MASSpy
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SBRG
When trying to import mass (or cobra), I get the following error: ``` ImportError: cannot import name 'object' from 'numpy' (C:\Users\Corentin offline\AppData\Roaming\Python\Python310\site-packages\numpy\__init__.py) ``` The full stack trace goes as follow:...
I really really really admire the person who wrote the tutorial, it is beyond good. Unfortunately I learned fast and so I discovered that somthing is broken. https://github.com/SBRG/masspy/blob/b29701ece7d81b4c5ca073e55e6485f867b7d55d/docs/tutorials/ensemble_modeling.ipynb In the...
The following example is much slower with 2.2.0 than 2.1.3 (the previous version) ```python import mass model_source = 'WholeCellRBC_MA_Rates.xml' mass_model = mass.io.sbml.read_sbml_model(model_source) mass_sim = mass.Simulation(reference_model=mass_model) mass_sim.roadrunner.setIntegrator('cvode') time = (0, 1000,...
Steps to reproduce ``` mass.io.sbml.read_sbml_model('path/to/WholeCellRBC_MA_Rates.xml') ``` Error ``` --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) ~/.local/lib/python3.9/site-packages/mass/io/sbml.py in read_sbml_model(filename, f_replace, **kwargs) 537 doc = _get_doc_from_filename(filename) --> 538 return _sbml_to_model(doc, f_replace=f_replace, **kwargs)...
Dockerfile needs to be cleaned up in order to better work with GitHub action
...... Collecting swiglpk Using cached swiglpk-4.65.1.tar.gz (30 kB) ERROR: Command errored out with exit status 1: command: 'C:\Users\Ilknur\anaconda3\envs\masspy\python.exe' -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\Ilknur\\AppData\\Local\\Temp\\pip-install-jkgdvhfk\\swiglpk_2f4580227db041b9b88e4cd94c33661c\\setup.py'"'"'; __file__='"'"'C:\\Users\\Ilknur\\AppData\\Local\\Temp\\pip-install-jkgdvhfk\\swiglpk_2f4580227db041b9b88e4cd94c33661c\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code,...
Specific use-case of masspy, might consider making a built-in function: Has a GEM for organism, as well as a kinetic model of a subsystem of the larger GEM. Integrate the...
I would suggest an option in the built-in visualization functions to display (perhaps below the legend, outside the plot) selected model parameters or initial conditions. This feature could just add...
