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CONTRIBUTING.md

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Contribution guidelines

We encourage contributions from the community. To contribute:

  • Star this repository: Click the star button in the top-right corner of the repository to show your support.
  • Fork the repository: Start by forking this repository to your account.
  • Develop your component: Create your Viash component, ensuring it aligns with our best practices (detailed below).
  • Submit a pull request: After testing your component, submit a pull request for review.

Installation

You need to have Docker, Java, and Viash installed. Follow these instructions to install the required dependencies.

Getting started

Cloning the repository

To get started, fork the repository and clone it to your local machine:

git clone <git url to fork> --recursive

cd <name of the repository>

NOTE: If you forgot to clone the repository with the --recursive flag, you can run the following command to update the submodules:

git submodule update --init --recursive

Downloading the test resources

Next, you should download the test resources:

scripts/sync_resources.sh

You may need to run this script again if the resources are updated.

Good first steps

Creating a new method

To create a new method, you can use the following command:

# in Python:
common/scripts/create_component \
  --name my_method \
  --language python \
  --type method

# or in R:
common/scripts/create_component \
  --name my_method \
  --language r \
  --type method

This will create a new method in src/methods/my_method. Next, you should:

  • Fill in the component's metadata
  • Specify dependencies
  • Implement the method's code
  • Run the unit test

Please review our documentation on creating a new method for more information on how to do this.

Creating a new metric

Creating a new metric is similar to creating a new method. You can use the following command:

# in Python:
common/scripts/create_component \
  --name my_metric \
  --language python \
  --type metric

# or in R:
common/scripts/create_component \
  --name my_metric \
  --language r \
  --type metric

This will create a new metric in src/metrics/my_metric. Next, you should:

  • Fill in the component's metadata
  • Specify dependencies
  • Implement the metric's code
  • Run the unit test

Please review our documentation on creating a new metric for more information.

Frequently used commands

To get started, you can run the following commands:

Sync the test data

To sync the test data, run the following command:

scripts/sync_resources.sh

Building the components

To run the benchmark, you first need to build the components.

viash ns build --parallel --setup cachedbuild

For each of the components, this will:

  • Build a Docker image
  • Build an executable at target/executable/<component_name>
  • Build a Nextflow module at target/nextflow/<component_name>

Running the unit tests

To run the unit test of one component, you can use the following command:

viash test src/path/to/config.vsh.yaml

To run the unit tests for all components, you can use the following command:

viash ns test --parallel

Running the benchmark

To run the benchmark, you can use the following command:

scripts/run_benchmark/run.sh