Contributing

Welcome to geno2phenoTB contributor’s guide.

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 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.

Issue Reports

If you experience bugs or general issues with geno2phenoTB, please have a look on the issue tracker. If you don’t see anything useful there, please feel free to fire an issue report.

Tip

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.

Code and Documentation Contributions

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.

Clone and set up the repository

Create an user account on GitHub if you do not already have one.
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.

Clone this copy to your local disk:

git clone git@github.com:YourLogin/geno2phenoTB.git
cd geno2phenoTB

Create an isolated conda environment with the required dependencies to avoid any problems with your installed Python packages:
```
conda env create -f tests/g2p-test.yaml
conda rename -n g2p-test g2p-dev
conda activate g2p-dev
```
Next, run:
```
pip install -U pip setuptools -e ".[dev]"
```
to install further packages required for development and to enable importing the package under development in the Python REPL.
Install pre-commit:
```
pre-commit install
```
geno2phenoTB comes with a lot of hooks configured to help the developer to check the code being written automatically.

Documentation Improvements

You can help to improve the geno2phenoTB docs by making them more readable and coherent, or by adding missing information and correcting mistakes.

The geno2phenoTB 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.

reStructuredText is used.

Tip

Please notice that the GitHub web interface provides a quick way of propose changes in geno2phenoTB’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, select the file for which you would like to propose changes, and click in the little pencil icon at the top, to open GitHub’s code editor. Once you finished editing the file, please write a message in the description field at the bottom of the page describing the changes you made and the motivations behind them and submit your proposal.

When working on documentation changes in your local machine, you can compile them using:

cd docs
make html

while being in the docs directory. 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'

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 potential issues.

Code Contributions

Create a branch to hold your changes:
```
git checkout -b my-feature-name
```
and start making changes. Never work on the main branch!
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.

Important

Don’t forget to add unit tests and documentation in case your contribution adds an additional feature and is not simply a bugfix.
Add yourself to the list of contributors in AUTHORS.rst.
While developing, you should regularly check that your changes don’t break unit tests with:
```
pytest .
```

Finally, check that your changes pass all unit and self tests with:

geno2phenotb test -f # fast test
geno2phenotb test -c # complete test

When you’re done editing, do:
```
git add <MODIFIED FILES>
git commit
```
to record your changes in git.

Please make sure to inspect the validation messages from pre-commit and fix any eventual issues.

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.

Isolated build testing

In order to test that everything works in an isolated build, this project uses act to run GitHub Actions locally.

Download and install Act from here: https://github.com/nektos/act and run:

act --artifact-server-path ./build/

The first run takes a while, since a clean docker container has to be be downloaded (~12GB).

Submit your contribution

If everything works fine, push your local branch to GitHub with:
```
git push -u origin my-feature-name
```
Go to the web page of your fork and click “Create pull request” to submit your changes for review.