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:

Main page

• Update diagram
• Change first paragraph to six components and nutrients cycle
• Add nutrient components to the Science Library doc links

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
  • Update version number of unifhy at start of tutorial when needed
  • Add data necessary for the example to work to the data folder of the repo

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

Science Library

• Add in LTLS (with proviso that it's not fully developed yet - this message should also be made more prominent in other places)

[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:

[mattjbr123]

@ThibHlln how about Fig2 here https://unifhy-org.github.io/unifhy/contributors/development.html ?
I'm sure I could create one similar from scratch, but it would good to keep things consistent, plus I like the style

[ThibHlln]

Hi Matt, this one was created on Inkscape. The file in the documentation is already a vector image (see SVG file https://unifhy-org.github.io/unifhy/_images/framework_detailed_transfers.svg), so you can open it with Inkscape too and start editing the shapes in it directly.

[mattjbr123]

Oh brilliant, thanks!

[mattjbr123]

New framework diagrams