Developer documentation

Development of exoplanet is actively happening on GitHub and we would love your contributions. There are a few different methods of contributing to exoplanet and the details are discussed below.

Reporting an issue

If you run into issues, bugs, or anything else, it is very useful if you can post an issue on the GitHub repository. When you post an issue, please provide the details to reproduce the issue. For example, if you find a bug, please provide a standalone and executable snippet of code that demonstrates the issue. It’s also useful to include details about your platform and the versions of key packages that your using.

Contributing code or documentation

If you’re not familiar with the workflow for contributing code to a GitHub repository, an excellent place to start is the AstroPy developer docs.

Set up your development environment

After getting some familiarity with the workflow, you should fork the exoplanet repository and clone it to your local machine:

git clone https://github.com/YOURUSERNAME/exoplanet.git
cd exoplanet
git checkout -b BRANCHNAME

for some name BRANCHNAME describing your contribution.

Then you should set up an isolated environment for development using a Conda environment, virtualenv, venv, or similar. If using conda, you can get the current development environment from the environment.yml file:

conda env create --prefix env -f environment.yml
conda activate ./env

If you have an existing conda environment for exoplanet, you can update it using:

conda env update --prefix ./env -f environment.yml  --prune

If you’re using a pip based environment, you can install the developer dependencies as follows:

python -m pip install -U pip
python -m pip install -U -r requirements-dev.txt

After your environment is set up, you can install the current development version of exoplanet:

python -m pip install -U setuptools setuptools_scm pep517
python -m pip uninstall -y exoplanet
python setup.py develop

Finding your way around the codebase

exoplanet is mostly arranged as a typical Python project with the module root in the src/exoplanet directory. But there are a few directions that can be useful before diving in:

1. Tutorials: The tutorials are written using the jupytext tool to keep the size of the repository from blowing up. The tutorial files are saved (using jupytext) in the docs/notebooks directory as .py files in the py:percent format. You can edit these files as if they are Jupyter notebooks by using the extension:

jupyter nbextension install --py jupytext
jupyter nbextension enable --py jupytext

If you are contributing a new tutorial, you should copy one of the existing ones and try to follow roughly the same format.

2. Case studies: These are more in depth tutorials that require more computational run time. These can be found in the case studies repo and there is more information there about how to contribute.

3. Theano ops: exoplanet comes bundled with a set of custom Theano ops that are implemented in src/exoplanet/theano_ops. As a user, you’ll rarely interact with these directly and we haven’t put a lot of work into making them user friendly, but if you are interested in diving in, here are some tips. First, you should check out the Theano docs that describe how to develop new ops in Python and C/C++. Most of the exoplanet ops are implemented in C++ for speed and we’ve made the design decision to separate the “science” code (which implements the actual operation without any dependency on Theano) and “wrapper” code (which sets up the interface). The science code is implemented as a header-only C++ library in src/exoplanet/theano_ops/lib/include/exoplanet and then the wrappers are implemented as submodules in src/exoplanet/theano_ops. A good place to start is the KeplerOp implemented in src/exoplanet/theano_ops/kepler and src/exoplanet/theano_ops/lib/include/exoplanet/kepler.h.

Testing your contribution

If you’re contributing a change to the code (either a new feature or bug fix), make sure that you implement at least one test that checks the behavior of your code. Then, you should run all of the unit tests before submitting a pull request using the following command:

python -m pytest -sv src/exoplanet

Code style

We have a pretty strict (but easy to implement!) set of style guidelines for the codebase. For Python code, we use isort, black, and black_nbconvert (for Jupyter notebooks). The custom settings for these projects can be found in pyproject.toml. Before opening a pull request, you can run the formatters as follows:

isort -rc src
black src
black_nbconvert .

Or, you can use pre-commit to automatically apply the formatting whenever you commit:

python -m pip install -U pre-commit
pre-commit install

Release management

Note

Most of this build process is based on the October 2019 update to this blog post so you should check that out if you want more info.

This section is mainly internal, but these are the steps that should be executed to produce a new release.

  1. Update citation date and version in src/exoplanet/citations.py.

  2. Update the notebooks in the case studies repo and run a release there.

  3. Update changelog date in HISTORY.rst.

  4. Tag a GitHub release.

After executing these steps, the release can be built as follows:

python -m pip install -U pip pep517 twine setuptools_scm
git pull
rm -rf build dist
python -m pep517.build .

Then you can test that the build installs as expected:

rm -rf venv-test
python -m venv venv-test
venv-test/bin/python -m pip install dist/exoplanet*.tar.gz
venv-test/bin/python -c "import exoplanet;print(exoplanet.__version__)"

This should print the current version number. Similarly you can test the wheel:

rm -rf venv-test
python -m venv venv-test
venv-test/bin/python -m pip install dist/exoplanet*.whl
venv-test/bin/python -c "import exoplanet;print(exoplanet.__version__)"

Once you’re satisfied with this build, you can upload it using twine:

twine upload dist/*