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vivarium_eye_vessels

Vivarium simulation model for the vivarium_eye_vessels project.

Contents

Installation

You will need conda to install all of this repository's requirements. We recommend installing Miniforge.

Once you have conda installed, you should open up your normal shell (if you're on linux or OSX) or the git bash shell if you're on windows. You'll then make an environment, clone this repository, then install all necessary requirements as follows:

:~$ conda create --name=vivarium_eye_vessels python=3.11 git git-lfs
...conda will download python and base dependencies...
:~$ conda activate vivarium_eye_vessels
(vivarium_eye_vessels) :~$ git clone https://github.com/ihmeuw/vivarium_eye_vessels.git
...git will copy the repository from github and place it in your current directory...
(vivarium_eye_vessels) :~$ cd vivarium_eye_vessels
(vivarium_eye_vessels) :~$ pip install -e .
...pip will install vivarium and other requirements...

Supported Python versions: 3.10, 3.11

Note the -e flag that follows pip install. This will install the python package in-place, which is important for making the model specifications later.

To install requirements from a provided requirements.txt (e.g. installing an archived repository with the exact same requirements it was run with), replace pip install -e . with the following:

(vivarium_eye_vessels) :~$ pip install -r requirements.txt

Cloning the repository should take a fair bit of time as git must fetch the data artifact associated with the demo (several GB of data) from the large file system storage (git-lfs). If your clone works quickly, you are likely only retrieving the checksum file that github holds onto, and your simulations will fail. If you are only retrieving checksum files you can explicitly pull the data by executing git-lfs pull.

Vivarium uses the Hierarchical Data Format (HDF) as the backing storage for the data artifacts that supply data to the simulation. You may not have the needed libraries on your system to interact with these files, and this is not something that can be specified and installed with the rest of the package's dependencies via pip. If you encounter HDF5-related errors, you should install hdf tooling from within your environment like so:

(vivarium_eye_vessels) :~$ conda install hdf5

The (vivarium_eye_vessels) that precedes your shell prompt will probably show up by default, though it may not. It's just a visual reminder that you are installing and running things in an isolated programming environment so it doesn't conflict with other source code and libraries on your system.

Usage

You'll find six directories inside the main src/vivarium_eye_vessels package directory:

  • artifacts

    This directory contains all input data used to run the simulations. You can open these files and examine the input data using the vivarium artifact tools. A tutorial can be found at https://vivarium.readthedocs.io/en/latest/tutorials/artifact.html#reading-data

  • components

    This directory is for Python modules containing custom components for the vivarium_eye_vessels project. You should work with the engineering staff to help scope out what you need and get them built.

  • data

    If you have small scale external data for use in your sim or in your results processing, it can live here. This is almost certainly not the right place for data, so make sure there's not a better place to put it first.

  • model_specifications

    This directory should hold all model specifications and branch files associated with the project.

  • results_processing

    Any post-processing and analysis code or notebooks you write should be stored in this directory.

  • tools

    This directory hold Python files used to run scripts used to prepare input data or process outputs.

Running Simulations

Before running a simulation, you should have a model specification file. A model specification is a complete description of a vivarium model in a yaml format. An example model specification is provided with this repository in the model_specifications directory.

With this model specification file and your conda environment active, you can then run simulations by, e.g.:

(vivarium_eye_vessels) :~$ simulate run -v src/vivarium_eye_vessels/model_specifications/model_spec.yaml

The -v flag will log verbosely, so you will get log messages every time step. For more ways to run simulations, see the tutorials at https://vivarium.readthedocs.io/en/latest/tutorials/running_a_simulation/index.html and https://vivarium.readthedocs.io/en/latest/tutorials/exploration.html