Add Quarto support #200

svilupp · 2022-08-07T15:15:19Z

Closes #199

Changes:

parse properly Quarto arguments #| echo:false
provide Quarto-specific codefence (refactored to a separate function)
save files with extension .qmd
all functionality tested
updated documentation with the new flavor

All tests are passing
Code formatted with JuliaFormatter (default setting as no specific preference was indicated)

- parse properly Quarto arguments `#| echo:false` - provide Quarto codefence (refactored to separate function) - save files with extension `.qmd` - all functionality tested - updated documentation

fredrikekre · 2022-08-07T21:55:00Z

Thanks for the PR. Can you drop all the formatting changes? Very difficult to review otherwise.

This reverts commit fa050c7.

svilupp · 2022-08-08T06:24:36Z

Thanks for the PR. Can you drop all the formatting changes? Very difficult to review otherwise.

Yes, of course. I've reverted it. I can open a separate PR with JuliaFormatter later.

svilupp · 2022-08-23T09:22:27Z

Hi @fredrikekre, would you have any thoughts on the PR?

fredrikekre · 2022-08-23T12:14:48Z

I'm om vacation but will have a look in a week or two.

svilupp · 2022-11-09T10:55:07Z

Hi @fredrikekre, I was wondering if you have any thoughts on the PR?

My team and I have been using it for several months now, so it seems to work pretty well.

svilupp · 2023-04-19T17:16:53Z

Hi @fredrikekre, I was wondering if there is anything I can do to get this merged.

I've updated to the latest and re-ran tests. All pass, including the additions for the functionality added.

Are there any suggestions or concerns that you have about this tweak?

lbenet · 2023-05-10T01:16:55Z

Is there an easy way to test your proposal (using my own .qmd files)?

svilupp · 2023-05-10T06:38:58Z

Is there an easy way to test your proposal (using my own .qmd files)?

Yeah, very simple. Just add my branch of Literate, eg, in your environment:
]add https://github.com/svilupp/Literate.jl.git#add-quarto-support

and then simply using Literate; Literate.markdown("filename.jl",flavor=Literate.QuartoFlavor())

My workflow is to have it in the global environment and call it with VSCode tasks. Ie, I simply click on "JL to HTML" when I have my script opened and separate process is spun to produce my Quarto report (while I can keep working in my project)

Example tasks.json (in VSCode)

    "version": "2.0.0",
    "tasks": [
        {
            "label": "JL to HTML",
            "type": "shell",
            "command": "echo Finished conversion to HTML",
            "dependsOrder": "sequence",
            "dependsOn": ["JL to QMD", "QMD: HTML Render"]
        },
        {
            "label": "JL to QMD",
            "type": "shell",
            "command": "julia --startup-file=no -e 'using Literate; Literate.markdown(\"${file}\",\"${fileDirname}\",flavor = Literate.QuartoFlavor(),credit=false)'"

        },
                {
            "label": "QMD: HTML Render",
            "type": "shell",
            "command": "quarto render ${fileDirname}${pathSeparator}${fileBasenameNoExtension}.qmd --to html",
            "problemMatcher": []
        }]

FYI. I think I'll create a fork/package extension to be able to register it and add it like a normal package.

src/Literate.jl

Co-authored-by: Fredrik Ekre <[email protected]>

docs/src/outputformats.md

svilupp · 2023-05-12T11:10:50Z

Docs checked. Output formats page renders correctly.

The question is where we should add also a full example to show the application / make it easier to start

fredrikekre · 2023-05-12T16:29:01Z

Thanks, will have a look.

The question is where we should add also a full example to show the application / make it easier to start

I have been thinking for some time to have a section where I link to real life usage of Literate as inspiration for setups etc. If you have something public let me know and I will get around to write up something.

svilupp · 2023-05-16T12:06:53Z

I have been thinking for some time to have a section where I link to real life usage of Literate as inspiration for setups etc. If you have something public let me know and I will get around to write up something.

Sorry, I forgot to reply. No, I don't have anything public, but I could easily sanitize a few examples to show the different quarto features (to be hosted in Literate.jl)

svilupp · 2023-05-29T19:58:37Z

I've looked into the Docs failure. It doesn't seem to be related.

I've refreshed Manifest.toml and local build works without a problem.

Looking at the failure, it's coming from StatsBase and Plots. I suspect it's due to JuliaStats/StatsBase.jl#840 and its removal of type aliases ("ERROR: LoadError: UndefVarError: Float not defined".

I'm unsure how to force Github Actions to load more up-to-date deps (I can build locally with StatsBase 0.34 vs StatsBase 0.33.21 in the CI)

fredrikekre · 2023-05-29T21:49:20Z

I've refreshed Manifest.toml and local build works without a problem.

You have to commit the changes then too.

I will review and merge this week, I should have some time. Sorry again for slow responses

svilupp · 2023-05-30T07:55:03Z

You have to commit the changes then too.

Sorry, I didn't make myself clear.
I couldn't replicate the error locally, I merely deleted and re-instantiated my Manifest.toml to check if its some breaking release (no changes to Project.toml, so nothing to commit)

To replicate the error, I'd have to explicitly ]add [email protected], which breaks. I'm hesitant to add a compat bound, because it's a 2nd-order dependency (docs -> Plots.jl -> StatsBase.jl -> SortingAlgorithms).

We could force Plots to something higher (1.38), but I'm not sure when the issue was introduced, so we could be overly
restrictive.

Would you prefer to be safe and set compat to [email protected]?

fredrikekre · 2023-05-30T08:11:39Z

I couldn't replicate the error locally, I merely deleted and re-instantiated my Manifest.toml to check if its some breaking release (no changes to Project.toml, so nothing to commit)

The manifest is commited.

svilupp · 2023-05-30T10:21:27Z

The manifest is commited.

Oh, I didn't clock that -- that explains the issues.
I've committed my Manifest (I run on an arm-based Mac machine, but hopefully nothing in there is platform specific)

docs/src/outputformats.md

svilupp · 2023-07-28T00:03:55Z

@fredrikekre, are you perhaps at JuliaCon? We could meet up and discuss the next steps?

fredrikekre · 2023-07-31T09:59:13Z

I wasn't. I think we can merge this. Perhaps in a version 3.0 it make sense to split up the flavors into Literate.quarto etc instead of trying to push it all into Literate.markdown.

svilupp · 2023-08-13T09:03:05Z

Hi @fredrikekre, would you mind merging this PR?

We're considering giving a presentation on benefits of Literate.jl + Quarto, but it would be odd to ask people to install from a fork...
I'm happy to review the structure for 3.0.

Updates:

updated to latest main
tests pass (tested on 1.10 and 1.9)
docs build

If people open issues related to the quarto functionality, just tag me. I have a lot of experience debugging it :)

Thank you!

svilupp · 2023-08-21T09:03:51Z

Happy Monday, @fredrikekre!

Is there something that I can do to get this merged?

Thank you

fredrikekre · 2023-08-28T16:10:43Z

src/Literate.jl

@@ -75,8 +76,9 @@ function parse(content; allow_continued = true)
 if !(chunks[end] isa CodeChunk)
 push!(chunks, CodeChunk())
 end
- # remove "## " and "##\n"
- line = replace(replace(line, r"^(\h*)#(# .*)$" => s"\1\2"), r"^(\h*#)#$" => s"\1")
+ # remove "## " and "##\n", strip the leading "#" from "## xyz" and "##| xyz"


Why not use #| directly in the source code and make no transformation? Alternatively, I think this transformation should only be done for quarto output.

svilupp · 2023-11-23T10:14:12Z

Hi @fredrikekre ,

Hope all is well! Is there any chance we could reach a conclusion on the PR?

I've responded in August to your comments but haven't heard back.
The current version isn't perfect but it works well for everyone (we have a bunch of people using it) and is simple to pick up as it follows an easy mental model -- could we consider merging this or rejecting this?

I'm happy to fork into LiterateQuarto.jl, because this is the only useful functionality of Literate for us.
However, I'm conscious that forks duplicate work, so I was hoping to prevent it.

Would you prefer we abandon this PR and create a separate package?

Thank you in advance for your response.

fredrikekre · 2023-11-23T10:46:05Z

I was waiting for #200 (comment)

svilupp · 2023-11-23T12:00:05Z

I was waiting for #200 (comment)

Thank you, I havent realized that my explanation wasn’t sufficient. I’ll follow your suggestion and update it within the next few days.

fredrikekre

Thanks, sorry it took a while to get this in.

CHANGELOG.md

fredrikekre · 2024-04-14T12:06:05Z

docs/src/outputformats.md

+ ```
+ # ---
+ # title: "My Report"
+ # jupyter: julia-1.9


Should this and the installation notes below be updated?

svilupp added 2 commits August 7, 2022 16:11

Add quarto support

24c2167

- parse properly Quarto arguments `#| echo:false` - provide Quarto codefence (refactored to separate function) - save files with extension `.qmd` - all functionality tested - updated documentation

Formatted

fa050c7

Revert "Formatted"

76183c0

This reverts commit fa050c7.

Merge remote-tracking branch 'upstream/master' into add-quarto-support

b0f94df

fredrikekre reviewed May 10, 2023

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fredrikekre reviewed May 10, 2023

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svilupp and others added 2 commits May 10, 2023 09:30

Update src/Literate.jl

77b8995

Co-authored-by: Fredrik Ekre <[email protected]>

quick draft - to be formatted

2a73c87

fredrikekre reviewed May 11, 2023

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updated examples

49d1bce

pat-alt mentioned this pull request May 30, 2023

blog/posts/tips-and-tricks-for-using-quarto-with-julia/ pat-alt/pat-alt.github.io#16

Open

pat-alt mentioned this pull request May 30, 2023

blog/posts/quarto-extensions/ pat-alt/pat-alt.github.io#15

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Updated Manifest.toml

b0fc948

olejorik reviewed Jul 14, 2023

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Merge remote-tracking branch 'upstream/master' into add-quarto-support

ac9a21a

fredrikekre reviewed Aug 28, 2023

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Merge remote-tracking branch 'upstream/master' into add-quarto-support

174fe96

svilupp and others added 7 commits November 26, 2023 13:51

update parser to have quarto-only functionality

9d6431c

Merge remote-tracking branch 'upstream/master' into add-quarto-support

ca07357

Code and doc formatting, changelog, mark as experimental.

4695060

fix tests

5d02038

fix test again

0cd17ff

testfix

292f1fc

Merge remote-tracking branch 'origin/master' into add-quarto-support

8122f5c

fredrikekre changed the title ~~Add quarto support~~ Add Quarto support Apr 14, 2024

fredrikekre merged commit 8abaeeb into fredrikekre:master Apr 14, 2024
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Add Quarto support #200

Add Quarto support #200

svilupp commented Aug 7, 2022

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Add Quarto support #200

Add Quarto support #200

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