Contributing to USGS-MAP-gwmodels

(Note: much of this page was cribbed from the geopandas project, which has similar guidelines to pandas and xarray.)

Overview

Contributions to usgs-map-gwmodels are very welcome. They are likely to be accepted more quickly if they follow these guidelines.

In general, usgs-map-gwmodels follows the conventions of the pandas project where applicable.

In particular, when submitting a pull request:

  • All existing tests should pass. Please make sure that the test suite passes, both locally and on Travis CI. Status on Travis will be visible on a pull request. If you want to enable Travis CI on your own fork, please read the pandas guidelines link above or the getting started docs.

  • New functionality should include tests. Please write reasonable tests for your code and make sure that they pass on your pull request.

  • Classes, methods, functions, etc. should have docstrings. The first line of a docstring should be a standalone summary. Parameters and return values should be documented explicitly. (Note: there are admittedly more than a few places in the existing code where docstrings are missing. Docstring contributions are especially welcome!

  • Follow PEP 8 when possible. For more details see below.

  • Following the FloPy Commit Message Guidelines (which are similar to the Conventional Commits specification) is encouraged. Structured commit messages like these can result in more explicit commit messages that are more informative, and also facilitate automation of project maintenance tasks.

  • Imports should be grouped with standard library imports first, 3rd-party libraries next, and usgs-map-gwmodels imports third. Within each grouping, imports should be alphabetized. Always use absolute imports when possible, and explicit relative imports for local imports when necessary in tests. Imports can be sorted automatically using the isort package with a pre-commit hook. For more details see below.

  • usgs-map-gwmodels supports Python 3.7+ only.

Seven Steps for Contributing

There are seven basic steps to contributing to usgs-map-gwmodels:

  1. Fork the usgs-map-gwmodels git repository

  2. Create a development environment

  3. Install usgs-map-gwmodels dependencies

  4. Installing the usgs-map-gwmodels source code

  5. Make changes to code and add tests

  6. Update the documentation

  7. Submit a Pull Request

Each of these 7 steps is detailed below.

1) Forking the usgs-map-gwmodels repository using Git

To the new user, working with Git is one of the more daunting aspects of contributing to usgs-map-gwmodels*. It can very quickly become overwhelming, but sticking to the guidelines below will help keep the process straightforward and mostly trouble free. As always, if you are having difficulties please feel free to ask for help.

The code is hosted on GitHub. To contribute you will need to sign up for a free GitHub account. We use Git for version control to allow many people to work together on the project.

Some great resources for learning Git:

Getting started with Git

GitHub has instructions for installing git, setting up your SSH key, and configuring git. All these steps need to be completed before you can work seamlessly between your local repository and GitHub.

Forking

You will need your own fork to work on the code. Go to the usgs-map-gwmodels project page and hit the Fork button. You will want to clone your fork to your machine:

git clone git@github.com:your-user-name/usgs-map-gwmodels.git usgs-map-gwmodels-yourname
cd usgs-map-gwmodels-yourname
git remote add upstream git://github.com/aleaf/usgs-map-gwmodels.git

This creates the directory usgs-map-gwmodels-yourname and connects your repository to the upstream (main project) usgs-map-gwmodels repository.

The testing suite will run automatically on Travis-CI once your pull request is submitted. However, if you wish to run the test suite on a branch prior to submitting the pull request, then Travis-CI needs to be hooked up to your GitHub repository. Instructions for doing so are here.

Creating a branch

You want your master branch to reflect only production-ready code, so create a feature branch for making your changes. For example:

git branch shiny-new-feature
git checkout shiny-new-feature

The above can be simplified to:

git checkout -b shiny-new-feature

This changes your working directory to the shiny-new-feature branch. Keep any changes in this branch specific to one bug or feature so it is clear what the branch brings to usgs-map-gwmodels. You can have many shiny-new-features and switch in between them using the git checkout command.

To update this branch, you need to retrieve the changes from the develop branch:

git fetch upstream
git rebase upstream/develop

This will replay your commits on top of the latest usgs-map-gwmodels git develop. If this leads to merge conflicts, you must resolve these before submitting your pull request. It’s a good idea to move slowly while doing this and pay attention to the messages from git. The wrong command at the wrong time can quickly spiral into a confusing mess.

If you have uncommitted changes, you will need to stash them prior to updating. This will effectively store your changes and they can be reapplied after updating.

2 & 3) Creating a development environment with the required dependencies

A development environment is a virtual space where you can keep an independent installation of usgs-map-gwmodels. This makes it easy to keep both a stable version of python in one place you use for work, and a development version (which you may break while playing with code) in another.

An easy way to create a usgs-map-gwmodels development environment is as follows:

Tell conda to create a new environment, named usgs-map-gwmodels_dev, that has all of the python packages needed to contribute to usgs-map-gwmodels. Note that in the geopandas instructions, this step is broken into two parts- 2) creating the environment, and 3) installing the dependencies. By using a yaml file that includes the environment name and package requirements, these two steps can be combined:

conda env create -f environment-dev.yml

This will create the new environment, and not touch any of your existing environments, nor any existing python installation.

To work in this environment, you need to activate it. The instructions below should work for both Windows, Mac and Linux:

conda activate usgs-map-gwmodels_dev

Once your environment is activated, you will see a confirmation message to indicate you are in the new development environment.

To view your environments:

conda info -e

To return to your home root environment:

conda deactivate

See the full conda docs here.

At this point you can easily do a development install, as detailed in the next sections.

4) Installing the usgs-map-gwmodels source code

Once dependencies are in place, install the usgs-map-gwmodels source code by navigating to the gitclone of the usgs-map-gwmodels repository and (with the usgs-map-gwmodels_dev environment activated) running:

python install -e .

5) Making changes and writing tests

usgs-map-gwmodels is serious about testing and strongly encourages contributors to embrace test-driven development (TDD). This development process “relies on the repetition of a very short development cycle: first the developer writes an (initially failing) automated test case that defines a desired improvement or new function, then produces the minimum amount of code to pass that test.” So, before actually writing any code, you should write your tests. Often the test can be taken from the original GitHub issue. However, it is always worth considering additional use cases and writing corresponding tests.

In general, tests are required for code pushed to usgs-map-gwmodels. Therefore, it is worth getting in the habit of writing tests ahead of time so this is never an issue.

usgs-map-gwmodels uses the pytest testing system and the convenient extensions in numpy.testing and pandas.testing.

Writing tests

All tests should go into the tests directory. This folder contains many current examples of tests, and we suggest looking to these for inspiration.

The .testing module has some special functions to facilitate writing tests. The easiest way to verify that your code is correct is to explicitly construct the result you expect, then compare the actual result to the expected correct result.

Running the test suite

The tests can then be run directly inside your Git clone (without having to install usgs-map-gwmodels) by typing:

pytest

6) Updating the Documentation

The usgs-map-gwmodels documentation resides in the docs folder. Changes to the docs are made by modifying the appropriate file in the source folder within docs. The usgs-map-gwmodels docs use reStructuredText syntax, which is explained here and the docstrings follow the Numpy Docstring standard.

Once you have made your changes, you can try building the docs using sphinx. To do so, you can navigate to the doc folder and type:

make -C docs html

The resulting html pages will be located in docs/build/html. It’s a good practice to rebuild the docs often while writing to stay on top of any mistakes. The reStructuredText extension in VS Code is another way to continuously preview a rendered documentation page while writing.

7) Submitting a Pull Request

Once you’ve made changes and pushed them to your forked repository, you then submit a pull request to have them integrated into the usgs-map-gwmodels code base.

You can find a pull request (or PR) tutorial in the GitHub’s Help Docs.

Style Guide & Linting

usgs-map-gwmodels tries to follow the PEP8 standard. At this point, there’s no enforcement of this, but I am considering implementing Black, which automates a code style that is PEP8-complient. Many editors perform automatic linting that makes following PEP8 easy.

usgs-map-gwmodels does use the isort package to automatically organize import statements. isort can installed via pip:

$ pip install isort

And then run with:

$ isort .

from the root level of the project.

Optionally (but recommended), you can setup pre-commit hooks to automatically run isort when you make a git commit. This can be done by installing pre-commit:

$ python -m pip install pre-commit

From the root of the usgs-map-gwmodels repository, you should then install the pre-commit included in usgs-map-gwmodels:

$ pre-commit install

Then isort will be run automatically each time you commit changes. You can skip these checks with git commit --no-verify.