Contributing¶

Welcome to SingleCellExperiment contributor’s guide.

This document focuses on getting any potential contributor familiarized with the development processes, but other kinds of contributions are also appreciated.

If you are new to using git or have never collaborated in a project previously, please have a look at contribution-guide.org. Other resources are also listed in the excellent guide created by FreeCodeCamp [1].

Please notice, all users and contributors are expected to be open, considerate, reasonable, and respectful. When in doubt, Python Software Foundation’s Code of Conduct is a good reference in terms of behavior guidelines.

Issue Reports¶

If you experience bugs or general issues with SingleCellExperiment, please have a look on the issue tracker. If you don’t see anything useful there, please feel free to fire an issue report.

Tip

Please don’t forget to include the closed issues in your search. Sometimes a solution was already reported, and the problem is considered solved.

New issue reports should include information about your programming environment (e.g., operating system, Python version) and steps to reproduce the problem. Please try also to simplify the reproduction steps to a very minimal example that still illustrates the problem you are facing. By removing other factors, you help us to identify the root cause of the issue.

Documentation Improvements¶

You can help improve SingleCellExperiment docs by making them more readable and coherent, or by adding missing information and correcting mistakes.

SingleCellExperiment documentation uses Sphinx as its main documentation compiler. This means that the docs are kept in the same repository as the project code, and that any documentation update is done in the same way was a code contribution.

When working on documentation changes in your local machine, you can compile them using tox :

tox -e docs

and use Python’s built-in web server for a preview in your web browser (http://localhost:8000):

python3 -m http.server --directory 'docs/_build/html'

Code Contributions¶

Submit an issue¶

Before you work on any non-trivial code contribution it’s best to first create a report in the issue tracker to start a discussion on the subject. This often provides additional considerations and avoids unnecessary work.

Create an environment¶

Before you start coding, we recommend creating an isolated virtual environment to avoid any problems with your installed Python packages. This can easily be done via either virtualenv:

virtualenv <PATH TO VENV>
source <PATH TO VENV>/bin/activate

or Miniconda:

conda create -n SingleCellExperiment python=3 six virtualenv pytest pytest-cov
conda activate SingleCellExperiment

Clone the repository¶

Create an user account on GitHub if you do not already have one.
Fork the project repository: click on the Fork button near the top of the page. This creates a copy of the code under your account on GitHub.

Clone this copy to your local disk:

git clone git@github.com:YourLogin/SingleCellExperiment.git
cd SingleCellExperiment

You should run:
```
pip install -U pip setuptools -e .
```
to be able to import the package under development in the Python REPL.
Install pre-commit:
```
pip install pre-commit
pre-commit install
```
SingleCellExperiment comes with a lot of hooks configured to automatically help the developer to check the code being written.

Implement your changes¶

Create a branch to hold your changes:
```
git checkout -b my-feature
```
and start making changes. Never work on the main branch!
Start your work on this branch. Don’t forget to add docstrings to new functions, modules and classes, especially if they are part of public APIs.
Add yourself to the list of contributors in AUTHORS.rst.
When you’re done editing, do:
```
git add <MODIFIED FILES>
git commit
```
to record your changes in git.

Please make sure to see the validation messages from pre-commit and fix any eventual issues. This should automatically use flake8/black to check/fix the code style in a way that is compatible with the project.
Important

Don’t forget to add unit tests and documentation in case your contribution adds an additional feature and is not just a bugfix.

Moreover, writing a descriptive commit message is highly recommended. In case of doubt, you can check the commit history with:
```
git log --graph --decorate --pretty=oneline --abbrev-commit --all
```
to look for recurring communication patterns.
Please check that your changes don’t break any unit tests with:
```
tox
```
(after having installed tox with pip install tox or pipx).

You can also use tox to run several other pre-configured tasks in the repository. Try tox -av to see a list of the available checks.

Submit your contribution¶

If everything works fine, push your local branch to the remote server with:
```
git push -u origin my-feature
```
Go to the web page of your fork and click “Create pull request” to send your changes for review.

Troubleshooting¶

The following tips can be used when facing problems to build or test the package:

Make sure to fetch all the tags from the upstream repository. The command git describe --abbrev=0 --tags should return the version you are expecting. If you are trying to run CI scripts in a fork repository, make sure to push all the tags. You can also try to remove all the egg files or the complete egg folder, i.e., .eggs, as well as the *.egg-info folders in the src folder or potentially in the root of your project.
Sometimes tox misses out when new dependencies are added, especially to setup.cfg and docs/requirements.txt. If you find any problems with missing dependencies when running a command with tox, try to recreate the tox environment using the -r flag. For example, instead of:
```
tox -e docs
```
Try running:
```
tox -r -e docs
```
Make sure to have a reliable tox installation that uses the correct Python version (e.g., 3.7+). When in doubt you can run:
```
tox --version
# OR
which tox
```
If you have trouble and are seeing weird errors upon running tox, you can also try to create a dedicated virtual environment with a tox binary freshly installed. For example:
```
virtualenv .venv
source .venv/bin/activate
.venv/bin/pip install tox
.venv/bin/tox -e all
```
Pytest can drop you in an interactive session in the case an error occurs. In order to do that you need to pass a --pdb option (for example by running tox -- -k <NAME OF THE FALLING TEST> --pdb). You can also setup breakpoints manually instead of using the --pdb option.

Maintainer tasks¶

Releases¶

If you are part of the group of maintainers and have correct user permissions on PyPI, the following steps can be used to release a new version for SingleCellExperiment:

Make sure all unit tests are successful.
Tag the current commit on the main branch with a release tag, e.g., v1.2.3.
Push the new tag to the upstream repository, e.g., git push upstream v1.2.3
Clean up the dist and build folders with tox -e clean (or rm -rf dist build) to avoid confusion with old builds and Sphinx docs.
Run tox -e build and check that the files in dist have the correct version (no .dirty or git hash) according to the git tag. Also check the sizes of the distributions, if they are too big (e.g., > 500KB), unwanted clutter may have been accidentally included.
Run tox -e publish -- --repository pypi and check that everything was uploaded to PyPI correctly.