[Non-urgent - Ready] GitHub readme update #843
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Seems like lots of unchanged text is getting unaligned / respaced for no reason which messes up the text file and then shows as a diff when none is present. There are also lots of @refs added which aren't going to work in the README. I'll give this a more careful read through after you fix these so the actual changes are easier to see.
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I think the reason that there is lots of diff is that there has been quite widespread rewriting and reordering to most parts of the text, i.e. the changes probably are more widespread than you first thought. But yes, let's first sort out the spatial SSA PR before we look at this. |
Co-authored-by: Sam Isaacson <[email protected]>
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| Finally, an overview of the package and its features (as of version 13) can also be found in its corresponding research paper, [Catalyst: Fast and flexible modeling of reaction networks](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011530). | ||
| An overview of the package, its features, and comparative benchmarking (as of version 13) can also | ||
| be found in its corresponding research paper, [Catalyst: Fast and flexible modeling of reaction networks](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011530). | ||
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| ## Features |
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Unfortunately, pretty much all of this is marked as changed. This is mainly due to:
- A large part of it (not all) has seen some modifications.
- Quite a few things were moved around (as we now divide stuff into Catalyst features, features of Catalyst composing with other packages, and features of packages building on Catalyst).
I.e. "Graphviz can be used to generate and visualize reaction network graphs. (Reusing the Graphviz interface created in Catlab.jl.)" wasn't really changed, but it got moved to the second section.
| [DifferentialEquations.jl](https://docs.sciml.ai/DiffEqDocs/stable/) | ||
| [ODE/SDE/jump solver](@ref ref), and can be used within `EnsembleProblem`s for carrying | ||
| out [parallelized parameter sweeps and statistical sampling](@ref ref). Plot recipes | ||
| are available for [visualization of all solutions](@ref ref). |
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I tried to keep American English here (so that we are consistent within the page). If you see anything I miswrote, feel free to point it out (or not to worry about it either. For a while I didn't really know what to do here, an in the end I decided to just try and be consistent within each file, mostly so that I know what to do, but if we end up mixing I do not mind either).
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| ## Elaborate example |
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Basically an example where I try to show off as much as possible while still keeping things simple/short.
| If you are interested in participating in the development of Catalyst, or integrating your package(s) | ||
| with it, developer documentation can be found [here](@ref ref). Are you a student (or similar) who | ||
| wishes to do a Google Summer of Code (or similar) project tied to Catalyst? Information on how to get | ||
| involved, including good first issues to get familiar with working on the package, can be found [here](@ref ref). |
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This last part we should remove, as we do not have any dev docs, information for people who want to get involved, or list of good issues. But if we ever get that, I think having something like this here would be nice. It is here so you can see it, then but I will remove it before we actually merge.
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| We also maintain a user survey, asking basic questions about how users utilise the package. The survey | ||
| is available [here](ref), and only takes about 5 minutes to fill out. We are grateful to those who | ||
| fill out the survey, as this helps us further develop the package. |
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Again, creating the survey should be rather simply, but we have other stuff to do before then.I will remove it after you have read (again I put it here when I thought we might have the survey ready, and now I keep it until you have read, just so you know it is an idea of mine to put something like this here)
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Ok, this one is read. Two additional comments:
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| ```julia | ||
| using Latexify | ||
| latexify(cell_model; form = :ode) | ||
| ``` |
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This will not work here, however, is there any good approach for making this work nicely on this page? If not, I might just skip it? I think we could just include some normal equations (copied from latexify) directly in the md file?
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Updates the GitHub readme page. Also updated the docs/Project.toml file for Catalyst v14.