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CONTRIBUTING.md

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Contributing to obnb

First and foremost, we thank you for your interest in contributing to the obnb pacakge! We welcome any kind of contribution, e.g.,

  • New features
  • Bug fixes and new tests
  • Typo fixes or improving the documentation in general

To get started,

  1. Make a fork of the repository, and create a new branch where you will be making your changes
  2. After you are done with the new changes, make a Pull Request https://github.com/krishnanlab/obnb/pulls of your changes

Dev notes

Installation

To develop obnb, first clone your forked repository to your machine (replace <your_github_handle> with your GitHub handle)

git clone https://github.com/<your_github_handle>/obnb
cd obnb

If you have done it before, make sure your fork is in-sync with the latest changes and pull the changes to your local copy

git pull

Then, create a conda environment for developing obnb (this is not required, but it is recommended to have an isolated development environment as it keeps the dependency versions clean)

conda create -n obnb-dev python=3.9
conda activate obnb-dev

Install obnb with development dependencies

pip install -r requirements.txt  # install dependencies with pinned version
pip install -e ".[dev]"  # install extra dependencies for dev

Finally, install pre-commit hooks to enable automated code quality control for each commit

pre-commit install

Testing

To run all existing unit-tests, simply run pytest at the project root directory

pytest

Linting

We provide some additional code quality control tools via tox to help catch early mistasks:

tox -e mypy,flake8

Continuous integration

We have set up continuous integration via GitHub Actions. Every time a pull request is made from a branch (and any following push to that branch) will trigger automated testing and linting to check the changes against out dev guidelines.

Building documentation

  1. Install obnb with doc dependencies (e.g., Sphinx)

    pip install -e .[full,doc]

  2. Install PyTorch if you have not done so yet, or simply install a minimal cpu version of PyTorch if you only want to build the obnb documentation:

    conda install pytorch cpuonly -c pytorch

  3. Build the documentation

    cd docs
make html

You can now view the documentation page by opening docs/build/html/index.html

Data preparation and releasing notes

First, bump data version in __init__.py to the next data release version, e.g., obnbdata-v0.1.0 -> obnbdata-v0.1.1-dev. Then, download and process all latest data by running

python script/release_data.py

By default, the data ready to be uploaded (e.g., to Zenodo) is saved under data_release/archived. After some necessary inspection and checking, if everything looks good, upload and publish the new archived data.

Note: dev data should be uploaded to the sandbox instead.

Check items:

  • Update __data_version__
  • Run release_data.py
  • Upload archived data to Zenodo (be sure to edit the data version there also)
  • Update url dict in config (will improve in the future to get info from Zenodo directly)
  • Update network stats in data test

Finally, commit and push the bumped version.