We welcome contribution to stemflow

1. Fork the git repository
2. Create a development environment
3. Create a new branch, make changes to code & add tests
4. Update the docs
5. Submit a pull request

We recommend you to open and issue of feature if you wish to add brand-new features before the PR, especially with heavy mathematics to resolve.

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

git clone [email protected]:YOUR-USER-NAME/stemflow.git stemflow-YOURNAME
cd stemflow-YOURNAME
git remote add upstream git://github.com/stemflow/stemflow.git

This creates the directory stemflow-YOURNAME and connects your repository to the upstream (main project) stemflow repository.

Although stemflow has only a few dependency, we recommend creating a new environment to keep everything neat.

To do this, first install miniconda or conda:

• Install miniconda or anaconda
• cd to the stemflow source directory

Next, start a new environment called stemflow, activate it, and install dependencies:

conda create -n stemflow -python=3.8 -y
activate stemflow
conda install --file requirement.txt
conda install pre-commit pytest pytest-cov pytest-xdist

pre-commit install
pip install -e .

This library uses black, flake8 and isort pre-commit hooks. You should be familiar with pre-commit before contributing.

Make changes to the code on a separate branch to keep you main branch clean:

git checkout -b shiny-new-feature

Make changes to your code and write tests as you go. Write clear, self-documenting code to spend more time developing and less time describing how the code works.

If your branch is no longer up-to-date with main, run the following code to update it:

git fetch upstream
git rebase upstream/main

Testing is done with pytest, which you can run with either:

pytest -x -n auto --cov --no-cov-on-fail --cov-report=term-missing:skip-covered

There are two places to update docs. One is required (docstrings), the other optional (mkdocs web documentation).

Adding docstrings to each new function/class is required. stemflow uses Google-style docstrings and, when you contribute to it, you should too. mkdocs automatically renders the API docs for all functions written with this style, so you don't need to re-document each function outside of the code.

If your code contributes important new features, or introduces novel/interesting concepts, write new documentation in the docs/ directory. The docs system is managed by mkdocs, which renders from Markdown.

You can install mkdocs and the associated plugins with:

pip install mkdocs-material pillow cairosvg mkdocs-jupyter 'mkdocstrings[crystal,python]'

Then you can render the docs locally with:

mkdocs serve

After you finish editing. Commit with words that summarize the changes.

git commit -m 'what I have changed'

You will possibly find that pre-commit trimmed your scripts. In this case you need to add those changed file again and commit again to save the changes.

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

For more information, you can find a PR tutorial in GitHub’s Help Docs.