Skip to content

Latest commit

 

History

History
110 lines (71 loc) · 5.84 KB

CONTRIBUTING.md

File metadata and controls

110 lines (71 loc) · 5.84 KB

Contributing to WSIMOD

Thank you for considering contributing to WSIMOD.

Bugs

Please create a new issues if you may have found a bug. Please describe the bug and instructions on recreating it (including OS and Python version). It may be helpful to use examples from the tutorials or how-to's to ensure that data is available.

Confusion

If you are confused about how a model component works, or why it is producing results that look the way they do, please first check the documentation and existing issues. If this does not answer your question, or your question has not yet been raised, then please create a new issue where we can discuss it.

Creating new functionality

Is there something in the water cycle that you would like to represent that is not included in WSIMOD? Whatever it is, you are probably not alone! If there is not one already, please create an issue where we can discuss it. Do this before you start developing as others may be working on the same thing!

Although the development of new functionality will depend highly on the case, there are a few generalisable points to bear in mind:

  • WSIMOD is highly object-oriented, thus, we will always try to implement a new component as a subclass of the closest component. We will collaboratively discuss this in the issue.
  • Our documentation relies heavily on use of docstrings, make sure to format it following the Google Python style, see the source code of Land.__init__ for an example. An admin will compile the documentation, but you can create your own pages to be added by following the directions below.
  • We are incredibly grateful for contributions that include new tutorials or how-to's, whether for new or existing functionality. Our use of the mkdocs-jupyter extension enables notebooks to form pages in the documentation, but that can also serve as downloadable examples that people can run.
  • Design new tests that instantiate your new functionality and test that it produces a specified response. New tests are stored in the wsi/tests/ folder.

Installation for development

To install WSIMOD in development mode, first you will need a virtual environment. Here we use a conda environment which let us use the version of python we want to use, but you can use any other tool you are familiar with. Just make sure you use a version of Python compatible with WSIMOD.

conda create --name wsimod python=3.10
conda activate wsimod

Once in the environment, you need to clone the WSIMOD GitHub repository locally and move into the right folder. You will need git for that, installed either following the official instructions or with conda install git, if you use conda.

git clone https://github.com/ImperialCollegeLondon/wsi.git
cd wsi

We use pip-tools to ensure consistency in the development process, ensuring all people contributing to WSIMOD uses the same versions for all the dependencies, which minimiese the conflicts. To install the development dependencies and then WISMO in development mode run:

pip install .[dev]
pip install -e .

You can also install the dependencies required to run the demos and tutorials with:

pip install .[demos]

Quality assurance and linting

WSIMOD uses a collection of tools that ensure that a specific code style and formatting is follow thoughout the software. The tools we used for that are ruff and markdownlint. You do not need to run them manually - unless you want to - but rather they are run automatically every time you make a commit thanks to pre-commit.

pre-commit should already have been installed when installing the dev dependencies, if you followed the instructions above, but you need to activate the hooks that git will run when making a commit. To do that just run:

pre-commit install

You can customise the checks that ruff will make with the settings in pyproject.toml. For markdownlint, you need to oedit the arguments included in the .pre-commit-config.yaml file.

Testing and coverage

WSIMOD uses pytests as testing suite. You can run tests by navigating to the folder and running:

pytest # run all tests
pytest tests/test_file.py # run a specific file's tests

You can check the coverage for these tests by running:

coverage run -m pytest
coverage report

And generate a new coverage html for the documentation with

coverage html

Create documentation

If you want to compile new documentation you will need some additional packages, installed with:

pip install .[doc]

From here, you can make changes to the documentation pages in docs and view how they appear by navigating to and hosting them locally:

mkdocs serve

If compiling and deploying documentation, you will need to have git installed (see above). Then:

mkdocs gh-deploy

Changing dependencies

Is as the development process moves forward you find you need to add a new dependency, just add it to the relevant section of the pyproject.toml file.