Making your first analysis contribution

This is the path that you can expect to follow when making your first contribution to an analysis.

• Planning
• Implementation
• Review

Planning

Make an analysis proposal

Start with GitHub Discussions to propose a new analysis or a modification to an existing analysis.

You will file a Discussion for:

• A new analysis in the Propose a new analysis category
• An update to an existing analysis in the Modify an existing analysis category

A Data Lab member will review your proposal and respond to your original post to discuss further. Together you will continue to develop your analysis plans and make decisions about next steps.

File an issue

• After you have proposed an analysis on Discussions and a plan has been developed, then you can file an issue in the AlexsLemonade/OpenScPCA-analysis repository.
• Refer to the documentation on how to write an issue.
• We use issue templates to prompt issue authors to include helpful information that helps us accomplish the work tracked in that Issue.

Pick an existing issue

• There may be existing issues in the AlexsLemonade/OpenScPCA-analysis repository for planned analyses that have not been started yet.
• If you would like to take on a planned analysis, you can comment on the issue to note your interest, ask any clarifying questions, and/or propose a solution for the Data Lab team to review and discuss further.

Getting access to resources

• Once you've met the criteria for Amazon Web Services (AWS) account creation, which includes discussing an analysis, we will create an AWS account for you.
• You will need to accept the invitation to join as described in our AWS documentation to complete one of the steps in environment setup mentioned below.

Implementation

Create local setup

Before starting any analyses, you need to set up your local environment.

Please refer to these linked instructions for the specific setup steps you need to take.

Scope work

• When working on an analysis, it's important to take some time to plan your work.
• Refer to this documentation on scoping your first pull request.

Implement your analysis

• Now that you have set up your local environment, discussed your proposed analysis, and filed an Issue, you're ready to create an analysis module.

• Refer to the documentation on creating an analysis module to make your first analysis folder.

• Document each step of your analysis.

• Once you have added or modified code for your analyses that you are happy with, you will need to commit your changes to your feature branch.

Review

File a pull request

• Once you have committed changes to your feature branch and pushed to origin, you are ready to file a pull request.

• Similar to issue templates, we use pull request templates to prompt you for information that will help us review your code.

Undergo analytical code review

• Pull requests must be reviewed and approved by a Data Lab member before they can be merged into the AlexsLemonade/OpenScPCA-analysis repository.
• All pull requests will undergo analytical code review.

Merge

• Once approved, a Data Lab staff member will merge your feature branch into the main branch of AlexsLemonade/OpenScPCA-analysis.