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 at https://github.com/YosefLab/scVI/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.
Look through the GitHub issues for bugs. Anything tagged with “bug” and “help wanted” is open to whoever wants to implement it.
Look through the GitHub issues for features. Anything tagged with “enhancement” and “help wanted” is open to whoever wants to implement it.
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.
The best way to send feedback is to file an issue at https://github.com/YosefLab/scVI/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 :)
Ready to contribute? Here’s how to set up scvi for local development.
Fork the scvi repo on GitHub.
Clone your fork locally:
$ git clone email@example.com:your_name_here/scvi.git
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 $ cd scvi/ $ pip install -e .[test,notebooks]
Install pre-commit, which will enforce the scvi code style (black, flake8) on each of your commit:
$ pip install pre-commit $ pre-commit install
Create a branch for local development:
$ git checkout -b name-of-your-bugfix-or-feature
Now you can make your changes locally.
When you’re done making changes, run the tests using tox:
$ python setup.py test or py.test $ tox
To get tox, just pip install it into your virtualenv.
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
Submit a pull request through the GitHub website.
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.
Almost all code should at least be run by a unit tests. No pull request should decrease unit test coverage by much.
Document each new method and each new class with a docstring.
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.
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.
Don’t commit data to the repository, except perhaps a few small (< 50 KB) files of test data.
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:
The pull request should include tests.
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.
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.
To run a subset of tests:
$ py.test tests.test_scvi
A reminder for the maintainers on how to deploy. Make sure all your changes are committed (including an entry in HISTORY.rst).
Also, make sure you’ve tested your code using tox by running:
$ bumpversion patch # possible: major / minor / patch $ git push $ git push --tags
Instructions on Uploading to pip¶
scvi is available on PyPI.
You can build and upload a new version to PyPI by running:
$ python3 setup.py sdist bdist_wheel $ twine upload dist/*
Instructions on Uploading to conda¶
scvi 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
$ 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.
Instructions on updating notebooks¶
In order to update the notebooks appearing in readthedocs, in scVI, merge the new tag onto the stable branch