bioindustrial-Park/blob/f56692d3bc06527b57dc77ed7cb929a40b59bc4d/BioSTEAM%202.x.x/biorefineries/lactic/results/2-2_ferm_concentrated.xlsx). The content is as follows and seems inconsistent with the data in Figure 4 of the article.

I have tried to download by using git clone or directly downloading the compressed package in BioSTEAMDevelopmentGroup/Bioindustrial-Park at f56692d3bc06527b57dc77ed7cb929a40b59bc4d. By entering the BioSTEAM 2.x.x folder and using the command "pip install .", with Python 3.10.9, the above code installs biosteam-2.52.0, biorefineries-2.16.1, and thermosteam-0.52.0. However, when running the code in Bioindustrial-Park/biorefineries/lactic/analyses/2_fermentation_TRY.py at master · BioSTEAMDevelopmentGroup/Bioindustrial-Park, an error occurs.

ModuleNotFoundError                       Traceback (most recent call last)
File D:\anaconda\envs\bio\lib\site-packages\lazypkg\__init__.py:53, in LazyPkg.__getattr__(self, name)
     52 try:
---> 53     attr = import_module('.'+name, self.__package__)
     54 except ModuleNotFoundError as Error:

File D:\anaconda\envs\bio\lib\importlib\__init__.py:126, in import_module(name, package)
    125         level += 1
--> 126 return _bootstrap._gcd_import(name[level:], package, level)

File <frozen importlib._bootstrap>:1050, in _gcd_import(name, package, level)

File <frozen importlib._bootstrap>:1027, in _find_and_load(name, import_)

File <frozen importlib._bootstrap>:1004, in _find_and_load_unlocked(name, import_)

ModuleNotFoundError: No module named 'biorefineries.lactic.load'

During handling of the above exception, another exception occurred:

ValueError                                Traceback (most recent call last)
Cell In[1], line 24
     22 from warnings import warn
     23 from biosteam.utils import Timer
---> 24 from biorefineries.lactic import load, create_funcs
     25 from biorefineries.lactic._chemicals import sugars
     26 from biorefineries.lactic.utils import set_yield

File <frozen importlib._bootstrap>:1075, in _handle_fromlist(module, fromlist, import_, recursive)

File D:\anaconda\envs\bio\lib\site-packages\lazypkg\__init__.py:62, in LazyPkg.__getattr__(self, name)
     60 unsearchable = self.__unsearchable
     61 for i in self.__all__:
---> 62     module = getattr(self, i)
     63     if (isinstance(module, ModuleType)
     64         and i not in unsearchable
     65         and hasattr(module, name)):
     66         attr = getattr(module, name)

File D:\anaconda\envs\bio\lib\site-packages\lazypkg\__init__.py:53, in LazyPkg.__getattr__(self, name)
     51 attempts = self.__import_attempts
     52 try:
---> 53     attr = import_module('.'+name, self.__package__)
     54 except ModuleNotFoundError as Error:
     55     if name in attempts:

File D:\anaconda\envs\bio\lib\importlib\__init__.py:126, in import_module(name, package)
    124             break
    125         level += 1
--> 126 return _bootstrap._gcd_import(name[level:], package, level)

File D:\anaconda\envs\bio\lib\site-packages\biorefineries\lactic\chemicals.py:117
    115 CaSO4 = chemical_database('CaSO4', phase='s', Hf=-342531*_cal2joule)
    116 # The default Perry 151 value is likely to be wrong, use another model instead
--> 117 CaSO4.Cn.move_up_model_priority('Constant', 0)
    119 # =============================================================================
    120 # Soluble organics
    121 # =============================================================================
    123 Ethanol = chemical_database('Ethanol')

File D:\anaconda\envs\bio\lib\site-packages\thermosteam\thermo\t_dependent_property.py:90, in move_up_model_priority(self, model, priority)
     87 if priority == 0:
     88     warn("'move_up_model_priority' is deprecated; set the 'method' "
     89          "attribute to change model", DeprecationWarning)
---> 90     self._set_method(model, 3)
     91 else:
     92     raise RuntimeError(
     93         "'move_up_model_priority' is deprecated; cannot set model "
     94         "priority as models are not cycled anymore")

File D:\anaconda\envs\bio\lib\site-packages\thermosteam\thermo\t_dependent_property.py:65, in _set_method(self, method, stacklevel)
     63     method = method.upper().replace(' ', '_').replace('_AND_', '_').strip('_').replace('SOLID', 'S').replace('SATURATION', 'SAT')
     64 if method not in self.all_methods and method != 'POLY_FIT':
---> 65     raise ValueError("Method '%s' is not available for this chemical; "
     66                      "available methods are %s" %(method, self.all_methods))
     67 if old_method != method:
     68     warn("Method '%s' does not exist, but was assummed to indicate '%s'" %(old_method, method),
     69          category=RuntimeWarning, stacklevel=stacklevel)

ValueError: Method 'CONSTANT' is not available for this chemical; available methods are {'PERRY151', 'LASTOVKA_S', 'CRCSTD'}

If I directly execute the command "pip install biosteam== 2.20.21", an error will encountered.

Collecting sklearn (from pipeml>=0.1->biosteam==2.20.21)
  Using cached sklearn-0.0.post12.tar.gz (2.6 kB)
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [15 lines of output]
      The 'sklearn' PyPI package is deprecated, use 'scikit-learn'
      rather than 'sklearn' for pip commands.

      Here is how to fix this error in the main use cases:
      - use 'pip install scikit-learn' rather than 'pip install sklearn'
      - replace 'sklearn' by 'scikit-learn' in your pip requirements files
        (requirements.txt, setup.py, setup.cfg, Pipfile, etc ...)
      - if the 'sklearn' package is used by one of your dependencies,
        it would be great if you take some time to track which package uses
        'sklearn' instead of 'scikit-learn' and report it to their issue tracker
      - as a last resort, set the environment variable
        SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True to avoid this error

      More information is available at
      https://github.com/scikit-learn/sklearn-pypi-package
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.