Update documentation to include Nutrient Components

[mattjbr123]

Documentation needs some small updates to incorporate the addition of Nutrient Components (#14)

[mattjbr123]

@ThibHlln how did you generate the nice diagram at https://unifhy-org.github.io/unifhy/api_reference.html ? It would be nice to create an up to date one with the Nutrient Components in.

[mattjbr123]

Changes to make:

User Guide

Tutorial

• [ ] Configuring a Model: Change mentions of three components to six
  • [ ] Change reference to water cycle to water and nutrient cycles
  • [ ] In Science subsection, at the start add in references to the Nutrient Component as well
  • [ ] In the Framework subsection, at the start change mentions of three Components to six and mention optionality of components through use of Data/NullComponents?
  • [ ] In the Data/Null Component Note change three to six
  • [ ] Update the two examples to include the Nutrient Components

    Files

• [ ] Add Nutrient Components to the example model configuration file, the dummy one developed for the tests will do the job.

Contributor Guide

Development

• [ ] Create your science component by subclassing a generic framework component: Add references to the three new Nutrient Components in the first paragraph
  • [ ] Update Fig. 2
  • [ ] Update Table 1

    Packaging

• [ ] At Bring in your component contribution(s): Edit text in first paragraph to reference the three new Nutrient Components
  • [ ] Add the nutrient components to the template repo
  • [ ] Edit the example to also include the new Nutrient Components

[ThibHlln]

@ThibHlln how did you generate the nice diagram at https://unifhy-org.github.io/unifhy/api_reference.html ? It would be nice to create an up to date one with the Nutrient Components in.

Hi @mattjbr123,

I used GraphViz and specified the relationships "manually" in a file using the DOT language.

I had created a simplified one:

and a more extensive version:

In order to feed our discussions from a while ago on the inclusion of the nutrient cycle in unifhy, I had also created this one:

But I don't think it represents what you have actually done, so it will certainly need adjusting, but this could be a starting point.

Once you have installed graphviz (e.g. with a mamba install graphviz), you can use the following commands to go from the DOT language files to PNG/SVG files: dot -Tpng unifhy-uml+diagram.gv -o png-unifhy+diagram.gv.png dot -Tsvg unifhy-uml+diagram.gv -o png-unifhy+diagram.gv.svg

I am attaching the files used to generate the three figures presented above: unifhy-uml_diagrams.zip

There are also tools that create UML class diagrams automatically (e.g. pyreverse in pylint), if you want to explore that route. Then, you will still need to manually handle the visual rendering.

Let me know if you need more info.

Cheers, T

[mattjbr123]

Great, thanks, this definitely gives me something to go on!

[mattjbr123]

Updated diagram, simplified version: