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[Non-urgent - Ready] GitHub readme update #843

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merged 28 commits into from
Jul 2, 2024
Merged

[Non-urgent - Ready] GitHub readme update #843

merged 28 commits into from
Jul 2, 2024

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TorkelE
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@TorkelE TorkelE commented May 18, 2024 •
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Updates the GitHub readme page. Also updated the docs/Project.toml file for Catalyst v14.

@TorkelE TorkelE mentioned this pull request May 18, 2024
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TorkelE
TorkelE commented May 18, 2024
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isaacsas requested changes May 21, 2024
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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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TorkelE commented May 22, 2024

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.

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TorkelE commented May 31, 2024
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TorkelE commented May 31, 2024

Ok, this one is read. Two additional comments:

  • The (@ref ref) mark where I want to put links to places in the docs. However, I cannot actually put these links in until the rest of the docs have been finished (and released, i.e. I do not want to link dev docs). They are there now so you can see where I want to link stuff. before we merge I will save this file somewhere on my computer (so I can go and see where I wanted to put links), and then remove all of these. And yes, you are totally right that I have to use normal links and cannot use Documenter references.
  • Ok, I think there was something else, but I have now forgotten. maybe it was one of the things I wrote as comments to the code though.

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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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I think you'd need to manually include the tex by hand. But I'd show the SDEs not the ODEs and just drop Latexify.

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Sounds good. Once Latexify+SDEs work we could reinstate it.

@TorkelE TorkelE changed the title GitHub readme remake [Ready] GitHub readme remake Jun 5, 2024
@TorkelE TorkelE changed the title [Ready] GitHub readme remake [Documentation - Ready] GitHub readme update Jun 5, 2024
@TorkelE TorkelE changed the title [Documentation - Ready] GitHub readme update [Non-urgent - Ready] GitHub readme update Jun 11, 2024
isaacsas
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Breaking changes and new functionality are summarized in the
[HISTORY.md](HISTORY.md) file.
Breaking changes and new functionality are summarized in the [HISTORY.md](HISTORY.md) file.
This also includes a special migration guide for version 14.
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Link this from the docs?

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will add a link

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```julia
using Latexify
latexify(cell_model; form = :ode)
```
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I think you'd need to manually include the tex by hand. But I'd show the SDEs not the ODEs and just drop Latexify.

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TorkelE and others added 2 commits June 28, 2024 18:08
@TorkelE @isaacsas
Update README.md
ccb5f6f 
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
@TorkelE @isaacsas
Update README.md
5653204 
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
TorkelE and others added 15 commits June 28, 2024 18:08
@TorkelE @isaacsas
Update README.md
c766ca6 
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
@TorkelE @isaacsas
Update README.md
4c64ea7 
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
@TorkelE @isaacsas
Update README.md
f6faa8f 
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
@TorkelE @isaacsas
Update README.md
052a460 
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
@TorkelE @isaacsas
Update README.md
171d399 
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
@TorkelE @isaacsas
Update README.md
37c660f 
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
@TorkelE @isaacsas
Update README.md
d42ee6a 
Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
@TorkelE
remove stuff that we should add back in later on
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up
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@TorkelE
link to stable docs
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@TorkelE
Merge branch 'master' into docs___proposed_updates___github_readme
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@TorkelE
update sde example
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@TorkelE
where the $dW_1(t)$ and $dW_2(t)$ terms described the noise added thr…
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…ough the Chemical Langevin Equations. Finally, we can simulate and plot the results.transfer text updates from home pr
@TorkelE
add using Plots in SDE example
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@TorkelE
minor fix after re reading
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@TorkelE TorkelE merged commit 8dba797 into master Jul 2, 2024
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@TorkelE TorkelE deleted the github_readme_remake branch July 2, 2024 08:01
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