Contributing

Welcome to SPACEc 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 SPACEc, 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 SPACEc docs by making them more readable and coherent, or by adding missing information and correcting mistakes.

Docstrings

The most important way to contribute to our documentation is completing missing docstrings.

We are using numpy style docstrings.

If you see differently styled docstrings feel free to change them. The updated docstrings will automatically be integrated into our Read the Docs documentation.

Tutorials

Tutorial notebooks are imported from notebooks. Please always start a notebook with a main header, e.g., # EXAMPLE HEADER.

Read the Docs

SPACEc documentation uses Sphinx as its main documentation compiler which helps us to automatically push our documentation to Read the Docs. 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.

We are using Markdown with the MyST extension for our documentations.

Tip

See MyST on how to get started writing documentation files, and install an editor extensions (e.g., MyST-Markdown for VS Code) for easier editing. It can also make sense to have a look at the Sphinx documentation for more advanced editing.

Tip

Please notice that the GitHub web interface provides a quick way of propose changes in SPACEc’s files. While this mechanism can be tricky for normal code contributions, it works perfectly fine for contributing to the docs, and can be quite handy.

If you are interested in trying this method out, please navigate to the docs folder in the source repository, find which file you would like to propose changes and click in the little pencil icon at the top, to open GitHub’s code editor. Once you finish editing the file, please write a message in the form at the bottom of the page describing which changes have you made and what are the motivations behind them and submit your proposal.

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

tox -e docs

Tip

If you are running within a conda environment first install tox with conda install tox.

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.

Quickstart

Note

Conventions:

  • numpy style docstrings

  • MyST documentation using Sphinx

Note

Tutorials: Tutorial notebooks are imported from notebooks. Please always start a notebook with a main header, e.g., # EXAMPLE HEADER.

# setup virtual environment
conda create -n SPACEc python=3.10 pytest pytest-cov tox pre-commit
conda activate SPACEc

# clone and install SPACEc
git clone git@github.com:yuqiyuqitan/SPACEc.git
cd SPACEc
pip install -e .

# for Apple Mx users, additional steps might be necessary
# also see `README.md`
# conda install tensorflow=2.10.0

# install pre-commit hooks (for automatic style checks)
pre-commit install

# try to run tests
tox

# build and look at docs
tox -e docs
python3 -m http.server --directory 'docs/_build/html'

Create an environment

Before you start coding, we recommend creating an isolated virtual environment to avoid any problems with your installed Python packages. We strongly recommend using some conda-style environment mangement system, e.g., Miniconda:

# create conda environment
conda create -n SPACEc python=3.10 pytest pytest-cov tox
conda activate SPACEc

Tip

Please also see the [Overview] for the most up to date instruction son how to set up the environment to use and develop SPACEc.

Clone the repository

  1. Create an user account on GitHub if you do not already have one.

  2. 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.

  3. Clone this copy to your local disk:

    git clone git@github.com:yuqiyuqitan/SPACEc.git
cd SPACEc

  4. You should run:

    pip install -U pip setuptools -e .

    to be able to import the package under development in the Python REPL.

  5. Install pre-commit:

    pip install pre-commit
pre-commit install

    SPACEc comes with a lot of hooks configured to automatically help the developer to check the code being written.

Implement your changes

  1. Create a branch to hold your changes:

    git checkout -b my-feature

    and start making changes. Never work on the main branch!

  2. 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. Please use numpy style docstrings.

  3. Add yourself to the list of contributors in AUTHORS.md.

  4. 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.

  5. Please check that your changes don’t break any unit tests with:

    tox

    (after having installed tox with conda install tox, 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

  1. If everything works fine, push your local branch to the remote server with:

    git push -u origin my-feature

  2. Go to the web page of your fork and click “Create pull request” to send your changes for review.

    Find more detailed information in creating a PR. You might also want to open the PR as a draft first and mark it as ready for review after the feedbacks from the continuous integration (CI) system or any required fixes.

    Pull requests automatically trigger tests via Github Actions. We can only merge a pull request if all tests succeed.

Tip

Every now and then Github Actions has a hick up and tests fail due to random reasons. For example saying THESE PACKAGES DO NOT MATCH THE HASHES FROM THE REQUIREMENTS FILE. You can make a small change and commit to update your pull request and trigger a re-run of the tests.

Troubleshooting

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

  1. 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.

  2. 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

  3. 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.

  4. 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 SPACEc:

  1. Make sure all unit tests are successful.

  2. Tag the current commit on the main branch with a release tag, e.g., v1.2.3.

  3. Push the new tag to the upstream repository, e.g., git push upstream v1.2.3

  4. This will automatically start a Github Action to deploy the new version to PyPI and update the documentation on Read the Docs.