Skip to content

Latest commit

 

History

History
351 lines (258 loc) · 13.3 KB

CONTRIBUTING.md

File metadata and controls

351 lines (258 loc) · 13.3 KB
Raw

Contributing

Welcome to TemporAI contributor's guide.

This guide is adapted from PyScaffold contributor's guide template.

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.

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.

🕮 Please also make sure to first familiarize yourself with the vanderschaarlab Code of Conduct.

Issue Reports

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

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

TemporAI 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.

We use CommonMark as the markup language for the documentation, facilitated by the MyST extension. This also allows the use of reStructuredText where necessary.

Please notice that the GitHub web interface provides a quick way of propose changes in TemporAI'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

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

TBC: Developer Guide

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 temporai python=3.8
conda activate temporai

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:YourLogin/temporai.git
cd temporai

  4. Run the following to install the package and all requirements, including dev requirements:

    pip install -U pip         # Update pip.
pip install -e .[dev]      # Install TemporAI in editable mode, with the `dev` extra.

  5. Install pre-commit:

    pip install pre-commit
pre-commit install

    TemporAI comes with a lot of pre-commit 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.

  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, among other things, automatically use flake8/black to check/fix the code style in a way that is compatible with the project. See also the full list of the configured pre-commit hooks.

    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 locally check that your changes don't break any tests. The same set of tests will be executed via GitHub workflows when you submit your PR.

    # Run unit tests on your current environment.
pytest

# [Optional] Run unit tests on different tox python environments (this may be slow).
# The tests will also include doctests, and a check that all notebooks execute without errors.
# The different environment cases will be tested by automated GitHub workflows, so doing this locally is optional.
tox
# If your code introduces new dependencies, use `tox -r`.

    (after having installed tox with pip install tox).

    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.

    Note on running tests faster:

    You may wish to first run a minimal set of tests, as this is faster:

    pytest -m "not slow and not extra"

    You may also with to use pytest-xdist (pre installed with the [dev] extra) to distribute test across multiple CPUs to make the test run faster, this requires the following parameters:

    # Split tests across all available CPUs (likely not optimal, may also cause running out of memory errors):
pytest -n auto

# Split tests across <INT> max number of CPUs. Optimal value varies by machine / system.
pytest -n <INT>
# Note that some code is multithreaded under the hood, which means more than <INT> CPUs will be utilized.
# From our testing, on a machine with ~20 CPUs (including hyperthreading), value of around 3-6 appears optimal.
# Try out different values and monitor your CPUs utilization -
# aim to keep high utilization *but below* 100% across all CPUs/threads.

    If your system has GPU that supports CUDA, you may wish to skip CPU-only tests for speed:

    pytest -m "not cpu"

  6. It is also useful to check that documentation generation succeeds after your changes, run this with the following command, and make sure you do not see any Sphinx WARNINGs or errors.

    tox -e docs
tox -e doctests

Submit your contribution

  1. Before submitting your contribution, make sure to read our code of conduct.

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

    git push -u origin my-feature

  3. 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.

    The PR template will guide you through the steps of preparing your PR.

  4. When your PR is submitted, some automated GitHub workflows will run to double check passing of tests, linting, etc. One of our maintainers will review your PR and help if any of the checks are failing.

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. For example:

    virtualenv .venv
source .venv/bin/activate
.venv/bin/pip install tox
.venv/bin/tox -e all

  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

We now use GitHub workflows for releases, see release.yml.