move to readme

CODE_OF_CONDUCT.md

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+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[INSERT CONTACT METHOD].
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations

CONTRIBUTING.md

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+# Contributing to `WSIMOD`
+
+Thank you for considering contributing to `WSIMOD`.
+
+## Bugs
+
+Please create a new [issues](https://github.com/ImperialCollegeLondon/wsi/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](https://imperialcollegelondon.github.io/wsi/tutorials/) or [how-to's](https://imperialcollegelondon.github.io/wsi/how-to/) 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](https://imperialcollegelondon.github.io/wsi/) and existing [issues](https://imperialcollegelondon.github.io/wsi/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](https://imperialcollegelondon.github.io/wsi/issues) 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](https://imperialcollegelondon.github.io/wsi) relies heavily on use of docstrings, make sure to format it following the [Google Python style](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html), see the source code of [`Land.__init__`](https://imperialcollegelondon.github.io/wsi/reference-land/#wsimod.nodes.land.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](#create-documentation).
+- We are incredibly grateful for contributions that include new [tutorials](https://imperialcollegelondon.github.io/wsi/tutorials/) or [how-to's](https://imperialcollegelondon.github.io/wsi/how-to/), whether for new or existing functionality. Our use of the [mkdocs-jupyter](https://github.com/danielfrg/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.
+
+```bash
+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](https://git-scm.com/downloads) or with `conda install git`, if you use `conda`.
+
+```bash
+git clone https://github.com/ImperialCollegeLondon/wsi.git
+cd wsi
+```
+
+We use [`pip-tools`](https://pip-tools.readthedocs.io/en/latest/) 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:
+
+```bash
+pip install -r requirements-dev.txt
+pip install -e .
+```
+
+You can also install the dependencies required to run the demos and tutorials with:
+
+```bash
+pip install -r requirements-demos.txt
+```
+
+## Quality assurance and linting
+
+WSIMOD uses a collection of tools that ensure that a specific code style and formatting is follow throughout the software. The tools we used for that are [`ruff`](https://docs.astral.sh/ruff/) and [`markdownlint`](https://github.com/igorshubovych/markdownlint-cli). 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:
+
+```bash
+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:
+
+```bash
+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:
+
+```bash
+coverage run -m pytest
+coverage report
+```
+
+And generate a new coverage html for the documentation with
+
+```bash
+coverage html
+```
+
+## Create documentation
+
+If you want to compile new documentation you will need some additional packages, installed with:
+
+```bash
+pip install -r requirements-doc.txt
+```
+
+From here, you can make changes to the documentation pages in `docs` and view how they appear by navigating to and hosting them locally:
+
+```bash
+mkdocs serve
+```
+
+If compiling and deploying documentation, you will need to have `git` installed (see above). Then:
+
+```bash
+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 and then run `pip-compile` as required to regenerate the different `requirements.txt` files. Read the [`pip-tools` documentation](https://pip-tools.readthedocs.io/en/latest/) for more information on the process.