Merge pull request #58 from ImperialCollegeLondon/update_docs2

Update installation instructions and CONTRIBUTING guidelines

docs/CONTRIBUTING.md

@@ -4,22 +4,68 @@ Thank you for considering contributing to `WSIMOD`.
 
 ## Bugs
 
-Please create a new [issues](https://github.com/barneydobson/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://barneydobson.github.io/wsi/tutorials/) or [how-to's](https://barneydobson.github.io/wsi/how-to/) to ensure that data is available.
+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://barneydobson.github.io/wsi) and existing [issues](https://github.com/barneydobson/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.
+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://github.com/barneydobson/wsi/issues) where we can discuss it. Do this _before_ you start developing as others may be working on the same thing!
+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://barneydobson.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://barneydobson.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://barneydobson.github.io/wsi/tutorials/) or [how-to's](https://barneydobson.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. You can run tests by navigating to the folder and running:
+- 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 thoughout 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
@@ -41,10 +87,10 @@ coverage html
 
 ## Create documentation
 
-If you want to compile new documentation you will need to clone the reposistory and `pip install` WSIMOD with some additional packages:
+If you want to compile new documentation you will need some additional packages, installed with:
 
 ```bash
-pip install .[doc]
+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:
@@ -53,14 +99,12 @@ From here, you can make changes to the documentation pages in `docs` and view ho
 mkdocs serve
 ```
 
-If compiling documentation, you will need to install `git`:
+If compiling and deploying documentation, you will need to have `git` installed (see above). Then:
 
 ```bash
-conda install git
+mkdocs gh-deploy
 ```
 
-And deploy:
+## Changing dependencies
 
-```bash
-mkdocs gh-deploy
-```
+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.

docs/installation.md

@@ -1,39 +1,38 @@
 # Installation
 
-Create and activate new conda environment
+It is highly recommended to setup a virtual environment to install WSIMOD into. This
+way, its installation and that of its dependencies will not interfere with any other
+tool in your system.
+
+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.
 
 ```bash
 conda create --name wsimod python=3.10
 conda activate wsimod
 ```
 
-Install a GUI if you like
+You can install the stable version of WSIMOD from [PyPI.org](https://pypi.org/) with:
 
 ```bash
-conda install spyder -c conda-forge
+pip install wsimod
 ```
 
-Install WSIMOD directly from GitHub
+If you want to install the development version, you can innstall WSIMOD directly from
+GitHub with:
 
 ```bash
-pip install https://github.com/barneydobson/wsi/archive/refs/heads/main.zip
+pip install git+https://github.com/ImperialCollegeLondon/wsi@main
 ```
 
-Use `[demos]` to include the demos and tutorials.
+Use `[demos]` to include the dependencies required to run the demos and tutorials.
 
 ```bash
-pip install https://github.com/barneydobson/wsi/archive/refs/heads/main.zip
 pip install wsimod[demos]
 ```
 
-If you want to make changes WSIMOD you can download/clone this folder, navigate to it, and run:
-
-```bash
-python setup.py develop
-```
+## Developing WSIMOD
 
-or (with demos)
-
-```bash
-python setup.py develop easy_install "wsimod[demos]"
-```
+If you want to help developing WSIMOD, or just modify it locally for your own interests,
+please read throgh the [CONTRIBUTING guidelines](https://github.com/ImperialCollegeLondon/wsi/blob/main/docs/CONTRIBUTING.md)
+in the GitHub repository.