🤝 How to Contribute

🤝 How to Contribute#

🎉 Thank you for considering contributions to this project! 🎉
We welcome new methods, enhancements, bug fixes, and improvements to the existing content.

Note

📋 Quick Start: To ensure consistency and smooth integration, please follow the guidelines below.

1. ➕ Add or Update Methods#

Each method is stored as an individual YAML file in the methods/ directory. This makes it easy to add new methods or edit existing ones without navigating through a large file.

🆕 To add a new method:#

  1. 📁 Create File: New YAML file in the methods/ directory with a descriptive filename (e.g., my_new_method.yaml)

  2. 📝 Follow Structure: Use existing method files as templates, including these required fields:

    Method: Method Name                    # 🏷️ Official method name
Year: 2024                            # 📅 Publication year
Published: true                        # ✅ Publication status (true/false)

Description: |                         # 📄 Detailed description
  A comprehensive description of the method, including its approach,
  key features, and how it works. This text appears in the
  expandable table rows on the website.

Task:                                  # 🎯 List of computational tasks
  - Task Category 1
  - Task Category 2

Publication: https://doi.org/10.1000/example     # 📖 DOI or URL
Code Availability: https://github.com/user/repo  # 💻 Repository link

    Additional optional fields:

    • Model: List of underlying models or frameworks

    • Inspired by: List of references or inspirations

✏️ To edit an existing method:#

  1. 🔍 Find File: Locate the corresponding YAML file in the methods/ directory

  2. ✏️ Edit Directly: Modify the file - filenames correspond to method names (lowercased with special characters replaced)

Tip

💡 File Naming: Use descriptive names based on the method name:

  • Method: cPCA → cpca.yaml

  • Method: GEARS → gears.yaml

  • Method: scGEN → scgen.yaml

Warning

⚠️ YAML Syntax: Please ensure valid YAML syntax and follow existing entries for examples.

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2. 🔄 Continuous Integration#

🚀 Automated Workflow

A GitHub Actions workflow automatically runs generate_methods.py against methods.rst.j2 whenever your pull request is merged into main. This regenerates source/methods.rst to reflect your changes.

Important

✅ No Manual Work Required: You do NOT need to run any commands manually for the table update!

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3. 🔍 Local Preview (Optional)#

If you wish to preview the changes locally before pushing your PR:

# 📦 Set up environment
conda env create -f environment.yml

# 🔄 Activate environment (once created)
conda activate iep-singlecell

# 🏗️ Generate docs and build
python generate_methods.py && make -C docs clean html

📱 View Results: Open docs/build/html/index.html in a browser.

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4. 🛡️ Quality Guidelines#

💡 Best Practices

For Method Descriptions:

  • 📝 Be comprehensive but concise - aim for 3-5 sentences

  • 🎯 Focus on the key innovation or distinguishing features

  • 🔗 Mention the main application area or use case

  • ⚙️ Include technical details that help users understand the approach

For Code Availability:

  • ✅ Use '-' if no code is available

  • 🔗 Prefer GitHub/GitLab links over personal websites

  • 📦 Link to the main repository, not individual files

For Publications:

  • 🏷️ Use DOI links when available (https://doi.org/10.xxxx/...)

  • 📰 For preprints, use bioRxiv/arXiv links

  • 📚 Ensure the link is publicly accessible

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5. 🆘 Getting Help#

❓ Need Assistance?

  • 💬 Questions: Open a GitHub issue with the question label

  • 🐛 Bug Reports: Use the bug label and provide details

  • 💡 Feature Requests: Use the enhancement label

  • 📧 Direct Contact: Reach out to the maintainers

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🙏 Thank You for Contributing! 🙏

Every contribution helps make this resource better for the entire single-cell community.

🌟 Don't forget to star the repository if you find it useful! 🌟

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