Contributing Guide

Contributions are welcome and greatly appreciated! Every little bit helps, and credit will always be given.

Types of Contributions

PCMDI Metrics Package (PMP) includes issue templates based on the contribution type: https://github.com/PCMDI/pcmdi_metrics/issues/new/choose. Note, new contributions must be made under the BSD-3-Clause license.

Bug Report

Look through the GitHub Issues for bugs to fix. Any unassigned issues tagged with “Type: Bug” is open for implementation.

Feature Request

Look through the GitHub Issues for feature suggestions. Any unassigned issues tagged with “Type: Enhancement” is open for implementation.

If you are proposing a feature:

Explain in detail how it would work.
Keep the scope as narrow as possible, to make it easier to implement.
Remember that this is a open-source project, and that contributions are welcome :)

Documentation Update

Help improve PMP’s documentation, whether that be the Sphinx documentation or the API docstrings.

Community Discussion

Take a look at the GitHub Discussions page to get involved, share ideas, or ask questions.

Contributing metrics

Developers working on new metrics to contribute to the PMP are highly encouraged to explore the PMP source code and examine how existing metrics are structured. Metrics are grouped into subpackages by topic; for example, the Mean Climate metrics, MJO metrics, and Extremes metrics are different subpackages.

In general each subpackage contains a driver script, additional library code needed to run the driver script, and example parameter files. Each subpackage must output a JSON file containing metrics and may also produce figures or other data files. New contributions may expand existing metrics subpackages or add a new subpackage.

Steps to contributing new metrics:

Open a Feature Request describing the planned metrics.
Follow the instructions in Get Started and Pull Request Guidelines (below) while working on code.
Update the GitHub.io documentation as needed.

Please keep in mind that:

It is never too early to open a Feature Request or contact the PMP team with your idea.
All metrics code must be in Python, and it is the responsibility of the contributor to deliver Python code. The PMP team has limited bandwidth to assist with code conversion to Python.
Current PMP dependencies can be found in dev.yml file. Dependencies cannot be added without the approval of the PMP team.
Input data sets are expected to follow the CF Metadata Conventions (e.g. CMIP, obs4mips).
Providing unit tests is highly encouraged.

Quick links to useful code sections:

See pcmdi_metrics/io and pcmdi_metrics/utils to find functions for tasks like land masking, grid subsetting, and more.
Graphics code for post-processing metrics is found in pcmdi_metrics/graphics

Version Control

The repository uses branch-based (core team) and fork-based (external collaborators) Git workflows with tagged software releases.

Guidelines

main must always be deployable
All changes are made through support branches
Branch names should follow the pattern “issuenumber_initials_description”
Rebase with the latest main to avoid/resolve conflicts
Make sure pre-commit quality assurance checks pass when committing (enforced in CI/CD build)
Open a pull request early for discussion
Once the CI/CD build passes and pull request is approved, squash and rebase your commits
Merge pull request into main and delete the branch

Things to Avoid

Don’t merge in broken or commented out code
Don’t commit directly to main
- There are branch-protection rules for main
Don’t merge with conflicts. Instead, handle conflicts upon rebasing

Source: https://gist.github.com/jbenet/ee6c9ac48068889b0912

Pre-commit

The repository uses the pre-commit package to manage pre-commit hooks. These hooks help with quality assurance standards by identifying simple issues at the commit level before submitting code reviews.

Get Started

Ready to contribute? Here’s how to set up PMP for local development.

VS Code, the editor of choice

We recommend using VS Code as your IDE because it is open-source and has great Python development support.

Get VS Code here: https://code.visualstudio.com

VS Code Setup

PMP includes a VS Code workspace file (.vscode/pcmdi_metrics.code-setting). This file automatically configures your IDE with the quality assurance tools, code line-length rulers, and more.

Make sure to follow the Local Development section below.

Recommended VS Code Extensions

Python

Pylance

Python Docstring Generator

Python Type Hint

Better Comments

Jupyter

Visual Studio Intellicode

Local Development

Download and install Conda

Linux

$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ bash ./Miniconda3-latest-Linux-x86_64.sh
Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no] yes

MacOS

$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
$ bash ./Miniconda3-latest-MacOSX-x86_64.sh
Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no] yes

Fork the pcmdi_metrics repo on GitHub.
- If you are a maintainer, you can clone and branch directly from the root repository here: https://github.com/PCMDI/pcmdi_metrics

Clone your fork locally:

$ git clone git@github.com:your_name_here/pcmdi_metrics.git

<OPTIONAL> Open .vscode/pcmdi_metrics.code-settings in VS Code

Create and activate Conda development environment:

$ cd pcmdi_metrics
$ conda env create -f conda-env/dev.yml
$ conda activate pcmdi_metrics_dev

<OPTIONAL> Set VS Code Python interpretor to pcmdi_metrics_dev

Install pre-commit:

$ pre-commit install
pre-commit installed at .git/hooks/pre-commit

Create a branch for local development and make changes:
```
$ git checkout -b <BRANCH-NAME>
```

<OPTIONAL> During or after making changes, check for formatting or linting issues using pre-commit:

# Step 9 performs this automatically on staged files in a commit
$ pre-commit run --all-files

Trim Trailing Whitespace.................................................Passed
Fix End of Files.........................................................Passed
Check Yaml...............................................................Passed
black....................................................................Passed
isort....................................................................Passed
flake8...................................................................Passed

Commit your changes:

$ git add .
$ git commit -m <Your detailed description of your changes>

Trim Trailing Whitespace.................................................Passed
Fix End of Files.........................................................Passed
Check Yaml...............................................................Passed
black....................................................................Passed
isort....................................................................Passed
flake8...................................................................Passed

Make sure pre-commit QA checks pass. Otherwise, fix any caught issues.
- Most of the tools fix issues automatically so you just need to re-stage the files.
- flake8 and mypy issues must be fixed automatically.
Push changes:
```
$ git push origin <BRANCH-NAME>
```
Submit a pull request through the GitHub website.

Pull Request Guidelines

Before you submit a pull request, check that it meets these guidelines:

The pull request should include tests for new or modified code.
Link issues to pull requests.
If the pull request adds functionality, the docs should be updated.
Squash and rebase commits for a clean and navigable Git history.

Style Guide

PMP integrates the Black code formatter for code styling. If you want to learn more, please read about it here.

PMP also leverages Python Type Annotations to help the project scale. mypy performs optional static type checking through pre-commit.

Testing

Testing your local changes are important to ensure long-term maintainability and extensibility of the project. Since PMP is an open source library, we aim to avoid as many bugs as possible from reaching the end-user.

To get started, here are guides on how to write tests using pytest:

In most cases, if a function is hard to test, it is usually a symptom of being too complex (high cyclomatic-complexity).

DOs for Testing

DO write tests for new or refactored code
DO try to follow test-driven-development
DO use the Coverage reports to see lines of code that need to be tested
DO focus on simplistic, small, reusable modules for unit testing
DO cover as many edge cases as possible when testing

DON’Ts for Testing

DON’T push or merge untested code
DON’T introduce tests that fail or produce warnings

Documenting Code

If you are using VS code, the Python Docstring Generator extension can be used to auto-generate a docstring snippet once a function/class has been written. If you want the extension to generate docstrings in Sphinx format, you must set the "autoDocstring.docstringFormat": "sphinx" setting, under File > Preferences > Settings.

Note that it is best to write the docstrings once you have fully defined the function/class, as then the extension will generate the full docstring. If you make any changes to the code once a docstring is generated, you will have to manually go and update the affected docstrings.

More info on docstrings here: https://sphinx-rtd-tutorial.readthedocs.io/en/latest/docstrings.html

DOs for Documenting Code

DO explain why something is done, its purpose, and its goal. The code shows how it is done, so commenting on this can be redundant.
DO explain ambiguity or complexities to avoid confusion
DO embrace documentation as an integral part of the overall development process
DO treat documenting as code and follow principles such as Don’t Repeat Yourself and Easier to Change

DON’Ts for Documenting Code

DON’T write comments as a crutch for poor code
DON’T comment every function, data structure, type declaration

Developer Tips

flake8 will warn you if the cyclomatic complexity of a function is too high.
- https://github.com/PyCQA/mccabe

FAQs

Why squash and rebase commits?

Before you merge a support branch back into main, the branch is typically squashed down to a single buildable commit, and then rebased on top of the main repo’s main branch.

Why?

Ensures build passes from the commit
Cleans up Git history for easy navigation
Makes collaboration and review process more efficient
Makes handling conflicts from rebasing simple since you only have to deal with conflicted commits

How do I squash and rebase commits?

Use GitHub’s Squash and Merge feature in the pull request
- You still need to rebase on the latest main if main is ahead of your branch.

Manually squash and rebase

<OPTIONAL if you are forking> Sync your fork of main (aka origin) with the root main (aka upstream)
git checkout main
git rebase upstream/main
git push -f origin main
Get the SHA of the commit OR number of commits to rebase to
git checkout <branch-name>
git log --graph --decorate --pretty=oneline --abbrev-commit
Squash commits:
git rebase -i [SHA]

# OR

git rebase -i HEAD~[NUMBER OF COMMITS]
Rebase branch onto main
git rebase main
git push -f origin <BRANCH-NAME>
Make sure your squashed commit messages are refined
Force push to remote branch
git push -f origin <BRANCH-NAME>