Example Step Workflow

An example step workflow that does a whole bunch of simple random matrix inversion.

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Workflow

This example step workflow generates random matrices, inverts them, does a cumulative sum over an axis, the finally plots them.

By default the workflow and all sub tasks are configured to run in a single process. However, there are example steps called mapped_raw and mapped_invert to give an idea of how to switch from single threaded / process to parallel data gathering and processing.

Distributed

If you want to run this in a distributed fashion be sure install the distributed dependencies (pip install -e .[distributed]) and additionally create a workflow_config.json file with the following contents:

{
    "project_local_staging_dir": "/allen/aics/modeling/{your_name}/results/example_step_workflow/"
}

Note: The path your provide in the JSON file can point to wherever you want, the path simply must be available to all the workers.

Installation

pip install git+https://github.com/AllenCellModeling/example_step_workflow.git

Development

See CONTRIBUTING.md for information related to developing the code.

Developer installation

pip install -e .[dev]

Free software: Allen Institute Software License