https://github.com/polusai/tools

https://github.com/polusai/tools

Last synced: about 1 year ago
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• Host: GitHub
• URL: https://github.com/polusai/tools
• Owner: PolusAI
• License: mit
• Created: 2024-02-21T15:32:25.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2025-02-28T14:04:01.000Z (over 1 year ago)
• Last Synced: 2025-02-28T19:56:02.509Z (over 1 year ago)
• Language: Python
• Size: 196 KB
• Stars: 0
• Watchers: 4
• Forks: 1
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE

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README

          
# Polus Tools

## polus.tool.workflows

This package provides model that represents CWL workflows and command line

tools following the latest [cwl spec](https://www.commonwl.org/v1.2/).

It also provides tools to load, save, build and execute cwl tools and workflows.

It requires no configuration and focus on ease of use and modularity.

### How to install

the workflow builder is written and tested for Python 3.x {x = 9, 10, 11}.

Use you prefered method to create a new environment then :

with pip: `pip install .`

or with poetry:  `poetry install`

### How to use

`python examples/workflows/demo_image_processing.py` for a basic example of use.

This tool allows people to load clts and workflows from a path or a URI.

The `CommandLineTool` and `Workflow` models are found in `polus.tools.workflow.model`.

Then workflows can be build thanks to two builder classes : `StepBuilder` and `WorkflowBuilder`.

Those builders are configurable to further customize how they operate.

The tool provide an easy way to configure a workflow through regular python assignments.

Ex:

assigning a value to a step input :  `step1.inputA = "input_message"`

linking an step output to another step input : `step2.inputA = step1.outputA`

Once configured and build, a `workflow` object can be persisted with `workflow.save()`

and its configuration with `workflow.save_config()`

Lastly we provide a convenience method to run workflows locally with `cwltool`

by calling `polus.tools.workflows.backends.run_cwl()`.

### Structure

`src/polus/tools/workflows` contains the source code.

`tests/workflows` contains the test suite.

`tests/worklflows/test_data` contains a variety of cwl processes definitions.

`examples` contains our examples.

Other data directories:

`cwl` contains cwl definitions of processes we use as building blocks.

`cwl_generated` contains cwl definitions of processes generated by the tool.

`tmp` will be created on the first run and will contains examples outputs.

### Current Workflow features

This tool supports creating workflows containing:

- subworkflows

- conditional clauses

- scattered inputs

- multiple inputs

### Developers

Some hooks should run on commits. Please run `pre-commit install` to set up the hooks

before contributing.