Added docs and assets for interactive simulation plotting tutorial #1053
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docs/src/model_simulation/examples/interactive_brusselator_simulation.md
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This looks really nice! I think my main comment is that it would be nice to run as much of the docs as possible dynamically, e.g. by using rather than (see rest of docs) That way, if there is an error in the code (of if an error is produced later on due to package updates) that is caught. I imagine this will become problems for the code doing the interactivity stuff, but some code blocks should be possible to make this way. |
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Made all the requested suggestions, including dynamically building the plot from the code blocks! The reason I didn't do this originally is because The last code block doesn't display the dynamically generated figure because I have the mp4 of the interaction instead |
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Looks like some tests and the documentation build weren't successful. This is the first time I've PRed docs, do I need to fix anything on my end? |
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(I usually use Gitkraken for such things as you can just drag master onto your local branch and tell it to merge master into your branch.) |
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There is something really weird going on with SI, possibly weirdest thing I've encountered. Currently faller quite sick, and don't think I will be able to do anything the next few days. I have disabled SI in the test fix PR. Please feel free to merge if we want to go ahead making updates without SI (ok for me). |
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@TorkelE no worries -- I hope you feel better soon! |
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@jonathanfischer97 can you merge master into this PR? I think that should allow tests to pass now. |
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@jonathanfischer97 looks like the StructuralIdentifiability extension is causing issues here still. I'll try to update master later today to completely remove it so things can work again. |
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@jonathanfischer97 just removed all the StructuralIdentifiability stuff if you want to merge master again. That will hopefully get this to pass CI for you. |
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@jonathanfischer97 looks like there is a link error in the tutorial. |
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Issue with GLMakie in CI without GPU, apparently requires using There's an example in the |
| - name: Install dependencies | ||
| run: julia --project=docs/ -e 'ENV["JULIA_PKG_SERVER"] = ""; using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()' | ||
| - name: Build and deploy | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token | ||
| DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key | ||
| GKSwstype: "100" # https://discourse.julialang.org/t/generation-of-documentation-fails-qt-qpa-xcb-could-not-connect-to-display/60988 | ||
| run: julia --project=docs/ --code-coverage=user docs/make.jl | ||
| run: | | ||
| DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24' julia --project=docs/ --code-coverage=user docs/make.jl |
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What practical impact does this have? Does it mean all our docs are now being built under the assumption they live in a virtual 1024x768 framebuffer?
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No, the use of xvfb with -screen 0 1024x768x24 does not mean all the plots rendered during doc build will be constrained to that resolution, if that's what you mean. This setup only applies during the CI build to provide a virtual display for GLMakie plots, which require OpenGL, but also doesn't dictate the final resolution of the GLMakie plots, which instead are determined by the plot settings themselves.
Plots rendered by Plots.jl (using GR) or CairoMakie.jl aren't affected, cause these libraries use software-based rendering that doesn't depend on an OpenGL display. Their output is generated independently of the xvfb virtual framebuffer, so that those final doc artifacts are unaffected by this temporary display configuration.
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However, if you'd rather not implement this change in the the docs CI, another option is I can just use CairoMakie as the backend for all the inline rendered plots, but make the presented code blocks look like they use GLMakie.
But this would obviously break some of the spirit of making the plots dynamically to ensure GLMakie functionality in the tutorial.
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No that's fine. I just wanted to understand the code.
If tests pass is this ready to merge on your end?
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@jonathanfischer97 if you feel this is done I'm happy to merge it. |
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@isaacsas This is ready on my end! I think this should fix most everything, so merge at your convenience! |
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Thanks for the PR! |
Added tutorial on how to simulate and plot a
Catalyst.jlgeneratedODEProblemusingGLMakie.jl.Additional embedded assets are SVG screenshots and an mp4 demoing the full interactive window.