Metadata-Version: 2.1
Name: vivarium-notebooks
Version: 0.0.4
Summary: UNKNOWN
Home-page: https://github.com/vivarium-collective/vivarium-notebooks
Author: Eran Agmon, William Poole
Author-email: agmon.eran@gmail.com, wpoole@caltech.edu
License: MIT
Description: # Vivarium notebooks
        
        ## Setup
        To run the code used in this work, you will need to install the following modules: `vivarium-core`, `vivarium-cobra`, 
        `vivarium-bioscrape`, and `vivarium-multibody`.
        These modules can be installed locally by executing the following command in the root directory:
        
        1. Clone the repository.
        
           ```console
           $ git clone https://github.com/vivarium-collective/vivarium-notebooks.git
           ```
        
           Alternatively, you can simply extract an archive of the source code
           if you got the code in that format.
        
        2. (recommended but optional) Setup a Python virtual environment.
        3. Install Python dependencies
        
           ```console
           $ pip install -r requirements.txt
           ```
        
           Note that you have to install numpy first because the `setup.py`
           script of one of our dependencies requires it.
        
        ## Notebooks
        Notebooks can be found under `notebooks/`. These include `Vivarium_interface_basics.ipynb` and `Multi-Paradigm-Composites.ipynb`.
        
        ## Python files
        All Python files can be found under `bioscrape_cobra/`.
        This includes Vivarium `Composers` for deterministic and stochastic versions of the Bioscrape/COBRA composite models 
        called `bioscrape_cobra_deterministic.py` and `bioscrape_cobra_stochastic.py`. 
        Simulation functions for running all of the examples in `Multi-Paradigm-Composites.ipynb` can be found in `simulate.py`.
        This file also includes command-line run options for six different simulations with these names: 
        [`deterministic`, `stochastic`, `deterministic_divide`, `stochastic_divide`, `deterministic_spatial`, `stochastic_spatial`].
        These can be called simply with:
        
        > python bioscrape_cobra/simulate --simulation_name
        
        Parallelization can be triggered with the `-p` option: 
        
        > python bioscrape_cobra/simulate --simulation_name -p
        
        Saving the simulation output to a mongoDB database requires a running mongoDB instance, as described in the
        [Vivarium docuentation](https://vivarium-core.readthedocs.io/en/latest/getting_started_dev.html). 
        It can then be triggered with the `-d` option: 
        
        > python bioscrape_cobra/simulate --simulation_name -d
        
        ## Tests
        Tests are performed with pytest. Simply call the following to ensure everything is working properly:
        ```
        $ pytest
        ```
        
        To run only the fast tests:
        ```
        $ pytest -m 'not slow'
        ```
        
        
Platform: UNKNOWN
Description-Content-Type: text/markdown
