Filter run_ribasim terminal output in docs

[Copilot]

Documentation pages render raw terminal output from run_ribasim() calls — the Unicode logo with blank lines, repeated progress bar lines, and log messages — wasting significant vertical space. Node icons in Python plots are also too small.

• Filter simulation output in docs: Modified docs/run_ribasim.py to capture stderr at the file descriptor level and filter out blank lines (invisible braille U+2800 characters) and progress bar repetitions from OrdinaryDiffEqCore. The logo art, startup info, and completion messages remain visible.

Original prompt

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This section details on the original issue you should resolve

<issue_title>Example documentation has formatting issues</issue_title>
<issue_description>The documentation at https://ribasim.org/getting-started/examples.html has:

• Terminal output with blank lines (stretching the logo)
• Repeated progressbar outputs

Ideally we can prevent both, saving a lot of space.

Also, the node icons are too small in the Python plots.</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes Example documentation has formatting issues #2979

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[evetion]

@copilot, we want to see the output of each run, just without all the newlines. Maybe we can tweak the terminal/shell output settings of run_ribasim?

[Copilot]

@copilot, we want to see the output of each run, just without all the newlines. Maybe we can tweak the terminal/shell output settings of run_ribasim?

Reverted the #| output: false directives. Instead, docs/run_ribasim.py now captures stderr at the fd level and filters it — removing blank/invisible braille lines (that stretched the logo) and progress bar repetitions from OrdinaryDiffEqCore, while preserving the logo art, startup info, and completion messages. See commit 046b94a.

[visr]

I set this size based on how it appear locally in a VSCode notebook. For that this seems to make it a bit too large:

NODE_ICON_SIZE = 17.0

NODE_ICON_SIZE = 25.0

Though in the docs at https://ribasim.org/reference/test-models.html#basic I agree they appear too small. I wonder how to best get this more in line?

[visr]

I changed it in #3007 to 22, so a bit smaller than here.