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JOSS Tutorial Fixes#2708

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tpike3 merged 1 commit intomesa:mainfrom
tpike3:JOSS_tutorial
Mar 11, 2025
Merged

JOSS Tutorial Fixes#2708
tpike3 merged 1 commit intomesa:mainfrom
tpike3:JOSS_tutorial

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@tpike3 tpike3 commented Mar 7, 2025 •
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Summary

Updates for JOSS paper #2666

Motive

Per request

Implementation

  • update line lengths (to 79) in tutorials
  • edit intro tutorial per JOSS requests
  • edit visualization tutorial per JOSS request
  • remove pyprojoect.toml info about line-length being taken care of through ruff formatter
  • add .virtual documents to .gitignore
  • test_agent was reformatted due to pyproject.toml changes

Additional Notes

The line-length is not formatting in pyproject.toml as discussed here what I am confused about is why it is only identifying some issues on my computer (like 1) but lots of issues when the workflow starts.So I will need to dig into this

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github-actions bot commented Mar 7, 2025

Performance benchmarks:

Model Size Init time [95% CI] Run time [95% CI]
BoltzmannWealth small 🔵 +1.8% [+1.1%, +2.5%] 🔵 -0.1% [-0.3%, +0.1%]
BoltzmannWealth large 🔵 +0.2% [-0.8%, +1.3%] 🔵 +0.9% [-0.9%, +2.7%]
Schelling small 🔵 -0.4% [-0.7%, -0.2%] 🔵 -0.9% [-1.6%, -0.4%]
Schelling large 🔵 +0.3% [-0.3%, +0.9%] 🔵 +0.6% [-1.5%, +3.0%]
WolfSheep small 🔵 -0.0% [-0.3%, +0.3%] 🔵 +0.1% [-0.2%, +0.4%]
WolfSheep large 🔵 -0.6% [-2.0%, +1.0%] 🔵 -0.8% [-2.5%, +1.2%]
BoidFlockers small 🔵 +0.2% [-0.6%, +1.0%] 🔵 +0.2% [+0.0%, +0.4%]
BoidFlockers large 🔵 -1.5% [-2.0%, -0.9%] 🔵 -0.4% [-0.8%, -0.0%]

@tpike3 tpike3 changed the title JOSS Intro Tutorial Fix JOSS Tutorial Fixes Mar 7, 2025
@tpike3 tpike3 added the docs Release notes label label Mar 7, 2025
@tpike3 tpike3 requested a review from EwoutH March 7, 2025 20:34
EwoutH
EwoutH approved these changes Mar 8, 2025
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pyproject.toml
# Reminder to update mesa-examples if the value below is changed.
target-version = "py311"
extend-exclude = ["docs", "build"]
extend-exclude = ["build"]
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@EwoutH EwoutH Mar 8, 2025

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This addresses the large package size right? How much does it help?

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@tpike3 tpike3 Mar 8, 2025

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Do you mean line-length or am I missing something?

This put docs through the ruff linter and formatter, but I also ignored a lot (see per-file-ignores)

To address the line-length across Mesa we need to add to E501 to [tool.ruff.lint] select and if we want to be compliant with pep 8 we would set the line-length to 79. I am trying to figure out why I am still get a discrepancy between the pre-commit on my machine and the pre-commit in github actions.

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@EwoutH EwoutH Mar 8, 2025

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Sorry I confused this with another comment, you're right.

Personally I won't worry too much about this.

@EwoutH EwoutH requested a review from jofmi March 8, 2025 06:47
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EwoutH commented Mar 8, 2025

Thanks Tom!

@martibosch could you checkout the rendered docs and confirm this resolves your comments?

@tpike3 are @jofmi’s comments also addressed in this PR?

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tpike3 commented Mar 8, 2025 •
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Thanks Tom!

@martibosch could you checkout the rendered docs and confirm this resolves your comments?

@tpike3 are @jofmi’s comments also addressed in this PR?

I addressed all the comments on the checklist except the choose version, this seems to be a readthedocs default, but their documentation on it is not very clear. It was in the conf.py, adding to pull request

@tpike3
update for JOSS
deaa239 
JOSS Intro Tutorial Fix

- update line lengths (to 79) in tutorials
- edit intro tutorial per JOSS requests
- edit visualization tutorial per JOSS request
- update pyproject.toml to autofix code cell lengths
- remove pyprojoect.toml spurious assumption about it being taken care of black formatting
- add .virtual documents to .gitignore
- test_agent was reformatted due to pyproject.toml changes
- remove upper left version switcher
- update email in pyproject.toml
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EwoutH commented Mar 8, 2025 •
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It was added in this PR:

If it’s easier, we could also just reverse this commit: 8d1dd13

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tpike3 commented Mar 9, 2025

It was added in this PR:

If it’s easier, we could also just reverse this commit: 8d1dd13

I removed yesterday and it was added to the PR. Every time I mess with the docs its like I have to relearn the whole process. Ohh well maybe this time it will stick. :)

EwoutH
EwoutH approved these changes Mar 9, 2025
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Sounds good, merge when you’re ready.

@tpike3 tpike3 merged commit 44308a8 into mesa:main Mar 11, 2025
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@EwoutH EwoutH mentioned this pull request Mar 13, 2025
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@quaquel quaquel quaquel approved these changes

@EwoutH EwoutH EwoutH approved these changes

@jofmi jofmi Awaiting requested review from jofmi

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