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Finish case scenarios + new devcontainer extension #14

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@M-PERSIC M-PERSIC commented Sep 30, 2023

  • Finish the industry case scenario
  • Finish tool installation guide
  • Add Rewrap to standardize markdown
  • Fix typos

- Finish the industry case scenario
- Add Rewrap to standardize markdown
- Fix typos
@M-PERSIC M-PERSIC marked this pull request as ready for review September 30, 2023 00:32
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M-PERSIC commented Nov 9, 2023

@kescobo

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kescobo commented Nov 15, 2023

I know I still owe you this review, sorry for the delay! It's on my list

docs/src/comparisons/bioconductor.md Show resolved Hide resolved
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This idea of a case scenario is not something I've noticed before. Is there a place that you're getting inspiration from?

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Some if is based on my own internship experience + experiences shared with me via Slack + some inspiration from JuliaHub case studies :)

alone can almost be considered a proper IDE. It should appear the moment you enter `julia` into your terminal:
The Julia REPL is included by default in every Julia installation and boasts a
number of features to the point that it alone can almost be considered a proper
IDE. It should appear the moment you enter `julia` into your terminal:
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Are we recommending people install julia via juliaup? I'm not sure how accessible the idea of a terminal is to windows users in particular, and I don't know how juliaup handles this on windows if installed through the app store. May be worth confirming.

3. Pkg mode for working with the included package manager and manipulating
dependencies/packages
4. Shell mode to execute system commands (run a terminal from Julia which
itself is running from a terminal!)
5. Search modes (forward, reverse) to look through your history of inputs

| Prompt | Key binding |
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I wonder if it's worth mentioning how to get out of these modes, the fact that Pkg / Shell are sticky, etc

[Revise](https://timholy.github.io/Revise.jl/stable/) package, although restarting the session is the simplest option.
* You can run a standalone script by entering `include("<name of script>")` in
Julian mode. For greater control, the equivalent of Python3's `if __name__ ==
__main__` condition would be `if abspath(<name of program file>) == @__FILE__`
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I don't think we want to recommend this. It's not idiomatic to have a file that's used as both a script and a library like it is in python

One common gotcha with the Julia REPL is that there are currently certain code changes that cannot be performed without
restarting your session, such as redefining structs (see the example below). You can mitigate this by adding the
[Revise](https://timholy.github.io/Revise.jl/stable/) package, although restarting the session is the simplest option.
* You can run a standalone script by entering `include("<name of script>")` in
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Mmm, I don't know if I would put it this way. Technically true, but really this is just evaluating the contents of another file. So for example any variables / functions that are defined will persist in your current session.

certain code changes that cannot be performed without restarting your
session, such as redefining structs (see the example below). You can
mitigate this by adding the
[Revise](https://timholy.github.io/Revise.jl/stable/) package, although
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This phrasing is a bit misleading - Revise doesn't help with redefining structs...

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This is still in progress?

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I won't add anything more to this PR as it's already pretty big. I think 2-3 more big PRs and the MVP for BioJuliaDocs will be ready! I will review the changes this weekend and ping you for any further feedback

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OK, maybe Just add a couple of WIP flags on that page so it doesn't look like you forgot about it 😉

@M-PERSIC M-PERSIC marked this pull request as draft November 20, 2023 18:08
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