https://github.com/allencellmodeling/example_step_workflow

An example step workflow that does a whole bunch of simple random matrix inversion.
https://github.com/allencellmodeling/example_step_workflow

Last synced: 10 months ago
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An example step workflow that does a whole bunch of simple random matrix inversion.

• Host: GitHub
• URL: https://github.com/allencellmodeling/example_step_workflow
• Owner: AllenCellModeling
• License: other
• Created: 2020-02-15T17:27:33.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2020-11-24T03:44:34.000Z (about 5 years ago)
• Last Synced: 2025-01-02T23:14:21.681Z (12 months ago)
• Language: Python
• Size: 69.3 KB
• Stars: 0
• Watchers: 5
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

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README

          
# Example Step Workflow

[![Build Status](https://github.com/AllenCellModeling/example_step_workflow/workflows/Build%20Master/badge.svg)](https://github.com/AllenCellModeling/example_step_workflow/actions)

[![Code Coverage](https://codecov.io/gh/AllenCellModeling/example_step_workflow/branch/master/graph/badge.svg)](https://codecov.io/gh/AllenCellModeling/example_step_workflow)

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

---

## Workflow

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

the finally plots them.

![DAG](docs/resources/workflow.png)

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:

```json

{

    "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](CONTRIBUTING.md) for information related to developing the code.

### Developer installation

`pip install -e .[dev]`

***Free software: Allen Institute Software License***