Development

Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.

You can contribute in many ways:

Types of Contributions

Report Bugs

Report bugs at https://github.com/YosefLab/scvi-tools/issues.

If you are reporting a bug, please include:

  • Your operating system name and version.

  • Any details about your local setup that might be helpful in troubleshooting.

  • Detailed steps to reproduce the bug.

Fix Bugs

Look through the GitHub issues for bugs. Anything tagged with “bug” and “help wanted” is open to whoever wants to implement it.

Implement Features

Look through the GitHub issues for features. Anything tagged with “enhancement” and “help wanted” is open to whoever wants to implement it.

Write Documentation

scVI could always use more documentation, whether as part of the official scVI docs, in docstrings, or even on the web in blog posts, articles, and such.

Submit Feedback

The best way to send feedback is to file an issue at https://github.com/YosefLab/scvi-tools/issues.

If you are proposing a feature:

  • Explain in detail how it would work.

  • Keep the scope as narrow as possible, to make it easier to implement.

  • Remember that this is a volunteer-driven project, and that contributions are welcome :)

Get Started!

Ready to contribute? Here’s how to set up scvi-tools for local development.

  1. Fork the scvi-tools repo on GitHub.

  2. Clone your fork locally:

    $ git clone git@github.com:your_name_here/scvi.git
    
  3. Install your local copy into a virtualenv (or conda environment). Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:

    $ mkvirtualenv scvi-dev
    $ cd scvi/
    $ pip install -e .[dev,tutorials]
    
  4. Install pre-commit, which will enforce the scvi code style (black, flake8) on each of your commit:

    $ pip install pre-commit
    $ pre-commit install
    
  5. Create a branch for local development:

    $ git checkout -b name-of-your-bugfix-or-feature
    

    Now you can make your changes locally.

  6. When you’re done making changes, run the tests using tox:

    $ pytest
    $ tox
    

    To get tox, just pip install it into your virtualenv.

  7. Commit your changes and push your branch to GitHub:

    $ git add <file> ...
    $ git commit -m "Your detailed description of your changes."
    $ git push origin name-of-your-bugfix-or-feature
    
  8. Submit a pull request through the GitHub website.

Coding Standards

  1. Don’t duplicate code. Certainly no blocks longer than a couple of lines. It’s almost always better to refactor than to duplicate blocks of code.

  2. Almost all code should at least be run by a unit tests. No pull request should decrease unit test coverage by much.

  3. Document each new method and each new class with a docstring.

  4. Don’t commit commented-out code. Just delete it or store it somewhere outside of the repo. You probably aren’t going to need it. At worse, it’s stored in previous commits, from before it was commented out.

  5. A pull request (PR) will typically close at least one Github issue. For these pull requests, write the issue it closes in the description, e.g. closes #210. The issue will be automatically closed when the PR is merged.

  6. Don’t commit data to the repository, except perhaps a few small (< 50 KB) files of test data.

  7. Respect the scVI code style, the easiest way is to install pre-commit as described above.

Pull Request Guidelines

Before you submit a pull request, check that it meets these guidelines:

  1. The pull request should include tests.

  2. If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in README.rst.

  3. The pull request should work for Python 3.7. Check https://travis-ci.org/YosefLab/scVI/pull_requests and make sure that the tests pass for all supported Python versions.

Tips

To run a subset of tests:

$ pytest tests/dataset/test_anndata.py

Deploying

A reminder for the maintainers on how to deploy. Make sure all your changes are committed (including an entry in history.rst). First, please install Poetry.

Also, make sure you’ve tested your code using tox by running:

$ tox

Then run:

$ poetry version preversion # possible: major / minor / patch
$ poetry build
$ poetry publish

This will upload scvi-tools to PyPi

Instructions on Uploading to conda

scvi-tools is available on bioconda channel.

Follow the below steps to upload a new version to bioconda channel.

Create a fork of bioconda-recipes on GitHub. Then:

$ git clone https://github.com/<USERNAME>/bioconda-recipes.git
$ git remote add upstream https://github.com/bioconda/bioconda-recipes.git

Update repo:

$ git checkout master
$ git pull origin master

Write a recipe:

$ git checkout -b my-recipe

Get the package’s hash:

$ pip hash dist/scvi-<NEW_VERSION_TAG>.tar.gz

Push changes, wait for tests to pass, submit pull request:

$ git push -u origin my-recipe

For this, it’s easier to look at old scVI PR’s.

Write a GitHub release

On the GitHub page, draft a release.