Metadata-Version: 2.1
Name: vivarium_cluster_tools
Version: 1.3.7
Summary: A set of tools for running simulation using vivarium on cluster.
Home-page: https://github.com/ihmeuw/vivarium_cluster_tools
Author: The vivarium developers
Author-email: vivarium.dev@gmail.com
License: UNKNOWN
Description: Vivarium Cluster Tools
        =======================
        
        .. image:: https://badge.fury.io/py/vivarium-cluster-tools.svg
            :target: https://badge.fury.io/py/vivarium-cluster-tools
        
        .. image:: https://travis-ci.org/ihmeuw/vivarium_cluster_tools.svg?branch=main
            :target: https://travis-ci.org/ihmeuw/vivarium_cluster_tools
            :alt: Latest Version
        
        .. image:: https://readthedocs.org/projects/vivarium-cluster-tools/badge/?version=latest
            :target: https://vivarium-cluster-tools.readthedocs.io/en/latest/?badge=latest
            :alt: Documentation Status
        
        Vivarium cluster tools is a python package that makes running ``vivarium``
        simulations at scale on a Univa Grid Engine cluster easy.
        
        Installation
        ------------
        
        You can install this package with
        
        .. code-block:: console
        
            pip install vivarium-cluster-tools
        
        In addition, this tool needs the redis client. This must be installed using conda.
        
        .. code-block:: console
        
            conda install redis
        
        A simple example
        ----------------
        
        If you have a ``vivarium`` model specifcation file defining a particular model,
        you can use that along side a **branches file** to launch a run of many
        simulations at once with variations in the input data, random seed, or with
        different parameter settings.
        
        .. code-block:: console
        
            psimulate run /path/to/model_specification.yaml /path/to/branches_file.yaml
        
        The simplest branches file defines a count of input data draws and random seeds
        to launch.
        
        .. code-block:: yaml
        
            input_draw_count: 25
            random_seed_count: 10
        
        
        This branches file defines a set of simulations for all combinations of 25
        input draws and 10 random seeds and so would run, in total, 250 simulations.
        
        You can also define a set of parameter variations to run your model over. Say
        your original model specification looked something like
        
        .. code-block:: yaml
        
            plugins:
              optional: ...
        
            components:
              vivarium_public_health:
                population:
                  - BasePopulation()
                  - Mortality()
                disease.models:
                  - SIS('lower_respiratory_infections')
              my_lri_intervention:
                components:
                  - GiveKidsVaccines()
        
            configuration:
              population:
                population_size: 1000
                age_start: 0
                age_end: 5
              lri_vaccine:
                coverage: 0.2
                efficacy: 0.8
        
        Defining a simple model of lower respiratory infections and a vaccine
        intervention. You could then write a branches file that varied over both
        input data draws and random seeds, but also over different levels of coverage
        and efficacy for the vaccine.  That file would look like
        
        .. code-block:: yaml
        
            input_draw_count: 25
            random_seed_count: 10
        
            branches:
              lri_vaccine:
                coverage: [0.0, 0.2, 0.4, 0.8, 1.0]
                efficacy: [0.4, 0.6, 0.8]
        
        The branches file would overwrite your original ``lri_vaccine`` configuration
        with each combination of coverage and efficacy in the branches file and launch
        a simulation. More, it would run each coverage-efficacy pair in the branches
        for each combination of input draw and random seed to produce 25 * 10 * 5 * 3 =
        3750 unique simulations.
        
        To read about more of the available features and get a better understanding
        of how to correctly write your own branches files, check out the
        `vivarium cluster tools documentation <https://vivarium-cluster-tools.readthedocs.io/en/latest/?badge=latest>`_.
        
Platform: UNKNOWN
Provides-Extra: docs
Provides-Extra: test
Provides-Extra: dev
